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free-energy principle

Y F Ouyang, H M Chen, X M Tao, F Gao, Q Peng, Y Du
The properties of precipitates are important in understanding the strengthening mechanism via precipitation during heat treatment and the aging process in Al-Cu based alloys, where the formation of precipitates is sensitive to temperature and pressure. Here we report a first-principles investigation of the effect of temperature and pressure on the structural stability, elastic constants and formation free energy for precipitates of Al2Cu, as well as their mechanical properties. Based on the formation enthalpy of Guinier-Preston (GP(I)) zones, the size of the GP(I) zone is predicted to be about 1...
December 12, 2017: Physical Chemistry Chemical Physics: PCCP
Gang Tang, Zewen Xiao, Hideo Hosono, Toshio Kamiya, Daining Fang, Jiawang Hong
Over the past few years, the development of lead-free and stabile perovskite absorbers with excellent performance has attracted extensive attention. Much effort has been devoted to screening and synthesizing this type of solar cell absorbers. Here, we present a general design strategy for designing the layered halide double perovskites Cs3+nM(II)nSb2X9+3n (M = Sn, Ge) with desired photovoltaic-relevant properties by inserting [MX6] octahedral layers, based on the principles of increased electronic dimensionality...
December 12, 2017: Journal of Physical Chemistry Letters
Xiaoyin Li, Shunhong Zhang, Cunzhi Zhang, Qian Wang
It is a longstanding quest to use the planar N6 ring as a structural unit to build stable atomic sheets. However, unlike C6H6, the neutral N6 ring is unstable due to the strong repulsion of the lone-pair of electrons. Using first-principles calculations and the global structure search method, we show that the N6 unit can be stabilized by the linkage of Be atoms, forming a h-BeN3 honeycomb monolayer, in which the geometry and the π-molecular orbitals of the N6 rings are well kept. This sheet is not only energetically, dynamically and thermally stable, but also can withstand high temperatures up to 1000 K...
December 7, 2017: Nanoscale
József Prechl
The homeostasis of antibodies can be characterized as a balanced production, target-binding and receptor-mediated elimination regulated by an interaction network, which controls B-cell development and selection. Recently, we proposed a quantitative model to describe how the concentration and affinity of interacting partners generates a network. Here we argue that this physical, quantitative approach can be extended for the interpretation of effector functions of antibodies. We define global antibody equilibrium as the zone of molar equivalence of free antibody, free antigen and immune complex concentrations and of dissociation constant of apparent affinity: [Ab]=[Ag]=[AbAg]=KD...
November 2017: Clinical & Translational Immunology
Zhibo Chen, Wei Zhou, Weiping Li
Stereoscopic video quality assessment (SVQA) is a challenging problem. It has not been well investigated on how to measure depth perception quality independently under different distortion categories and degrees, especially exploit the depth perception to assist the overall quality assessment of 3D videos. In this paper, we propose a new depth perception quality metric (DPQM) and verify that it outperforms existing metrics on our published 3D video extension of High Efficiency Video Coding (3D-HEVC) video database...
February 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Tingting Zheng, Wei Sang, Zhihai He, Qiushi Wei, Bowen Chen, Hongliang Li, Cong Cao, Ruijie Huang, Xupeng Yan, Bicai Pan, Shiming Zhou, Jie Zeng
Exploring efficient and economical electrocatalysts for hydrogen evolution reaction is of great significance for water splitting in industrial scale. Tungsten oxide WO3 has been long expected as a promising non-precious electrocatalysts for hydrogen production. However, the poor intrinsic activity of this material hampers its development. Herein, we design a highly efficient hydrogen evolution electrocatalyst via introducing oxygen vacancies into WO3 nanosheets. Our first-principles calculations demonstrate that the gap states introduced by O vacancies make WO3 act as a degenerate semiconductor with high conductivity and desirable hydrogen adsorption free energy...
November 27, 2017: Nano Letters
Shuang-Fei Zhu, Shu-Hai Zhang, Rui-Jun Gou, Gang Han, Chun-Lei Wu, Fu-de Ren
The effects of the molar ratio, temperature, and solvent on the formation of the cocrystal explosive DNP/CL-20 were investigated using molecular dynamics (MD) simulation. The cocrystal structure was predicted through Monte Carlo (MC) simulation and using first-principles methods. The results showed that the DNP/CL-20 cocrystal might be more stable in the molar ratio 1:1 near to 318 K, and the most probable cocrystal crystallizes in the triclinic crystal system with the space group P[Formula: see text]. Cocrystallization was more likely to occur in methanol and ethanol at 308 K as a result of solvent effects...
