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free-energy principle

Sohag Biswas, Bhabani S Mallik
We present the characteristic proton transfer process from water to the pyrazole anion, infrared signatures of hydroxyl groups and the free energy profile of the process in aqueous solution combining first principles simulations, wavelet analysis and metadynamics. Our results show that the presence of minimum three water molecules in the gas phase cluster with a particular arrangement is sufficient to facilitate the proton transfer process from water to the anion. The overall reaction is very rapid in aqueous solution, and the free energy barrier for this process is found to be 4...
October 21, 2016: Physical Chemistry Chemical Physics: PCCP
Fredrik Elinder, Michael Madeja, Hugo Zeberg, Peter Århem
The transmembrane voltage needed to open different voltage-gated K (Kv) channels differs by up to 50 mV from each other. In this study we test the hypothesis that the channels' voltage dependences to a large extent are set by charged amino-acid residues of the extracellular linkers of the Kv channels, which electrostatically affect the charged amino-acid residues of the voltage sensor S4. Extracellular cations shift the conductance-versus-voltage curve, G(V), by interfering with these extracellular charges...
October 18, 2016: Biophysical Journal
Gregory J O Beran, Joshua D Hartman, Yonaton N Heit
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties...
October 18, 2016: Accounts of Chemical Research
Katsuyuki Nobusada
A simple and efficient method to inhibit aggregation of Pt clusters supported on metal-oxide is presented and assessed. This method preserves the accessible clusters surface where catalytic active sites are located and is effective even at relatively high temperatures up to 700K. The key idea is the inclusion of transition metal atoms, such as Ni, into the Pt clusters realizing the anchoring via the formation of strong chemical bonds with oxygen atoms of the metal-oxide support. To elucidate the efficiency of the method, we use first-principles molecular dynamics enhanced with free-energy sampling methods...
October 15, 2016: Chemistry: a European Journal
Zhun Liu, Ru-Zhi Wang, Peter Zapol
Elucidation of homoepitaxial growth mechanisms on vicinal non-polar surfaces of GaN is highly important for gaining an understanding of and control thin film surface morphology and properties. Using first-principles calculations, we study the step-flow growth in m-plane GaN based on atomic row nucleation and kink propagation kinetics. Ga-N dimer adsorption onto the m-plane is energetically more favorable than that of Ga and N isolated adatoms. Therefore, we have treated the dimers as the dominant growth species attached to the step edges...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
Bolin Liao, A A Maznev, Keith A Nelson, Gang Chen
There is a growing interest in the mode-by-mode understanding of electron and phonon transport for improving energy conversion technologies, such as thermoelectrics and photovoltaics. Whereas remarkable progress has been made in probing phonon-phonon interactions, it has been a challenge to directly measure electron-phonon interactions at the single-mode level, especially their effect on phonon transport above cryogenic temperatures. Here we use three-pulse photoacoustic spectroscopy to investigate the damping of a single sub-terahertz coherent phonon mode by free charge carriers in silicon at room temperature...
October 12, 2016: Nature Communications
Jonny Proppe, Tamara Husch, Gregor N Simm, Markus Reiher
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided...
October 12, 2016: Faraday Discussions
Shaobin Tang, Weihua Wu, Liangxian Liu, Junjing Gu
The BCN graphene are attractive for metal-free oxygen reduction reaction (ORR) electrocatalysts and other catalysts due to its unique structures and electronic properties. In the present work, we first report the structure of active site of BCN graphene with different types of BN cluster towards the O2 dissociation using density functional theory. Our results show that the edge termination and shape of substitutional BN clusters are two important factors, determining the catalytic activity of BCN graphene for the oxygen molecules dissociation...
September 29, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Mariana Rossi, Piero Gasparotto, Michele Ceriotti
Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects...
September 9, 2016: Physical Review Letters
Daniele Pelliccia, Alexander Rack, Mario Scheel, Valentina Cantelli, David M Paganin
We report an experimental proof of principle for ghost imaging in the hard-x-ray energy range. We use a synchrotron x-ray beam that is split using a thin crystal in Laue diffraction geometry. With an ultrafast imaging camera, we are able to image x rays generated by isolated electron bunches. At this time scale, the shot noise of the synchrotron emission process is measurable as speckles, leading to speckle correlation between the two beams. The integrated transmitted intensity from a sample located in the first beam is correlated with the spatially resolved intensity measured in the second, empty, beam to retrieve the shadow of the sample...
September 9, 2016: Physical Review Letters
Rajkumar Jana, Anupam Bhim, Pallavi Bothra, Swapan K Pati, Sebastian C Peter
Manipulating the d-band center of the metal surface and hence optimizing the free energy of hydrogen adsorption (ΔGH ) close to the optimal adsorption energy (ΔGH =0) for hydrogen evolution reaction (HER), is an efficient strategy to enhance the activity for HER. Herein, we report a oleylamine-mediated (acting as the solvent, stabilizer, and reducing agent) strategy to synthesize intermetallic PdCu3 nanoparticles (NPs) without using any external reducing agent. Upon electrochemical cycling, PdCu3 transforms into Pd-rich PdCu (ΔGH =0...
