The increasingly common occurrence of antibiotic-resistant bacteria has become an urgent public health issue. There are currently some infections without any effective treatment, which require new therapeutic strategies. An attractive alternative is the design of compounds capable of disrupting bacterial communication known as quorum sensing (QS). In gram-negative bacteria, such communication is regulated by acyl-homoserine lactones (AHLs). QS allows bacteria to proliferate before expressing virulence factors. Our group previously reported that hexyloxy phenyl imidazoline (9) demonstrated 71% inhibitory activity of QS at 100 µM (IC50=90.9 µM) in Chomobacterium violaceum, a gram-negative bacterium. The aim of the present study was to take 9 as a lead compound to design and synthesize three 2-imidazolines (13-15) and three 2-oxazolines (16-18), to be evaluated as quorum sensing inhibitors on C. violaceum CV026. We were looking for compounds with a higher affinity towards the Cvi receptor of this bacterium and the ability to inhibit QS. The binding mode of the test compounds on the Cvi receptor was explored with docking studies and molecular dynamics. It was found that 8-pentyloxyphenyl-2-imidazoline 13 reduced the production of violacein (IC50=56.38 µM) without affecting bacterial growth, suggesting inhibition of quorum sensing. Indeed, compound 13 is apparently one of the best QS inhibitors known to date. Molecular docking revealed the affinity of compound 13 for the orthosteric site of the N-hexanoyl homoserine lactone (C₆-AHL) on the CviR protein. Ten aminoacid residues in the active site of C₆-AHL interacted with 13, and 7 of these are the same as those interacting with AHL. Contrarily, 8-octyloxyphenyl-2-imidazoline 14, 8-decyloxyphenyl-2-imidazoline 15 and 9-decyloxyphenyl-2-oxazoline 18 bound only to an allosteric site and thus did not compete with C₆-AHL for the orthosteric site.

The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.

The current study presents a computational fluid dynamics model designed to simulate the isolation of 2D graphene components from their dispersion using a microfiltration hollow fiber membrane unit. The model utilizes Navier-Stokes and mass conservation equations to predict the flow and concentration behaviors in the system, and it employs the resistance-in-series approach to couple the fouling of the non-exfoliated graphites in the dispersion to the model. Specifically, the model accounts for the effects of the concentration polarization and cake formation of the fouling component, resulting in the increment of the transmembrane pressure (TMP) of the system. Additionally, we assumed the wettability of polymeric membrane’s inner wall enhances upon fouling by the flat layered structure material, leading to the reduction of the transmemrabe pressure. This approach demosntrates accurate reproduction of the exceptional experimental TMP behavior corresponding to the fouling of the graphite.

This project aims to simulate and analyze population dynamics in evolutionary systems, using stochastic differential equations and probabilistic rules for crossbreeding and benefits. The study employs advanced computational techniques to model the evolution of populations over an extended period. Specifically, we explore a scenario with ten distinct groups, each starting with an equal population and evolving under defined genetic and cooperative behaviors. The simulation spans 1000 years, incorporating individual lifespans, stochastic updates, and probabilistic interactions. To ensure robustness and reliability, the study includes detailed statistical analysis, encompassing descriptive statistics, confidence intervals, and ANOVA tests. We further visualize the temporal behavior of populations and subpopulations, providing insights into the evolutionary dynamics and stability of the system. The results demonstrate the effectiveness of balanced cooperation and genetic diversity in maintaining stable population distributions. The project showcases the integration of mathematical modeling, statistical analysis, and computational simulations, contributing valuable insights into evolutionary biology and complex systems. It highlights the importance of interdisciplinary approaches in understanding and predicting population behaviors, with implications for both theoretical research and practical applications in fields such as ecology, genetics, probability and social sciences.

In view of the inability to directly and accurately obtain the athlete's aerodynamic force during take-off phase through wind tunnel test, the athlete's aerodynamic force and surrounding flow field form under different take-off postures are obtained through numerical simulation research, and the effects of different take-off modes on the aerodynamic characteristics during take-off in ski jumping are discussed. The multi-body system composed of the athlete and skis was selected as the research objects. By using partially averaged Navier-Stokes (PANS) turbulence model and 3D numerical simulation of computational fluid dynamics (CFD), the aerodynamic characteristics of the athlete under different take-off postures were predicted. Take-off modes include knee-push-hip (KPH) mode and hip-drive-knee (HDK) mode, and the hip joint angle of HDK mode is significantly greater than KPH mode. First, the aerodynamic force ratio of the athlete’s torso and legs is obviously large. Although the aerodynamic force of arms themselves is not obvious, they have a great impact on the overall aerodynamic characteristics of the athlete, so the posture of arms cannot be ignored. Then, the total drag and moment of HDK mode are significantly higher than that of KPH mode, and the lift-to-drag ratio of HDK mode is significantly lower than that of KPH mode. At first the total lift of HDK mode is higher than that of KPH mode, but in the last attitude the total lift of HDK mode does not rise but fall, and finally the total lift of HDK mode is lower than KPH mode. The aerodynamic characteristics change dramatically during take-off phase, and the aerodynamic characteristics of the two take-off modes are quite different, and these changes and differences are difficult to be observed in real training and competition site. KPH mode has obvious aerodynamic advantage over HDK mode. During the take-off process, the athlete should increasethe force generated by the knee joint extension and appropriately reduce the speed of hip joint extension, and control the using force order of the lower limb joints, and push hip joint extension by knee joint extension, in order to avoid issues such as the hip joint angle is too large, the hip joint extension angle is too fast, the center of gravity is to back and other problems. Studying the aerodynamic characteristics during the take-off phase provides valuable insights for athletes to achieve favorable flight postures after take-off, offering scientific guidance to improve training strategies and enhance competitive performance.

Phytoseiidae inhabit a wide range of herbs, shrubs and trees. Aesculus hippocastanum is an important ornamental tree in Europe and is likely reservoir of these mites. We therefore assessed the species composition and the spatial and seasonal variability in the abundance of Phytoseiidae in city parks in South Bohemia, Czech Republic. Leaf samples were randomly collected from horse chestnut tree branches at eight sites, five times during the vegetation season in 2013. The mites were collected by washing technique and mounted on slides for identification. In total, 13,903 specimens of phytoseiid mites were found, and eight species were identified: Amblyseius andersoni, Euseius finlandicus, Kampimodromus aberrans, Neoseiulella tiliarum, Phytoseilus macropilis, Paraseiulus talbii, Paraseiulus triporus and Typhlodromus (Typhlodromus) pyri. Paraseiulus talbii and P. macropilis were recorded on the leaves of horse chestnut trees for the first time in the Czech Republic in this study. The predominant species was E. finlandicus (96.25%). The number of mites per compound leaf was, on average, 2.53, 10.40, 23.54, 11.59 and 9.27 on the sampling dates in each month between May and September, respectively. The mite density was significantly affected by the sampling site and date.

The search for new antibacterial agents that could decrease bacterial resistance is a subject that is continuously developing. The Gram-negative and Gram-positive bacteria have a metalloproteins group belonging to the M4 family. That is the main virulence factor of these bacteria. In this work, we have used a computational protocol based on the comprehensive analysis of the results of docking, molecular dynamics simulation, MM-PBSA, ligand efficiency, and ADME-Tox properties of ligand designed in silico in the previous manuscript using the Thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family as a target. The principal results obtained were the designed ligands were adequately oriented in the thermolysin active center. The Lig783, Lig2177, and Lig3444 compounds were those with better dynamic behavior, however, when analyzing the results extracted from the ADME-Tox properties, only Lig783 was the best antibacterial agent candidate.

The present work highlights some of the dynamic couplings observed in a series of tests performed in a wave basin with a scaled-model of a FOWT with semi-submersible substructure. The model was moored by means of a conventional chain catenary system and an actively controlled fan was used for emulating the thrust loads during the tests. A set of wave tests comprising regular and irregular waves was done for different wave angles and wind velocities. The experimental records illustrate the main coupling effects involved and how they affect the FOWT motions in waves, especially when the floater presents a non-negligible tilt angle.. In addition, an analysis of the frequency-domain dynamic model was made in order to evaluate its ability to capture these effects properly. The influence of different modes of fan response, floater trim angles (changeable with ballast compensation) and variations of the mooring stiffness with the offsets were investigated in the analysis. Results attest that significant changes in the FOWT responses may indeed arise from coupling effects, thus indicating that caution must be taken when simplifying the hydrodynamic frequency-domain models often used as a basis for the simulation of FOWTs in waves and in in optimization procedures for the design of the floater and mooring lines.

The emergence of electric vehicles has brought new issues such as the problem of rolling element bearings (REBs) operating at high speeds. Losses due to these components in mechanical transmissions are a key issue and must therefore be taken into account right from the design stage of these systems. Among these losses, the one induced by the motion of rolling elements , known as drag loss, becomes predominant in high-speed REBs. Although an experimental approach is still possible, it is difficult to isolate this loss in order to study it properly. A numerical approach based on CFD is therefore a possible way forward, even if other issues arise. The aim of this article is to study the ability of such an approach to correctly estimate the drag coefficient associated with the motion of rolling elements. The influence of the numerical domain extension, the mesh refinement, the simplification of the ring shape and the presence of the cage, on the values of the drag coefficient is presented. While it seems possible to compromise on the calculation domain and mesh size, it appears that the other parameters must be taken into account as much as possible to obtain realistic results.

Explosive boiling is a fast phase transition from an ultra-thin liquid film to vapor under an extremely high heat flux, which typically has been studied using molecular dynamics simulation (MDS) method. The present MDS study investigated the explosive boiling of a liquid argon nanofilm over different solid copper surfaces with different nanowall patterns including parallel and cross nanowalls. For each surface, atomic motion trajectories, number of liquid and vapor argon atoms, heat flux, and, mainly, onset time of explosive boiling were investigated. The simulation results indicated that explosive boiling occurs earlier on parallel and cross nanowall surfaces than on an ideally smooth surface, regardless of the topology and configuration of nanowalls. Moreover, the results revealed that by using the cross nanowall surfaces, the onset time of explosive boiling decreased by 0.7–4% compared to the parallel nanowall surfaces. In addition, it was found that the onset time of explosive boiling strongly depends on the potential energy barrier and the movement space between nanowalls for both parallel and cross nanowall surfaces. Furthermore, simulation findings showed that even though increasing the height of cross nanowalls increases heat flux and temperature of the fluid argon domain, it does not necessarily result in a shorter onset time of explosive boiling. These findings demonstrate the capability of cross nanowall surfaces for explosive boiling, thereby could be utilized in future surface design for thermal management applications.

The population parameters of the ecologically important mud shrimp Upogebia major were analyzed from 2012 to 2015 in tidal flats in Seonjaedo and Jugyo on the West coast of Korea. The shrimp density averaged 265/m2 in Seonjaedo and 118/m2 in Jugyo. The sex ratio varied monthly, often male-biased, but by size, males were significantly dominant, with a carapace length (CL) over 30 mm. Although the shrimp settled almost annually, only a single size-group was observed from 2012 to 2014. The recruitment in Jugyo in 2014 was notably successful, resulting in two cohorts persisting until 2015. Many shrimp were parasitized at varying local rates: 6.0% in Seonjaedo and 37.1% in Jugyo. The growth curves revealed that the shrimp grew annually after settlement, reaching CLs of 11.90, 18.24, and 23.02 mm in Seonjaedo and 13.73, 20.86, and 25.82 mm in Jugyo. Annual mortality was 77.2% in Seonjaedo and 67.4% in Jugyo. The estimated lifespan (tmax) was 10 years in Seonjaedo and 8 years in Jugyo, whereas the 2010 cohort in Jugyo largely disappeared in 5 years. Ovigerous females appeared from November to June and benthic juveniles between June and September. The shrimp’s growth was slower relative to other East Asian populations, likely due to colder sea water temperatures and altered food conditions from a higher shrimp density.