November 24, 2017: Journal of Molecular Modeling
T Gopinath, Sarah E D Nelson, Gianluigi Veglia
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is emerging as a unique method for the atomic resolution structure determination of native membrane proteins in lipid bilayers. Although 13C-detected ssNMR experiments continue to play a major role, recent technological developments have made it possible to carry out 1H-detected experiments, boosting both sensitivity and resolution. Here, we describe a new set of 1H-detected hybrid pulse sequences that combine through-bond and through-space correlation elements into single experiments, enabling the simultaneous detection of rigid and dynamic domains of membrane proteins...
December 2017: Journal of Magnetic Resonance
Somayeh Khazaei, Daniel Sebastiani
We study the influence of rotational coupling between a pair of methyl rotators on the tunneling spectrum in condensed phase. Two interacting adjacent methyl groups are simulated within a coupled-pair model composed of static rotational potential created by the chemical environment and the interaction potential between two methyl groups. We solve the two-dimensional time-independent Schrödinger equation analytically by expanding the wave functions on the basis set of two independent free-rotor functions. We investigate three scenarios which differ with respect to the relative strength of single-rotor and coupling potential...
November 21, 2017: Journal of Chemical Physics
Emre Bukusoglu, Jose A Martinez-Gonzalez, Xiaoguang Wang, Ye Zhou, Juan J de Pablo, Nicholas L Abbott
We report on the influence of surface confinement on the phase behavior and strain-induced alignment of thin films of blue phase liquid crystals (BPs). Confining surfaces comprised of bare glass, dimethyloctadecyl [3-(trimethoxysilyl)propyl] ammonium chloride (DMOAP)-functionalized glass, or polyvinyl alcohol (PVA)-coated glass were used with or without mechanically rubbing to influence the azimuthal anchoring of the BPs. These experiments reveal that confinement can change the phase behavior of the BP films...
November 22, 2017: Soft Matter
Gregor Deichmann, Nico F A van der Vegt
Scale bridging simulations of soft matter rely on the availability of transferable coarse-grained models. In systematic coarse-graining approaches, core principles of statistical mechanics are used to relate the coarse-grained models to the underlying molecular interactions. The conditional reversible work (CRW) method provides effective, nonbonded pair potentials by means of computing coupling free energies between mapped chemical groups. This method has so far been used almost exclusively for systems composed of apolar organic molecules, but additional challenges arise when developing coarse-grained models for polar molecules in which (long-ranged) electrostatic interactions are important...
November 21, 2017: Journal of Chemical Theory and Computation
Leonid L Rusevich, Guntars Zvejnieks, Alessandro Erba, Roberto Dovesi, Eugene E Kotomin
An enhancement of the piezoelectric properties of lead-free materials, which allow conversion of mechanical energy into electricity, is a task of great importance and interest. Results of first-principles calculations of piezoelectric/electromechanical properties of the Ba(1-x)SrxTiO3 (BSTO) ferroelectric solid solution with perovskite structure are presented and discussed. Calculations are performed within the linear combination of atomic orbitals (LCAO) approximation and periodic-boundary conditions, using advanced hybrid functionals of the density-functional-theory (DFT)...
November 17, 2017: Journal of Physical Chemistry. A
Alexander B Kuhn, Sebastian Kube, Anne R Karow-Zwick, Daniel Seeliger, Patrick Garidel, Michaela Blech, Lars V Schäfer
Monoclonal antibody (mAb) based therapeutics often require high concentration formulations. Unfortunately, highly concentrated antibody solutions often have biophysical properties that are disadvantageous for therapeutic development, such as high viscosity, solubility limitations, precipitation issues, or liquid-liquid phase separation. In this work, we present a computational rational design principle for improving the thermodynamic stability of mAb solutions through targeted point mutations. Two publicly available IgG1 monoclonal antibodies that exhibit high viscosity at high concentrations were used as model systems...
