相关论文: A new method for reactive constant pH simulations
We present a clear and rigorous derivation of the Ewald-like method for calculation of the electrostatic energy of the systems infinitely periodic in two-dimensions and of finite size in the third dimension (slabs) which is significantly…
Molecular dynamics (MD) simulations are used to determine the diffusion coefficients, electrophoretic mobilities and electrical conductivity of a charged colloidal suspension in the salt-free regime as a function of the colloid charge. The…
Port-Hamiltonian (pH) systems are a very important modeling tool in almost all areas of systems and control, in particular in network based model of multi-physics multi-scale systems. They lead to remarkably robust models that can be easily…
Suspensions of swimming particles exhibit complex collective behaviors driven by hydrodynamic interactions, showing persistent large-scale flows and long-range correlations. While heavily studied, it remains unclear how such structures…
Quasi two-dimensional Coulomb systems have drawn widespread interest. The reduced symmetry of these systems leads to complex collective behaviors, yet simultaneously poses significant challenges for particle-based simulations. In this…
When liquids are cooled sufficiently rapidly below their melting temperature, they may bypass crystalization and, instead, enter a long-lived metastable supercooled state that has long been the focus of intense research. Although they…
Quantum simulations can provide new insights into the physics of strongly correlated electronic systems. A well studied system, but still open in many regards, is the Hubbard-Holstein Hamiltonian, where electronic repulsion is in…
We propose a quantum simulation of small-polaron physics using a one-dimensional system of trapped ions acted upon by off-resonant standing waves. This system, envisioned as an array of microtraps, in the single-excitation case allows the…
We propose a numerical methodology for the numerical simulation of distinct, interacting physical processes described by a combination of compressible, inert and reactive forms of the Euler equations, multiphase equations and elastoplastic…
The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is…
Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the…
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…
Smoothed Dissipative Particle Dynamics (SDPD) is a mesoscopic method which allows to select the level of resolution at which a fluid is simulated. The aim of this work is to extend SDPD to chemically reactive systems.To this end, an…
We describe a method to simulate the dynamics of charged colloidal particles suspended in a liquid containing dissociated ions and salt ions. Regimes of prime current interest are those of large volume fraction of colloids, highly charged…
A new modified Poisson-Boltzmann equation accounting for the finite size of the ions valid for realistic salt-free concentrated suspensions has been derived, extending the formalism developed for pure salt-free suspensions [Roa et al.,…
[ This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics, 157, 024504 (2022) and may be found at:…
In density functional-theoretic studies of photoionized water-based systems, the role of charge localization in proton-transfer dynamics is not well understood. This is due to the inherent complexity in extracting the contributions of…
Our ability to numerically model and understand the complex flow behavior of solid-bearing suspensions has increased significantly over the last couple of years, partly due to direct numerical simulations that compute flow around individual…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Hydrogen bonds play a pivotal role in chemistry, biology, and condensed-matter physics, where quantum tunnelling can strongly influence structure and dynamics. Isotope substitution (H $\rightarrow$ D) provides a sensitive probe of such…