Related papers: Non-equilibrium dynamics of gene expression and th…
We give a field-theoretic proof of the nonequilibrium work relations for a space dependent field with stochastic dynamics. The path integral representation and its symmetries allow us to derive Jarzynski's equality. In addition, we derive a…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
Thermodynamics constrains changes to the energy of a system, both deliberate and random, via its first and second laws. When the system is not in equilibrium, fluctuation theorems such as the Jarzynski equality further restrict the…
We extend the Jarzynski equality, which is an exact identity between the equilibrium and nonequilibrium averages, to be useful to compute the value of the entropy difference by changing the Hamiltonian. To derive our result, we introduce…
We study the long-term behavior of two piecewise-deterministic Markov processes used to model stochastic gene regulatory networks with bursting dynamics. Under regularity assumptions on the jump rate, we prove the existence and uniqueness…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein…
This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a…
The different cell types in a living organism acquire their identity through the process of cell differentiation in which the multipotent progenitor cells differentiate into distinct cell types. Experimental evidence and analysis of…
We study nonequilibrium work relations for a space-dependent field with stochastic dynamics (Model A). Jarzynski's equality is obtained through symmetries of the dynamical action in the path integral representation. We derive a set of exact…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
In the study of gas dynamics, theoretical modeling and numerical simulation are mostly set up with deterministic settings. Given the coarse-grained modeling in theories of fluids, considerable uncertainties may exist between flow-field…
The number of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy model to study the trade-off between the ribosomal supply and the…
We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of…
The nonequilibrium fluctuation relation is a cornerstone of quantum thermodynamics. It is widely believed that the system-bath heat exchange obeys the famous Jarzynski-W\'{o}jcik fluctuation theorem. However, this theorem is established in…
The processes, resulting in the transcription of RNA, are intrinsically noisy. It was observed experimentally that the synthesis of mRNA molecules is driven by short, burst-like, events. An accurate prediction of the protein level often…
In this paper, we consider two stochastic models of gene expression in prokaryotic cells. In the first model, sixteen biochemical reactions involved in transcription, translation and transcriptional regulation in the presence of inducer…
A detailed stochastic model of single-gene auto-regulation is established and its solutions are explored when mRNA dynamics is fast compared with protein dynamics and in the opposite regime. The model includes all the sources of randomness…