September 21, 2016: ChemSusChem
Xun Sun, Thomas E Morrell, Haw Yang
Protein conformational changes are known to play important roles in assorted biochemical and biological processes. Driven by thermal motions of surrounding solvent molecules, such a structural remodeling often occurs stochastically. Yet, regardless of how random the conformational reconfiguration may appear, it could in principle be described by a linear combination of a set of orthogonal modes which, in turn, are contained in the intramolecular distance distributions. The central challenge is how to obtain the distribution...
October 13, 2016: Journal of Physical Chemistry. B
Johannes T Margraf, Prakash Verma, Rodney J Bartlett
Double-hybrid density functional approximations (DH-DFAs) provide an accurate description of the electronic structure of molecules by semiempirically mixing density functional and wavefunction theory. In this paper, we investigate the properties of the potential used in such approximations. By using the optimized effective potential approach, the consistent Kohn-Sham (KS) potential for a double-hybrid functional (including the second-order perturbational contribution) can be generated. This potential is shown to provide an improved description of orbital energies as vertical ionization potentials (IPs), relative to the perturbation-free KS potential typically used...
September 14, 2016: Journal of Chemical Physics
Wei He, Zhengping Li, Chao Wen, Hong Liu, Wenzhong Shen
Doping of silicon nanocrystals (Si-NCs) is one of the major challenges for silicon nanoscale devices. In this work, phosphorus (P) doping in Si-NCs which are embedded within an amorphous silicon matrix is realized together with the growth of Si-NCs by plasma-enhanced chemical vapor deposition under a tunable substrate direct current (DC) bias. The variation of phosphorus concentration with substrate bias can be explained by the competition of bonding processes of Si-Si and P-Si bonds. The formation of Si-Si and P-Si bonds is differently influenced by the ion bombardment controlled by the substrate bias, due to their bonding energy difference...
October 21, 2016: Nanotechnology
Dimitrios Spiliotopoulos, Panagiotis L Kastritis, Adrien S J Melquiond, Alexandre M J J Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Molecular-docking programs coupled with suitable scoring functions are now established and very useful tools enabling computational chemists to rapidly screen large chemical databases and thereby to identify promising candidate compounds for further experimental processing. In a broader scenario, predicting binding affinity is one of the most critical and challenging components of computer-aided structure-based drug design. The development of a molecular docking scoring function which in principle could combine both features, namely ranking putative poses and predicting complex affinity, would be of paramount importance...
2016: Frontiers in Molecular Biosciences
Ram M Adar, David Andelman, Haim Diamant
Two overall neutral surfaces with positively and negatively charged domains ("patches") have been shown in recent experiments to exhibit long-range attraction when immersed in an ionic solution. Motivated by the experiments, we calculate analytically the osmotic pressure between such surfaces within the Poisson-Boltzmann framework, using a variational principle for the surface-averaged free energy. The electrostatic potential, calculated beyond the linear Debye-Hückel theory, yields an overall attraction at large intersurface separations, over a wide range of the system's controlled length scales...
August 2016: Physical Review. E
Gaetano Napoli, Luigi Vergori
We derive the hydrodynamic equations for nematic liquid crystals lying on curved substrates. We invoke the Lagrange-Rayleigh variational principle to adapt the Ericksen-Leslie theory to two-dimensional nematics in which a degenerate anchoring of the molecules on the substrate is enforced. The only constitutive assumptions in this scheme concern the free-energy density, given by the two-dimensional Frank potential, and the density of dissipation which is required to satisfy appropriate invariance requirements...
August 2016: Physical Review. E
Mandy J Peffers, John Collins, John Loughlin, Carole Proctor, Peter D Clegg
BACKGROUND: Mesenchymal stem cells (MSCs) have prospective applications in regenerative medicine and tissue engineering but to what extent phenotype and differentiation capacity alter with ageing is uncertain. Consequently, any loss in functionality with age would have profound consequences for the maintenance of tissue viability and the quality of tissues. Proteomics enables the set of proteins responsible for a particular cell phenotype to be identified, as well as enabling insights into mechanisms responsible for age-related alterations in musculoskeletal tissues...
September 14, 2016: Stem Cell Research & Therapy
Todor Dudev, Cédric Grauffel, Carmay Lim
The homotetrameric M2 proton channel of influenza A plays a crucial role in the viral life cycle and is thus an important therapeutic target. It selectively conducts protons against a background of other competing cations whose concentrations are up to a million times greater than the proton concentration. Its selectivity is largely determined by a constricted region of its open pore known as the selectivity filter, which is lined by four absolutely conserved histidines. While the mechanism of proton transport through the channel has been studied, the physical principles underlying the selectivity for protons over other cations in the channel's His4 selectivity filter remain elusive...
October 5, 2016: Journal of the American Chemical Society
Werner Crous, Kevin J Naidoo
Mammalian sialyltransferases play a role in the metastasis of various cancers in humans. Inhibitors of these enzymes will in principle be able to directly inhibit aberrant sialylation in cancer. Inhibitors of ST3Gal-I resembling the donor component of SN1 Transition State structures were previously evaluated as part of a kinetics study. Here, using classical dynamics simulations and free energy perturbation calculations, we rationalize the performance of three of these donor analogue ST3Gal-I enzyme inhibitors...
October 15, 2016: Bioorganic & Medicinal Chemistry
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