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We study the effect of thermal fluctuations of the s-wave order parameter of a quasi two dimensional superconductor on the nuclear spin relaxation rate near the transition temperature Tc. We consider both the effects of the amplitude…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
We consider the trapping reaction, $A+B\to B$, where $A$ and $B$ particles have a diffusive dynamics characterized by diffusion constants $D_A$ and $D_B$. The interaction with $B$ particles can be formally incorporated in an effective…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
A series of asymmetric dimers with an odd number of atoms in the spacer were found to form different types of twisted structures despite being achiral. The formation of a variety of helical structures is accompanied by a gradual freezing of…
We present a numerical method that consistently implements thermal fluctuations and hydrodynamic interactions to the motion of Brownian particles dispersed in incompressible host fluids. In this method, the thermal fluctuations are…
We study helical structures in spin-spiral single crystals. In the continuum approach for the helicity potential energy the simple electronic band splits into two non-parabolic bands. For the Fermi energy greater than the splitting between…
We study the localization properties of the quasiperiodic one-dimensional helical chain with two tunneling paths: nearest-neighbor and a long-range hop that connects sites of consecutive helical turns. Using exact diagonalization, we…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the worm-like chain…
This is an archival document; the work contains theoretical development to be used in new publications and to stimulate further development. Here, we develop a statistical mechanical treatment of a braid formed of two molecules subject to…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
We follow the temporal evolution of mesoscopic intensity fluctuations and correlation in strongly localized samples. We find an initial burst in relative transmission fluctuations in random one dimensional (1D) samples due to fluctuations…
Motivated by cold-atom experiments and a desire to understand far-from-equilibrium quantum transport, we analytically study the dynamics of spin helices in the one-dimensional $XX$ model. We use a Jordan-Wigner transformation to map the…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
We study the effects of thermal flucutations on thin elastic filaments with spontaneous curvature and torsion. We derive analytical expressions for the orientational correlation functions and for the persistence length of helices, and find…
We consider an electron-phonon system in two and three dimensions on square, hexagonal and cubic lattices. The model is a modification of the standard Holstein model where the optical branch is appropriately curved in order to have a…
Conventional X-ray methods use incoming plane waves and result in discrete diffraction patterns when scattered at crystals. Here we find, by a systematic method, incoming waveforms which exhibit discrete diffraction patterns when scattered…
We study the spin and charge fluctuations of the extended Hubbard model (EHM) with on-site interaction U and first neighbor interaction V on the two-dimensional square lattice in the weak to intermediate coupling regime. We propose an…