相关论文: Entropy loss in long-distance DNA looping

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…

The non-equilibrium dynamics of disordered many-body quantum systems after a global quantum quench unveils important insights about the competition between interactions and disorder, yielding in particular an insightful perspective on many…

In this work we implement the so-called matching time estimators for estimating the entropy rate as well as the entropy production rate for symbolic sequences. These estimators are based on recurrence properties of the system, which have…

We consider Hidden Markov Chains obtained by passing a Markov Chain with rare transitions through a noisy memoryless channel. We obtain asymptotic estimates for the entropy of the resulting Hidden Markov Chain as the transition rate is…

In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…

Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…

A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on…

For a closed-loop control system with a digital channel between the sensor and the controller, the notion of invariance entropy quantifies the smallest average rate of information transmission above which a given compact subset of the state…

Microscopic formula to describe the entropy of biomolecular solutions are derived based on the Gibbs formula of entropy, and the generalized Langevin theory combined with the RISM/3D-RISM theory. Two formula are derived: one is concerned…

Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…

Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…

We study Nielsen's circuit complexity in a periodic harmonic oscillator chain, under single and multiple quenches. In a multiple quench scenario, it is shown that the complexity shows remarkably different behaviour compared to the other…

We discuss algorithms for estimating the Shannon entropy h of finite symbol sequences with long range correlations. In particular, we consider algorithms which estimate h from the code lengths produced by some compression algorithm. Our…

We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in…

We discuss the scaling of entanglement entropy in the random singlet phase (RSP) of disordered quantum magnetic chains of general spin-S. Through an analysis of the general structure of the RSP, we show that the entanglement entropy scales…

We study solvable spin chains where either fields or couplings vary linearly in space and create a sandwich-like structure of the ground state. We find that the entanglement entropy between two halves of a chain varies logarithmically with…

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…

Products of truncated unitary matrices, independently and uniformly drawn from the unitary group, can be used to study universal aspects of monitored quantum circuits. The von Neumann entropy of the corresponding density matrix decreases…

We investigate the diagonal entropy for ground states of the extended Kitaev chains with extensive pairing and hopping terms. The systems contain rich topological phases equivalently represented by topological invariant winding numbers and…