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Theory of simulation

Christine Prouty, Shima Mohebbi, Qiong Zhang
Given the increasing vulnerability of communities to the negative impacts of untreated wastewater, resource recovery (RR) systems provide a paradigm shift away from a traditional approach of waste separation and treatment towards a productive recovery of water, energy and nutrients. The aim of this research is to understand the relationships between factors that influence the adoption and sustainability of wastewater-based RR systems to inform technology implementation strategies. The study presents a theory-informed, community-influenced system dynamics (SD) model to provide decision-makers with an adaptable tool that simulates system-level responses to the strategies that are developed for the coastal town of Placencia, Belize...
March 7, 2018: Water Research
Marcin Maździarz, Adam Mrozek, Wacław Kuś, Tadeusz Burczyński
A potentially new, single-atom thick semiconducting 2D- graphene -like material, called Anisotropic-cyclicgraphene , has been generated by the two stage searching strategy linking molecular and ab initio approach. The candidate was derived from the evolutionary-based algorithm and molecular simulations was then profoundly analysed using first-principles density functional theory from the structural, mechanical, phonon, and electronic properties point of view. The proposed polymorph of graphene ( rP16 -P1m1) is mechanically, dynamically, and thermally stable and can achieve semiconducting with a direct band gap of 0...
March 16, 2018: Materials
Brodie Pearson, Baylor Fox-Kemper
Data from turbulent numerical simulations of the global ocean demonstrate that the dissipation of kinetic energy obeys a nearly log-normal distribution even at large horizontal scales O(10  km). As the horizontal scales of resolved turbulence are larger than the ocean is deep, the Kolmogorov-Yaglom theory for intermittency in 3D homogeneous, isotropic turbulence cannot apply; instead, the down-scale potential enstrophy cascade of quasigeostrophic turbulence should. Yet, energy dissipation obeys approximate log-normality-robustly across depths, seasons, regions, and subgrid schemes...
March 2, 2018: Physical Review Letters
Ruili Shi, Pengju Wang, Lingli Tang, Xiaoming Huang, Yonggang Chen, Yan Su, Jijun Zhao
Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F-(H2O)n with n = 1-10. The F-(H2O)n clusters prefer structures in which the F- anion remains at the surface of the structure and coordinates with four water molecules, as the F-(H2O)n clusters have strong F--H2O interactions as well as strong hydrogen bonds between H2O molecules. The strong interaction between the F- anion and adjacent H2O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule...
March 16, 2018: Journal of Physical Chemistry. A
Kara Pham, Emma Turian, Kai Liu, Shuwang Li, John Lowengrub
We consider the nonlinear dynamics of an avascular tumor at the tissue scale using a two-fluid flow Stokes model, where the viscosity of the tumor and host microenvironment may be different. The viscosities reflect the combined properties of cell and extracellular matrix mixtures. We perform a linear morphological stability analysis of the tumors, and we investigate the role of nonlinearity using boundary-integral simulations in two dimensions. The tumor is non-necrotic, although cell death may occur through apoptosis...
March 15, 2018: Journal of Mathematical Biology
Angelica Nakagawa Lima, Ronaldo Junio de Oliveira, Antônio Sérgio Kimus Braz, Maurício Garcia de Souza Costa, David Perahia, Luis Paulo Barbour Scott
There are two different prion conformations: (1) the cellular natural (PrPC ) and (2) the scrapie (PrPSc ), an infectious form that tends to aggregate under specific conditions. PrPC and PrPSc are widely different regarding secondary and tertiary structures. PrPSc contains more and longer β-strands compared to PrPC . The lack of solved PrPSc structures precludes a proper understanding of the mechanisms related to the transition between cellular and scrapie forms, as well as the aggregation process. In order to investigate the conformational transition between PrPC and PrPSc , we applied MDeNM (molecular dynamics with excited normal modes), an enhanced sampling simulation technique that has been recently developed to probe large structural changes...
March 15, 2018: European Biophysics Journal: EBJ
Jeliazko R Jeliazkov, Adnan Sljoka, Daisuke Kuroda, Nobuyuki Tsuchimura, Naoki Katoh, Kouhei Tsumoto, Jeffrey J Gray
Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody's antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the complementarity determining region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts...
2018: Frontiers in Immunology
Zhenyu Zhu, Rubin Wang, Fengyun Zhu
Based on the Hodgkin-Huxley model, the present study established a fully connected structural neural network to simulate the neural activity and energy consumption of the network by neural energy coding theory. The numerical simulation result showed that the periodicity of the network energy distribution was positively correlated to the number of neurons and coupling strength, but negatively correlated to signal transmitting delay. Moreover, a relationship was established between the energy distribution feature and the synchronous oscillation of the neural network, which showed that when the proportion of negative energy in power consumption curve was high, the synchronous oscillation of the neural network was apparent...
