Related papers: The Joint Solvation Interaction
The effect of hydrodynamic interactions on the free-solution electrophoresis of polyelectrolytes is investigated with coarse-grained molecular dynamics simulations. By comparing the results to simulations with switched-off hydrodynamic…
After discussing the significance of interactions to understand complex multiscale stochastic systems (CMSS), we turn our attention to the construction of a Generalised Theory of Interactions (GToI). We define interactions as discrete,…
One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable…
The development of a coherent conceptual basis for the treatment of non-linear microscopic phenomena, such as, hydrodynamic interaction, finite extensibility, excluded volume and internal viscosity, in molecular theories of dilute polymer…
Articulated objects used in simulation and embodied AI are typically specified by geometry and kinematic structure, but lack the fine-grained dynamical effects that govern realistic mechanical behavior, such as frictional holding, detents,…
Using classical density functional theory (DFT) we calculate the density profile $\rho({\mathbf r})$ and local compressibility $\chi({\mathbf r})$ of a simple liquid solvent in which a pair of blocks with (microscopic) rectangular…
We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved…
Many-body effects on superfluidity and transition temperatures are calculated for optical lattices and uniform systems with ultracold multi-component Fermi gases. The induced interactions depend sensitively on the interactions between the…
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 propose a novel fluid-structure interaction (FSI) scheme using the entropic multi-relaxation time lattice Boltzmann (KBC) model for the fluid domain in combination with a nonlinear finite element solver for the structural part. We show…
The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
The Perdew-Zunger self-interaction correction(PZ-SIC) improves the performance of density functional approximations(DFAs) for the properties that involve significant self-interaction error(SIE), as in stretched bond situations, but…
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has…
Solvent often manifests itself as the key determinant of the kinetic aspect of molecular recognition process. While the solvent is often depicted as a source of barrier in the ligand recognition process by polar cavity, the nature of…
Standard spin-density functionals for the exchange-correlation energy of a many-electron ground state make serious self-interaction errors which can be corrected by the Perdew-Zunger self-interaction correction (SIC). We propose a…
When a hydrophilic solute in water is suddenly turned into a hydrophobic species, for instance, by photoionization, a layer of hydrated water molecules forms around the solute on a time scale of a few picoseconds. We study the dynamic…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…
It is shown that lattice kinetic theory based on short-lived quasiparticles proves very effective in simulating the complex dynamics of strongly interacting fluids (SIF). In particular, it is pointed out that the shear viscosity of lattice…