The Hollow fiber membrane contactor (HFMC) is an intensification process that combines membrane and absorption technologies, being a technology in expansion, so the dynamics of this process is crucial for an increase in industrial scale-up. In this manuscript a rigorous dynamic model of an HFMC is developed and simulated in Python software for the absorption of post-combustion CO2 using a monoethanolamine (MEA) solution, which was validated using available data in literature in steady state. Dynamic simulations were performed to analyze the model's capability to predict the effect of disturbances on the responses of CO2 capture ratio and loading. Four distinct experiments were conducted by step changes and pulse disturbances at the following variables: gas and liquid volumetric flow rates, CO2 composition in flue gases, and CO2 lean load. The gas phase showed a faster response compared to the liquid. The CO2 capture ratio and rich loading presented opposite responses when disturbing both liquid flows, and for the composition and lean loading variations, the capture ratio presented an inverse response characteristic, while the loading showed a delayed response. As the model proved to be capable of returning to the reference state, it can potentially be used for control studies purposes.

Wear usually occurs in the loaded part of hydrodynamic bearings and leads the bearing geometry imperfections. This paper investigates the effects of wear-induced geometric imperfections of tilting pad journal bearings (TPJBs) on the dynamic behavior of the system. Furthermore, the effect of wear on the journal-bearing rub-induced contact pressure severity is investigated. A novel tribo-dynamic model is proposed for a flexible rotor-worn TPJB which integrates a mixed elastohydrodynamic model with a rotor-worn TPJB thermal and dynamic model to assess the effects of the bearing wear progression on the rotor-TPJB behavior. Based on the results, wear changes the temperature distribution of the pads and oil film as well as the dynamic behavior of the system. Dynamic simulations reveal a higher vibration level and contact pressure for the worn TPJBs near the system's critical speed and service speed. Finally, thermal and dynamic condition indicators are suggested to detect TPJB wear severity at its early stages.

This paper proposes the use of non-uniform extended surfaces installed externally to the tubes of the radiation section of fired heaters, in order to obtain a better heat flux distribution to the coils. To this end, the heat transfer mechanisms present in such equipment were studied through computational fluid dynamics (CFD), using simplified geometries that represent typical sizes of fired heaters. Also, a simplified model for the combustion was considered. Although this model oversimplifies the physics of the problem, it was able to give satisfactory results for the parameters being optimized, considering the main objective of this paper, that is to minimize the non-uniformity of heat flux in the tubes of the radiant section of fired heaters. It was possible to obtain optimized geometric parameters for different types of extended surfaces evaluated, coupling the results of these models with the Particle Swarm optimization method through the use of a response surface technique,. The results indicate a significant improvement in the uniformity of the heat flux distribution to the tubes through the use of the proposed extended surfaces. Thus, this solution reveals to be an interesting alternative to reduce the risks of fluid degradation and coking formation. Future studies must investigate the non-uniformity of the heat flux due to the presence of the flame and consider the interaction between the reactive flow and the participating medium. Nevertheless, this paper presents some results that justify the optimization of such extended surfaces taking into consideration thermal radiation.

Backgroumd: The feeling of nasal obstruction is one of the most complaints of the Ear Nose and Throats (ENT) patients. The reason of this complaint is variable, such as Nasal Septal Deviation (NSD). NSD is a significant obstacle to normal respiration and the volume of air entering the lungs. Understanding how the deviation causes the obstruction is so important, because it leads to better management of this disease. Rhinomanometry and acoustic rhinometry are methods that are used for objective evaluation of upper airway, but they are semi invasive and the accuracy are not guaranteed. With development of Computed Tomography (CT scan) and Computational Fluid Dynamics (CFD), numerical studies on airflow in different parts of the nasal cavity have been performed. Objectives: The purpose of this study was to compare nasal airflow patterns between patient with NSD and healthy nasal cavity using a computational fluid dynamics (CFD) Methods: A patient with NSD and a healthy human were selected. Using CFD, the maximal airflow velocity, nasal resistance, maximal Wall Shear Stress (WSS), and pressure drop in bilateral nostrils of both cases were assessed. Results: Pressure and velocity profiles are evaluated at a mass flow rate of 17.4 Liters Per Minute (LPM). The velocity profile shows an abnormal flow profile in the septal deviated nasal cavity and the peak velocity is observed at the middle nasal region, whereas this point is at the nasal valve level in a healthy nasal cavity. Wall shear stress (WSS) caused by NSD is lower than in normal nasal cavities. The pressure drop in a nasal cavity with deviated septum is higher than in a healthy nasal cavity. Based on the results of this investigation nasal resistance in NSD was higher than in normal, healthy nasal cavity. Conclusions: NSD plays an important role in nasal airflow regime and it results in the feeling of obstruction comparing to normal nasal cavity. Also there is a promising future for CFD to become a useful tool in understanding airflow physiology and pathology.

The human serotonin transporter (hSERT) terminates neurotransmission by removing serotonin from the synaptic cleft, which is an essential process plays an important role in depression. In addition to substrate serotonin, hSERT is also the target of drugs of abuse like cocaine and clinically used antidepressants such as escitalopram and paroxetine. To date, few studies attempt to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of hSERT. The high-resolution X-ray structure of hSERT resolved recently enables us to theoretically study the unbinding of the above four ligands against the S1 or S2 site of hSERT, by means of molecular docking, molecular dynamics (MD) and potential of mean force (PMF) simulations. We proved that for either the S1 or S2 site, the other three ligands (cocaine, escitalopram and paroxetine) are much more favorable than the original substrate serotonin, whether in kinetics along the unbinding pathways or in thermodynamics at the equilibrium states. Furthermore, the S1 site is much more favorable than the S2 site, for each ligand. Interestingly, inspection revealed that there are ~ 3Å lengths between the allosteric site of serotonin and cocaine, and an unseen un-binding pathway for escitalopram at the S1 site except for verification of the broadest trail.

The gravitational charge should be the energy instead of mass. This modification will lead to some different results and the experiments to test are also presented. Especially, we propose a scheme to achieve the negative energy and gravitational repulsive force in the lab.

Remote sensing plays a central role in the assessment of environmental phenomena and has increasingly become a powerful tool for monitoring shorelines, rivers morphology, flood waves delineation and floods assessment. Optical based monitoring and characterization of river evolution at long time scales is a key tool in fluvial geomorphology. However, the evolution occurring during extreme events is crucial for the understanding of the river dynamics under severe flow conditions and requires the processing of data from active sensors to overcome cloud obstructions. This work proposes a cloud-based unsupervised algorithm for the intra-event monitoring of river dynamics during extreme flow conditions based on time series of Sentinel-1 SAR data. The method allows the extraction of multi-temporal series of spatially explicit geometric parameters at high time and spatial resolutions, linking them to the hydrometric levels acquired by reference gauge stations. Intra-event reconstruction of inundation dynamics has led to the estimation of the relationship between hydrometric level and wet area extension and the assessment of bank erosion phenomena. Time series of SAR acquisitions, provided by Copernicus Sentinel-1 satellites, were analyzed to quantify changes in the wet area of a reach of the Tagliamento river under different flow conditions. The algorithm, developed within the Python-API of GEE, first empowers the Sentinel-1 images with the hydrometric level, then involves radiometric slope correction and speckle noise filtering. The Otsu method is then used for image segmentation leading to a water and dry land binary classification. Results support many types of analysis about river dynamics, including morphological changes, floods monitoring and relief efforts and bio-physical habitat dynamics. The results encourage future advancements and applications of the algorithm, specifically exploring SAR data from ICEYE and Capella Space constellations, which offer significantly higher spatial and temporal resolutions compared to Sentinel-1 data.

Background: Colorectal cancer is considered the third most fetal among all type of cancer. Spleen tyrosine kinase (SYK) is a non-receptor type tyrosine-protein that plays crucial role in signaling mediated via immune receptor. We adopted an onco-informatics analysis to evaluate the SYK expression and prognostic value of SYK in colorectal cancer, and identification of potential phytochemicals which may inhibit overexpression of SYK protein as well as minimized colorectal cancer. Materials & Methods: Differential expression of SYK gene was analyzed using the several transcriptomic databases including Oncomine, UALCAN, GENT2 and GEPIA2. The server, cBioPortal was used to analyze mutation and copy number alterations whereas GENT2, GEPIA, OncoLnc and PrognoScan were employed to examine the survival rate. A protein-protein interaction network of SYK and co-expressed genes of SYK was conducted via GeneMANIA. Considering SYK gene encoding protein as drug target, selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. YASARA molecular dynamics simulators were applied for the post validation of the molecular docking data. Results: We have observed significant overexpression of mRNA expression levels of SYK gene colorectal adenocarcinoma (COAD) samples compared with normal tissues. Significant methylation level and various genetic alterations are assembled in SYK gene which can lead to the development of colorectal cancer. As a result, lower level of SYK expression was related to the more chances of patients’ survival by which all the outcomes from the multiple bioinformatics platforms and web resources have demonstrated the significant evidences that the SYK kinsase can possess as a potential biomarker for the treatment of colorectal cancer. Here, aromatic phytochemicals namely, Kaempferol and Glabridin targeting SYK showed more stability compared to controls and may be useful for the treatment of colorectal cancer. Conclusion: Our study showed dysregulated expression of SYK in colorectal cancer and potentiality to act as a biomarker for the prognosis of CRC. Moreover, we have shown phytochemicals (Kaempferol and Glabridin) target SYK as potential treatment strategies and drug repositioning potentiality in colorectal cancer.

Assessment of the trends of land cover and vegetation dynamics (VD) using remote sensing (RS) and indicators such as anthropogenic activities and the socio-demographic information is essential in order to make proper planning for sustainable management. This paper attempts to evaluate land cover change (LCC) and VD in Kebbi State, Nigeria using historical Landsat data from 1986-2016 by means of remote sensing. The Driver-Pressure-State-Impact-Response (DPSIR) framework was later employed using both primary and secondary data for a better understanding of the drivers, the state of the environmental condition, the causes as well as the impact of the change. The images were classified into five thematic land cover classes as Dense Vegetation, shrubs/built area, farmland, bare/grassland and water body by means of Maximum likelihood supervised classification technique in accordance with Anderson classification scheme level 1, with acceptable accuracy. Pre-classification and post-classification change detection (CD) methodologies were executed using Normalized difference vegetation index (NDVI) and Image differencing respectively. The study illustrates a steady decline in dense vegetation and shrubs/build areas while farmland and bare/grassland increases, however, water bodies remain unchanged. The DPSIR pin-point that the major drivers of change in the study area have been the pressing need for farming land as the population grows and socioeconomic demands including fuelwood consumption and endemic poverty. Expansion of Farming land, fuelwood consumption and the need for construction materials are identified as the main key elements exerting pressure for the change. The state of the condition indicates a steady decline in dense vegetation and shrubs areas while farmland and bare/grassland are increasing significantly. The impacts include land degradation, the decline in the provision ecosystem goods and services, biodiversity loss through loss of habitats. The study, however, noted that many international and national policies in response to land degradation are channelled toward land restoration and remediating of the environment, through afforestation programs and improving the livelihood of the rural people through providing alternative income sources since they depend heavily on land for sustenance. However, the state governments, communities and individual commonly organized annual tree planting campaign with the main purpose of environmental protection.

In this paper an integrated methodology for the coupling between 1D- and 3D-CFD simulation codes is presented, which has been developed to support the design and calibration of new diesel engines. The aim of the proposed methodology is to couple 1D engine models, which may be available in the early-stage engine development phases, with 3D predictive combustion simulations, in order to obtain reliable estimates of engine performance and emissions for newly designed automotive diesel engines. The coupling procedure features simulations performed in 1D-CFD by means of GT-SUITE and in 3D-CFD by means of Converge, executed within a specifically designed calculation methodology. An assessment of the coupling procedure has been performed by comparing its results with experimental data acquired on an automotive Diesel engine, considering different working points including both part load and full load conditions. Different multiple injection schedules have been evaluated for part-load operation, including pre and post injections. The proposed methodology, featuring detailed 3D chemistry modeling, was proven to be capable to properly assess pollutant formation, specifically to estimate NOx concentrations. Soot formation trend was also well-matched for most of the explored working points. The proposed procedure can therefore be considered as a suitable methodology to support the design and calibration of new Diesel engines, thanks to its ability to provide reliable engine performance and emissions estimations from the early-stage of a new engine development.

In this essay, I revisit Neural Networks (NNs) through the lens of evolutionary dynamics. From the two most important features of NNs, I recover the two most general equations of evolutionary dynamics. These two equations may thus serve as a connection between NNs and a body of knowledge that has been built over multiple centuries and has found application across a vast range of disciplines. This connection may therefore also help explain why NNs with the two features in question are applicable across a much broader range of domains than initially envisioned.

