Refinement of Thermostated Molecular Dynamics Using Backward Error AnalysisKinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems,…Ana J. Silveira, Charlles R. A. Abreu·Nov 12, 2018SaveLearn
Path integral Monte Carlo method for the quantum anharmonic oscillatorThe Markov chain Monte Carlo (MCMC) method is used to evaluate the imaginary-time path integral of a quantum oscillator with a potential that includes both a quadratic term and a quartic term whose…Shikhar Mittal, Marise J. E. Westbroek, Peter R. King et al.·Nov 12, 2018SaveLearn
Load balancing strategies for the DSMC simulation of hypersonic flows using HPCIn the context of the validation of PICLas, a kinetic particle suite for the simulation of rarefied, non-equilibrium plasma flows, the biased hypersonic nitrogen flow around a blunted cone was…T. Binder, S. Copplestone, A. Mirza et al.·Nov 12, 2018SaveLearn
Parallelization and implementation of multi-spin Monte Carlo simulation of 2D square Ising model using MPI and C++In this paper, we present a parallel algorithm for Monte Carlo simulation of the 2D Ising Model to perform efficiently on a cluster computer using MPI. We use C++ programming language to implement…Dariush Hassani, Shahnoosh Rafibakhsh·Nov 11, 2018SaveLearn
Parallelized and Vectorized Tracking Using Kalman Filters with CMS Detector Geometry and EventsThe High-Luminosity Large Hadron Collider at CERN will be characterized by greater pileup of events and higher occupancy, making the track reconstruction even more computationally demanding. Existing…Giuseppe Cerati, Peter Elmer, Brian Gravelle et al.·Nov 9, 2018SaveLearn
Artificial neural networks for density-functional optimizations in fermionic systemsIn this work we propose an artificial neural network functional to the ground-state energy of fermionic interacting particles in homogeneous chains described by the Hubbard model. Our neural network…C. A. Custodio, E. R. Filletti, V. V. França·Nov 9, 2018SaveLearn
Multi-resolution dimer models in heat baths with short-range and long-range interactionsThis work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct…Ravinda Gunaratne, Daniel Wilson, Mark Flegg et al.·Nov 8, 2018SaveLearn
A Numerical Scheme for Non-Newtonian Fluids and Plastic Solids under the GPR ModelA method for modelling non-Newtonian fluids (dilatants and pseudoplastics) by a power law under the Godunov-Peshkov-Romenski model is presented, along with a new numerical scheme for solving this…Haran Jackson, Nikos Nikiforakis·Nov 8, 2018SaveLearn
Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTPMany-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of…Jens Wehner, Lothar Brombacher, Joshua Brown et al.·Nov 8, 2018SaveLearn
Deep Learning Accelerated Gold Nanocluster SynthesisThe understanding of inorganic reactions, especially those far from the equilibrium state, is relatively limited due to their inherent complexity. Poor understandings on the underlying synthetic…Jiali Li, Tiankai Chen, Kaizhuo Lim et al.·Nov 7, 2018SaveLearn
The Lorentz sphere visualizedFrom the inception of Nuclear Magnetic Resonance as a spectroscopic technique, the local origin of chemical shifts has been a topic of discussion. A useful concept employed to describe it has been…Simone Sturniolo, Jonathan Yates·Nov 6, 2018SaveLearn
GPU Acceleration of an Established Solar MHD Code using OpenACCGPU accelerators have had a notable impact on high-performance computing across many disciplines. They provide high performance with low cost/power, and therefore have become a primary compute…R. M. Caplan, J. A. Linker, Z. Mikić et al.·Nov 6, 2018SaveLearn
HIJING++, a Heavy Ion Jet INteraction Generator for the High-luminosity Era of the LHC and BeyondHIJING++ (Heavy Ion Jet INteraction Generator) is the successor of the widely used original HIJING, developed almost three decades ago. While the old versions (1.x and 2.x) were written in FORTRAN,…Gábor Bíró, Gábor Papp, Gergely Gábor Barnaföldi et al.·Nov 6, 2018SaveLearn
