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An analytical method is advanced for constructing interpolation formulae for complicated problems of statistical mechanics, in which just a few terms of asymptotic expansions are available. The method is based on the self-similar…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
We characterize the dynamic non-equilibrium steady state behavior of active particles using density fluctuations in the system. We analyze the effective local density around a particle in the steady state and numerically calculate its mean,…
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
Simple homogeneous shear flows of frictionless, deformable particles are studied by particle simulations at large shear rates and for differently soft, deformable particles. The particle stiffness sets a time-scale that can be used to scale…
Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and…
One of the most widely used methods for determination of the bending elasticity modulus of model lipid membranes is the analysis of the shape fluctuations of nearly spherical lipid vesicles. The theoretical basis of this analysis is given…
The deep connection between thermodynamics, computation, and information is now well established both theoretically and experimentally. Here, we extend these ideas to show that thermodynamics also places fundamental constraints on…
Based on Brownian dynamics simulations, we investigate the thermodynamic signatures of non-equilibrium steady states in a confined colloidal suspensions under shear flow. Specifically, we consider a thin film consisting of charged particles…
We extend the generating function technique for calculation of single molecule photon emission statistics [Y. Zheng and F. L. H. Brown, Phys. Rev. Lett., 90,238305 (2003)] to systems governed by multi-level quantum dynamics. This opens up…
Engineers in the manufacturing industries have used accelerated test (AT) experiments for many decades. The purpose of AT experiments is to acquire reliability information quickly. Test units of a material, component, subsystem or entire…
We study the swelling of a flexible linear chain composed of active particles by analytical theory and computer simulation. Three different situations are considered: a free chain, a chain confined to an external harmonic trap, and a chain…
We study a system of diffusing point particles in which any triplet of particles reacts and is removed from the system when the relative proximity of the constituent particles satisfies a predefined condition. Proximity-based reaction…
Achieving dynamic manipulation and control of single molecules at high spatio-temporal resolution is pivotal for advancing atomic-scale computing and nanorobotics. However, this endeavour is critically challenged by complex nature of atomic…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
For studying the thermodynamic properties of systems using statistical mechanics we propose an ensemble that lies in between the familiar canonical and microcanonical ensembles. From a comparative study of these ensembles we conclude that…
The recently established connection between stochastic thermodynamics and fluctuating hydrodynamics is applied to a study of efficiencies in the coupled transport of heat and matter on a small scale. A stochastic model for a mesoscopic cell…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…