相关论文: Particle-based simulations of reaction-diffusion p…
We introduce mesoscopic and macroscopic model equations of chemotaxis with anomalous subdiffusion for modelling chemically directed transport of biological organisms in changing chemical environments with diffusion hindered by traps or…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Active Brownian particles (ABPs) function as self-driving agents that display non-equilibrium behavior through their pairwise interactions which lead to phase separation and vortex patterns in both soft matter and living systems. A…
A firm cognitive subject or ``individual'' is presupposed for the emergence of mind. However, with the development of recent information technology, the ``individual'' has become more dispersed in society and the cognitive subject has…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
We present Aurora, an open-source package for particle transport, neutrals and radiation modeling in magnetic confinement fusion plasmas. Aurora's modern multi-language interface enables simulations of 1.5D impurity transport within…
We present and study a Particle method for the stationary solutions of a class of transport equations. This method is inspired by non-stationary Particle methods, the time variable being replaced by one spatial variable. Particles…
Spatially distributed problems are often approximately modelled in terms of partial differential equations (PDEs) for appropriate coarse-grained quantities (e.g. concentrations). The derivation of accurate such PDEs starting from finer…
Models defined by stochastic differential equations (SDEs) allow for the representation of random variability in dynamical systems. The relevance of this class of models is growing in many applied research areas and is already a standard…
The Eulerian advection-dispersion-reaction equation (ADRE) suffers the well-known scale-effect of reduced apparent reaction rates between chemically dissimilar fluids at larger scales (or dimensional averaging). The dispersion tensor in the…
The random phase approximation (RPA) has received a considerable interest in the field of modeling systems where noncovalent interactions are important. Its advantages over widely used density functional theory (DFT) approximations are the…
Analyses of individual atherosclerotic plaques are mostly descriptive, relying -- for example -- on histological classification by spectral analysis of ultrasound waves or staining and observing particular cellular components. Such passive…
In this paper we introduce and discuss kinetic equations for the evolution of the probability distribution of the number of particles in a population subject to binary interactions. The microscopic binary law of interaction is assumed to be…
Complex biological processes involve collective behavior of entities (bacteria, cells, animals) over many length and time scales and can be described by discrete models that track individuals or by continuum models involving densities and…
We present a data-driven framework for learning hydrodynamic equations from particle-based simulations of active matter. Our method leverages coarse-graining in both space and time to bridge microscopic particle dynamics with macroscopic…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Reaction diffusion equations have been used to model a wide range of biological phenomenon related to population spread and proliferation from ecology to cancer. It is commonly assumed that individuals in a population have homogeneous…
A quantum unitary evolution alternated with measurements is simulated by a bubble filled with fictitious particles called amplitude quanta that move chaotically and can be transformed by the simple rules that look like chemical reactions. A…
We study a system of self-propelled disks that perform run-and-tumble motion, where particles can adopt more than one internal state. One of those internal states can be transmitted to another particle if the particle carrying this state…
Recent advances in high-resolution imaging techniques and particle-based simulation methods have enabled the precise microscopic characterization of collective dynamics in various biological and engineered active matter systems. In…