Exit times of totally asymmetric simple exclusion processes.

We address the question of the time needed by N particles, initially located on the first sites of a finite one-dimensional lattice of size L, to exit that lattice when they move according to a TASEP transport model. Using analytical calculations and numerical simulations, we show that when N≪L, the mean exit time of the particles is asymptotically given by T_{N}(L)∼L+β_{N}sqrt[L] for large lattices. Building upon exact results obtained for two particles, we devise an approximate continuous space and time description of the random motion of the particles that provides an analytical recursive relation for the coefficients β_{N}.

Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model.

Gene expression is the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions.

Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor.

The bacterial flagellar motor is the membrane-embedded rotary motor, which turns the flagellum that provides thrust to many bacteria. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels that dynamically bind to the peptidoglycan at the rotor periphery and apply torque.

Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex.

ParABS, the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS-anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParBS complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS.

Modelling the effect of ribosome mobility on the rate of protein synthesis.

Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm.

Physical Modeling of a Sliding Clamp Mechanism for the Spreading of ParB at Short Genomic Distance from Bacterial Centromere Sites.

Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are cytosine triphosphate (CTP)-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from centromere sites where ParB is specifically loaded.

A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids.

Chromosome and plasmid segregation in bacteria are mostly driven by ParAB systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (). However, the mechanism of how a few -bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models.

Dynamical response of nanomechanical oscillators in immiscible viscous fluid for in vitro biomolecular recognition.

Dynamical response of nanomechanical cantilever structures immersed in a viscous fluid is important to in vitro single-molecule force spectroscopy, biomolecular recognition of disease-specific proteins, and the study of microscopic protein dynamics. Here we study the stochastic response of biofunctionalized nanomechanical cantilever beams in a viscous fluid. Using the fluctuation-dissipation theorem we derive an exact expression for the spectral density of displacement and a linear approximation for resonance frequency shift.