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In this article we address the three-dimensional modeling and simulation of biological ion channels using a continuum-based approach. Our multi-physics formulation self-consistently combines, to the best of our knowledge for the first time,…

Numerical Analysis · Mathematics 2015-09-25 Riccardo Sacco , Paolo Airoldi , Aurelio G. Mauri , Joseph W. Jerome

In this work, a force field for several ions in water is proposed. In particular, we consider the cations Li$^+$ , Na$^+$ , K$^+$, Mg$^{2+}$, Ca$^{2+}$ and the anions Cl$^-$, and SO$_4^{2-}$ . These ions were selected as they appear in the…

Chemical Physics · Physics 2024-01-25 I. M. Zeron , J. L. F. Abascal , C. Vega

Long-range ion induced water-water correlations were recently observed in femtosecond elastic second harmonic scattering experiments of electrolyte solutions. To further the qualitative understanding of these correlations, we derive an…

Statistical Mechanics · Physics 2017-09-06 David M. Wilkins , David E. Manolopoulos , Sylvie Roke , Michele Ceriotti

We describe how the fast quasi-centroid molecular dynamics (f-QCMD) method can be applied to condensed phase systems by approximating the quasi-centroid potential of mean force as a sum of inter- and intra-molecular corrections to the…

Chemical Physics · Physics 2023-10-20 Joseph E. Lawrence , Annina Z. Lieberherr , Theo Fletcher , David E. Manolopoulos

We investigate the dissociation and ionization equilibria of deuterium fluid over a wide range of temperatures and densities. The partition functions for molecular and atomic species are evaluated, in a statistical-mechanically consistent…

Plasma Physics · Physics 2015-11-19 Mofreh R. Zaghloul

An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…

Chemical Physics · Physics 2018-11-14 Linfeng Zhang , Han Wang , Weinan E

Molecular dynamics simulations of aqueous electrolytes generally rely on empirical force fields, combining dispersion interactions - described by a truncated Lennard-Jones (LJ) potential - and electrostatic interactions - described by a…

Soft Condensed Matter · Physics 2020-06-30 Guillaume Le Breton , Laurent Joly

Inspired by recent experimental observations of anomalously large decay lengths in concentrated electrolytes, we revisit the Restricted Primitive Model (RPM) for an aqueous electrolyte. We investigate the asymptotic decay lengths of the…

Soft Condensed Matter · Physics 2021-04-02 P. Cats , R. Evans , A. Härtel , R. van Roij

We develop Electrochemical Mean-Field Kinetic Equations (EMFKE) to simulate electrochemical cells. We start from a microscopic lattice-gas model with charged particles, and build mean-field kinetic equations following the lines of earlier…

Materials Science · Physics 2009-11-10 Marc-Olivier Bernard , Mathis Plapp , Jean-Francois Gouyet

The aim of this paper is to propose a new numerical model to simulate 2D vesicles interacting with a newtonian fluid. The inextensible membrane is modeled by a chain of circular rigid particles which are maintained in cohesion by using two…

Mathematical Physics · Physics 2012-02-15 Mourad Ismail , Aline Lefebvre-Lepot

In high energy collisions of heavy-ions, experimental findings of collective flow are customarily associated with the presence of a thermalized medium expanding according to the laws of hydrodynamics. Recently, the ATLAS, CMS and ALICE…

Nuclear Theory · Physics 2016-08-24 M. Habich , G. A. Miller , P. Romatschke , W. Xiang

Hypotheses: The aggregation number and length of spherocylindrical (rodlike, wormlike) micelles in solutions of an ionic surfactant and salt can be predicted knowing the molecular parameters and the input concentrations of the species. This…

Soft Condensed Matter · Physics 2020-10-20 K. D. Danov , P. A. Kralchevsky , R. D. Stanimirova , S. D. Stoyanov , J. L. Cook , I. P. Stott

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…

Chemical Physics · Physics 2022-01-26 Xiangwen Wang , Simon L. Clegg , Devis Di Tommaso

A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle…

Soft Condensed Matter · Physics 2015-05-13 Erkan Tuzel , Guoai Pan , Thomas Ihle , Daniel M. Kroll

The magnetic properties of the two-channel periodic Anderson model for uranium ions, comprised of a quadrupolar and a magnetic doublet are investigated through the crossover from the mixed-valent to the stable moment regime using dynamical…

Strongly Correlated Electrons · Physics 2009-10-31 Frithjof B. Anders

Chemically-active colloids modify the concentration of chemical solutes surrounding them in order to self-propel. In doing so, they generate long-ranged hydrodynamic flows and chemical gradients that modify the trajectories of other…

Fluid Dynamics · Physics 2021-11-29 Francisco Rojas-Perez , Blaise Delmotte , Sebastien Michelin

In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…

Computational Physics · Physics 2024-07-18 Benjamin Bobin Ye , Shensheng Chen , Zhen-Gang Wang

Experimental measurements of interactions in ionic liquids and concentrated electrolytes over the past decade or so have revealed simultaneous monotonic and oscillatory decay modes. These observations have been hard to interpret using…

Soft Condensed Matter · Physics 2024-02-28 Timothy S. Groves , Susan Perkin

We present a multiscale simulation framework that couples the Finite Element Method with molecular dynamics. Bypassing traditional equations of state (EOS) by using in-line atomistic simulations, the method offers the advantage of…

Out-of-equilibrium reactions between different particle species are the main processes contributing to bulk viscosity in neutron stars. In this work, we numerically compare three different approaches to the modeling of bulk viscosity: the…

General Relativity and Quantum Cosmology · Physics 2023-05-23 Giovanni Camelio , Lorenzo Gavassino , Marco Antonelli , Sebastiano Bernuzzi , Brynmor Haskell
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