25 citations · 65 across the 3 of their papers we have counts for
6 papers
Chemical diffusion master equation: formulations of reaction--diffusion processes on the molecular level
Mauricio J. del Razo, Stefanie Winkelmann, Rupert Klein +1
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,…
A probabilistic framework for particle-based reaction-diffusion dynamics using classical Fock space representations
Mauricio J. del Razo, Daniela Frömberg, Arthur V. Straube +3
The modeling and simulation of stochastic reaction-diffusion processes is a topic of steady interest that is approached with a wide range of methods. \rev{At the level of particle-…
Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics
Mauricio J. del Razo, Manuel Dibak, Christof Schütte +1
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 reacti…
Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs
Margarita Kostré, Christof Schütte, Frank Noé +1
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mos…
MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations
Manuel Dibak, Mauricio J. del Razo, David De Sancho +2
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throug…
Numerical methods for interface coupling of compressible and almost incompressible media
Mauricio J. Del Razo, Randall J. LeVeque
Many experiments in biomedical applications and other disciplines use a shock tube. These experiments often involve placing an experimental sample within a fluid-filled container,…