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Terry Farrelly, Fernando G S L Brandão, Marcus Cramer
Thermal states are the bedrock of statistical physics. Nevertheless, when and how they actually arise in closed quantum systems is not fully understood. We consider this question for systems with local Hamiltonians on finite quantum lattices. In a first step, we show that states with exponentially decaying correlations equilibrate after a quantum quench. Then, we show that the equilibrium state is locally equivalent to a thermal state, provided that the free energy of the equilibrium state is sufficiently small and the thermal state has exponentially decaying correlations...
April 7, 2017: Physical Review Letters
Y Lu, T Sun, Ping Zhang, P Zhang, D-B Zhang, R M Wentzcovitch
Beryllium (Be) is an important material with wide applications ranging from aerospace components to x-ray equipment. Yet a precise understanding of its phase diagram remains elusive. We have investigated the phase stability of Be using a recently developed hybrid free energy computation method that accounts for anharmonic effects by invoking phonon quasiparticles. We find that the hcp → bcc transition occurs near the melting curve at 0<P<11  GPa with a positive Clapeyron slope of 41±4  K/GPa, which is more consistent with recent experimental measurements...
April 7, 2017: Physical Review Letters
Bing Xie, Trung Hai Nguyen, David D L Minh
We demonstrate the feasibility of estimating protein-ligand binding free energies using multiple rigid receptor configurations. Based on T4 lysozyme snapshots extracted from six alchemical binding free energy calculations with a flexible receptor, binding free energies were estimated for a total of 141 ligands. For 24 ligands, the calculations reproduced flexible-receptor estimates with a correlation coefficient of 0.90 and a root mean square error of 1.59 kcal/mol. The accuracy of calculations based on Poisson-Boltzmann/Surface Area implicit solvent was comparable to previously reported free energy calculations...
April 21, 2017: Journal of Chemical Theory and Computation
Jenna L Logsdon, Patrick E Hartnett, Jordan N Nelson, Michelle A Harris, Tobin J Marks, Michael R Wasielewski
Orthogonal attachment of polar and nonpolar side-chains to a zinc porphyrin-perylenediimide dyad (ZnP-PDI, 1a) is shown to result in self-assembly of ordered supramolecular ribbons in which the ZnP and PDI molecules form segregated π-stacked columns. Following photoexcitation of the ordered ribbons, ZnP(+•)-PDI(-•) radical ion pairs form in <200 fs and subsequently produce a 30 ± 3% yield of free charge carriers that live for about 100 μs. Elongating the side chains on ZnP and PDI in 1b enhances the order of the films, but does not result in an increase in free charge carrier yield...
April 21, 2017: ACS Applied Materials & Interfaces
Jinfan Chen, Patrick H-L Sit
The catalytic hydrogen-producing processes of two prototypical cobaloxime catalysts Co(dmgBF2)2 (dmgBF2=difluoroboryl-dimethylglyoxime) and Co(dmgH)2 (dmgH=dimethylglyoxime), were studied by Density Functional Theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent. Our study demonstrates the key role of water molecules as shuttles to deliver protons to the cobalt active centers of these catalysts. However, the transfer of protons to the cobalt centers also competes with the diffusion of the proton away from the complex via the hydrogen bond network of water...
April 21, 2017: Journal of Physical Chemistry. A
Shuang Zhou, Sergij V Shiyanovskii, Heung-Shik Park, Oleg D Lavrentovich
The detailed structure of singularities of ordered field represents a fundamental problem in diverse areas of physics. At the defect cores, the deformations are so strong that the system explores states with symmetry different from that of an undistorted material. These regions are difficult to explore experimentally as their spatial extension is very small, a few molecular lengths in the condensed matter. Here we explore the cores of disclinations in the so-called chromonic nematics that extend over macroscopic length scales accessible for optical characterization...
April 21, 2017: Nature Communications
Miyabi Hiyama, Hidefumi Akiyama, Nobuaki Koga
To elucidate the emission process of firefly d-luciferin oxidation across the pH range of 7-9, we identified the emission process by comparison of the potential and free-energy profiles for the formation of the firefly substrate and emitter, including intermediate molecules such as d-luciferyl adenylate, 4-membered dioxetanone, and their deprotonated chemical species. From these relative free energies, it is observed that the oxidation pathway changes from d-luciferin → deprotonated d-luciferyl adenylate → deprotonated 4-membered dioxetanone → oxyluciferin to deprotonated d-luciferin → deprotonated d-luciferyl adenylate → deprotonated 4-membered dioxetanone → oxyluciferin with increasing pH value...
