Markovian dynamics on complex reaction networks
J Goutsias, G Jenkinson - Physics reports, 2013 - Elsevier
Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …
reaction channels, are ubiquitous across many scientific and engineering disciplines …
Time-dependent variational principle for open quantum systems with artificial neural networks
We develop a variational approach to simulating the dynamics of open quantum many-body
systems using deep autoregressive neural networks. The parameters of a compressed …
systems using deep autoregressive neural networks. The parameters of a compressed …
Moment-based inference predicts bimodality in transient gene expression
Recent computational studies indicate that the molecular noise of a cellular process may be
a rich source of information about process dynamics and parameters. However, accessing …
a rich source of information about process dynamics and parameters. However, accessing …
Design and analysis of DNA strand displacement devices using probabilistic model checking
Designing correct, robust DNA devices is difficult because of the many possibilities for
unwanted interference between molecules in the system. DNA strand displacement has …
unwanted interference between molecules in the system. DNA strand displacement has …
Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry
Most of the fascinating phenomena studied in cell biology emerge from interactions among
highly organized multimolecular structures embedded into complex and frequently dynamic …
highly organized multimolecular structures embedded into complex and frequently dynamic …
[HTML][HTML] Stochastic analysis of chemical reaction networks using linear noise approximation
Abstract Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually
analyzed through solving the Chemical Master Equation (CME) or performing extensive …
analyzed through solving the Chemical Master Equation (CME) or performing extensive …
[图书][B] Simulation algorithms for computational systems biology
The dynamics of molecular systems is an essential tool of systems biology. It helps figuring
out what is the effect of the perturbation of a system, or what is the best dose for a drug or …
out what is the effect of the perturbation of a system, or what is the best dose for a drug or …
[HTML][HTML] Tensor-train approximation of the chemical master equation and its application for parameter inference
In this work, we perform Bayesian inference tasks for the chemical master equation in the
tensor-train format. The tensor-train approximation has been proven to be very efficient in …
tensor-train format. The tensor-train approximation has been proven to be very efficient in …
A hierarchical dynamical low-rank algorithm for the stochastic description of large reaction networks
L Einkemmer, J Mangott, M Prugger - arXiv preprint arXiv:2407.11792, 2024 - arxiv.org
The stochastic description of chemical reaction networks with the kinetic chemical master
equation (CME) is important for studying biological cells, but it suffers from the curse of …
equation (CME) is important for studying biological cells, but it suffers from the curse of …
Bye bye, linearity, bye: quantification of the mean for linear CRNs in a random environment
M Sinzger-D'Angelo, S Startceva, H Koeppl - Journal of Mathematical …, 2023 - Springer
Molecular reactions within a cell are inherently stochastic, and cells often differ in
morphological properties or interact with a heterogeneous environment. Consequently, cell …
morphological properties or interact with a heterogeneous environment. Consequently, cell …