Computational Insights into the Charge Relaying Properties of β‐Turn Peptides in Protein Charge Transfers

Density functional theory calculations suggest that β‐turn peptide segments can act as a novel dual‐relay elements to facilitate long‐range charge hopping transport in proteins, with the N terminus relaying electron hopping transfer and the C terminus relaying hole hopping migration. The electron‐ or hole‐binding ability of such a β‐turn is subject to the conformations of oligopeptides and lengths of its linking strands. On the one hand, strand extension at the C‐terminal end of a β‐turn considerably enhances the electron‐binding of the β‐turn N terminus, due to its unique electropositivity in the macro‐dipole, but does not enhance hole‐forming of the β‐turn C terminus because of competition from other sites within the β‐strand. On the other hand, strand extension at the N terminal end of the β‐turn greatly enhances hole‐binding of the β‐turn C terminus, due to its distinct electronegativity in the macro‐dipole, but does not considerably enhance electron‐binding ability of the N terminus because of the shared responsibility of other sites in the β‐strand. Thus, in the β‐hairpin structures, electron‐ or hole‐binding abilities of both termini of the β‐turn motif degenerate compared with those of the two hook structures, due to the decreased macro‐dipole polarity caused by the extending the two terminal strands. In general, the high polarity of a macro‐dipole always plays a principal role in determining charge‐relay properties through modifying the components and energies of the highest occupied and lowest unoccupied molecular orbitals of the β‐turn motif, whereas local dipoles with low polarity only play a cooperative assisting role. Further exploration is needed to identify other factors that influence relay properties in these protein motifs.     

‘Pourbaix sensors’: fluorescent molecular logic gates for pE and pH

Abstract

From the cross-fertilisation of fluorescent pH indicators and fluorescent redox switches, our group has established a new class of molecular sensor that operates as two-input molecular logic gates. These molecular sensors, known as ‘Pourbaix sensors’, are named in honour of Marcel Pourbaix, who developed the pH–potential diagrams for the various states of metal ion species in aqueous solution. This review highlights the evolution of ‘Pourbaix sensors’ based on anthracene and naphthalimide fluorophores. Potential applications of this class of molecule in fields such as corrosion science, cell biology and biomedical diagnostics are highlighted.     

Partial atomic multipoles for internally consistent microelectrostatic calculations

An extension of the extant microelectrostatic methodologies, based on the concept of distributed generalized polarizability matrix derived from the Coupled Perturbed Hartree–Fock (CPHF) equations, is proposed for self‐consistent calculation of charge carrier and charge‐transfer (CT) state electrostatic energies in molecular solids, including the doped, defected and disordered ones. The CPHF equations are solved only once and the generalized molecular polarizability they yield enables low cost iterations that mutually adjust the molecular electronic distributions and the local electric field in which the molecules are immersed. The approach offers a precise picture of molecular charge densities, accounting for atomic partial multipoles up to order 2, which allows one to reproduce the recently reported large charge‐quadrupole contributions to CT state energies in low‐symmetry local environments. It is particularly well suited for repetitive calculations for large clusters (up to 300,000 atoms), and may potentially be useful for describing electrostatic solvent effects. © 2017 Wiley Periodicals, Inc.     

Electrochemical energy for living systems

Plastoquinone and ubiquinone play essential roles in the electron transport chains of chloroplasts and mitochondria by coupling electron transport to the transfer of protons across membranes. The energy of the resulting proton gradient is used to synthesize adenosine triphosphate (ATP), the energy currency of all life. How did quinones first become involved in this process? We have detected several quinone compounds in carbonaceous meteorites that can transport protons in a liposome model system. It is possible that such compounds were available to transport protons in primitive versions of electron transport in early life.     

Theoretical and photophysical investigation of biologically active fluorophore: 2-amino-6-chlorofluoren-9-one

The optimized geometric parameters of the 2-Amino-6-chlorofluoren-9-one (2A6CF9O) compound were estimated by employing density functional theory. The electronic characteristics of the molecule were explored using molecular frontier orbital energies and the MEP surface. Kamlet's and Catalan's multiple linear regression techniques along with different polarity functions were used to investigate the influence of pure solvents on spectral properties. In the system, both general solute-solvent and hydrogen bonding interactions are active. However, as compared to normal solute-solvent interactions, hydrogen bonding interactions have a smaller role. In addition, using computed ground state dipole moment, solvatochromic correlations were employed to infer excited state dipole moment.     