2018: Frontiers in Neuroscience
Masahiko Machida, Koichiro Kato, Motoyuki Shiga
The isotopologs of liquid water, H2 O, D2 O, and T2 O, are studied systematically by first principles PIMD simulations, in which the whole entity of the electrons and nuclei are treated quantum mechanically. The simulation results are in reasonable agreement with available experimental data on isotope effects, in particular, on the peak shift in the radial distributions of H2 O and D2 O and the shift in the evaporation energies. It is found that, due to differences in nuclear quantum effects, the H atoms in the OH bonds more easily access the dissociative region up to the hydrogen bond center than the D (T) atoms in the OD (OT) bonds...
March 14, 2018: Journal of Chemical Physics
Shuai Zhang, Burkhard Militzer, Lorin X Benedict, François Soubiran, Philip A Sterne, Kevin P Driver
Carbon-hydrogen plasmas and hydrocarbon materials are of broad interest to laser shock experimentalists, high energy density physicists, and astrophysicists. Accurate equations of state (EOSs) of hydrocarbons are valuable for various studies from inertial confinement fusion to planetary science. By combining path integral Monte Carlo (PIMC) results at high temperatures and density functional theory molecular dynamics results at lower temperatures, we compute the EOSs for hydrocarbons from simulations performed at 1473 separate (ρ, T)-points distributed over a range of compositions...
March 14, 2018: Journal of Chemical Physics
Giovanni Rillo, Miguel A Morales, David M Ceperley, Carlo Pierleoni
We performed simulations for solid molecular hydrogen at high pressures (250 GPa ≤ P ≤ 500 GPa) along two isotherms at T = 200 K (phase III) and at T = 414 K (phase IV). At T = 200 K, we considered likely candidates for phase III, the C2c and Cmca12 structures, while at T = 414 K in phase IV, we studied the Pc48 structure. We employed both Coupled Electron-Ion Monte Carlo (CEIMC) and Path Integral Molecular Dynamics (PIMD). The latter is based on Density Functional Theory (DFT) with the van der Waals approximation (vdW-DF)...
March 14, 2018: Journal of Chemical Physics
Igor Poltavsky, Robert A DiStasio, Alexandre Tkatchenko
Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials. In this work, we extend our recently proposed perturbed path-integral (PPI) approach for modeling NQE in molecular systems [I. Poltavsky and A. Tkatchenko, Chem. Sci. 7, 1368 (2016)], which successfully combines the advantages of thermodynamic perturbation theory with path-integral molecular dynamics (PIMD), in a number of important directions...
March 14, 2018: Journal of Chemical Physics
Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao
To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures...
March 14, 2018: Journal of Chemical Physics
Yining Han, Jaehyeok Jin, Jacob W Wagner, Gregory A Voth
Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals...
March 14, 2018: Journal of Chemical Physics
A R Hopkinson, M I J Probert
We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment...
March 14, 2018: Journal of Chemical Physics
Y K Law, A A Hassanali
In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups...
March 14, 2018: Journal of Chemical Physics
Trung Hai Nguyen, David D L Minh
Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)-the binding free energy between a flexible ligand and rigid receptor-over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble...
March 14, 2018: Journal of Chemical Physics
Ali Mirzaeinia, Farzaneh Feyzi, Seyed Majid Hashemianzadeh
Based on Wertheim's second order thermodynamic perturbation theory (TPT2), equations of state (EOSs) are presented for the fluid and solid phases of tangent, freely jointed spheres. It is considered that the spheres interact with each other through the Weeks-Chandler-Anderson (WCA) potential. The developed TPT2 EOS is the sum of a monomeric reference term and a perturbation contribution due to bonding. MC NVT simulations are performed to determine the structural properties of the reference system in the reduced temperature range of 0...
March 14, 2018: Journal of Chemical Physics
Yang Xu, Kai Song, Qiang Shi
The hydride transfer reaction catalyzed by dihydrofolate reductase is studied using a recently developed mixed quantum-classical method to investigate the nuclear quantum effects on the reaction. Molecular dynamics simulation is first performed based on a two-state empirical valence bond potential to map the atomistic model to an effective double-well potential coupled to a harmonic bath. In the mixed quantum-classical simulation, the hydride degree of freedom is quantized, and the effective harmonic oscillator modes are treated classically...
March 14, 2018: Journal of Chemical Physics
Giovanni Di Liberto, Riccardo Conte, Michele Ceotto
We present an investigation of vibrational features in water clusters performed by means of our recently established divide-and-conquer semiclassical approach [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)]. This technique allows us to simulate quantum vibrational spectra of high-dimensional systems starting from full-dimensional classical trajectories and projection of the semiclassical propagator onto a set of lower dimensional subspaces. The potential energy surface employed is a many-body representation up to three-body terms, in which monomers and two-body interactions are described by the high level Wang-Huang-Braams-Bowman (WHBB) water potential, while, for three-body interactions, calculations adopt a fast permutationally invariant ab initio surface at the same level of theory of the WHBB 3-body potential...
March 14, 2018: Journal of Chemical Physics
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