Related papers: Quantifying Broken Detailed Balance in Transcripti…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
The past few decades have seen great leaps in technologies to analyze cells and tissues. Omics methods in particular now allow us unprecedented access to their the molecular composition where the base-level resolution of transcripts and…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time $t$. Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed…
Adaptive physical and biological systems continually process fluctuating information from their environments. When the environment is nonstationary, inference itself becomes a nonequilibrium process with thermodynamic cost. We analyse a…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
New experimental methods make it possible to measure the expression levels of many genes, simultaneously, in snapshots from thousands or even millions of individual cells. Current approaches to analyze these experiments involve clustering…
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…
The bulk of stochastic gene expression models in the literature do not have an explicit description of the age of a cell within a generation and hence they cannot capture events such as cell division and DNA replication. Instead, many…
Entropy production plays a fundamental role in the study of non-equilibrium systems by offering a quantitative handle on the degree of time-reversal symmetry breaking. It depends crucially on the degree of freedom considered as well as on…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…
We evaluate entropy production in a photovoltaic cell that is modeled by four electronic levels resonantly coupled to thermally populated field modes at different temperatures. We use a formalism recently proposed, the so-called multiple…
The information on a quantum process acquired through measurements plays a crucial role in the determination of its non-equilibrium thermodynamic properties. We report on the experimental inference of the stochastic entropy production rate…
The theory of stochastic transcription termination based on free-energy competition requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules…
Nonequilibrium steady-state currents, unlike their equilibrium counterparts, continuously dissipate energy into their physical surroundings leading to entropy production and time-reversal symmetry breaking. This letter discusses these…
Generative diffusion models have achieved spectacular performance in many areas of machine learning and generative modeling. While the fundamental ideas behind these models come from non-equilibrium physics, variational inference and…
Equations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general…
A typical strategy of realizing an adiabatic change of a many-particle system is to vary parameters very slowly on a time scale $t_\text{r}$ much larger than intrinsic equilibration time scales. In the ideal case of adiabatic state…