Related papers: Modeling sRNA-regulated Plasmid Maintenance
Plants both lose water and take in carbon dioxide through microscopic stomatal pores, each of which is regulated by a surrounding pair of guard cells. During drought, the plant hormone abscisic acid (ABA) inhibits stomatal opening and…
This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
Plasmas are highly nonlinear and multi-scale, motivating a hierarchy of models to understand and describe their behavior. However, there is a scarcity of plasma models of lower fidelity than magnetohydrodynamics (MHD). Galerkin models,…
The recent progress in high-temperature superconductor technologies has led to the design and construction of SPARC, a compact tokamak device expected to reach plasma breakeven with up to $25$MW of external ion cyclotron resonant heating…
Trapped atoms and ions are among the best controlled quantum systems which find widespread applications in quantum information, sensing and metrology. For molecules, however, a similar degree of control is currently lacking owing to their…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…
In this paper, we study through mathematical modelling the combined effect of transcriptional and translational regulation by proteins and small noncoding RNAs (sRNA) in a genetic feedback motif that has an important role in the survival of…
We consider the generalization of the Kramers escape over a barrier problem to the case of a long chain molecule. The problem involves the motion of a chain molecule of $N$ segments across a region where the free energy per segment is…
Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is typically condensed into a compact body - the nucleoid. This compaction influences the localization and dynamics of many cellular processes including transcription,…
We studied in silico effects of structural stress in Mycoplasma pneumoniae, a genome-reduced model bacterial organism, by tracking the damage propagating on its metabolic network after a deleterious perturbation. First, we analyzed failure…
Kinetic Monte-Carlo simulation is applied to study the partial oxidation of methane over a nickel catalyst. Based on the Langmuir-Hinshelwood mechanism, the kinetic behavior of this reaction is analyzed and the results are compared with…
We study a three-species cyclic game system where organisms face a contagious disease whose virulence may change by a pathogen mutation. As a responsive defence strategy, organisms' mobility is restricted to reduce disease dissemination in…
Soil-transmitted helminth (STH) infections, one of the most prevalent neglected tropical diseases, pose a significant threat to public health in tropical and subtropical areas. These parasites infect humans and animals through direct…
A wealth of new research has highlighted the critical roles of small RNAs (sRNAs) in diverse processes such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif comprising…
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
In this paper, we develop a stochastic Asymptotic-Preserving (sAP) scheme for the kinetic chemotaxis system with random inputs, which will converge to the modified Keller-Segel model with random inputs in the diffusive regime. Based on the…
We present a generic mechanism by which reproducing microorganisms, with a diffusivity that depends on the local population density, can form stable patterns. It is known that a decrease of swimming speed with density can promote separation…
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to…