April 20, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
Xiaohua Zhou, Erhu Zhang, Minggang Xia, Lei Zhang, Zhiqi Tian, Jianlin Liu, Shengli Zhang
Gaining insight into the relationships between the self-organized cell structures and the properties of biotissues is helpful for revealing the function of biomaterials and its designing principle. However, the traditionally used random foam model neglects several important details of the frameworks of cell clusters resulting in incomplete conclusions. Herein, we use a more complete model, the cell adhesion model, to investigate the mechanical and morphological properties of the two-dimensional (2D) dry cell foams...
April 21, 2017: Physical Chemistry Chemical Physics: PCCP
Yu Cheng, Yun Liu, Juan Wu, Prince Ofori Donkor, Ting Li, Haile Ma
The thermodynamics and kinetics of traditional and simultaneous dual frequency energy-gathered ultrasound (SDFU) assisted enzymolysis of potato protein were investigated to get the knowledge of the mechanisms on the SDFU's promoting efficiency during enzymolysis. The concentration of potato protein hydrolysate and parameters of thermodynamic and kinetic during traditional and SDFU assisted enzymolysis were determined. The results showed that potato protein hydrolysate concentration of SDFU assisted enzymolysis was higher than traditional enzymolysis at the hydrolysis time of 60min (p<0...
July 2017: Ultrasonics Sonochemistry
Jiaqi Lin, Roozbeh Dargazany, Alfredo Alexander-Katz
Lipid flip-flop and its associated transient pore formation are key thermodynamic properties of living cell membranes. However, there is a lack of understanding of whether ionic imbalance that exists ubiquitously across cell membranes affects lipid flip-flop and its associated functions. Potential of mean force calculations show that the free-energy barrier of lipid flip-flop on the extracellular leaflet reduces with the presence of ionic imbalance, whereas the barrier on the intracellular leaflet is generally not affected...
April 20, 2017: Small
Tugce Senturk Parreidt, Markus Schmid, Carolin Hauser
Characterizing the physical properties of a surface is largely dependent on determining the contact angle exhibited by a liquid. Contact angles on the surfaces of rough and irregularly-shaped food samples are difficult to measure using a contact angle meter (goniometer). As a consequence, values for the surface energy and its components can be mismeasured. The aim of this work was to use a novel contact angle measurement method, namely the snake-based ImageJ program, to accurately measure the contact angles of rough and irregular shapes, such as food samples, and so enable more accurate calculation of the surface energy of food materials...
April 20, 2017: Foods (Basel, Switzerland)
Melek N Ucisik, Sharon Hammes-Schiffer
Human DNA polymerase η (Pol η) plays a vital role in protection against skin cancer caused by damage from ultraviolet light. This enzyme rescues stalled replication forks at cyclobutane thymine-thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions. Residue R61 is conserved in the Pol η enzymes across species, but the corresponding residue, as well as its neighbor S62, is different in other Y-family polymerases, Pol ι and Pol κ. Herein, R61 and S62 are mutated to their Pol ι and Pol κ counterparts...
April 20, 2017: Journal of Physical Chemistry. B
Abhishek Singharoy, Christophe Chipot
Millisecond-scale conformational transitions represent a seminal challenge for traditional molecular dynamics simulations, even with the help of high-end supercomputer architectures. Such events are particularly relevant to the study of molecular motors-proteins or abiological constructs that convert chemical energy into mechanical work. Here, we present a hybrid-simulation scheme combining an array of methods including elastic network models, transition path sampling, and advanced free-energy methods, possibly in conjunction with generalized-ensemble schemes to deliver a viable option for capturing the millisecond-scale motor steps of biological motors...
