Related papers: A new method for reactive constant pH simulations
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH…
The influence of the chain degree of ionization on the adsorption of weak polyelectrolytes on neutral and on oppositely and likely charged surfaces is investigated for the first time, by means of Monte Carlo simulations with the mesoscopic…
Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between…
Discrete particle simulation, a combined approach of computational fluid dynamics and discrete methods such as DEM (Discrete Element Method), DSMC (Direct Simulation Monte Carlo), SPH (Smoothed Particle Hydrodynamics), PIC…
Dense suspensions of small strongly interacting particles are complex systems, which are rarely understood on the microscopic level. We investigate properties of dense suspensions and sediments of small spherical Al_2O_3 particles in a…
A new computational method is presented to resolve hydrodynamic interactions acting on solid particles immersed in incompressible host fluids. In this method, boundaries between solid particles and host fluids are replaced with a continuous…
By performing an ensemble of molecular dynamics simulations, the model-dependent ionisation state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimisation framework based on the…
We present a study of hydrogen at pressures higher than molecular dissociation using the Coupled Electron-Ion Monte Carlo method. These calculations use the accurate Reptation Quantum Monte Carlo method to estimate the electronic energy and…
In a recent review~Landsgesell et al., Soft Matter {\bf 15}, 1155 (2019) stated that $\text{pH} - \text{pK}_a$ is a ``universal parameter" for titrating systems. We show that this is not the case. This broken symmetry has important…
Variational methods are used to calculate structural and thermodynamical properties of a titrating polyelectrolyte in a discrete representation. The Coulomb interactions are emulated by harmonic repulsive forces, the force constants being…
Different schemes for the treatment of long-ranged electrostatic interactions will be examined for water simulations using the polarizable fluctuating charge potential. Several different methods are compared, including Ewald sums, potential…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…
We present a new approach to efficiently simulate electrolytes confined between infinite charged walls using a 3d Ewald summation method. The optimal performance is achieved by separating the electrostatic potential produced by the charged…
Electronically excited atoms or molecules in an environment are often subject to interatomic/intermolecular Coulombic decay (ICD) and/or electron transfer mediated decay (ETMD) mechanisms. A few of the numerous variables that can impact…
We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…
We use the extension of scaled particle theory (ESPT) presented in the accompanying paper [Stillinger et al. J. Chem. Phys. xxx, xxx (2007)] to calculate numerically pair correlation function of the hard sphere fluid over the density range…
Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs),…
We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework,…
Recently an improved long-range model for electrolyte solutions was developed that is applicable from infinite dilution to pure salt. This paper tests this claim for the first time applying it to the calculation of liquid-liquid equilibria…