Related papers: Modeling sRNA-regulated Plasmid Maintenance
Motivated by biological membrane-containing organelles in plants and photosynthetic bacteria, we study charge regulation in a model membrane stack. Considering (de)protonation as the simplest mechanism of charge equilibration between the…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
We introduce and systematically investigate a new class of topological magnetic textures, skyrmionium meta-matter, composed of skyrmioniums (Skm, $Q=0$) and skyrmions (Sk, $Q=-1$) arranged in periodic lattices mimicking the richness of…
Adaptive therapy is a promising paradigm for treating cancers, that exploits competitive interactions between drug-sensitive and drug-resistant cells, thereby avoiding or delaying treatment failure due to evolution of drug resistance within…
As a model for molecular traffic control (MTC) we investigate the diffusion of hard core particles in crossed single-file systems. We consider a square lattice of single-files being connected to external reservoirs. The (vertical)…
We study a simplified, solvable model of a fully-connected metabolic network with constrained quenched disorder to mimic the conservation laws imposed by stoichiometry on chemical reactions. Within a spin-glass type of approach, we show…
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such…
Mechanisms of plasmoid drift following massive material injection are studied via 3D non-linear MHD modelling with the JOREK code, using a transient neutral source deposited at the low field side midplane of a JET H-mode plasma to clarify…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…
We investigate a mathematical model for a bacterial population in a continuously stirred tank reactor with wall attachment. The model couples a free-boundary value problem for substrate diffusion in the one-dimensional biofilm with a system…
The external-kink stability of a toroidal plasma surrounded by a rigid resistive wall is investigated. The well-known analysis of Haney & Freidberg is rigorously extended to allow for a wall that is sufficiently thick that the thin-shell…
We perform stability analysis of a kinetic bacterial chemotaxis model of bacterial self-organization, assuming that bacteria respond sharply to chemical signals. The resulting discontinuous tumbling kernel represents the key challenge for…
Contention resolution schemes have proven to be an incredibly powerful concept which allows to tackle a broad class of problems. The framework has been initially designed to handle submodular optimization under various types of constraints,…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling.…
The twin-arginine translocation (Tat) system transports folded proteins of various sizes across both bacterial and plant thylakoid membranes. The membrane-associated TatA protein is an essential component of the Tat translocon, and a broad…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
The tokamak offers a promising path to fusion energy, but plasma disruptions pose a major economic risk, motivating considerable advances in disruption avoidance. This work develops a reinforcement learning approach to this problem by…