A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations
The modeling and simulation of stochastic reaction–diffusion processes is a topic of steady
interest that is approached with a wide range of methods. At the level of particle-resolved …
interest that is approached with a wide range of methods. At the level of particle-resolved …
[HTML][HTML] Chemical diffusion master equation: Formulations of reaction–diffusion processes on the molecular level
The chemical diffusion master equation (CDME) describes the probabilistic dynamics of
reaction–diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112, 49 …
reaction–diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112, 49 …
Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics
A novel approach to simulate simple protein–ligand systems at large time and length scales
is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction …
is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction …
Dynamics of systems with varying number of particles: from Liouville equations to general master equations for open systems
A varying number of particles is one of the most relevant characteristics of systems of interest
in nature and technology, ranging from the exchange of energy and matter with the …
in nature and technology, ranging from the exchange of energy and matter with the …
MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations
Molecular dynamics (MD) simulations can model the interactions between macromolecules
with high spatiotemporal resolution but at a high computational cost. By combining high …
with high spatiotemporal resolution but at a high computational cost. By combining high …
Reversible interacting-particle reaction dynamics
Interacting-particle reaction dynamics (iPRD) simulates the spatiotemporal evolution of
particles that experience interaction forces and can react with one another. The combination …
particles that experience interaction forces and can react with one another. The combination …
[HTML][HTML] Efficient reactive Brownian dynamics
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations
of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of …
of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of …
Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion pdes
Open biochemical systems of interacting molecules are ubiquitous in life-related processes.
However, established computational methodologies, like molecular dynamics, are still …
However, established computational methodologies, like molecular dynamics, are still …
Grand canonical diffusion-influenced reactions: A stochastic theory with applications to multiscale reaction-diffusion simulations
Smoluchowski-type models for diffusion-influenced reactions (A+ B→ C) can be formulated
within two frameworks: the probabilistic-based approach for a pair A, B of reacting particles …
within two frameworks: the probabilistic-based approach for a pair A, B of reacting particles …
Models for randomly distributed nanoscopic domains on spherical vesicles
The existence of lipid domains in the plasma membrane of biological systems has proven
controversial, primarily due to their nanoscopic size—a length scale difficult to interrogate …
controversial, primarily due to their nanoscopic size—a length scale difficult to interrogate …