Related papers: Peeling and Sliding in Nucleosome Repositioning
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Particle resuspension refers to the physical process by which solid particles deposited on a surface are, first, detached and, then, entrained away by the action of a fluid flow. In this study, we explore the dynamics of large and heavy…
The viscosity of dilute and semidilute unentangled DNA solutions, in steady simple shear flow, has been measured across a range of temperatures and concentrations. For polystyrene solutions, measurements of viscosity have been carried out…
Motor-driven cytoskeletal remodeling in cellular systems can often be accompanied by a diffusive-like effect at local scales, but distinguishing the contributions of the ordering process, such as active contraction of a network, from this…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Predicting the behaviour of complex systems is one of the main goals of science. An important example is plastic deformation of micron-scale crystals, a process mediated by collective dynamics of dislocations, manifested as broadly…
We study strain-controlled plastic deformation of crystalline solids via two-dimensional discrete dislocation dynamics simulations. To this end, we characterize the average stress-strain curves as well as the statistical properties of…
Plastic deformation of crystals is a physical phenomenon, which has immensely driven the development of human civilisation since the onset of the Chalcolithic period. This process is primarily governed by the motion of line defects, called…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
We perform physical and numerical experiments to study the stick-slip response of a stack of slabs in contact through dry frictional interfaces driven in quasistatic shear. The ratio between the drive's stiffness and the slab's shear…
Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1)…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
The motility of eukaryotic cells is strongly influenced by their environment, with confined cells often developing qualitatively different motility patterns from those migrating on simple two-dimensional substrates. Recent experiments,…
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the…
Motivated by the experiments on DNA under torsion, we consider the problem of pulling a polymer out of a potential well by a force applied to one of its ends. If the force is less than a critical value, then the process is activated and has…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
Helicases are molecular motors that unwind double-stranded nucleic acids (dsNA), such as DNA and RNA). Typically a helicase translocates along one of the NA single strands while unwinding and uses adenosine triphosphate (ATP) hydrolysis as…
This work unravels the atomic details of the interaction of solute atoms with nanoscale crystalline defects. The complexity of this phenomenon is elucidated through detailed atom probe tomographic investigations on epitaxially-strained,…