Related papers: Macroscopic loop formation in circular DNA denatur…
We carry out molecular dynamics (MD) and Monte Carlo (MC) simulations to characterize nucleation in liquid clusters of 600 Lennard-Jones particles over a broad range of temperatures. We use the formalism of mean first-passage times to…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
It is shown that many anomalies observed in underdoped cuprates, including anomalous spectral weight transfer and a large pseudogap, appear to have a common nature due to both the cluster structure of the underdoped phase and the specific…
The wormlike chain (WLC) model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for…
We study the evolution of the superconducting state in a perforated disk by varying the size of the hole. The superconducting properties are investigated by means of transport measurements around the superconducting/normal phase boundary…
We present our current results from ongoing lattice investigations of the Berenstein--Maldacena--Nastase deformation of maximally supersymmetric Yang--Mills quantum mechanics. We focus on the thermal phase structure of this theory, which…
In this paper, we propose a thermodynamic mechanism for the formation of transcriptional foci via the joint agglomeration of DNA-looping proteins and protein-binding domains on DNA: The competition between the gain in protein-DNA binding…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
Using a consistent quantum-mechanical treatment for the electromagnetic radiation, we theoretically investigate the magnetic spin-flip scatterings of a neutral two-level atom trapped in the vicinity of a superconducting body. We derive a…
We investigate the crystallization of crosslinked and entangled polymers under external deformation using a coarse-grained poly(vinyl alcohol) (CG-PVA) model and molecular dynamics simulations. Following uniaxial deformation, the systems…
A broad fundamental understanding of the mechanisms underlying the phenomenology of supercooled liquids has remained elusive, despite decades of intense exploration. When supercooled beneath its characteristic melting temperature, a liquid…
We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops…
The loop-current state discovered in under-doped cuprates is characterized by a vector ${\bf \Omega}$ which has four possible orientations which correspond to different domains of order in a perfect sample. Since translational symmetry…
We describe the approach of the superconducting state as a sequence of cross-over phenomena. As the temperature is decreased, uncorrelated pairing of the electrons leads to the opening of a pseudogap at T_F^*. Upon further lowering the…
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…
We elucidate the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect is the driving…
It is shown that in a structure consisting of a superconducting ring-shaped electrode overlapped by a normal metal contact through a thin oxide barrier, measurements of the tunnel current in magnetic field can probe persistent currents in…
Crystal growth and crystal coalescence processes in supercooled systems strongly depend on the concentration of crystallization centers. We perform atomistic dynamics simulations of the crystallization process in the ultrathin metallic film…