Related papers: Kinesin's backsteps under mechanical load
Molecular motor proteins such as Myosin V, Dynein or Kinesin are no ratchets, at least not with a flashing asymmetric potential; the crucial asymmetry is in the dynamical activity. We make that explicit in terms of a simple Markov model,…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
The stochastic driving force exerted by a single molecular motor (e.g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
FoF1-ATP synthases are ubiquitous membrane-bound, rotary motor enzymes that can catalyze ATP synthesis and hydrolysis. Their enzyme kinetics are controlled by internal subunit rotation, by substrate and product concentrations, by mechanical…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Current molecular dynamic simulations of biomolecules using multiple time steps to update the slowingly changing force are hampered by an instability occuring at time step equal to half the period of the fastest vibrating mode. This has…
We identify a mechanism for a type of hysteresis which we predict to occur in a variety of depinning transitions. We show that the phenomenon of one-way hysteresis is generic to stress-overshoot models of the depinning transition, and we…
Active motion of molecules along filamentous structures is a crucial feature of cell biology and is often modeled with the paradigmatic asymmetric simple exclusion process. Motivated by recent experimental studies that have addressed the…
The reduction of 4-nitrophenol (4-NiP) with sodium borohydride is widely used to benchmark heterogeneous catalysts, yet its kinetics are commonly oversimplified as pseudo-first-order. In reality, borohydride hydrolysis and hydrogenation by…
We study the stochastic dynamics of growth and shrinkage of single actin filaments or microtubules taking into account insertion, removal, and ATP/GTP hydrolysis of subunits. The resulting phase diagram contains three different phases: a…
The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular…
This Chapter is devoted to unravel the relaxation processes taking place after photoexcitation of isolated DNA/RNA nucleobases in gas phase from a time-dependent perspective. To this aim, several methods are at hand, ranging from full…
We introduce a general framework to study the processivity of molecular motors moving along a polar filament and discuss the average time spent attached to the filament as a function of a tangentially applied load. Our study of specific…
Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Actin is one of the most studied cytoskeleton proteins showing a very rich span of structures. It can self-assemble actively into dynamical structures that govern the mechanical properties of the cell, its motility and its division.…
We show that a reversible pumping mechanism operating between two states of a kinetic network can give rise to Poisson transitions between these two states. An external observer, for whom the pumping mechanism is not accessible, will…
One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which…
Kinetic approaches provide an effective description of the process of particle acceleration at shock fronts and allow to take into account the dynamical reaction of the accelerated particles as well as the amplification of the turbulent…