Related papers: Non-equilibrium dynamics of gene expression and th…
We investigate the low-temperature dynamics of a simple stochastic model, introduced recently in the context of the physics of glasses. The slowest characteristic time at equilibrium diverges exponentially at low temperature. On smaller…
We present an application of the theory of stochastic processes to model and categorize non-equilibrium physical phenomena. The concepts of uniformly continuous probability measures and modular evolution lead to a systematic hierarchical…
There are two related theorems which hold even in far from equilibrium, namely fluctuation theorem and Jarzynski equality. Fluctuation theorem states the existence of symmetry of fluctuation of entropy production, while Jarzynski equality…
The Jarzynski Equality relates the free energy difference between two equilibrium states of a system to the average of the work over all irreversible paths to go from one state to the other. We claim that the derivation of this equality is…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
The Jarzynski equality is one of the most influential results in the field of non equilibrium statistical mechanics. This celebrated equality allows to calculate equilibrium free energy differences from work distributions of nonequilibrium…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
We present a generalization of Jarzynski's Equality, applicable to quantum systems, relating discretized mechanical work and free-energy changes. The theory is based on a step-wise pulling protocol. We find that work distribution functions…
We present a derivation of the Jarzynski identity and the Crooks fluctuation theorem for systems governed by deterministic dynamics that conserves the canonical distribution such as Hamiltonian dynamics, Nose-Hoover dynamics, Nose-Hoover…
There are multiple ways in which a stochastic system can be out of statistical equilibrium. It might be subject to time-varying forcing; or be in a transient phase on its way towards equilibrium; it might even be in equilibrium without us…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
We consider the paradigm of an overdamped Brownian particle in a potential well, which is modulated through an external protocol, in the presence of stochastic resetting. Thus, in addition to the short range diffusive motion, the particle…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify the error that is made in a free energy…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
Gene regulatory circuits show significant stochastic fluctuations in their circuit signals due to the low copy number of transcription factors. When a gene circuit component is connected to an existing circuit, the dynamic properties of the…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…
In this short communication, I give a very simple derivation of the Jarzynski equality, which allows to compute the free energy difference of a body, which is driven between two equilibrium states $A$ and $B$ by an external (time-dependent)…