Related papers: Balanced Branching in Transcription Termination
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
Recent experiments have shown that stochastic effects exerted at the level of translation contribute a substantial portion of the variation in abundance of proteins expressed at moderate to high levels. This study analyzes translational…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…
Selective rationalization aims to produce decisions along with rationales (e.g., text highlights or word alignments between two sentences). Commonly, rationales are modeled as stochastic binary masks, requiring sampling-based gradient…
Training Memory-based transformers can require a large amount of memory and can be quite inefficient. We propose a novel two-phase training mechanism and a novel regularization technique to improve the training efficiency of memory-based…
Flowing blood displays a phenomenon called margination, in which leukocytes and platelets are preferentially found near blood vessel walls, while erythrocytes are depleted from these regions. Here margination is investigated using direct…
We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively. We show through analytic…
We present a reduction of the termination problem for a Turing machine (in the simplified form of the Post correspondence problem) to the problem of determining whether a continuous-time Markov chain presented as a set of Kappa…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…
In this second part of our two-part paper, we invoke the stochastic maximum principle, conditional Hamiltonian and the coupled backward-forward stochastic differential equations of the first part [1] to derive team optimal decentralized…
Resistance switching memory cells such as electrochemical metallization cells and valence change mechanism cells have the potential to revolutionize information processing and storage. However, the creation of deterministic resistance…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
We perform an analytic study on the stochastic thermodynamics of a small classical particle trapped in a time dependent single-well potential in the highly underdamped limit. It is shown that the nonequilibrium probability density function…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene,…
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of non-equilibrium statistical physics, the totally…
We consider binary infinite order stochastic chains perturbed by a random noise. This means that at each time step, the value assumed by the chain can be randomly and independently flipped with a small fixed probability. We show that the…
Coherence distillation is one of the central problems in the resource theory of coherence. In this Letter, we complete the deterministic distillation of quantum coherence for a finite number of coherent states under strictly incoherent…
This paper considers linear quadratic team decision problems where the players in the team affect each other's information structure through their decisions. Whereas the stochastic version of the problem is well known to be complex with…
We demonstrate the advantages of randomization in coherent quantum dynamical control. For systems which are either time-varying or require decoupling cycles involving a large number of operations, we find that simple randomized protocols…