Grid-based diffusion Monte Carlo for fermions without the fixed-node approximationA diffusion Monte Carlo algorithm is introduced that can determine the correct nodal structure of the wave function of a few-fermion system and its ground-state energy without an uncontrolled bias.…Alexander A. Kunitsa, So Hirata·Nov 5, 2018SaveLearn
GPU-accelerated Simulation of Massive Spatial Data based on the Modified Planar Rotator ModelA novel Gibbs Markov random field for spatial data on Cartesian grids based on the modified planar rotator (MPR) model of statistical physics has been recently introduced for efficient and automatic…Milan Žukovič, Michal Borovský, Matúš Lach et al.·Nov 5, 2018SaveLearn
Mxdrfile: read and write Gromacs trajectories with MatlabProgress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a…Jon Kapla, Martin Lindén·Nov 5, 2018SaveLearn
A simple algorithm to implement jump boundary conditions within the lattice Boltzmann methodAn algorithm is proposed to implement unsteady jump boundary conditions, presenting discontinuity in physical quantities, within the lattice Boltzmann method (LBM). This is useful to tackle problems…Badr Kaoui·Nov 5, 2018SaveLearn
A fifth-order shock capturing scheme with BVD algorithmA novel 5th-order shock capturing scheme is presented in this paper. The scheme, so-called P4-THINC-BVD (4th degree polynomial and THINC reconstruction based on BVD algorithm), is formulated as a…Xi Deng, Yuya Shimizu, Feng Xiao·Nov 4, 2018SaveLearn
New interaction potentials for alkali and alkaline-earth aluminosilicate glassesWe apply a recently developed optimization scheme to obtain effective potentials for alkali and alkaline-earth aluminosilicate glasses that contains lithium, sodium, potassium, or calcium as…Siddharth Sundararaman, Liping Huang, Simona Ispas et al.·Nov 3, 2018SaveLearn
Numerical phase reduction beyond the first order approximationWe develop a numerical approach to reconstruct the phase dynamics of driven or coupled self-sustained oscillators. Employing a simple algorithm for computation of the phase of a perturbed system, we…Michael Rosenblum, Arkady Pikovsky·Nov 2, 2018SaveLearn
Acoustic scattering from a fluid cylinder with Willis constitutive propertiesA material that exhibits Willis coupling has constitutive equations that couple the pressure-strain and momentum-velocity relationships. This coupling arises from subwavelength asymmetry and…Michael B. Muhlestein, Benjamin M. Goldsberry, Andrew N. Norris et al.·Nov 2, 2018SaveLearn
First-principles investigation of Ag-, Co-, Cr-, Cu-, Fe-, Mn-, Ni-, Pd- and Rh-hexaaminobenzene 2D metal-organic frameworksIn the latest experimental advances, Ni-, Co- and Cu-HAB MOFs were synthesized in 2D forms, with high electrical conductivities and capacitances as well. Motivated by these experimental advances, we…Bohayra Mortazavi, Masoud Shahrokhi, Meysam Makaremi et al.·Nov 2, 2018SaveLearn
A Discontinuous Galerkin Fast Spectral Method for the Full Boltzmann Equation with General Collision KernelsThe Boltzmann equation, an integro-differential equation for the molecular distribution function in the physical and velocity phase space, governs the fluid flow behavior at a wide range of physical…Shashank Jaiswal, Alina A. Alexeenko, Jingwei Hu·Nov 2, 2018SaveLearn
Capacities and the Free Passage of Entropic BarriersWe propose an approach for estimating the probability that a given small target, among many, will be the first to be reached in a molecular dynamics simulation. Reaching small targets out of a vast…Jackson Loper, Guangyao Zhou, Stuart Geman·Nov 1, 2018SaveLearn
Stochastic turbulence modeling in RANS simulations via Multilevel Monte CarloA multilevel Monte Carlo (MLMC) method for quantifying model-form uncertainties associated with the Reynolds-Averaged Navier-Stokes (RANS) simulations is presented. Two, high-dimensional, stochastic…Prashant Kumar, Martin Schmelzer, Richard P. Dwight·Nov 1, 2018SaveLearn