Related papers: Computer Simulations of a Heterogeneous Membrane w…
The present paper deals with the problem of improving the efficiency of large scale turbulent flow simulations. The high-fidelity methods for modelling turbulent flows become available for a wider range of applications thanks to the…
The miscibility in several polymer blend mixtures (polymethylmethacrylate/polystyrene, (1,4-cis) polyisoprene/polystyrene, and polymethylmethacrylate/polyoxyethylene) has been investigated using Molecular Dynamics simulations for atomistic…
The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplasm has a very complex geometric structure which cannot be handled by standard…
We report a numerical simulation for the phase diagram of a simple two dimensional model, similar to one proposed by Noro and Frenkel [J. Chem. Phys. \textbf{114}, 2477 (2001)] for membrane proteins, but one that includes the role of the…
Successful computer studies of glass-forming materials need to overcome both the natural tendency to structural ordering and the dramatic increase of relaxation times at low temperatures. We present a comprehensive analysis of eleven…
Many modern production and measurement facilities incorporate multiphase systems at low pressures. In this region of flows at small, non-zero Knudsen- and low Mach numbers the classical mesoscopic Monte Carlo methods become increasingly…
We apply the recently developed adaptive ensemble optimization technique to simulate dense Lennard-Jones fluids and a particle-solvent model by broad-histogram Monte Carlo techniques. Equilibration of the simulated fluid is improved by…
Simulating quantum many-body systems (QMBS) is one of the long-standing, highly non-trivial challenges in condensed matter physics and quantum information due to the exponentially growing size of the system's Hilbert space. To date, tensor…
We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS…
We develop a new Lagrangian material particle -- dynamical domain decomposition method (MPD^3) for large scale parallel molecular dynamics (MD) simulation of nonstationary heterogeneous systems on a heterogeneous computing net. MPD^3 is…
Multiphase flows frequently occur in many important engineering and scientific applications, but modeling of such flows is a rather challenging task due to complex interfacial dynamics between different phases, let alone if the flow is…
Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the complexity, heterogeneity and multi-scale nature of cancer pose significant computational challenges. Coupling discrete cell-based models…
The development of novel materials in recent years has been accelerated greatly by the use of computational modelling techniques aimed at elucidating the complex physics controlling microstructure formation in materials, the properties of…
The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We…
The space-time dynamics of rigid inhomogeneities (inclusions) free to move in a randomly fluctuating fluid bio-membrane is derived and numerically simulated as a function of the membrane shape changes. Both vertically placed (embedded)…
Markov Chain Monte Carlo methods are algorithms used to sample probability distributions, commonly used to sample the Boltzmann distribution of physical/chemical models (e.g., protein folding, Ising model, etc.). This allows us to study…
Mixtures of linear dynamical systems (MoLDS) provide a path to model time-series data that exhibit diverse temporal dynamics across trajectories. However, its application remains challenging in complex and noisy settings, limiting its…
Fluorescence microscopy is widely employed for the analysis of living biological samples; however, the utility of the resulting recordings is frequently constrained by noise, temporal variability, and inconsistent visualisation of signals…
A discrete model for computer simulations of the clustering dynamics of Social Amoebae is presented. This model incorporates the wavelike propagation of extracellular signaling cAMP, the sporadic firing of cells at early stage of…
This paper presents our work on developing parallel computational methods for two-phase flow on modern parallel computers, where techniques for linear solvers and nonlinear methods are studied and the standard and inexact Newton methods are…