Related papers: Hierarchical Reaction-Diffusion Master Equation
Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be…
In contrast to normal diffusion, there is no canonical model for reactions between chemical species which move by anomalous subdiffusion. Indeed, the type of mesoscopic equation describing reaction-subdiffusion depends on subtle assumptions…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
We poorly understand the macroscopic properties of complex fluids and of amorphous bodies in general. This is mainly due to the interplay between phenomena at different levels and length-scales. In particular, it is not necessarily true…
We present the advantages of a multiscale modelling strategy for the understanding of systems with charged interfaces. On the one hand, one can simulate a complex system at different levels, depending on the relevant length and time scales…
The paper presents an approach for overcoming modeling problems of typical life science applications with partly unknown mechanisms and lacking quantitative data: A model family of reaction diffusion equations is built up on a mesoscopic…
It is increasingly realized that taking stochastic effects into account is important in order to study biological cells. However, the corresponding mathematical formulation, the chemical master equation (CME), suffers from the curse of…
We present a mathematical study for the development of Multiple Sclerosis in which a spatio-temporal kinetic { theory} model describes, at the mesoscopic level, the dynamics of a high number of interacting agents. We consider both…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
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…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Chemical reaction network is an important method for modeling and exploring complex biological processes, bio-chemical interactions and the behavior of different dynamics in system biology. But, formulating such reaction kinetics takes…
Derivation of macroscopic models for advection-diffusion processes in the presence of dominant heterogeneous (e.g., surface) reactions using homogenisation theory or volume averaging is often deemed unfeasible due to the strong coupling…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Simulating chemical systems is highly sought after and computationally challenging, as the number of degrees of freedom increases exponentially with the size of the system. Quantum computers have been proposed as a computational means to…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
In this paper physical multi-scale processes governed by their own principles for evolution or equilibrium on each scale are coupled by matching the stored and dissipated energy, in line with the Hill-Mandel principle. In our view the…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…