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We investigate the impact of intermittent energy injections on a Brownian particle, modeled as stochastic renewals of its kinetic energy to a fixed value. Between renewals, the particle follows standard underdamped Langevin dynamics. For…
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic…
We review our recent studies on selective solvation effects in phase separation in polar binary mixtures with a small amount of solutes. Such hydrophilic or hydrophobic particles are preferentially attracted to one of the solvent…
Financial markets have long since been modeled using stochastic methods such as Brownian motion, and more recently, rough volatility models have been built using fractional Brownian motion. This fractional aspect brings memory into the…
Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system…
We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the…
We theoretically investigate electrostatic properties between two charged surfaces with a grafted polyelectrolyte layer in an aqueous electrolyte solution by using the Poisson-Boltzmann approach accounting for ion partitioning. In order to…
We present new results on the ionization by electron impacts in a dense plasma. We are interested in the density effect known as the ionization potential depression and in its role in atomic structure. Rather than using the well-known…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
We develop two-dimensional Brownian dynamics simulations to examine the motion of disks under thermal fluctuations and Hookean forces. Our simulations are designed to be experimental-like, since the experimental conditions define the…
A colloidal particle is a prominent example of a stochastic system, and, if suspended in a simple viscous liquid, very closely resembles the case of an ideal random walker. A variety of new phenomena have been observed when such colloid is…
It is quite clear from a wide range of experiments that gating phenomena of ion channels is inherently stochastic. It has been discussed using BD simulations in a recent paper that memory effects in ion transport is negligible, unless the…
In this study, we investigate the behaviour of sedimenting solid particles and the influence of microscopic particle dynamics on the collective motion of a sedimenting cloud. Departing from conventional direct numerical simulations (DNS),…
Seemingly unrelated experiments such as electrolyte transport through nanotubes, nano-scale electrochemistry, NMR relaxometry and Surface Force Balance measurements, all probe electrical fluctuations: of the electric current, the charge and…
The behaviour and stability of soft and biological matter depend significantly on electrostatic interactions, as particles such as proteins and colloids acquire a charge when dispersed in an electrolytic solution. A typical simplification…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
Equations of motion for the microscopic number density $\hat{\rho}({\bf x},t)$ and the momentum density $\hat{\bf g}({\bf x},t)$ of a fluid have been obtained in the past from the corresponding Langevin equations representing the dynamics…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting…
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 present a diagrammatic formulation of a theory for the time dependence of density fluctuations in equilibrium systems of interacting Brownian particles. To facilitate derivation of the diagrammatic expansion we introduce a basis that…