Macromolecules with well-defined structures in terms of molar mass and monomer sequence became interesting building blocks for modern materials. The precision of the macromolecular structure makes fine-tuning of the properties of resulting materials possible. Conjugated macromolecules exhibit excellent optoelectronic properties that make them exceptional candidates for sensors construction. The importance of chain length and monomer sequence is particularly important in conjugated systems. The sequence lengths, monomer sequence and structural modification often influence the energy bang gap between HOMO and LUMO orbitals of the molecules that reflect in their properties. Moreover, the supramolecular aggregation that is often observed in oligo-conjugated systems is usually strongly affected by even minor structural changes that are used for sensor designs. This review summarizes the examples of well-defined conjugated macromolecules based on oligo(arylene ethynylene)s skeleton used for sensor applications. The sensing mechanisms and importance of uniformity of structure are discussed.

The intricate orchestration of molecular events that constitutes life, as we know it, is oftentimes ascribed to an intelligent design motive. It is portrayed as if a paranormal watch maker has engineered the assemblage of parts and events that eventually manifests as the clockwork precision with which ontogeny and evolution operate within the boundary conditions imposed by what we know as life. The debate between those who advocate evolution versus intelligent design as the shaping force for modern life forms persists. However, that is not the motive for this essay. Though there has been several studies and scholarly articles that aspire to decipher and present the complexity of the molecular events that constitutes life in an insular fashion, there is a paucity of resources for undergraduates that summarizes the complexity cogently, as parts of a whole, for appreciating the enormity of the multidimensional nature of biological information and the inherent contradictions that are embedded therein. The fluidity inherent in the way information flows through signalling networks, the way biomolecular architectures maintain homeostasis in the ying-yang of life and the way multicellular complexity evolves through precise cell-cycle control is inherent in the evolution, maintenance and reproduction of biological systems. The matrix of events that encode information at the sequential and structural level across different macromolecules is a fascinating jungle of information. Combining these with how small-molecule metabolites interact with macromolecules in a spatially and temporally coordinated manner to evolve signal over random noise generates a staggering picture of informational organization and relays that, most often, defies human comprehension. This perspective is an attempt to array the various sources of information and put them together in context to appreciate the nuances of how information is stored and relayed within the biological systems. Further, it speculates on how these multitiered organization of biological information could be adapted to guide synthetic biology approaches and the future of information storage and organization.

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment which considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard-Dauxois-Bishop model we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables when going from the bp local scale to the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

We apply principles of Gibbs phase plane chemistry to and across the entire ocean-atmospheric interface. Surface tension increments support a two dimensional, tangential pressure well known to determine rates of bulk gas, bubble, salt, spray and momentum transfer plus both sensible and latent heat fluxes. Hence it is worth asking whether tension mapping follows from current understanding of two dimensional composition. A history is provided dating back centuries and demonstrating that detrital organic macromolecules are central; subtle surfactant functional variation creates a microforcing field which dissipates turbulent energy at the sub-meter scale. Since we have just distributed major biopolymeric classes emitted as primary organic aerosol, further climate links can be established by considering full planar thermochemistry. Organic microlayer behaviors are reviewed with attention to confined, analog phase transitions among two dimensional “solid, liquid, (and) gaseous” states serving as elasticity indicators. We also discuss surfactant properties of general marine dissolved organic carbon, demonstrating that only proteins and lipids are capable of occupying significant local micro-area. The literature often suggests albumin and stearic acid as best proxies, and so we distribute their concentrations through multilevel global ecodynamic simulations. Consensus distributions are obtained in order to control adsorptive equilibria. Working from conservation of planar free energy, a parametric equation of state is devised relating excess coverage to the surface pressure-modulus. Constant settings for the proxy pair are drawn from laboratory study, and they successfully reproduce frequencies for surfactant solid-to-gas occurrence in ambient compression experiments. Functionally resolved organic measurements are rare and so we group them into super-ecological province tables showing that our bulk concentration estimates are reasonable. Outputs are then fed into a coverage-tension-elasticity code. Resulting contours traverse the critical range for piston velocity, bubble-spray and damping effects on either a regional or seasonal basis. There is also a possibility for widespread microlayer crystallization in polar seas. The concepts are a direct extension of our organic aerosol work, and the two approaches could be inserted into Earth System Models in tandem. Uncertainties in the logic are enumerated and include kinetic and thermochemical factors at multiple scales. But the problems are reducible through molecular modeling coupled to renewed laboratory and field study. Connections to marine colloids-gels, microlayer iron chelation, and linings of the ice channel network are discussed additionally.

Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of fifteen modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications like protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in their science and engineering research. All materials are freely available at https://github.com/RosettaCommons/PyRosetta.notebooks.