Related papers: Path Integral Method for DNA Denaturation
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…
The tunneling density of states in dirty superconductors is often well described by the phenomenological Dynes formula. Recently we have shown that this formula can be derived, within the coherent potential approximation, for…
We consider decay of an initial density or current perturbation at finite temperature $T$ near a quantum critical point with emergent Lorentz invariance. We argue that decay of perturbations with wavenumbers $k \gg T$ (in natural units) is…
The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…
We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the $\lambda$ space, with $\lambda$ being any thermodynamic variable that characterizes…
The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
The hot nucleus $^{162}\mathrm{Dy}$ is investigated using covariant density functional theory, where the shell-model-like approach treats the pairing correlation. Lee-Yang's theorem is applied to classify the pairing phase transition by…
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…
An analysis of the stability of a duplex containing G.A mispairs or G.A/A.G tandem during DNA melting has revealed that duplex stability depends on both DNA sequences and on the conformations of the G.A mispairs. The thermodynamics of…
A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of…
We investigate a thermally isolated quantum many-body system with an external control represented by a time-dependent parameter. We formulate a path integral in terms of thermal pure states and derive an effective action for trajectories in…
The well-known formal analogy between time and absolute temperature, existing on the quantum level, is considered as a profound duality relationship requiring some modifications in the conventional quantum dynamics. They consist of tiny…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Work belongs to the most basic notions in thermodynamics but it is not well understood in quantum systems, especially in open quantum systems. By introducing a novel concept of work functional along individual Feynman path, we invent a new…
Germanium is an extremely important material used for numerous functional applications in many fields of nanotechnology. In this paper, we study the crystallization of amorphous Ge using atomistic simulations of critical nano-metric nuclei…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…