Related papers: Extrusion of chromatin loops by a composite loop e…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Excitons, Coulomb-bound electron-hole pairs, play a fundamental role in both optical excitation and correlated phenomena in solids. When an exciton interacts with other quasi-particles, few- and many-body excited states, such as trions,…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
The mitotic spindle partitions chromosomes during cell division by connecting the poles to kinetochores through microtubules (MTs). Their plus-ends, facing the chromosomes, exhibit dynamic instability, which is critical for proper…
Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal,…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
The composite cytoskeleton, comprising interacting networks of semiflexible actin and rigid microtubules, actively generates forces and restructures using motor proteins such as myosins to enable key mechanical processes including cell…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
Cellular migration is crucial for biological processes including embryonic development, immune response, and wound healing. The myosin-clutch model is a framework that describes how cells control migration through the interactions between…
We investigated the effect of torsional rigidity of a semiflexible chain on the wrapping transition around a spherical core, as a model of nucleosome, the fundamental unit of chromatin. Through molecular dynamics simulation, we show that…
The deep inelastic scattering of leptons off nuclei is considered within the the Bethe-Salpeter formalism. It is shown that nuclear short-range structure can be expressed in terms of the nucleon structure functions and four-dimensional…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
We demonstrate how center-of-mass (COM) motion influences polymer segment fluctuations. Cancellation of internal forces, together with spatially uncorrelated external noise, generally yields COM diffusivity scaling as $1/s$ with segment…
In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Singlet Fission (SF) into two triplets offers exciting avenues for high-efficiency photovoltaics and optically initializable qubits. While the chemical space of SF chromophores is ever-expanding, the mechanistic details of…
Null Polygon Wilson Loops (WL) in N=4 SYM can be computed using the Operator Product Expansion in terms of a transition amplitude on top of a color flux tube (FT). That picture is valid at any value of the 't Hooft coupling. So far it has…