Dynamics of human populations can be affected by various socio-economic factors through their influence on the natality and mortality rates, and on the migration intensity and directions. In this work we study an economic-demographic model which takes into account the dependence of the wealth production rate on the available resources. In the case of nonlocal consumption of resources the homogeneous in space wealth-population distribution is replaced by a periodic in space distribution for which the total wealth increases. For the global consumption of resources, if the wealth redistribution is small enough, then the homogeneous distribution is replaced by a heterogeneous one with a single wealth accumulation center. Thus, economic and demographic characteristics of nonlocal and global economies can be quite different in comparison with the local economy.

Climate projections show that southern Indonesia such as West Nusa Tenggara is projected to experience a lower precipitation and higher temperatures. To date, research on climate change impact on Indonesian rice production yield is limited. As climate change is projected to decrease rainfall and to increase temperatures, this paper offers a qualitative analysis using system archetypes to understand the impacts of climate change on rice production. Two system archetypes are identified including Limits to Growth and Success to Successful. Both archetypes explain that rice production is hampered by high minimum temperature as photosynthesis output is decreased by increasing respiration. This paper shows that using a simple tool, system archetypes, we can describe the impacts of climate change on rice production. The outputs of this study such as a causal loop diagram and system archetypes can be a basis to develop a simulation model in understanding the impacts of climate change on main crops.

We have recently proposed a pre-quantum, pre-space-time theory as a matrix-valued Lagrangian dynamics on an octonionic space-time. This pre-theory offers the prospect of unifying the internal symmetries of the standard model with gravity. It can also predict the values of free parameters of the standard model, because these parameters arising in the Lagrangian are related to the algebra of the octonions which define the underlying non-commutative space-time on which the dynamical degrees of freedom evolve. These free parameters are related to the algebra $J_3(\mathbb O)$ [exceptional Jordan algebra] which in turn is related to the three fermion generations. The exceptional Jordan algebra [also known as the Albert algebra] is the finite dimensional algebra of 3x3 Hermitean matrices with octonionic entries. Its automorphism group is the exceptional Lie group $F_4$. These matrices admit a cubic characteristic equation whose eigenvalues are real and depend on the invariant trace, determinant, and an inner product made from the Jordan matrix. Also, there is some evidence in the literature that the groups $F_4$ and $E_6$ could play a role in the unification of the standard model symmetries, including the Lorentz symmetry. The octonion algebra is known to correctly yield the electric charge values (0, 1/3, 2/3, 1) for standard model fermions, via the eigenvalues of a $U(1)$ number operator, identified with $U(1)_{em}$. In the present article, we use the same octonionic representation of the fermions to compute the eigenvalues of the characteristic equation of the Albert algebra, and compare the resulting eigenvalues with the known mass ratios for quarks and leptons. We find that the ratios of the eigenvalues correctly reproduce the [square root of the] known mass ratios for quarks and charged leptons. We also propose a diagrammatic representation of the standard model bosons, Higgs and three fermion generations, in terms of the octonions, exhibiting an $F_4$ and $E_6$ symmetry. In conjunction with the trace dynamics Lagrangian, the Jordan eigenvalues also provide a first principles theoretical derivation of the low energy value of the fine structure constant, yielding the value $1/137.04006$. The Karolyhazy correction to this value gives an exact match with the measured value of the constant, after assuming a specific value for the electro-weak symmetry breaking energy scale.

We report the results of the characterization of local Monte Carlo (MC) dynamics of an equilibrium bond fluctuation model polymer matrix (BFM), in time interval typical for MC simulations of non-linear optical phenomena in host-guest systems. The study contributes to the physical picture of the dynamical aspects of quasi-binary mosaic states characterized previously in the static regime. The polymer dynamics was studied at three temperatures (below, above and close to the glass transition), using time-dependent generalization of the static parameters which characterize local free volume and local mobility of the matrix. Those parameters play the central role in the kinetic MC model of host-guest systems. The analysis was done in terms of the probability distributions of instantaneous and time-averaged local parameters. The main result is the characterization of time scales characteristic of various local structural processes. Slowing down effects close to the glass transition are clearly marked. The approach yields an elegant geometric criterion for the glass transition temperature. A simplified quantitative physical picture of the dynamics of guest molecules dispersed in BFM matrix at low temperatures offers a starting point for stochastic modeling of host-guest systems.

Shut-in after fracturing is generally adopted for wells in shale oil reservoirs, and imbibition occurring in matrix nanopores has been proven as an effective way to improve recovery. In this research, the molecular dynamics (MD) simulation was used to investigate the effects of wettability and pressure on nanopores imbibition during shut-in for a typical shale reservoir Jimsar. The results indicate that the microscopic advancement mechanism of the imbibition front is the competitive adsorption between “interfacial water molecules” at the imbibition front and “adsorbed oil molecules” on the pore wall. The essence of spontaneous imbibition involves the adsorption and aggregation of water molecules onto the hydroxyl groups on the pore wall. The flow characteristics of shale oil suggest that the overall push of the injected water to the oil phase is the main reason for the displacement of adsorbed oil molecules. Thus, shale oil especially the heavy hydrocarbon component in the adsorbed layer tends to slip on the walls. However, the weak slip ability of heavy components on the wall surface is an important reason that restricts the displacement efficiency of shale oil during spontaneous imbibition. The effectiveness of spontaneous imbibition is strongly dependent on the hydrophilicity of the matrix pore's wall. The better hydrophilicity of the matrix pore's wall facilitates higher levels of adsorption and accumulation of water molecules on the pore wall and requires less time for “interfacial water molecules” to compete with adsorbed oil molecules. During the forced imbibition process, the pressure difference acts on both the bulk oil and the boundary adsorption oil, but mainly on the bulk oil, which leads to the occurrence of wetting hysteresis. Meanwhile, shale oil still existing in the pore always maintains a good stratified adsorption structure. Because of the wetting hysteresis phenomenon, as the pressure difference increases, the imbibition effect gradually increases, but the actual capillary pressure gradually decreases and there is a loss in the imbibition velocity relative to the theoretical value. Simultaneously, the decline in hydrophilicity further weakens the synergistic effect of pressure difference because of the more pronounced wetting hysteresis. Thus, selecting an appropriate well pressure enables cost savings and maximizes the utilization of the formation's natural power for EOR.

Stability considerations play a central role in structural dynamics to determine states that are robust against perturbations during the operation. Linear stability concepts, such as the complex eigenvalue analysis, constitute the core of analysis approaches in engineering reality. However, most stability concepts are limited to local perturbations, i.e. they can only measure a state’s stability against small perturbations. Recently, the concept of basin stability has been proposed as a global stability concept for multi-stable systems. As multi-stability is a well-known property of a range of nonlinear dynamical systems, this work studies the basin stability of bi-stable mechanical oscillators that are affected and self-excited by dry friction. The results indicate how the basin stability complements the classical binary stability concepts for quantifying how stable a state is given a set of permissible perturbations.

The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Recent experimental studies, however, have started to shed more light on the mechanisms and spatial dynamics of viral spread within hosts. Here, we review these experimental studies as well as the limited number of computational modeling efforts that have begun to integrate spatial considerations for understanding within-host viral spread. We limit our review to influenza virus to highlight key mechanisms affecting spatial aspects of viral spread for pathogens of the respiratory tract. There is considerable empirical evidence for highly spatial within-host spread of influenza virus, yet few computational modeling studies that shed light on possible factors that structure the dynamics of this spatial spread. In existing modeling studies, there is also a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature to provide informed theoretical expectations for what viral and host factors may impact the spatial patterns of within-host viral dynamics and for how spatial spread will affect the genetic composition of within-host viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host influenza virus spread and the potential for within-host spatial considerations to inform the development of disease control strategies.

The construction of 22 dams on the Euphrates has reduced the flow of this river, changed the hydrology and destroyed the ecosystem. In order to understand the effect of extreme management on water, 4 coastal points from the Euphrates catchment area were selected to investigate the dynamics of the water level. Using the Cadmium method, the radius of each point was calculated to be 140 meters to study the NDWI index and satellite monitoring. 546 Landsat 8 OLI/TIRS satellite images from 2013 to 2022 were used. The analysis showed that the water level of the Euphrates in the fourth coordinate is directly related to the data of the first and third coordinates and the dynamics of the water level in the fourth coordinate is 3.6 to 4.2 percent of the first coordinate and another 5.2 to 5.9 percent is affected by the third coordinate. Is. Also, the data from August 2013 to 2022 were analyzed. The results showed that the correlation coefficients of the data related to the first coordinates are related to the third and fourth coordinates. It was proved that fluctuations in the first coordinate led to 27% change in the third coordinate in the months of August. Also, the changes in the first point caused 18-19.8% change in the dynamic level of water in the fourth point, and 22.5% of the changes in the water level in the fourth coordinate were affected by the third point.

Turbulence is a fluid dynamic problem refractory to mathematical treatment. Examining a theoretical model of liquid water flowing in a cylinder at different Raleigh numbers, we propose a novel approach to elucidate the first stages of turbulent flows. The weakly bonded molecular assemblies of liquid water form a fluctuating branched polymer in which every micro-cluster displays different density. Against the common view of liquid water as an incompressible and continuous fluid, we suggest that the occurrence of transient local aggregates could be able to generate the vortices and eddies that are the hallmarks of turbulence. We quantify the local changes in velocity, diameter and density required to engender “obstacles” to the average flow. Then, we show how these microstructures, equipped with different Raleigh numbers and characterized by high percolation index, could generate boundary layers that contribute to micro-vortices production. We conclude that the genesis of turbulence cannot be assessed in terms of collective phenomena, rather is sustained, among many other factors, by the underrated microscopic inhomogeneities of fluids like liquid water.

Deep eutectic solvents (DESs) are one of the most rapidly evolving types of solvents, appearing in a broad range of applications such as nanotechnology, electrochemistry, biomass transformation, pharmaceuticals, membrane technology, biocomposite development, modern 3D-printing, and many others. The range of their applicability continues to expand, which demands the development of new DESs with improved properties. To do so requires an understanding of the fundamental relationship between the structure and properties of DESs. Computer simulation and machine learning techniques provide a fruitful approach as they can provide predictions, reveal physical mechanisms and readily be linked to experiments. This review is devoted to the computational research of DESs and describes technical features of DES simulations and the corresponding perspectives on various DES applications. The aim is to demonstrate the current frontiers of computational research of DESs and discuss future perspectives.

Carcinus maenas (the “shore crab” or “European green crab”) is a very proficient invader (considered to be one of the world’s 100 worst invaders by the IUCN) due to its phenotypic plasticity, wide temperature and salinity tolerance, and an extensive omnivorous diet. Native to Atlantic Europe, it has established two well‐studied nonindigenous populations in the northwestern Atlantic and northeastern Pacific and less‐studied populations in Australia, Argentina and South Africa. Green crabs are eurythermal and euryhaline as adults, but they are limited to temperate coastlines due to more restrictive temperature requirements for breeding and larval development. They cannot tolerate wave‐swept open shores so are found in wave‐protected sheltered bays, estuaries and harbors. Carcinus maenas has been the subject of numerous papers, with over 1000 published in the past decade. This review provides an up‐to‐date account of the current published information on the life history and population dynamics of this very important species, including genetic differentiation, habitat preferences, physical parameter tolerances, reproduction and larval development, sizes of crabs, densities of populations, sex ratios, ecosystem dynamics and ecological impacts in the various established global populations of green crabs.

This work focused on Diplectanum aequans, a gill parasite of Dicentrarchus labrax. Analyzes allowed us to detect factors regulating parasites distribution on Corsican fish-farms, and to highlight the ecological structure of D. aequans communities on gills of fish. The study of parasite distribution showed that bigger fish appear more parasitized and that the infection dynamics of D. aequans can be explained by several factors such as biotic factors or farm environment conditions. The study of gill repartition of D. aequans showed that parasites tend to have a homogeneous distribution with no statistically significant difference in infection between two sides on each fish. However, the distribution of the number of parasites on gill arches varies according to the total number of parasites. Results differ depending on infection degree and host weight. When parasites are numerous, the individuals are distributed on the gill arches according to an antero-posterior gradient, while with low rates of infection, the parasites are randomly distributed on the 4 arches. The spatial distribution of D. aequans appears to be determined by the differential action of water flow through gill arch and the size of anterior arches. We also proposed a tool in order to reduce the sampling effort and allow optimal exploitation for fish farmers.

