Related papers: Lengthscales and Cooperativity in DNA Bubble Forma…
The phase separation of purely-repulsive particles induced by self-propulsion is among the most well-studied non-equilibrium phase transitions. However, some notable features of this transition remain open questions, including the origin of…
Material mixing induced by a Rayleigh-Taylor instability occurs ubiquitously in either nature or engineering when a light fluid pushes against a heavy fluid, accompanying with the formation and evolution of chaotic bubbles. Its general…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
The impact of a sessile droplet with a moving meniscus, as encountered in processes such as dip-coating, generically leads to the entrapment of small air bubbles. Here we experimentally study this process of bubble formation by looking…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a…
The first JWST observations of nearby galaxies have unveiled a rich population of bubbles that trace the stellar feedback mechanisms responsible for their creation. Studying these bubbles therefore allows us to chart the interaction between…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…
We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
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…
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct…
In cosmological first-order phase transitions, the progress of true-vacuum bubbles is expected to be significantly retarded by the interaction between the bubble wall and the hot plasma. It has been claimed that this leads to a significant…
The nucleation of bubbles in first-order phase transitions is traditionally characterised by the critical bubble: defined as the saddle-point solution of the Euclidean action that separates collapsing from expanding field configurations.…
We compute the dynamical prefactor in the nucleation rate of bubbles or droplets in first order phase transitions for the case where both viscous damping and thermal dissipation are significant. This result, which generalizes previous work…
We investigate nuclear pasta structures at high temperatures in the framework of relativistic mean field model with Thomas-Fermi approximation. Typical pasta structures (droplet, rod, slab, tube, and bubble) are obtained, which form various…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…