相关论文: A new method for reactive constant pH simulations
The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we show…
We use a reactive Monte Carlo simulation method and primitive model of electrolyte to study acid-base equilibrium that controls charge regulation in colloidal systems. The simulations are performed in a semi-grand canonical ensemble in…
We discuss problems associated with the notion of pH in heterogeneous systems. For homogeneous systems, standardization protocols lead to a well defined quantity, which although different from S\o rensen's original idea of pH, is well…
Ion partitioning between different compartments (\emph{e.g.} a porous material and a bulk solution reservoir), known as Donnan equilibrium, plays a fundamental role in various contexts such as energy, environment, or water treatment. The…
In this work we study the tertiary structure of ionic surfactants when the pH in the system is modified using electrostatic dissipative particle dynamics simulations (DPD). The dependence with pH and kind of surfactant is presented. Our…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes.…
We have studied a bulk electrolyte, and polyelectrolyte solutions with surfactants or multivalent salt with the explicit presence of counterions and solvent molecules by means of the mesoscopic dissipative particle dynamics (DPD) method in…
We present a theory that enables us to calculate the effective surface charge of colloidal particles and to efficiently obtain titration curves for different salt concentrations. The theory accounts for the shift of pH of solution due to…
A new and very general technique for simulating solid-fluid suspensions is described; its most important feature is that the computational cost scales linearly with the number of particles. The method combines Newtonian dynamics of the…
A new and very general technique for simulating solid-fluid suspensions has been described in a previous paper (Part I); the most important feature of the new method is that the computational cost scales with the number of particles. In…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
We carry out the Ewald summation for the Rotne-Prager-Yamakawa mobility tensor, the Oseen mobility tensor and further variations of both, relevant for the hydrodynamic interactions in colloidal suspensions, where all interacting particles…
Several statistical mechanical theories predict that colloidal suspensions of highly charged macroions and monovalent microions can exhibit unusual thermodynamic phase behavior when strongly deionized. Density-functional, extended…
We discuss the application of Widom insertion method for calculation of the chemical potential of individual ions in computer simulations with Ewald summation. Two approaches are considered. In the first approach, an individual ion is…
Recently, Maassen et al. measured an appreciable pH difference between the bulk solution and the solution in the lumen of virus-like particles, self-assembled in an aqueous buffer solution containing the coat proteins of a simple plant…
The strongly coupled electron liquid provides a unique opportunity to study the complex interplay of strong coupling with quantum degeneracy effects and thermal excitations. To this end, we carry out extensive \textit{ab initio} path…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
Ewald summation and physically equivalent methods such as particle-mesh Ewald, kubic-harmonic expansions, or Lekner sums are commonly used to calculate long-range electrostatic interactions in computer simulations of polar and charged…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn,…