The definitive negative results of various direct searches for dark matter particles and non-observation of them has increasingly indicated that we should consider alternate models like the Modification of Newtonian Dynamics (MOND) and Modification of Newtonian Gravity (MONG). It is puzzling how the Oort cloud, despite its great distance from the Sun, is gravitationally bound to the Sun’s gravity. In this work, we suggest that this could be explained by the modifications to Newtonian dynamics (MOND) and to gravity (MONG).

The phenomenon of droplet impact on moving surfaces is widely observed in fields such as transportation, rotating machinery, and inkjet printing. Droplets exhibit non-axisymmetric behavior due to the motion of solid surfaces which significantly determines core parameters such as contact time, maximum spreading radius, and bounding velocity, thereby affecting the efficiency of related applications. In this study, we focus on kinetics and morphology of the non-axisymmetric bouncing behaviors for droplets impacting on a moving superhydrophobic surface (SHPS) within the normal (Wen) and tangential (Wet) Weber numbers. Considering the influences of moving surface on the contact area and contact time, the previous scaling formula for the horizontal velocity of droplets has been improved. Based on the velocity superposition hypothesis, we establish a theoretical model for the ratio of the maximum spreading radius at both ends depending on Wen and Wet. This research provides both experimental and theoretical evidence for understanding and controlling the non-axisymmetric behavior of droplets impacting on moving surfaces.

Studying the dynamics of urban form means questioning the processes of evolution of the form in general. The discussion on the architecture of buildings and urban spaces has drawn the concept of adaptation from the theories of natural evolution. These notes propose a reflection on the opposite concept of exaptation proposed by the biologist and paleontologist Stephen Jay Gould in 1982. Through some examples (some different transformations of the Roman amphitheaters of the imperial age and the metamorphoses that occurred to the Chinese urban fabrics, originally made by courtyard houses, in the contemporary city), it is possible to extend to urban form the idea of casual co-optation for new uses of organs and anatomical parts developed for other reasons. This kind of reflections opens up innovative considerations on the potential of transitional urban analysis and its repercussions on evolutive urban transformation processes.

This article belongs in the emerging area of research seeking ways to depolarize societies in the short run (around events such elections) as well as in a sustainable fashion. We approach the depolarization process with a model of three homophilic groups (US Democrats, Republicans and Independents interacting in the context of upcoming federal elections). We expand a previous polarization model, which assumed that each individual interacts with all other individuals in its group with mean-field interactions. We add a depolarization field which is analogous to the Blume-Capel model’s crystal field. There are currently numerous depolarization efforts around the world, some of which act in ways similar to this depolarization field. We find that for low values of the depolarization field, the system continues to be polarized. When the depolarization field increases, the polarization decreases.

Norepinephrine (NE) uptake through the NE transporter (NET) is the primary mechanism to ter-minate the action of this neurotransmitter. Dysregulation of brain NE levels is associated with various conditions, including attention deficits, depression, and Alzheimer's disease. Recently, we identified an interaction between the related dopamine (DA) transporter (DAT) and G protein βγ subunits. Activation of Gβγ in cells and brain slices leads to DA efflux through DAT. However, the potential interaction between Gβγ and NET has not been reported. Here, we used a combina-tion of molecular modeling approaches to elucidate the structural details of the NET/Gβγ inter-action, supported by experimental evidence. Through 1.5µs of molecular dynamic simulation, we observed a favorable NET/Gβγ interaction mediated by the intracellular carboxy terminus of NET. As a consequence, the binding energy of NE for NET also changes resulting in alterations of the electrostatic profile of NET. We propose that these changes mediate the NE efflux effect. Fi-nally, we provide experimental evidence demonstrating that Gβγ physically interacts with NET and that the Gβγ activator mSIRK induces NE efflux through the transporter. These findings identified a novel interaction between Gβγ and NET and highlighted its potential implications in the regulation of NE neurotransmission and associated disorders.

In this study, we present more than 8 years of observations of the quasi-16-day wave (Q16DW) in the mesosphere and lower thermosphere (MLT) wind at middle latitudes observed by the Mengcheng (33.4°N, 116.5°E) meteor radar. The long-term variation in amplitudes calculated from the data between April 2014 and December 2022 shows enhanced wave activity during winter and early spring (near equinox) and suppressed wave activity during the summer. The Q16DWs are relatively weak in the meridional wind. During the winter months, the Q16DWs in the zonal component exhibit a burst below 85 km, and their amplitudes reach up to 10 m/s. In the early spring, the Q16DWs strengthen above 90 km with amplitudes in excess of 12 m/s. The phase differences between the zonal and meridional components of the Q16DW are, on average, slightly smaller than 90°, suggesting the existence of orthogonal relationships between them. During strong bursts, the periods of the Q16DW in winter range between 15 and 18 d, whereas in winter, the periods tend to be more diffuse. The wintertime Q16DW is amplified, on average, when the zonal wind shear peaks, suggesting that barotropic instability may be one source of Q16DW. Q16DW amplitudes exhibit considerable interannual variability; however, a relationship between the 11-year solar cycle and the Q16DW is not found.

The temperature-assisted laser shock process has shown promising prospects in the fields of forming manufacturing and surface strengthening. However, large-scale application of this process is limited by the instability and failure of confinement medium at high temperatures (≥300 ℃). Aiming at this problem, we propose a novel laser shock strategy based on Leidenfrost effect, where the suspended droplets are utilized as the confinement medium. According to the sequence of images acquired by time delay system and high-speed camera, the droplet dynamics behavior is studied. The focusing enhancement effect of the droplet is comprehensively explored. And the correlations between droplet size, ambient temperature, vapor layer thickness and focusing effect are investigated. Combining the dynamics and focusing enhancement effect of droplets, a theoretical model of laser shock pressure under droplet confinement is established. Finally, the effectiveness and feasibility of the droplet-based laser shock strategy in high temperature processing environments are verified by typical applications in laser shock forming and laser shock peening fields. The results show that the droplet-based laser shock process presents better forming effect. And the mechanical property tests demonstrate that this process can obtain the simultaneous improvement of the strength (~51%) and ductility (~6.4%) of annealed Cu. The multiscale plasticity mechanisms of the strengthened material are comprehensively investigated. We believe that this low-energy, low-cost and high-quality process can provide a new solution for the industrial application of laser shock at high temperatures.

The spread of ideas is a fundamental concern of today’s news ecology. Understanding the dynamics of the spread of information and its co-option by interested parties is of critical importance. Research on this topic has shown that individuals tend to cluster in echo-chambers and are driven by confirmation bias. In this paper, we leverage the active inference framework to provide an in silico model of confirmation bias and its effect on echo-chamber formation. We build a model based on active inference, where agents tend to sample information in order to justify their own view of reality, which eventually leads to them to have a high degree of certainty about their own beliefs. We show that, once agents have reached a certain level of certainty about their beliefs, it becomes very difficult to get them to change their views. This system of self-confirming beliefs is upheld and reinforced by the evolving relationship between agent's beliefs and its observations, which over time will continue to provide evidence for their ingrained ideas about the world. The epistemic communities that are consolidated by these shared beliefs, in turn, tend to produce perceptions of reality that reinforce those shared beliefs. We provide an active inference account of this community formation mechanism. We postulate that agents are driven by the epistemic value that they obtain from sampling or observing the behaviors of other agents. Inspired by digital social networks like Twitter, we build a generative model in which agents generate observable social claims or posts (e.g. `tweets') while reading the socially-observable claims of other agents, that lend support towards one of two mutually-exclusive abstract topics. Agents can choose which other agent they pay attention to at each timestep, and crucially who they attend to and what they choose to read influences their beliefs about the world. Agents also assess their local network’s perspective, influencing which kinds of posts they expect to see other agents making. The model was built and simulated simulated using the freely-available Python package pymdp. The proposed active inference model can reproduce the formation of echo-chambers over social networks, and gives us insight into the cognitive processes that lead to this phenomenon.

Molecular Dynamics (MD) simulations model motion of molecules in atomistic detail and aid in drug design. While simulations on large systems may require several days to complete, analysis of terabytes of data generated in the process could also be time consuming. Recent studies captured exciting and dramatic drug-receptor interactions under cell-like complex conditions. Such advances make simulations of biomolecular interactions more realistic, insightful, and informative and have potential to make drug design more realistic. However, currently available resources and techniques do not provide, in reasonable time, a comprehensive understanding of events seen in simulations. We demonstrate that big data approach results in significant speedups, and provides rapid insights into simulations performed. Advancing this improvement, we propose a scalable, self-tuning, and responsive framework based on Cloud-infrastructure to accomplish the best possible MD studies with given priorities and within available resources.

Leigh Van Valen was an American evolutionary biologist who made major contributions to evolutionary theory and is particularly remembered by his groundbreaking paper "A New Evolutionary Law" (1973) where he provided evidence from fossil record data that this law maintains that the probability of extinction within any group remains es­sentially constant through time. In order to explain such unexpected result, Van Valen formulated a very influential idea that he dubbed the "Red Queen hypothesis". It states that the constant decay must be a consequence of evolutionary interactions among connected species within ecological networks. In Van Valen's picture, species do not merely evolve: they also coevolve with other species. As a consequence, when thinking in adaptation to an external environment, the other species must be considered as part (may be a major part) of such external world. Van Valen's law provided the first complex systems theory of coevolutionary dynamics and inspired a whole range of theoretical and experimental developments and scholars from very diverse fields, from economics to physics. In that respect, Leigh Van Valen's contribution percolated far beyond its original formulation. Red Queen arms races are nowadays considered a widespread feature of complex adaptive systems.

The COVID-19 pandemic of 2020 changed the way we interact and engage in commerce at a fundamental level. Social distancing and stay-at-home orders leave businesses and cities wondering what economic activity will look like in the future. Given a likely reduction in face-to-face interactions, it is important to better understand how social interactivity influences economic outcomes. Here we measure the effect of social interactions in the workforce on patent production and economic efficiency. We decompose U.S. occupations into individual work activities, determine which of those activities are associated with face-to-face interactions, and reaggregate the labor force of each U.S. metropolitan statistical area (MSA) into a metric of social interactiveness. We then calculate each MSA’s density of social work activities and find that this measure is more highly correlated with an MSA’s per capita patent production than simple population density. This suggests that density of face-to-face interactions is the important driver of a city’s rate of invention. We close by exploring analogies between the development of cities and the development of stars, suggesting ways these analogies may help frame future research on cities.

In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial physics, droplet evaporation, super hydrophobic surfaces, and wettability etc.

Decoherence with recurrences appear in the dynamics of the one-body density matrix of an $F = 1$ spinor Bose-Einstein condensate, initially prepared in coherent states, in the presence of an external uniform magnetic field and within the single mode approximation. The phenomenon emerges as a many-body effect of the interplay of the quadratic Zeeman effect, that breaks the rotational symmetry, and the spin-spin interactions. By performing full quantum diagonalizations very accurate time evolution of large condensates are analyzed, leading to heuristic analytic expressions for the time dependence of the density matrix, in the weak and strong interacting regimes. We are able to find accurate analytical expressions for both the decoherence and the recurrence times, in terms of the number of atoms and strength parameters, that show remarkable differences depending on the strength of the spin-spin interactions. We discuss the nature of these limits in the light of the thermodynamic limit.

This research article presents the integration of participatory modeling and system dynamics as a novel methodology for the consolidation of social dynamic models for the subsequent evaluation and prioritization of green projects in Colombian post-conflict communities. In the first instance, through participatory work carried out along with the community, it was possible to identify, evaluate and systematize citizen factors in relation to the problems and needs of the region. Second, based on the results obtained, to calibrate a simulation model based on system dynamics that facilitates decision making with regard to the evaluation of green projects. The proposed methodology leads to the conclusion that, with the participation of the community and with a model based on the dynamics of variables such as supply and demand for natural resources of water and land, it is possible to warn decision makers about the variables that can lead to the maximization of investments and thus prioritize and select the most appropriate environmental, social or economic initiatives, that certainly meet the needs or expectations of the involved community. In the future, the model could be used to facilitate the management, administration and control of water and land resources by creating alerts called reserve margins.

