Related papers: Thermal Denaturation of Fluctuating DNA Driven by …
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
The state function entropy and its quantum thermodynamical implication for two typical dissipative systems with anomalous spectral densities are studied by investigating on their low-temperature quantum behavior. In all cases it is found…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles sub jected to…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…
We report an experimental and theoretical analysis of the energy exchanged between two conductors kept at different temperature and coupled by the electric thermal noise. Experimentally we determine, as functions of the temperature…
Despite its fundamental and technological importance, a microscopic understanding of the crystallization process is still elusive. By computer simulations of the hard-sphere model we reveal the mechanism by which thermal fluctuations drive…
Jamming is a geometric phase transition occurring in dense particle systems in the absence of temperature. We use computer simulations to analyse the effect of thermal fluctuations on several signatures of the transition. We show that…
The effects of thermal diffuse scattering on the transmission and eventual diffraction of highly accelerated electrons are investigated with a method that incorporates the frozen phonon approximation to the exact numerical solution of the…
The effect of thermal fluctuations on the dynamics of a gapped quantum magnet is studied using inelastic neutron scattering on copper nitrate, a model material for the one-dimensional (1D) bond alternating Heisenberg chain, combined with…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in…
We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both…
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with…
We use the Heat Kernel method to calculate the Entanglement Entropy for a given entangling region on a fractal. The leading divergent term of the entropy is obtained as a function of the fractal dimension as well as the walk dimension. The…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
A single mechanism, endemic to the standard model of physics, is proposed to explain wavefunction collapse, classical motion, dissipation, equilibration, and the transition from pure quantum mechanics through open system decoherence to the…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…