相关论文: Integral equation models for solvent in macromolec…
In this work we consider the semi-batch process of precipitation of calcium carbonate solids from a solution containing calcium ions by adjusting the pH of the solution. The change in pH is induced either by the addition of alkaline…
We describe an approach for modeling fluid concentration profiles in grid-based microfluidic chips for fluid mixing. This approach provides an algorithm that predicts fluid concentrations at the chip outlets. Our algorithm significantly…
Vlasov solvers that operate on a phase-space grid are highly accurate but also numerically demanding. Coarse velocity space resolutions, which are unproblematic in particle-in-cell (PIC) simulations, can lead to numerical heating or…
A method for enhancing the stability and robustness of explicit schemes in computational fluid dynamics is presented. The method is based in reformulating explicit schemes in matrix form, which cane modified gradually into semi or…
We determine the liquid-solid phase diagram for carbon-oxygen and oxygen-selenium plasma mixtures using two-phase MD simulations. We identified liquid, solid, and interface regions using a bond angle metric. To study finite size effects, we…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…
Two-fluid ideal plasma equations are a generalized form of the ideal MHD equations in which electrons and ions are considered as separate species. The design of efficient numerical schemes for the these equations is complicated on account…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of…
We introduce the PRISM interstellar medium (ISM) model for thermochemistry and its implementation in the RAMSES-RTZ code. The model includes a non-equilibrium primordial, metal, and molecular chemistry network for 115 species coupled to…
Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new…
In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free…
Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…
The magnetohydrodynamics (MHD) equations are continuum models used in the study of a wide range of plasma physics systems, including the evolution of complex plasma dynamics in tokamak disruptions. However, efficient numerical solution…
The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al. [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations…
Dust plays a key role in the evolution of the ISM and its correct modelling in numerical simulations is therefore fundamental. We present a new and self-consistent model that treats grain thermal coupling with the gas, radiation balance,…
Efficient differential equation solvers have significantly reduced the sampling time of diffusion models (DMs) while retaining high sampling quality. Among these solvers, exponential integrators (EI) have gained prominence by demonstrating…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…