Related Experiment Video
Updated: Jul 5, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte
1Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden. andreas.hellander@it.uu.se
Abstract:
A quasi-Monte Carlo method for the simulation of discrete time Markov chains is applied to the simulation of biochemical reaction networks. The continuous process is formulated as a discrete chain subordinate to a Poisson process using the method of uniformization. It is shown that a substantial reduction of the number of trajectories that is required for an accurate estimation of the probability density functions (PDFs) can be achieved with this technique. The method is applied to the simulation of two model problems. Although the technique employed here does not address the typical stiffness of biochemical reaction networks, it is useful when computing the PDF by replication. The method can also be used in conjuncture with hybrid methods that reduce the stiffness.
More Related Videos
05:51Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
Published on: July 19, 2019
10:52Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
Published on: April 12, 2019
Related Concept Videos
Chemical Equilibria: Systematic Approach to Equilibrium Calculations
The first step is to identify all the chemical reactions involved, The...
Reaction Mechanisms: The Steady-State Approximation
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Reaction Mechanisms: Rate-limiting Step Approximation
Calculating Equilibrium Concentrations
A more...
Dynamic Equilibrium