Related papers: A PDE model for bleb formation and interaction wit…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We study phase behaviours of lipid--bilayer vesicles functionalised by ligand--receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
We provide a review of recent advancements in nonlocal continuous models for migration, mainly from the perspective of its involvement in embryonal development and cancer invasion. Particular emphasis is placed on spatial nonlocality…
In assumed probability density function (pdf) methods of turbulent combustion, the shape of the scalar pdf is assumed a priori and the pdf is parametrized by its moments for which model equations are solved. In non-premixed flows the beta…
In this work we examine thermodynamics of fluid with "molecules" represented by two fused hard spheres, decorated by the attractive square-well sites. Interactions between these sites are of short-range and cause association between the…
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
We derive mathematical models of the elementary process of dissolution/growth of bubbles in a liquid under pressure control. The modeling starts with a fully compressible version, both for the liquid and the gas phase so that the entropy…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
We analyze the asymptotic behavior of a partial differential equation (PDE) model for hematopoiesis. This PDE model is derived from the original agent-based model formulated by (Roeder et al., Nat. Med., 2006), and it describes the…
The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we…
We discuss the use of the hydrodynamic model for the description of the evolution of dense matter formed in ultrarelativistic heavy-ion collisions. The collective flow observed in heavy-ion collisions at the BNL Relativistic Heavy Ion…
We investigate general aspects of molecular line formation under conditions which are typical of prestellar cores. Focusing on simple linear molecules, we study formation of their rotational lines by radiative transfer simulations. We…
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the…
In this article an upscaled model is presented, for complex networks with highly clustered regions exchanging some abstract quantities in both, microscale and macroscale level. Such an intricate system is approximated by a partitioned open…
Models of adhesion of extended particles on linear and planar substrates are of interest in interpreting surface deposition in colloid, polymer, and certain biological systems. An introduction is presented to recent theoretical advances in…
The general description of formation the cellular structure in the system of interacting particles is proposed. Interactions between particles are presumably well-understood and the phase transition in which can be studied in the scale of…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
For a wide range of applications, we need DEM simulations of granular matter in contact with flexible elastic boundaries. We present a novel method to describe the interaction between granular particles and a flexible elastic membrane.…