Related papers: Near-critical gene expression in embryonic boundar…
Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate…
Stochastic motion of particles in a highly unstable potential generates a number of diverging trajectories leading to undefined statistical moments of the particle position. This makes experiments challenging and breaks down a standard…
Using the Density Matrix Renormalization Group (DMRG), we calculate critical exponents for the one-dimensional Hubbard model with open boundary conditions with and without additional boundary potentials at both ends. A direct comparison…
An adiabatic approach is developed for the problem of boundary friction between two atomically smooth and incommensurate solid surfaces, separated by a monolayer of lubricant atoms. This method permits to consider very slow macroscopic…
Growth models with internal habit formation have been studied in various settings under the assumption of deterministic dynamics. The purpose of this paper is to explore a stochastic version of the model in Carroll et al. [1997, 2000], one…
Deep reinforcement learning (RL) works impressively in some environments and fails catastrophically in others. Ideally, RL theory should be able to provide an understanding of why this is, i.e. bounds predictive of practical performance.…
We derive the boundary condition for a subdiffusive particle interacting with a reactive boundary with finite reaction rate. Molecular crowding conditions, that are found to cause subdiffusion of larger molecules in biological cells, are…
We experimentally demonstrate boundary-induced helical bulk states (BI-HBSs) for RF acoustic transport in LiNbO3 thin-film phononic crystals (approximately 175-200 MHz). A boundary-symmetry selection rule at an accidental {\Gamma}-point…
Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the…
A linear growth-diffusion equation is studied in a time-dependent interval whose location and length both vary. We prove conditions on the boundary motion for which the solution can be found in exact form, and derive the explicit expression…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
We consider pattern formation in periodically forced binary systems. In particular we focus on systems in which the two species are differentially forced, one being accelerated with respect to the other. Using a continuum model consisting…
In this paper, we study pattern formations in an aggregation and diffusion cell migration model with Dirichlet boundary condition. The formal continuum limit of the model is a nonlinear parabolic equation with a diffusivity which can become…
A weak formulation for a class of parabolic free boundary problems (FBP) is proposed that does not involve the notion of a free boundary but reduces to a FBP when classical solutions exist. It is aimed at hydrodynamic limits (HDL) of…
Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by the computational cost. To address this, a surge of deep…
Direct Preference Optimization (DPO) is often tuned as if increasing alignment pressure (controlled by $\beta$) yields progressively "better" behavior. We instead treat $\beta$ as a control parameter and densely sweep it for three 7B…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
Grain boundaries (GBs) in polycrystalline materials are powerful sinks for irradiation defects. While standard theories assume that the sink efficiency of a grain boundary is defined solely by its character before irradiation, recent…
Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed…
In this article we demonstrate that the so-called bursting production of molecular species during gene expression may be an artifact caused by low time resolution in experimental data collection and not an actual burst in production. We…