November 14, 2017: Journal of Physical Chemistry. B
Jiu Pang, Qun Yang, Xiaosong Ma, Liming Wang, Chunjian Tan, Daxi Xiong, Huaiyu Ye, Xianping Chen
The sensing performances of pristine and X-doped phosphorene substrates (X = Al, Si, and S atoms) toward the adsorption of the toxic gases HCN and HNC were systematically investigated by first-principles simulations. The numerical results show that the pristine phosphorene is sensitive to HCN and HNC molecules with moderate adsorption energy, excellent charge transfer, high sensitivity and selectivity, implying its potential applications as excellent HCN and HNC sensors. In addition, the Al-doped phosphorene exhibits extremely high reactive activity toward HCN and HNC gases; thus, it has potential for use as a metal-free catalyst for activating or catalyzing HCN or HNC adsorbates...
November 22, 2017: Physical Chemistry Chemical Physics: PCCP
Xin Zhao, Cai-Zhuang Wang, Minsung Kim, Kai-Ming Ho
Fe-cluster-based crystal structures are predicted for chalcogenides Fe3X4 (X = S, Se, Te) using an adaptive genetic algorithm. Topologically different from the well-studied layered structures of iron chalcogenides, the newly predicted structures consist of Fe clusters that are either separated by the chalcogen atoms or connected via sharing of the vertex Fe atoms. Using first-principles calculations, we demonstrate that these structures have competitive or even lower formation energies than the experimentally synthesized Fe3X4 compounds and exhibit interesting magnetic and electronic properties...
November 13, 2017: Inorganic Chemistry
Ruben Demuynck, Sven M J Rogge, Louis Vanduyfhuys, Jelle Wieme, Michel Waroquier, Veronique Van Speybroeck
In order to reliably predict and understand the breathing behavior of highly flexible metal-organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling...
November 13, 2017: Journal of Chemical Theory and Computation
Vytautas Gapsys, Bert L de Groot
Nucleotide sequence dependent interactions between proteins and DNA are responsible for a wide range of gene regulatory functions. Accurate and generalizable methods to evaluate the strength of protein-DNA binding have been long sought after. While numerous computational approaches have been developed, most of them require fitting parameters to experimental data to a certain degree, e.g. machine learning algorithms or knowledge based statistical potentials. Molecular dynamics based free energy calculations offer a robust, system independent, first principles based method to calculate free energy differences upon nucleotide mutation...
November 10, 2017: Journal of Chemical Theory and Computation
Qiang Shao, Weiliang Zhu
Protein folding has been posing challenges for molecular simulation for decades. Implicit solvent models are sought as routes to increase the capability of simulation, with trade-offs between computational speed and accuracy. Here, we systematically investigate the folding of a variety of α-helix bundle proteins ranging in size from 46 to 102 amino acids using state-of-the-art force field and implicit solvent model. The accurate all-atom simulated folding is enabled for six proteins, including for the first time a successful folding of protein with >100 amino acids in implicit solvent...
November 9, 2017: Journal of Chemical Theory and Computation
Ang Bian, Yafei Dai, Jinlong Yang
Using a gas separation membrane as a simple gas separation device has an obvious advantage because of the low energy consumption and pollution-free manufacturing. The first-principles calculations used in this work show that germanene with its divacancy is an excellent material for use as a hydrogen (H2) and helium (He) separation membrane, and that it displays an even better competitive advantage than porous graphene and porous silicene. Porous germanene with its divacancy is chemically inert to gas molecules, because it lacks additional atoms to protect the edged dangling germanium atoms in defects, and thus shows great advantages for gas separation over previously prepared graphene...
November 16, 2017: Nanoscale
Ukrae Cho, Daniel P Riordan, Paulina Ciepla, Kiranmai S Kocherlakota, James K Chen, Pehr B Harbury
In principle, the millisecond emission lifetimes of lanthanide chelates should enable their ultrasensitive detection in biological systems by time-resolved optical microscopy. In practice, however, lanthanide imaging techniques have provided no better sensitivity than conventional fluorescence microscopy. Here, we identified three fundamental problems that have impeded lanthanide microscopy: low photon flux, inefficient excitation, and optics-derived background luminescence. We overcame these limitations with a new lanthanide imaging modality, transreflected illumination with luminescence resonance energy transfer (trLRET), which increases the time-integrated signal intensities of lanthanide lumiphores by 170-fold and the signal-to-background ratios by 75-fold...
November 6, 2017: Nature Chemical Biology
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