We introduce a new, and quite general variational model for opinion dynamics based on pairwise interaction potentials and a range of opinion evolution protocols ranging from random interactions to global synchronous flows in the opinion state space. The model supports the concept of topic “coupling”, allowing opinions held by individuals to be changed via indirect interaction with others on different subjects. Interaction topology is governed by a graph that determines interactions. Our model, which is really a family of variational models, has, as special cases, many of the previously established models for the opinion dynamics. After introducing the model, we study the dynamics of the special case in which the potential is either a tent function or a constructed bell-like curve. We find that even in these relatively simple potential function examples there emerges interesting behavior. We also present results of preliminary numerical explorations of the behavior of the model to motivate questions that can be explored analytically

In a thin-volume photobioreactor where a concentrated suspension of microalgae is circulated throughout the established spatial irradiance gradient, microalgal cells experience a time-variable irradiance. Deploying this feature is the most convenient way of obtaining the so-called “flashing light” effect, improving biomass production in high irradiance. This work investigates the light flashing features of sloping wavy photobioreactors, a recently proposed type, by introducing and validating a Computational Fluid Dynamics model. Two characteristic flow zones (straight top-bottom stream and local recirculation stream), both effective toward light flashing, have been found and characterised: a recirculation-induced frequency of 3.7 Hz and straight flow-induced frequency of 5.6 Hz were estimated. If the channel slope is increased, the recirculation area becomes less stable while the recirculation frequency is nearly constant with flow rate. The validated CFD model is a mighty tool that could be reliably used to further increase the flashing frequency by optimising the design, the dimensions, the installation and the operational parameters of the sloping wavy photobioreactor.

The aim of this paper is to attempt to understand why the popular academic and policy field of promoting, studying and evangelising “entrepreneurship” should have been associated with great success but, in the past twenty years or more in many advanced economies, so much failure. From the US to lesser and developing countries, emerging economies and the European Union, entrepreneurship, especially in regard to start-ups and particularly high-tech start-ups have been in constant more or less recent decline. This is seldom registered in the mainstream literature where a positive and benign profile is generally presented. The paper examines this phenomenon, ties it partly with the “productivity paradox” and seeks tentative hypotheses in relation to the apparent illusions if not delusions regarding “entrepreneurship”.

HIV-1 assembly is a complex mechanism taking place at the plasma membrane of the host cell. It requires nice spatial and temporal coordination to end up with a full immature virus. Researchers have extensively studied HIV-1 assembly molecular mechanism during the past decades, in order to dissect the respective roles of viral proteins, viral genome and host cell factors. Nevertheless, the time course of the process has been observed in living cells only a decade ago. The very recent revolution of optical microscopy, combining high speed and high spatial resolution now permit to study assemblies and their consequences at the single molecule level within (living) cells. In this review, after a short description of these new approaches, we will show how HIV-1 assembly in cells has been revisited using these advanced super resolution microscopy techniques and how much it could make a bridge in studying assembly from the single molecule to the host cell.

Utility perceived by individuals is believed to be different from the utility experienced by that individual. System dynamicists implicitly categorize this phenomenon as a form of bounded rationality and traditionally employ a simple smoothing function to capture it. We challenge this generalization by testing it against an alternative formulation of utility perception that is suggested by modern theories of behavioral economics. In particular, the traditional smoothing formulation is compared with the peak-end rule in a simple theoretical model as well as in a medium-size model of electronic health record implementation. Experimentation with the models reveals that the way utility perception is formulated is important and might affect behavior and policy implications of system dynamics models.

The coordination planning between land use and transportation system is an important premise of solving urban transportation problems and realizing land use integration. This study investigates the interactive and feedback relationship between land use and transportation system from the perspective of access management. By integrating the land use and traffic data from Las Vegas Metropolitan area with the system dynamics model, the causal relationship and causal loop diagrams (CLDs) are introduced to analyze the cause-and-effect relationship and quantitative relationship between the factors of the combined system of land use and transportation, and then sub-models partition and system simulation are performed. The systems dynamics model is established by analyzing the relationship between a series of access management techniques, traffic characteristics, and land use features. The results show that system dynamics model can be used as an effective alternative to model the symbiosis relationship of land use and transportation system for urban planning and construction.

The molecular dynamics simulation has been used to investigate the structural and transport properties of (Ba_0.5-xSr_x)La_0.5InO_3-δ (x=0, 0.1, 0.2) oxygen-ion conductor. The previous studies reported that the ionic conductivity of Ba-doped LaInO3 decreases because Ba dopant forms narrow oxygen path in the lattice, which could hinder the diffusion of oxygen ion. In this study, we reveal the mechanism to improve the ionic conductivity by Ba and Sr co-doping on La site in LaInO3 perovskite oxide. The results show that the ionic conductivity of (Ba_0.5-xSr_x)La_0.5InO_3-δ increases with increasing numbers of Sr ions, which oxygen diffusion paths including Sr ion have larger critical radius than Ba ions. The RDF calculations showed the heights of peak in composition including Sr ions is lower and broaden, so oxygen ions moved easily into other oxygen sites.

Stratified Taylor Couette Flow (STCF) undergoes transient growth. Recent studies have shown that there exists transient amplification in the linear regime of counter-rotating STCF. It is reported that as Gr increases, the maximum amplification factor ($G_0$) initially decays before it eventually starts growing after reaching a certain critical value Gr$_{c}$. Assuming other parameters of the model are kept constant, the value Gr$_{c}$ changes with respect to different speed ratios of the cylinders. The observed decay/growth pattern of $G_0$ is attributed to the interplay between the induced shear and buoyancy. In this study, the mechanism that triggers this observed pattern is investigated. The kinetic budget of the optimal transient perturbation is analysed numerically to simulate the interaction of the shear production (SP), buoyancy production (BP) and other energy components that contributes to the total optimal transient kinetic energy. These contributions affect the total energy by influencing the perturbation to extract kinetic energy (KE) from the mean flow. The decay of $G_0$ resulted from the positive amplification of both BP and SP, while the growth is attributed to the negative and positive amplification of BP and SP, respectively. The optimal SP is positively amplified, implying that there is the possibility of constant linear growth. These findings agree with the linear growth rate for increasing values of Gr.

Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain DNA of living cells. To do so, it needs to interact with and permeate through cell membranes. The pH of biological media may vary quite significantly and this influences H33342 ionization state, and may change its rate of permeation through biomembranes. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 < pH < 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics simulations. While probe insertion occurs for all ionization states, with similar overall equilibrium location, orientation was found to depend on the probe charge, with the neutral form lying mostly parallel and the doubly charged displaying a significant tilt relative to the membrane plane. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy of interaction is negative and is larger at lower pH values. This suggests efficient hydrogen bonding between the probe and the lipid, namely for the protonated +2 form. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from water and octanol partition. This highlights the distinction between lipophilicity and hydrophobicity, and the importance of considering association with lipid bilayers when predicting the affinity for biomembranes.

The main objective of this work is to study the effects of carbon nanotubes (CNT) on the strength and electrical properties of cement mortar. Molecular dynamic simulations (MDS) were carried out for the mechanical and electrical properties of the cementitious composite and the associated mechanisms. To model the atomic structure of the Calcium-Silicate-Hydrates (C-S-H) gel, tobermorite 11Å was chosen. Single-walled carbon nanotubes (SWCNTs) embedded in tobermorite structure were tested numerically. In particular, the effect of the concentration of CNT in cement paste was studied. An innovative experiment of electrical characterization of a cementitious composite of carbon nanotubes has been developed.

Experimental test facilities are generally characterised using linear transfer functions to relate the wavemaker forcing amplitude to wave elevation at a probe located in the wavetank. Second and third order correction methods are becoming available but are limited to certain ranges of waves in their applicability. Artificial intelligence has been shown to be a suitable tool to find even highly nonlinear functional relationships. This paper reports on a numerical wavetank implemented using the OpenFOAM software package which is characterised using artificial intelligence. The aim of the research is to train neural networks to represent non-linear transfer functions mapping a desired surface-elevation time-trace at a probe to the wavemaker input required to create it. These first results already demonstrate the viability of the approach and the suitability of a single setup to find solutions over a wide range of sea states and wave characteristics.

Let f : V → V be a Cohomological Expanding Mapping¹ of a smooth complex compact homogeneous manifold with $ dim_{\mathbb{C}}(\Vc)=k \ge 1$ and Kodaira Dimension $\leq 0$. We study the dynamics of such mapping from a probabilistic point of view, that is, we describe the asymptotic behavior of the orbit $ O_{h} (x) = \{h^{n} (x), n \in \mathbb{N} \quad \mbox{or}\quad \mathbb{Z}\}$ of a generic point. Using pluripotential methods, we have constructed in our previous paper \cite{Armand4} a natural invariant canonical probability measure of maximal Cohomological Entropy $ \nu_{h} $ such that ${\chi_{2l}^{-m}} (h^m)^\ast \Omega \to \nu_h \qquad \mbox{as} \quad m\to\infty$ for each smooth probability measure $\Omega $ in $\Vc$ . We have also studied the main stochastic properties of $ \nu_{h}$ and have shown that $ \nu_{h}$ is a smooth equilibrium measure , ergodic, mixing, K-mixing, exponential-mixing. In this paper we are interested on equidistribution problems and we show in particular that $ \nu_{h}$ reflects a property of equidistribution of periodic points by setting out the Third and Fourth Main Results in our study. Finally we conjecture that $$\nu_h:=T_l^+ \wedge T_{k-l}^-,$$ $$\dim_\HH(\nu_h)= \Psi h_{\chi}(h) , $$ $$\dim_\HH( \mbox{Supp} T_l^+) \geq 2(k-l) + \frac{\log \chi_{2l}}{\psi_l},$$ $$|\langle \nu_m^x-\nu_h,\zeta\rangle|\leq M \Big[1+\log^+{1\over D(x,\Tc)}\Big]^{\beta/2}\|\zeta\|_{\Cc^\beta} \gamma^{-\beta m/2}$$ and $$|\langle \nu_m^x-\nu_h,\zeta\rangle|\leq M \Big[1 +\log^+{1\over D(x,E_\gamma)}\Big]^{\beta/2}\|\zeta\|_{\Cc^\beta} \gamma^{-\beta m/2}.$$

Let $f:V\rightarrow V $ be a Cohomological Expanding Mapping¹ of a smooth complex compact homogeneous manifold with dim_C(V) = k ≥ 1 and Kodaira Dimension $\leq 0$. We study the dynamics of such mapping from a probabilistic point of view, that is, we describe the asymptotic behavior of the orbit $ O_{f} (x) = \{f^{n} (x), n \in \mathbb{N} \quad \mbox{or}\quad \mathbb{Z}\}$ of a generic point. Using pluripotential methods, we construct a natural invariant canonical probability measure of maximum Cohomological Entropy $ \mu_{f} $ such that ${\chi_{2l}^{-m}} (f^m)^\ast \Omega \to \mu_f \qquad \mbox{as} \quad m\to\infty$ for each smooth probability measure $\Omega $ on V . Then we study the main stochastic properties of $ \mu_{f}$ and show that $ \mu_{f}$ is a measure of equilibrium, smooth, ergodic, mixing, K-mixing, exponential-mixing and the unique measure with maximum Cohomological Entropy. We also conjectured that $\mu_f:=T_l^+ \wedge T_{k-l}^-$, $\dim_\H(\mu_f)= \Psi h_{\chi}(f) $ and $\dim_\H( \mbox{Supp} T_l^+) \geq 2(k-l) + \frac{\log \chi_{2l}}{\psi_l}.$

The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we present an improved innovative sequence–activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this improved approach, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability than that predicted using the existing data. We successfully improved the determination coefficient (R2) of the model from 0.66 to 0.92. In addition, root mean square deviation (RMSD) and root mean square fluctuation (RMSF) were estimated and conformation analysis based on molecular dynamics simulations was performed to verify the enhanced thermal stability of the screened mutants. The improved innov'SAR algorithm enhanced the predictive accuracy, suggesting a method for modifying the stability of AT-ATA, which may help in directed evolutionary screening and open up new avenues for protein engineering.

