Related papers: Quantifying Broken Detailed Balance in Transcripti…
Here we develop an effective approach to simplify two-time-scale Markov chains with infinite state spaces by removal of states with fast leaving rates, which improves the simplification method of finite Markov chains. We introduce the…
Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…
We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equivalently as a 1D Rouse chain or as an approximate model of single file diffusion. We discuss mainly two levels of description of this system:…
This article considers the generative modeling of the (mixed) states of quantum systems, and an approach based on denoising diffusion model is proposed. The key contribution is an algorithmic innovation that respects the physical nature of…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
We derive, for a bistochastic strictly contractive quantum channel on a matrix algebra, a relation between the contraction rate and the rate of entropy production. We also sketch some applications of our result to the statistical physics of…
Over the last several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Though many stochastic effects have been explained, the source of transcriptional bursting (one of the most…
Tissue heterogeneity is a major confounding factor in studying individual populations that cannot be resolved directly by global profiling. Experimental solutions to mitigate tissue heterogeneity are expensive, time consuming, inapplicable…
Gene expression estimation from pathology images has the potential to reduce the RNA sequencing cost. Point-wise loss functions have been widely used to minimize the discrepancy between predicted and absolute gene expression values.…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
Metriplectic systems are learned from data in a way that scales quadratically in both the size of the state and the rank of the metriplectic data. Besides being provably energy conserving and entropy stable, the proposed approach comes with…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
Observational entropy captures both the intrinsic uncertainty of a thermodynamic state and the lack of knowledge due to coarse-graining. We demonstrate two interpretations of observational entropy, one as the statistical deficiency…
A central task in stochastic thermodynamics is the estimation of entropy production for partially accessible Markov networks. We establish an effective transition-based description for such networks with transitions that are not…
The metriplectic formalism is useful for describing complete dynamical systems which conserve energy and produce entropy. This creates challenges for model reduction, as the elimination of high-frequency information will generally not…
This paper considers adiabatic reduction in both discrete and continuous models of stochastic gene expression. In gene expression models, the concept of bursting is a production of several molecules simultaneously and is generally…
This work explores entropy analysis as a tool for probing information distribution within Transformer-based architectures. By quantifying token-level uncertainty and examining entropy patterns across different stages of processing, we aim…
We propose an expression for the production of entropy for system described by a stochastic dynamics which is appropriate for the case where the reverse transition rate vanishes but the forward transition is nonzero. The expression is…
A major goal of stochastic thermodynamics is to estimate the inevitable dissipation that accompanies particular observable phenomena in an otherwise not fully accessible system. Quantitative results are often formulated as lower bounds on…
We adopt a stochastic approach to study the charge transport in transistors. In this approach, the hole and electron densities are ruled by diffusion-reaction stochastic partial differential equations satisfying local detailed balance…