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Snap-buckling is a rapid shape transition in slender structures, appearing as a fundamental switching mechanism of natural and man-made systems. Boundary conditions of structures are crucial to predict and control their snap-buckling…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
Rheological characterization of complex fluids subjected to cyclic shear-rate sweep often exhibits hysteresis. Since both viscoelastic and thixotropic materials show hysteresis loops, it is important to understand distinguishing features…
Kinesins move processively toward the plus end of microtubules by hydrolyzing ATP for each step. From an enzymatic perspective, the mechanism of mechanical motion coupled to the nucleotide chemistry is often well explained using a…
Motor proteins display widely different stepping patterns as they move on microtubule tracks, from the deterministic linear or helical motion performed by the protein kinesin to the uncoordinated random steps made by dynein. How these…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
Kinesin and related motor proteins utilize ATP fuel to propel themselves along the external surface of microtubules in a processive and directional fashion. We show that the observed step-like motion is possible through time varying charge…
The translocation of biopolymers, such as DNA and proteins, across cellular or nuclear membranes is essential for numerous biological processes. The translocation dynamics are influenced by the properties of the polymers, such as polymer…
Directional locking occurs when a particle moving over a periodic substrate becomes constrained to travel along certain substrate symmetry directions. Such locking effects arise for colloids and superconducting vortices moving over ordered…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
During the past century, biologists and mathematicians investigated two mechanisms underlying bacteria motion: the run phase during which bacteria move in straight lines and the tumble phase in which they change their orientation. When…
Conventional kinesin is a homodimeric motor protein that is capable of walking unidirectionally along a cytoskeletal filament. While previous experiments indicated unyielding unidirectionality against an opposing load up to the so-called…
The actin cytoskeleton is an active semi-flexible polymer network whose non-equilibrium properties coordinate both stable and contractile behaviors to maintain or change cell shape. While myosin motors drive the actin cytoskeleton…
To develop a minimal model for a cell moving in a crowded environment such as in tissue, we investigate the response of a liquid drop of active matter moving on a flat rigid substrate to forces applied at its boundaries. We consider two…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a…