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Accurate prediction of phase equilibria remains a central challenge in chemical engineering. Physics-consistent machine learning methods that incorporate thermodynamic structure into neural networks have recently shown strong performance…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
The task of accurately locating fluid phase boundaries by means of computer simulation is hampered by problems associated with sampling both coexisting phases in a single simulation run. We explain the physical background to these problems…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
The basic problem in equilibrium statistical mechanics is to compute phase space average, in which Monte Carlo method plays a very important role. We begin with a review of nonlocal algorithms for Markov chain Monte Carlo simulation in…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
We present Monte Carlo simulations of an ultra coarse-grained lipid bilayer with different number of lipids on both leaflets. In the simulations, we employ a new method for measuring the elastic parameters of the membrane, including the…
Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modelling this process can provide novel insights into development and the principles that orchestrate the…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
We present different methods to increase the performance of Hybrid Monte Carlo simulations of the Hubbard model in two-dimensions. Our simulations concentrate on a hexagonal lattice, though can be easily generalized to other lattices. It is…
Spherical symmetry is ubiquitous in nature. It's therefore unfortunate that spherical system simulations are so hard, and require complete spheres with millions of interacting particles. Here we introduce an approach to model spherical…
Metastable structures in macromolecular and colloidal systems are non-equilibrium states that often have long lifetimes and cause difficulties in simulating equilibrium. In order to escape from the long-lived metastable states, we propose a…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Phase separation plays an role in determining the self-assembly of biological and soft-matter systems. In biological systems, liquid-liquid phase separation inside a cell leads to the formation of various macromolecular aggregates. The…
Lipid phase heterogeneity in the plasma membrane is thought to be crucial for many aspects of cell signaling, but the physical basis of participating membrane domains such as "lipid rafts" remains controversial. Here we consider a lattice…