Related papers: Multicanonical molecular dynamics by variable-temp…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
We propose a novel type of ergostats and thermostats for molecular dynamics simulations. A general class of active particle swarm models is considered, where any specific total energy (alternatively any specific temperature) can be provided…
Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
We present a dynamical model of lipoprotein metabolism derived by combining a cascading process in the blood stream and cellular level regulatory dynamics. We analyse the existence and stability of equilibria and show that this…
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations describing dynamics of cellular density. Cells move towards chemical gradient (process called…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
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…
We demonstrate that the multicanonical approach is not restricted to Monte Carlo simulations, but can also be applied to simulation techniques such as molecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The effectiveness of the…
We study the dynamics of particles in a multi-component 2d Lennard-Jones (LJ) fluid in the limiting case where {\it all the particles are different} (APD). The equilibrium properties of this APD system were studied in our earlier work…
Small thermodynamic systems exhibit peculiar behavior different from that observed in long-scale systems. Non-equilibrium processes taking place in those systems are strongly influenced by the presence of fluctuations which can be large.…
Multiscale dynamics are frequently present in real-world processes, such as the atmosphere-ocean and climate science. Because of time scale separation between a small set of slowly evolving variables and much larger set of rapidly changing…
Cellular automata can simulate many complex physical phenomena using the power of simple rules. The presented methodological platform expresses the concept of programmable matter in which Newtons laws of motion are one of examples. Energy…
We develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
Stochastic and dynamical processes lie at the heart of all physical, chemical, and biological systems. However, kinetic and thermodynamic properties which characterize these processes have largely been treated separately as they can be…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
Molecular dynamics simulations of a quasi-harmonic solid are conducted to elucidate the meaning of temperature fluctuations in canonical systems and validate a well-known but frequently contested equation predicting the mean square of such…