COVID-19 appeared as an infectious disease of global health emergency and the highest public health concern of 21st century for this world due to its high-speed of spread across the globe. The disease started as one single case to a cluster of cases in Wuhan, China (Dec 2019) and within few months with its continuous upsurge of cases spreading globally which has created enormous threat and tension across the global Public health care field. Most significantly to share the fact that, this disease caused high level of Risk Group mortality, high morbidity, health care services burden, panic anxiety, mental trauma and tension, social and economic insecurity, which also collectively surfaced by diverse range of social reaction and political pressure across the world. Also with the appearance of new and unknown pathogenesis of the disease has created the most and significant attention and concern for the scientific community and political leaders as well. The disease also varies much with its pattern of virus, sign, symptoms, characteristics including its epidemiological and public health response (like prevention strategy, diagnoses, case management, treatment pattern) across the countries. However, this variance is comparatively less rather even more in commonality while it comes to basic public health prevention interventions like frequent hand washing, wearing face mask, maintaining social/physical distancing (2 - 6 meter in between), individual isolation and community quarantine for suspected exposure and lockdown in community areas where cases are identified. These are with the most commonly practiced public health interventions to deal with this disease in majority of the epicenters across countries. Also with the progress of the disease with its diverse categorical appearance of sign symptoms which are uniquely portraying this disease is more of a kind of COVID-19 syndrome than as COVID-19. Moreover, various factors including socio economic status, health status, population dynamics, health system and infrastructure, health behavioral pattern, nutrition and food habit and access to information and knowledge made this viral disease one of the historically counted on expensive disease of the modern world to fight for. Specially to mention here, the case fatality rate distinctively vary with the population dynamics and the health system infrastructure and ability factors which have already created clear evidence as explained in this paper how these factors are uniquely distinguished and different from country to country. Apart from the contextual differences, the various kind of ongoing preventive measures (like prevention, diagnosis and treatment) learnt every day from the emerging characteristics and pattern of this viral disease which are most commonly practiced across countries with a variance. According to the Public health prevention practice and interventions, the total world is connected and learning from each other’s public health experiences to fight for the virus. However, the world communities are eagerly waiting to see the result and outcome of the ongoing therapeutics and vaccine trial initiated in several countries, the people of the world are quite optimistic and hopeful that, global scientific community will be able to invent some miraculous and magic solution in upcoming months which ultimately will free the world from this most terrifying COVID-19 pandemic of 21st century.

In this paper we develop from first principles a unique law pertaining to the flow of fluids through closed conduits. This law, which we call “Quinn’s Law”, may be described as follows: When fluids are forced to flow through closed conduits under the driving force of a pressure gradient, there is a linear relationship between the normalized dimensionless pressure gradient, P_Q, and the normalized dimensionless fluid current, C_Q. The relationship is expressed mathematically as: P_Q = k₁ +k₂C_Q. This linear relationship remains the same whether the conduit is filled with or devoid of solid obstacles. The law differentiates, however, between a packed and an empty conduit by virtue of the tortuosity of the fluid path, which is seamlessly accommodated within the normalization framework of the law itself. When movement of the fluid is very close to being at rest, i.e., very slow, this relationship has the unique minimum constant value of k₁, and as the fluid acceleration increases, it varies with a slope of k₂ as a function of normalized fluid current. Quinn’s Law is validated herein by applying it to the data from published classical studies of measured permeability in both packed and empty conduits, as well as to the data generated by home grown experiments performed in the author’s own laboratory.

Modeling brain dynamics to better understand and control complex behaviors underlying various cognitive brain functions are of interests to engineers, mathematicians, and physicists from the last several decades. With a motivation of developing computationally efficient models of brain dynamics to use in designing control-theoretic neurostimulation strategies, we have developed a novel data-driven approach in a long short-term memory (LSTM) neural network architecture to predict the temporal dynamics of complex systems over an extended long time-horizon in future. In contrast to recent LSTM-based dynamical modeling approaches that make use of multi-layer perceptrons or linear combination layers as output layers, our architecture uses a single fully connected output layer and reversed-order sequence-to-sequence mapping to improve short time-horizon prediction accuracy and to make multi-timestep predictions of dynamical behaviors. We demonstrate the efficacy of our approach in reconstructing the regular spiking to bursting dynamics exhibited by an experimentally-validated 9-dimensional Hodgkin-Huxley model of hippocampal CA1 pyramidal neurons. Through simulations, we show that our LSTM neural network can predict the multi-time scale temporal dynamics underlying various spiking patterns with reasonable accuracy. Moreover, our results show that the predictions improve with increasing predictive time-horizon in the multi-timestep deep LSTM neural network.

Electrostatic interactions have a determining role in conformational and dynamic behavior of polyelectrolyte molecules [1]. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in water solution with the most commonly used K+ or Na+ counterions were investigated using atomistic molecular dynamics (MD) simulations. Seven common force fields, AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and with the non-bonded fix (NBFIX) and electronic continuum corrections (ECC) to were studied. These corrections have bene introduced to correct for the problem of overbinding of ions to the charged groups of polyelectrolytes. Physical properties, such as molecular sizes, local structure and dynamics, were studied using two types of common counterions, potassium and sodium. The results show that in some cases, the macroion size and dynamics depend strongly on the models (parameters) for the counterions due to strong overbinding of ions and charged side chain groups. The local structures and dynamics are more sensitive on dihedral angle parameterization resulting in a preference for defined monomer conformations amd the type of correction used.

Most fully developed galaxies have vivid spiral structure, but the formation and evolution of spiral structure is still a mystery that is not fully understood in astrophysics. We find that the currently used equations of galactic dynamics contain some unreasonable components. In this paper, the following three working assumptions are introduced to simplify the galactic structural equations. 1. In the research of large-scale structure, the retarded potential of the gravitational field should be taken into account. The propagating time of the gravitational field from center to border is longer than the revolution periods of the stars near the center of galaxy. Newton's gravitational potential is unreasonable for such case, and the weak field and low velocity approximation of Einstein's field equation should be adopted. 2. The stars in a fully developed galaxy should be zero-pressure and inviscid fluid, and the equation of motion is different from that of ordinary continuum mechanics. Stars move along geodesics. 3. The structure of the galaxy is only related to the total mass density distribution. The equation of state of dark halo is different from that of ordinary luminous interstellar matter, so their trajectories are also very different. Dark halo and ordinary matter in galaxy are automatically separated. The total mass density distribution can be presupposed according to the observation data, and then it can be determined by comparing the solution of the equations with the observed data. These assumptions and treatments are supported by theory and observation. The variables of the equations of simplified galactic dynamics are separated from each other, and the equations are well-posed and can be solved according to a definite procedure. Therefore, this simplified dynamic equation system provides a more reasonable and practical framework for the further study of galactic structure, and can solve many practical problems. Besides, it is closely related to the study of dark energy and dark matter.

I present an experimental paradigm to explore the interpersonal dynamics generating a collective mind. I hypothesized that collective organization is based on dual interpersonal modes: (1) symmetrical and (2) anti‑symmetrical. I specified the geometric topology of these modes by detecting the spatiotemporal patterns that embed cooperative agents in a three‑dimensional matrix. I found that the symmetrical mode is executed automatically and without guidance. Conversely, the anti‑symmetrical mode required explicit direction and recruited attention for execution. I demonstrate that self‑other mirror‑symmetry stabilized group dynamics, enabled fast and efficient symmetrical imitation that optimized information transmission, whereas anti‑symmetrical imitation was comparatively slow, inefficient, and unstable. I determined that the anti‑symmetrical mode spontaneously transitioned to the symmetrical mode under perturbations. Crucially, this renormalization mechanism never transitioned from symmetrical to anti‑symmetrical. These self-organizing dynamics speak to interpersonal symmetry‑breaking. In the present work, spontaneous group choice mandated that agents synchronize cooperative cycles in symmetrical space under internal or external perturbations. I provide examples to illustrate that this self-regulating pullback attractor manifests in invertebrates and vertebrates alike. I conclude by suggesting that inter‑agent symmetry provides the social stability manifold through which attention-driven interactions enable intrapersonal and interpersonal change.

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

Matrix Metaloproteinase-2 (MMP-2) is an extracellular Zn²⁺ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed 10 families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamics cross correlation analysis indicated domain movements corresponding to opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the MMPBSA-interaction entropy analysis method and revealed strong binding energies for the catalytic Zn²⁺ ion 1, Ca²⁺ ion 1, and Ca²⁺ ion 3 with significant conformational stability at the binding sites of Zn²⁺ ion 1 and Ca²⁺ ion 1. Ca²⁺ ion 2 diffuses freely away from its crystallographically defined binding site. Zn²⁺ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca²⁺ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain.

A computational simulation of a PT6A gas turbine engine operating at off-design conditions is described in the present article. The model consists of a 0-dimensional thermo-fluidic description of the engine by applying the mass, linear momentum, angular momentum, and energy balances in each engine's component. The transient behavior of the engine is simulated for different blends of the original JET-A1 fuel with bio-diesel. Simulated thermodynamic variables of the air at each engine's component, as well as some performance parameters correspond to the reported experimental measurements. The numerical results also demonstrate the ability of the computational simulation to predict acceptable fuel blends, such that the efficiency of the engine is maximized and its structural integrity is maintained.

The present study shows a methodology for analyzing and designing a cylindrical packed-bed reactor considering stationary and dynamic models. The design comprises the reactor's stationary and dynamic governing differential equations for mass and heat transfer under multi-dimensional approaches. The results included simulation of concentration, temperature, and reaction rate profiles via the 1-D and 2-D differential equations solution with FlexPDE software. The analysis was complemented with a scaled 3-D dynamic model implemented in COMSOL Multiphysics. Both FlexPDE and COMSOL Multiphysics relied on the finite element technique to solve the governing differential equations. The simulated concentration and temperature profiles from both FlexPDE and COMSOL models were compared to experimental data gathered from literature (specifically from a Fischer-Tropsch process to produce low-molecular-weight hydrocarbons in a configuration of cylindrical packed-bed reactors). Simulated concentration and temperature profiles from the 2-dimensional dynamic model and the COMSOL model were in good agreement with the trend observed in experimental data. Finally, the predicted reaction rate profiles from the COMSOL model and the 2-dimensional dynamic model followed the temperature trend, thus reflecting the temperature dependence of the reaction.

We performed for the first time to our knowledge fully ab initio molecular dynamics simulations of additive tribochemistry in boundary lubrication conditions. We consider an organophosphourus additive that has been experimentally shown to reduce friction in steel-on-steel sliding contacts thanks to the tribologically-induced formation of an iron phosphide tribofilm. The simulations allow us to observe in real time the molecular dissociation at the sliding iron interface under pressure and to understand the mechanism of iron phosphide formation. We discuss the role played by the mechanical stress by comparing the activation times for molecular dissociation observed in the tribological simulations at different applied loads with that expected on the basis of the dissociation barrier.

This paper numerically investigates a 3D mesh independency study of a straight blade horizontal axis tidal turbine modelled using Computational Fluid Dynamics (CFD). The solution was produced by employing two turbulence models, the standard k-ε model and Shear Stress Transport (SST) in ANSYS CFX. Three parameters were investigated: mesh resolution, turbulence model, and power coefficient in the initial CFD, analysis. It was found that the mesh resolution and the turbulence model affect the power coefficient results. The power coefficients obtained from the standard k-ε model are 15% to 20% lower than the accuracy of the SST model. It can also be demonstrated that the torque coefficient increases with the increasing Tip Speed Ratio (TSR), but drops drastically after TSR = 5 and k-ε model failing to capture the non-linearity in the torque coefficient with the increasing TSR.

In order to perceive the behavior presented by the multiphase chemical reactors, the ant colony optimization algorithm was combined with computational fluid dynamics (CFD) data. This intelligent algorithm creates a probabilistic technique for computing flow and it can predict various levels of three-dimensional bubble column reactor (BCR). This artificial ant algorithm is mimicking real ant behavior. This method can anticipate the flow characteristics in the reactor using almost 30 % of the whole data in the domain. Following discovering the suitable parameters, the method is used for predicting the points not being simulated with CFD, which represent mesh refinement of Ant colony method. In addition, it is possible to anticipate the bubble-column reactors in the absence of numerical results or training of exact values of evaluated data. The major benefits include reduced computational costs and time savings. The results show a great agreement between ant colony prediction and CFD outputs in different sections of the BCR. The combination of ant colony system and neural network framework can provide the smart structure to estimate biological and nature physics base phenomena. The ant colony optimization algorithm (ACO) framework based on ant behavior can solve all local mathematical answers throughout 3D bubble column reactor. The integration of all local answers can provide the overall solution in the reactor for different characteristics. This new overview of modelling can illustrate new sight into biological behavior in nature.

