Related papers: Quantifying Broken Detailed Balance in Transcripti…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
We explore the idea that non-equilibrium steady states breaking detailed balance are obtained by deforming trajectories (lines in space-time) that have been sampled in a reference system with stochastic dynamics obeying detailed balance,…
It is argued that a typical many body energy eigenstate has a well defined thermodynamic entropy and that individual eigenstates possess thermodynamic characteristics analogous to those of generic isolated systems. We examine large systems…
We investigate the entropic consequences of the relaxation of an open two-level quantum system towards a thermalised statistical state, using a framework of quantum state diffusion with a minimal set of raising and lowering Lindblad…
MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to…
Large Genomic Foundation Models have recently achieved remarkable results and in-vivo translation capabilities. However these models quickly grow to over a few Billion of parameters and are expensive to run when compute is limited. To…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
Resonance states of a two-electron quantum dot are studied using a variational expansion with both real basis-set functions and complex scaling methods. The two-electron entanglement (linear entropy) is calculated as a function of the…
A system that violates detailed balance evolves asymptotically into a nonequilibrium steady state with non-vanishing currents. Analogously, when detailed balance holds at any instant of time but the system is driven through time-periodic…
Gene expression data, or transcription data, are surrogates for actual protein concentrations in the cells. In addition protein-protein interactions are static diagrams of all the protein-protein interactions in the cell. These interactions…
1-Dimensional (1D) photonics crystals with and without defects have been numerically studied using efficient Transfer Matrix Method (TMM). Detailed numerical recipe of the TMM has been laid out. Dispersion relation is verified for the…
The study of generic properties of quantum states has led to an abundance of insightful results. A meaningful set of states that can be efficiently prepared in experiments are ground states of gapped local Hamiltonians, which are well…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential…
In this paper, we investigate the open tight-binding model with $N$ sites coupled to two reservoirs on its edges with the nonequilibrium Green function method to understand effects of open boundaries. As a result, we obtain an analytical…
Generative diffusion models have emerged as a powerful class of models in machine learning, yet a unified theoretical understanding of their operation is still developing. This paper provides an integrated perspective on generative…
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 that result from coarse-graining the internal states of…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
At the nanoscale, random effects govern not only the dynamics of a physical system but may also affect its observation. This work introduces a novel paradigm for coarse graining that eschews the assignment of a unique coarse-grained…