April 20, 2017: Journal of Physical Chemistry. B
Ranajit Saha, Sudip Pan, Pratim Kumar Chattaraj
Structures, bonding and stability half-sandwich complexes with general formula, NgMCp+ (Ng = He-Rn, M = Be-Ba, Cp = 5-C5H5) are analyzed through ab initio computation. MCp+ complexes possess remarkable Ng binding ability, particularly for M = Be and Mg. While for Ar-Rn bound analogues the bond dissociation energy in the former complex ranges within 17.5-28.0 kcal mol-1, it becomes 10.4-18.7 kcal mol-1 in the latter complex. In fact, BeCp+ is able to form strong bond with the two most inert elements, He and Ne...
April 19, 2017: Journal of Physical Chemistry. A
Alessandra Magistrato, Jacopo Sgrignani, Rolf Krause, Andrea Cavalli
Cytochromes P450 (CYP450), in particular CYP19A1 and CYP17A1, are key clinical targets of breast and prostate anticancer therapies, critical players in drug metabolism and their overexpression in tumours is associated with drug resistance. In these enzymes ligands (substrates, drugs) metabolism occurs in deeply buried active sites accessible only via several gruelling channels, whose exact biological role remains unclear. Gaining direct insights on the mechanism by which ligands travel in and out, is becoming increasingly important given that channels are involved in the modulation of binding/dissociation kinetics and the specificity of ligands toward a CYP450...
April 19, 2017: Journal of Physical Chemistry Letters
Thomas P Burghardt, Xiaojing Sun, Yihua Wang, Katalin Ajtai
Myosin motors in cardiac ventriculum convert ATP free energy to the work of moving blood volume under pressure. The actin bound motor cyclically rotates its lever-arm/light-chain complex linking motor generated torque to the myosin filament backbone and translating actin against resisting force. Previous research showed that the unloaded in vitro motor is described with high precision by single molecule mechanical characteristics including unitary step-sizes of approximately 3, 5, and 8 nm and their relative step-frequencies of approximately 13, 50, and 37%...
2017: PloS One
Xianbo Jia, Yonghua Guo, Xinjian Lin, Minsheng You, Chenqiang Lin, Longjun Chen, Jichen Chen
Cyclodextrin glycosyltransferase (CGTase) is an important industrial enzyme for production of cyclodextrins (CDs) from starch by intramolecular transglycosylation. CGTase consists of five domains labeled A to E. For optimizing catalytic activity of CGTase, CGTase of Geobacillus sp. was fused with the family 20 carbohydrate-binding module (CBM) of the Bacillus circulans strain 251 CGTase. The CBMbc251 that has a low binding free energy with maltohexaose, was selected by in silico design. Then the fusion enzyme, CGTΔE-CBMbc251, was constructed by fusing the CBMbc251 to the C-terminal region of CGTΔE...
April 19, 2017: Journal of Basic Microbiology
Kai Huang, Igal Szleifer
Nature uses the interplay between hydrophobic and electrostatic interactions of disordered proteins to orchestrate complicated molecular gate such as the nuclear pore complex to control the transport of biological masses. Inspired by nature, we here theoretically show that well-defined gate shape, sensitive response to pH and salt concentration, and selectivity in cargo transport can be simultaneously achieved by grafting amphiphilic diblock copolymers made of sequence-controlled hydrophobic and ionizable monomers on the inner surface of solid-state nanopore...
April 19, 2017: Journal of the American Chemical Society
Pfano Mathews Nekhunguni, Nikita Tawanda Tavengwa, Hlanganani Tutu
In this work, the synthesis of iron (hydr) oxide modified zeolite was achieved through precipitation of iron on the zeolite. The structure and surface morphology of iron (hydr) oxide modified zeolite (IHOMZ) was studied by scanning electron microscopy (SEM), coupled with an energy-dispersive X-ray spectroscopy (EDX), and Fourier transform infrared (FT-IR) spectra. The efficiency of IHOMZ was then investigated through batch technique for the extraction of As(V) from mine waste water. The optimum parameters for maximum As(V) adsorption were: an initial As(V) concentration (10 mg L(-1)), adsorbent dosage (3...
April 15, 2017: Journal of Environmental Management
Shuai Wei, Charles L Brooks, Aaron T Frank
The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on Cα-only protein structures...
April 16, 2017: Journal of Computational Chemistry
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