Approximation and inference methods for stochastic biochemical kinetics—a tutorial review
D Schnoerr, G Sanguinetti… - Journal of Physics A …, 2017 - iopscience.iop.org
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important
examples include gene expression and enzymatic processes in living cells. Such systems …
examples include gene expression and enzymatic processes in living cells. Such systems …
[图书][B] Stochastic thermodynamics: an introduction
L Peliti, S Pigolotti - 2021 - books.google.com
The first comprehensive graduate-level introduction to stochastic thermodynamics
Stochastic thermodynamics is a well-defined subfield of statistical physics that aims to …
Stochastic thermodynamics is a well-defined subfield of statistical physics that aims to …
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 …
Thermodynamic inference in partially accessible Markov networks: a unifying perspective from transition-based waiting time distributions
J Van der Meer, B Ertel, U Seifert - Physical Review X, 2022 - APS
The inference of thermodynamic quantities from the description of an only partially
accessible physical system is a central challenge in stochastic thermodynamics. A common …
accessible physical system is a central challenge in stochastic thermodynamics. A common …
What to learn from a few visible transitions' statistics?
Interpreting partial information collected from systems subject to noise is a key problem
across scientific disciplines. Theoretical frameworks often focus on the dynamics of variables …
across scientific disciplines. Theoretical frameworks often focus on the dynamics of variables …
Stochastic thermodynamics under coarse graining
M Esposito - Physical Review E—Statistical, Nonlinear, and Soft …, 2012 - APS
A general formulation of stochastic thermodynamics is presented for open systems
exchanging energy and particles with multiple reservoirs. By introducing a partition in terms …
exchanging energy and particles with multiple reservoirs. By introducing a partition in terms …
Small protein number effects in stochastic models of autoregulated bursty gene expression
A stochastic model of autoregulated bursty gene expression by Kumar et al.[Phys. Rev. Lett.
113, 268105 (2014)] has been exactly solved in steady-state conditions under the implicit …
113, 268105 (2014)] has been exactly solved in steady-state conditions under the implicit …
Inference of time irreversibility from incomplete information: Linear systems and its pitfalls
Data from experiments and theoretical arguments are the two pillars sustaining the job of
modeling physical systems through inference. In order to solve the inference problem, the …
modeling physical systems through inference. In order to solve the inference problem, the …
Multiple-scale stochastic processes: decimation, averaging and beyond
The recent experimental progresses in handling microscopic systems have allowed to probe
them at levels where fluctuations are prominent, calling for stochastic modeling in a large …
them at levels where fluctuations are prominent, calling for stochastic modeling in a large …
Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining
The entropy production rate (EPR) measures time-irreversibility in systems operating far
from equilibrium. The challenge in estimating the EPR for a continuous variable system is …
from equilibrium. The challenge in estimating the EPR for a continuous variable system is …