The buildup dynamics of diode-pumped passively mode-locked solid-state laser is thoroughly explored by the real-time measurement with temporal sampling rate up to 40 GHz. A concise cavity is developed to ensure the transient dynamics purely arising from the gain medium and saturable absorber. Experimental results reveal that the laser output in the buildup process exhibits numerous passively Q-switched pulses followed with a damped relaxation oscillation prior to the stable mode locking. Furthermore, it is confirmed that the laser output has already displayed single clean mode-locked pulses inside the first several Q-switched envelopes before stepping into the stage of relaxation oscillation. The present real-time exploration is expected to provide important information for practical applications with temporal modulation of the pump intensity.

The airborne inoculum of Fusarium circinatum, the fungal pathogen causing Pine Pitch Canker (PPC), is one of the main means of spread of the disease in forest stands and forest nurseries. Since this world-wide known pathogen was introduced in Europe, its biology in this newly infected area still remains scarcely known. To shed more light on this topic, we set an experiment on a naturally PPC infected forest of Monterey pine in Galicia (NW Spain) with the following two goals: (i) to describe the seasonal spore dispersal pattern during one year of regular sampling and (ii) to assess the spatial spore dispersal pattern around the infested plot. Portable rotating arm spore traps were used and complemented with meteorological measurements. The abundance of F. circinatum spores in the samples was evaluated by quantitative PCR (qPCR) with hydrolysis probe. The results showed almost permanent occurrence of the air inoculum throughout the whole year, being detected in 27 of the 30 samplings. No clear temporal trends were observed, but higher air inoculum was favoured by previous lower air temperatures and lower leaf wetness. Conversely, neither rainfall nor air humidity seemed to have any significant importance. The spatial spread of the inoculum was noted to be successful up to a distance of 1000 m in the wind direction, even with winds of just 5 m s^-1. Our study shows that rotating arm spore traps combined with qPCR may be an efficient tool for F. circinatum detection.

We used population reconstruction techniques to assess for the first time the population dynamics of a seagrass, Cymodocea nodosa, exposed to long-term elevated CO₂ near three volcanic seeps and compare them with reference sites away from the seeps. Under high CO₂, the density of shoots and of individuals (apical shoots), and the vertical and horizontal elongation and production rates, were higher. Nitrogen effects on rhizome elongation and production rates and on biomass, were stronger than CO₂ as these were highest at the location where the availability of nitrogen was highest. At the seep where the availability of CO₂ was highest and nitrogen lowest, density of shoots and individuals were highest, probably due to CO₂ effects on shoot differentiation and induced reproductive output, respectively. In all three seeps there was higher short- and long-term recruitment and growth rates around zero, indicating that elevated CO₂ increases the turnover of C. nodosa shoots.

Background: Understanding the factors that influence the market entry, exit, and stability of community pharmacies (i.e., market dynamics) is important for stakeholders ranging from patients to health policymakers and small business owners to large corporate institutions. The purpose of this article is to provide an update to a 15-year ecological comparison for the market dynamics of Minnesota community pharmacies from 2002 to 2017 [1]. Objectives: The first objective was to update the 15-year study [1] by describing the market dynamics of community pharmacies for each county in the state of Minnesota every five years over a 20-year period (i.e., 2002-2022). The second objective was to update the 15-year study by describing the number and proportion of community pharmacies for each county in the state of Minnesota every five years over a 20-year period (i.e., 2002-2022) by (1) ‘Business Organization Structure’ and (2) ‘Pharmacy Type.’ The third and fourth objectives were new for the 2022 study. In response to evolutionary trends in the pharmacy market, objective three described the number of Minnesota licensed pharmacies located in-state and out-of-state between 2002 and 2022. Objective four described the primary type of service provided by licensed pharmacies categorized as out-of-state in 2002 and in 2022. Methods: Data were obtained from the Minnesota Board of Pharmacy, US Census Bureau, and Minnesota State Demographic Center for 2002, 2007, 2012, 2017, and 2022. Descriptive statistics were used to tabulate and summarize the findings and test associations between study variables. Results: Over the 20-year study period, the total number of community pharmacies in Minnesota remained steady. Findings for 2022 were similar to those for 2017 regarding the effects of population density and metropolitan designation on the market dynamics of community pharmacies and regarding the organizational structures and types of pharmacies. The findings revealed significant growth in the number of proportion of pharmacies licensed in Minnesota that were located out-of-state. In 2002, there were 283 of these pharmacies (19% of the total). By 2022, this grew to 960 (46% of the total). Over that 20-year period, the number of mail order and medical supply service pharmacies rose from 196 to 413. The number of specialty pharmacy distributors rose from 37 to 230 and the number of compounding pharmacies rose from 33 to 202. Discussion: The findings confirmed the shift over the past 20 years from traditional retail convenience models to healthcare access models based on population health metrics. National scalability was another detected shift in order to have profitable margins for some services and was feasible due to advances in technologies. Conclusion: The findings showed that community pharmacy distribution in Minnesota’s 87 counties shifted between 2002 and 2022 from traditional retail convenience models to healthcare access models based on population health metrics and to nationally scalable models based on economic pressures. This signals the need for not only new approaches for tracking community pharmacy market dynamics but also adjustments by community pharmacies to remain relevant in a new environment of patient care services.

The adsorption of proteins on polymer is widely used in biosensors. Here, molecular dynamics (MD) simulation was used to study the immobilization of angiotensin converting enzyme II (ACE2) with six initial orientations proposed on polystyrene (PS) at the ambient conditions of pH (4.5, 6, 7, 8, 9.5) and NaCl (0.01, 0.05, 0.1, 0.15, 0.2, 0.25 M). ACE2 immobilization under favorable ambient conditions was characterized by minimum distance (short), settlement time (fast), interaction energy (substantial) and protein configuration (stable). ACE2 orientations proposed in 0.15M NaCl were respectively preferable to (90, 0, 0), (0, 0, 0) and (0, 270, 0), (180, 0, 0) and (0, 90, 0), (90, 0, 0) at pH 4.5, 6, 7, 9.5. ACE2 immobilization was further evaluated at pH 7 by optimizing NaCl concentration. Its proposed orientations of (i) (0, 270, 0), (ii) (0, 0, 0) and (90, 0, 0), and (iii) (0, 90, 0) and (90, 0, 0) were preferable in 0.05, 0.1 and 0.2 M NaCl, respectively. The great significance of cubic-orientation settlement mode provides tangible improvement for the microfabrication of biochips for rapid diagnosis of severe acute respiratory syndrome coronavirus II (SARS-CoV-2).

In this research, the computational fluid dynamic (CFD) approach that has been used in wind power generation field was applied for the solution of the problems of local strong wind areas in railway fields, and the mechanism of wind generation was discussed. At the same time, the affectivity of the application of computational fluid dynamic approach to railway field was discussed. The problem of local wind that occurs on the railway line in winter was taken up in this research. A computational simulation for the prediction of wind conditions by LES was implemented and it was clarified that the local strong wind area is mainly caused by separated flows originating from the small‐scale terrain positioned at its upstream (at approximately 180.0 m above sea level). Meanwhile, the effects of the size of calculation area and spatial grid resolution on the result of calculation and the effect of atmospheric stability were also discussed. It was clarified that when the air flow characteristic of the separated flow originating from the small‐scale terrain (at altitude of approximately 180.0 m) targeted in this research is reproduced at high accuracy by computational simulation of wind conditions, approximately 10.0 m of spatial resolution of computational grid in horizontal direction is required. As a result of the computational simulation of wind conditions of stably stratified flow (Fr = 1.0), lee waves were excited at the downstream of the terrain over time. As a result, the reverse‐flow region lying behind the terrain that had been observed at a neutral time was inhibited. Consequently, local strong wind area was generated at the downstream of the terrain and the strong wind area passing through the observation mast was observed. By investigating the speed increasing rate of local strong wind area induced at the time of stable stratification, it was found that the wind was approximately 1.2 times stronger than what was generated at a neutral time.

Molecular dynamics(MD) simulations are carried out to characterize the mechanicalproperties and failure behavior of van der Waals heterostructures composed ofgraphene and hexagonal boron nitride(hBN) single layer sheets. The graphene–hBNand hBN–graphene–hBN heterostructures simulations are carried out under tensileand shear deformation. Accordingly, stress versus strain curves of each systemare plotted and various properties of heterostructures, namely elastic modulusand shear modulus as well as failure stress and failure strain, are evaluatedand compared with one another as well as with the pristine graphene and hBNsheets. Subsequently, the failure mechanism/characterization of each sheet in theheterostructures is described. Alternatively, the elastic and shear modulus of eachheterostructure are computed by means of rule of mixture(ROM) which are in goodagreement with results that are obtained from MD simulations.

In this age of mass media and, in particular, social media-driven perception of reality, coupling disease and prophylactic opinion dynamics models can provide better insights into disease evolution than using a disease model alone. We develop in this work two disease-opinion dynamics models based on the epidemiology of the new coronavirus disease (COVID-19) and the availability or not of imperfect vaccines. We assume that susceptibility to infection decreases with the level of prophylactic attitude (personal hygiene, social distancing), and changes in prophylactic attitudes of susceptible individuals occur in response to perceived disease prevalence and vaccination coverage and efficacy in the population. We derive and discuss the disease-free equilibriums and reproduction numbers in the introduced models. We further assess the impacts of the distribution of opinions at disease introduction, the ability to detect presymptomatic, asymptomatic and symptomatic positive COVID-19 cases, the behavioural responses to the outbreak and the introduction of vaccination, and the effects of distortions of disease prevalence by public policy and mass media on disease dynamics. The insights highlighted from the proposed models are expected to make informative contributions to public policy in a context of opinion fluxes in response to perceived disease prevalence.

Regeneration is crucial for forest continuity in natural and managed stands. Analyzing intra-annual dynamics improves the understanding between growth and climate, identifying survival thresholds. The objective was to determine microclimate constraints (rainfall, air and soil temperatures) over Nothofagus antarctica regeneration growing at closed, open, and edge forests in Patagonia. We measured stand characteristics (forest structure, understory, soil properties, animal use), microclimate, and daily growth of regeneration using dendrometers (n = 6) during two growing seasons. We found significant differences in the studied variables (e.g. overstory, light, soil, understory, animal use). These changes defined microclimate across overstory gradient (e.g. soil moisture), influencing the daily growth across seasons (lag, exponential, stationary). Rainfall influenced more than temperature. Daily growth in closed forests indicating shrinkage (-0.0082 mm day-1 without rain, and -0.0008 mm day-1 with 0.0-0.2 mm day-1 rainfall), while above 0.2 mm day-1 rainfall, growth always increased. Open forests presented shrinkage during days without rain (-0.0051 mm day-1), showing positive growths according rainfall. Edge forests always presented positive daily growths. The resilience of regeneration under these changed conditions was related with overstory. Main outputs indicated that regeneration was vulnerable during non-rainy days, suggesting the needs of long-term monitoring to develop better silvicultural proposals.

The hyper-arid environment is characterized by high inter-annual climatic fluctuations. The yearly average rainfall can change substantially for several years, forming wet or dry sub-periods. Observing rainfall trends over a sub-period can lead to a false perception of a change in the trend but may in fact represent a periodic cycle when examined on a larger time scale. We aimed to better characterize the rainfall regime prevailing in the hyper-arid Arava Valley (Israel/Jordan), and to examine the response of vegetation to annual rainfall. We hypothesized that annual and perennial vegetation would respond differently to wet and dry sub-periods, and that grazing activities will impact vegetation growth. We used a time series of monthly rainfall, from which we calculated Standard Precipitation Index (SPI), and calculated proxies of perennial and annual vegetation over the last four decades using Landsat-derived Normalized Difference Vegetation Index (NDVI). We found no clear trend in rainfall amounts during this period, however we did identify wet and dry sub-periods which were statistically distinct in rain and in vegetation patterns from each other. The highest levels of correlation between rainfall and the NDVI derived proxies were found when examining average rainfall over a period of two- three years for the annual vegetation and over four years for perennial vegetation. Using the Mann-Kendall test, we identified a time lag of two to four years, with the proxies of annual vegetation responding faster than the proxies of perennial vegetation, to shifts between wet and dry sub-period. In addition, we found a consistent difference between natural vegetation cover in Jordan (grazed) and Israel (non-grazed), favoring the development of natural vegetation on the Israeli side. We conclude that integrating between long-term remote sensing satellite imagery and climatic records revealed the greater resilience of perennial vegetation in the hyper-arid region to climatic fluctuation, and enabled us to identify the vegetation’s sensitivity to anthropogenic impact.