Approximate analytical solutions for solute transport in two-layer porous media

Mathematical models for transport in layered media are important for investigating how restricting layers affect rates of solute migration in soil profiles; they may also improve the analysis of solute displacement experiments. This study reports an (approximate) analytical solution for solute transport during steady-state flow in a two-layer medium requiring continuity of solute fluxes and resident concentrations at the interface. The solutions were derived with Laplace transformations making use of the binomial theorem. Results based on this solution were found to be in relatively good agreement with those obtained using numerical inversion of the Laplace transform. An expression for the flux-averaged concentration in the second layer was also obtained. Zero- and first-order approximations for the solute distribution in the second layer were derived for a thin first layer representing a water film or crust on top of the medium. These thin-layer approximations did not perform as well as the binomial solution, except for the first-order approximation when the Peclet number,P, of the first layer, was low (P<5). Results of this study indicate that the ordering of two layers will affect the predicted breakthrough curves at the outlet of the medium. The two-layer solution was used to illustrate the effects of dispersion in the inlet or outlet reservoirs using previously published data on apparatus-induced dispersion.The U.S. Government right to retain a non-exclusive, royalty free licence in and to any copyright is acknowledged.     

Theory of Disappearance of the Electric Signal Induced by an Aircraft Jet Engine in the Afterburner Regime

Electrical aspects of aircraft jet engine operation are considered. A phenomenon previously observed experimentally, namely, the disappearance of the engine current and alternating electric signal induced by the engine jet in the afterburner regime, is explained. It is shown that this phenomenon results from the detachment of electrons from negative ions when the gas temperature in the afterburner increases. This leads to an increase in the effective conductivity of the gas. As a result, the engine current circuit is closed on the internal duct walls and engine charging becomes insignificant.A physico-mathematical model of the electrical processes in the afterburner is formulated and model problems are solved.     

Cloud dispersion models

A new technique has been developed to compute mean and fluctuating concentrations in complex turbulent flows. An initial distribution of material is discretised into any small clouds which are advected by a combination of the mean flow and large scale turbulence. The turbulence can be simulated either by Kinematic Simulation or by a stochastic model for the motion of each cloud centroid. The clouds also diffuse relative to their centroids; the statistics for this are obtained from a separate calculation of the growth of individual clouds in small scale turbulence, generated by Kinematic Simulation. The ensemble of discrete clouds is periodically rediscretised, to limit the size of the small clouds and prevent overlapping. The model is illustrated with simulations of dispersion in uniform flow and in a coastal flow, and the results are compared with analytic, steady state solutions where available.     

AP Shadow Net: A Remote Sensing Shadow Removal Network Based on Atmospheric Transport and Poisson’s Equation

Shadow is one of the fundamental indicators of remote sensing image which could cause loss or interference of the target data. As a result, the detection and removal of shadow has already been the hotspot of current study because of the complicated background information. In the following passage, a model combining the Atmospheric Transport Model (hereinafter abbreviated as ATM) with the Poisson Equation, AP ShadowNet, is proposed for the shadow detection and removal of remote sensing images by unsupervised learning. This network based on a preprocessing network based on ATM, A Net, and a network based on the Poisson Equation, P Net. Firstly, corresponding mapping between shadow and unshaded area is generated by the ATM. The brightened image will then enter the Confrontation identification in the P Net. Lastly, the reconstructed image is optimized on color consistency and edge transition by Poisson Equation. At present, most shadow removal models based on neural networks are significantly data-driven. Fortunately, by the model in this passage, the unsupervised shadow detection and removal could be released from the data source restrictions from the remote sensing images themselves. By verifying the shadow removal on our model, the result shows a satisfying effect from a both qualitative and quantitative angle. From a qualitative point of view, our results have a prominent effect on tone consistency and removal of detailed shadows. From the quantitative point of view, we adopt the non-reference evaluation indicators: gradient structure similarity (NRSS) and Natural Image Quality Evaluator (NIQE). Combining various evaluation factors such as reasoning speed and memory occupation, it shows that it is outstanding among other current algorithms.