Related papers: Dynamical phase transition of a periodically drive…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a…
In this manuscript, we study the quench dynamics of a transverse-field XY model starting from coherent Gibbs states. The results reveal that the initial strength of magnetization plays a crucial role in the emergence of dynamical quantum…
Using numerical simulations, we examine the dynamics of driven two-dimensional bidisperse disks flowing over quenched disorder. The system exhibits a series of distinct dynamical phases as a function of applied driving force and packing…
We examine the dynamics and stripe formation in a system with competing short and long range interactions in the presence of both an applied dc drive and quenched disorder. Without disorder, the system forms stripes organized in a labyrinth…
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
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…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for…
We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation…
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the…
The dynamical motion of the magnetization plays a key role in the properties of magnetic materials. If the magnetization is initially away from the equilibrium direction in a magnetic nanoparticle, it will precess at a natural frequency…
It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional…
DNA methylation is usually treated as an epigenetic memory mark: transcriptional history is written into regulatory DNA and later stabilizes a chosen cell identity. This picture explains persistence, but it makes memory passive. Here we…
A class of models of driven diffusive systems which is shown to exhibit phase separation in $d=1$ dimensions is introduced. Unlike all previously studied models exhibiting similar phenomena, here the phase separated state is fluctuating in…
Two known distinct examples of one-dimensional systems which are known to exhibit a phase transition are critically examined: (A) a lattice model with harmonic nearest-neighbor elastic interactions and an on-site Morse potential, and (B)…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…