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes, respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related H3K4me3. However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with transcriptional changes, in a developmental series including Arabidopsis leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prime over changes in H3K27me3 and quantitatively correlate with transcription changes, while H3K27me3 changes occur after prolonged expression changes. Notably, early activation of PcG target genes is dominated by increases in H3K4me3 while H3K27me3 remains present at the locus. Our results reveal H3K4me3 as greater predictor over H3K27me3 for transcription dynamics, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.

This research paper presents a comprehensive study on the gasification of wheat straw pellets in a 10-kW fixed bed gasifier through a combination of Computational Fluid Dynamics (CFD) simulation and experimental validation. The developed 2D CFD model in ANSYS meshing simulates the gasification process in ANSYS Fluent software. The investigation evaluates key parameters such as equivalence ratio, higher heating value, and temperature distribution within the gasifier to enhance syngas production efficiency. The simulated results exhibit a noteworthy agreement with experimental data obtained from gasification. The impact of the equivalence ratio on gas production and lower heating value (LHV) is systematically explored, revealing that an equivalence ratio of 0.35 is optimal for syngas production. The resulting producer gas composition at this optimum condition includes CO (~27.67%), CH4 (~3.29%), CO2 (~11.09%), H2 (~11.09%), and N2 (~51%). The study further investigates the positive influence of reactor temperature on increasing syngas quantity while considering the uneven shape of the reactor and various thermal reactions affecting temperature, static pressure, velocity, and density. The findings contribute valuable insights to improve the efficiency of fixed-bed gasifiers, offering essential information on performance parameters for sustainable and optimized syngas production.

In every agricultural setting, weed seeds can be found in every cubic centimeter of soil. Weed seeds, as a valuable trait underlying the fate of weed populations, exhibit differing levels of seed dormancy, ensuring their survival under uncertain conditions. Seed dormancy is considered as an innate mechanism that constrains germination under suitable conditions that would otherwise stimulate germination of non-dormant seeds. This work provides new insight into changes in germination patterns along the dormant to nondormancy continuum in seeds with physiological dormancy. Notable findings are: (1) germination synchrony can act as a new parameter that quantitatively describes dormancy patterns and subsequently weed population dynamics, (2) germination synchrony is dynamic, suggesting that the more dormancy decreases, the more synchrony is obtainable, (3) after-ripening and stratification can function as a synchronizing agent that regulates germination behavior. Brassica napus showed the most synchronous germination with the value of 3.14, while lower level of germination asynchrony was for Sinapis arvensis, with the asynchrony value of 2.25. After-ripening and stratification can act as a synchronizing factor through decreasing asynchrony level and increasing synchrony. Weed establish a firm relationship between dormancy cycling and germination synchrony patterns, ensuring their survival and reproductive strategies. By germinating in synchrony, which is accompanied by cycling mechanisms, weeds have more opportunities to persist. The synchrony model used in the present study predicts germination behavior and synchrony along the dormant to nondormancy continuum in weed seeds with physiological dormancy, suggesting a useful method for quantification of germination strategies and weed population dynamics.

Self-organized criticality (SOC) is a universal mechanism for self-sustained critical behavior in large-scale systems evolving outside equilibrium. Our report explores a tentative link between SOC and Lagrangian field theory, with the long-term goal of bridging the gap between complex dynamics and the non-perturbative behavior of quantum fields.

As a widely used plastic, the aging and degradation of polyethylene (PE) are inevitable problems, whether the goal is to prolong the life of PE products or address the issue of white pollution. Molecular simulation is a vital scientific tool in elucidating the mechanisms and processes of chemical reactions. To obtain the distribution and evolution process of PE's thermal oxidation products, this work employs the self-consistent charge density functional tight binding (SCC-DFTB) method to perform molecular simulations of the thermal oxidation of PE with different crystallinity and branched structures. We discovered that crystallinity does not affect the thermal oxidation mechanism of PE, but higher crystallinity makes PE more susceptible to cross-linking and carbon chain growth, reducing the degree of PE carbon chain breakage. The branched structure of PE results in differences in pore size between the carbon chains, with larger pores leading to a concentrated distribution of O2 and free radicals subsequently formed. The breakdown of PE is slowed down when free radicals are localized in low-density regions of the carbon chain. The specifics and mechanism of PE's thermal oxidation are clearly revealed in this paper, which is essential for understanding the process in-depth and for the development of anti-aging PE products.

User-generated passwords often pose a security risk in authentication systems. However, providing a comparative substitute poses a challenge, given the common tradeoff between security and user experience. This paper integrates cryptographic methods (both asymmetric and symmetric), steganography, and a combination of physiological and behavioral biometrics to construct a prototype for a passwordless authentication system. We demonstrate the feasibility of scalable passwordless authentication while maintaining a balance between usability and security. We employed threat modeling techniques to pinpoint the security prerequisites for the system, along with choosing appropriate cryptographic protocols. In addition, a comparative analysis is conducted, examining the security impacts of the proposed system in contrast to that of traditional password-based systems. Results from the prototype indicate that authentication is possible within a timeframe similar to passwords (within 2 seconds), without imposing additional hardware costs on users to enhance security or compromising usability. Given the scalable nature of the system design and the elimination of shared secrets, the financial and efficiency burdens associated with password resets are alleviated. Furthermore, the risk of breaches is mitigated, as there is no longer a need to store passwords and/or their hashes. Differing from prior research, our study presents a pragmatic design and prototype that deserves consideration as a viable alternative for both password-based and passwordless authentication systems.

The article proposes an amendment to the relativistic continuum mechanics which introduces the relationship between density tensors and the curvature of spacetime. The resulting formulation of a symmetric stress-energy tensor for a system with an electromagnetic field, leads to the solution of Einstein Field Equations indicating a relationship between the electromagnetic field tensor and the metric tensor. In this EFE solution, the cosmological constant is related to the invariant of the electromagnetic field tensor, and additional pulls appear, dependent on the vacuum energy contained in the system. In flat Minkowski spacetime, the vanishing four-divergence of the proposed stress-energy tensor expresses relativistic Cauchy's momentum equation, leading to the emergence of force densities which can be developed and parameterized to obtain known interactions. Transformation equations were also obtained between spacetime with fields and forces, and a curved spacetime reproducing the motion resulting from the fields under consideration, which allows for the extension of the solution with new fields.

Turbulent flow is the first and fundamental physical phenomena to evaluate when optimising cost and reducing emissions from an Anode Baking Furnace (ABF). Gas flow patterns, velocity field, pressure drop, shear stress, and turbulent dissipation rate variables are the main operational parameters to be optimised, considering a specific geometry. Computational Fluid Dynamics (CFD) allows simulating physical phenomena using numerical methods with computer resources. In particular, the finite element method is one of the most used methods to solve the flow equations. This method requires a discretisation of the geometry of the ABF, called mesh. Hence, mesh is the main input to the finite element method. A suitable mesh for applying a discretisation method determines whether the problem can be simulated or not. Generating an appropriate mesh remains a challenge to perform accurate simulations. In this work, a comparison between meshes generated using two mesh generation tools is presented. Results of different study cases are included.

Bimetallic nanoparticles are of interest since they lead to many interesting electrical, chemical, catalytic, and optical properties. They are particularly important in the field of catalysis since they show superior catalytic properties than their monometallic counterparts. The structures of bimetallic nanoparticles depend mainly on the synthesis conditions and the miscibility of the two components. In this work, PdPt alloyed-bimetallic nanoparticles (NPs) were synthesized through the polyol method, and characterized using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). High-angle annular dark-field (HAADF)-STEM images of bimetallic nanoparticles were obtained. The contrast of images shows that nanoparticles have an alloy structure with an average size of 8.2 nm. Together with the characterization of nanoparticles, a systematic molecular dynamics simulations study, focused on the structural stability and atomic surface segregation trends in 923-atom PdPt alloyed-bimetallic NPs was carried out.

Human NAD(P)H:quinone oxidoreductase 1 (NQO1) is a multi-functional protein whose alteration is associated with cancer, Parkinson´s and Alzheimer´s diseases. NQO1 displays a remarkable functional chemistry, capable of binding different functional ligands that modulate its activity, stability and interaction with proteins and nucleic acids. Our understanding on this functional chemistry is limited by the difficulty of obtaining structural and dynamic information on many of these states. Herein, we have used hydrogen/deuterium exchange monitored by mass-spectrometry (HDXMS) to investigate the structural dynamics of NQO1 in three ligation states: without ligands (NQO1apo), with FAD (NQO1holo) and with FAD and the inhibitor dicoumarol (NQO1dic). We show that NQO1apo has a minimally stable folded core holding the protein dimer and with FAD and dicoumarol ligand binding sites populating binding non-competent conformations. Binding of FAD significantly decreases protein dynamics and stabilizes the FAD and dicoumarol binding sites as well as the monomer:monomer interface. Dicoumarol binding further stabilizes all three functional sites, a result not previously anticipated by available crystallographic models. Our work provides an experimental perspective into the communication of stability effects through the NQO1 dimer, valuable to understand at the molecular level the effects of disease-associated variants, post-translation modifications and ligand binding cooperativity in NQO1.

By employing the stochastic extension of the Madelung quantum-hydrodynamic description within a discrete methodology, we establish a solution using the path integral approach to explore the progression of quantum states' superposition. This investigation aims to understand the eventual establishment of a stable end-state configuration amid the backdrop of gravitational background fluctuations. The model identifies the circumstances that lead to a limited range of interaction for the quantum potential, allowing for the emergence of sizeable, classically described macroscopic phenomena. The theory unveils the lowest achievable level of uncertainty in an open quantum system and investigate its congruence with the localized behaviors of macroscopic classical systems. The study examines agreements and differences with decoherence theory and the Copenhagen interpretation of quantum mechanics, and evaluates the impact of wave function decay on the measurement process.

The genetic code conceals a ‘code within the codons’, which hints at biophysical interactions between amino acids and their cognate nucleotides. But research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and four RNA mononucleotides in three charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least one of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomized assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.

It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.

We prepared heterogeneous alumina-silicate glasses by consolidating nanoparticles using molecular dynamics simulations. Consolidated glasses from either low alumina content alumina-silicate glasses or high alumina content alumina-silicate glasses show significantly improved ductility around consolidation pressure of ~3 GPa. The introduced structural heterogeneities, namely over-coordinated network formers and their neighboring oxygen atoms, are identified as plasticity carriers due to their high rearrangement propensity. In addition, consolidated oxide glass from both 23.4Al₂O₃76.6SiO₂ and 73.1Al₂O₃26.9SiO₂ nanoparticles show improved flow strength (up to 1 GPa) due to the introduction of chemical heterogeneities. Last but not least, apparent hardening behavior appears upon cold work in consolidated glasses, with an increase of yield strength from ~3.3 GPa to ~6.4 GPa. This method is a big advancement toward ultra-strong and ultra-tough glasses by breaking the structure, composition and size limitations in traditional melt-quench process.

Electrowetting – induced detachment of droplets from solid surfaces is important for numerous applications in the fields of heat transfer and fluid mechanics. The forced oscillations of droplets on solid surfaces and their ability to detach are studied. In this study the process is efficiently simulated by implementing a powerful methodology developed by our team. Our results agree with experiments, showing that optimal detachment, in terms of actuation energy, is achieved when the application of voltage is synchronized with the spreading time of the droplet. Under these conditions, the droplet oscillates with a period close to that of a mirrored Rayleigh droplet. The relation between the droplet’s oscillation period and its physical properties is examined. During voltage-droplet synchronization, the droplet’s ability to detach depends mostly on its contact angle, its viscosity, and the applied voltage. An energy analysis is also conducted, revealing how energy is supplied to the droplet by electrowetting-induced detachment.