Related papers: A combined on-the-fly/interpolation procedure for …
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
Using previous experimental data of diffusion in metallic alloys, we obtain real values for an interpolation parameter introduced in a mean-field theory for diffusion with interaction. Values of order 1 were found as expected, finding…
Quantum Monte Carlo methods are used to calculate various ground state properties of charged bosons in two dimensions, throughout the whole density range where the fluid phase is stable. Wigner crystallization is predicted at $r_s\simeq…
Using the Monte Carlo method, we have studied the pulsed laser deposition process at the sub-monolayer regime. In our simulations, dissociation of an atom from a cluster is incorporated. Our results indicate that the pulsed laser deposition…
We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev.…
Monte Carlo (MC) simulations are extensively used for various purposes in modern high-energy physics (HEP) experiments. Precision measurements of established Standard Model processes or searches for new physics often require the collection…
We describe and analyze some Monte Carlo methods for manifolds in Euclidean space defined by equality and inequality constraints. First, we give an MCMC sampler for probability distributions defined by un-normalized densities on such…
We apply the Direct Simulation Monte Carlo (DSMC) method, developed originally to calculate rarefied gas dynamical problems, to study the gas flow in an accretion disc in a close binary system. The method involves viscosity and thermal…
In order to resolve the pressure checkerboard field problem with collocated grid, it is essential to employ the momentum interpolation method when formulating the pressure equation, and the flux reconstruction method when updating the…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
Monte Carlo simulations are a unique tool to check the response of a detector and to monitor its performance. For a deep-sea neutrino telescope, the variability of the environmental conditions that can affect the behaviour of the data…
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble…
Membrane filtration is widely used in water treatment to remove foulants from contaminated water. Foulant build-up on the membrane occludes the area open for fluid flow, which impairs the efficiency of the filtration operation by decreasing…
This chapter is devoted to the computation of equilibrium (thermodynamic) properties of quantum systems. In particular, we will be interested in the situation where the interaction between particles is so strong that it cannot be treated as…
One way to investigate the precision of estimates likely to result from planned experiments and planned epidemiological studies is to simulate a large number of possible outcomes and analyse the sets of possible results. This appears to be…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by periodically updating the system with a Metropolis criteria, where the integration step is…