相关论文: Spin-oscillator model for DNA/RNA unzipping by mec…

Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…

A harmonic oscillator linearly coupled with a linear chain of Ising spins is investigated. The $N$ spins in the chain interact with their nearest neighbours with a coupling constant proportional to the oscillator position and to $N^{-1/2}$,…

Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…

The Laessig-Wiese (LW) field theory for the freezing transition of random RNA secondary structures is generalized to the situation of an external force. We find a second-order phase transition at a critical applied force f = f_c. For f <…

The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…

The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…

Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…

We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…

This study investigates spin squeezed states in nuclear magnetic resonance (NMR) quadrupolar systems with spins $I=3/2$ and $I=7/2$ at room temperature, taking into account the effects of relaxation on the dynamics. The origin of spin…

We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…

Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It…

Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…

We study the surface scaling behavior of a semi-infinite $d$-dimensional O(N) spin system in the presence of quenched random field and random anisotropy disorders. It is known that above the lower critical dimension $d_{\mathrm{lc}}=4$ the…

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…

We describe the dynamics of an antiferromagnetic nano-oscillator in an external magnetic field of any given time distribution. The oscillator is powered by a spin current originating from spin-orbit effects in a neighboring heavy metal…

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…

Using a Brownian dynamics simulation, we numerically studied the interaction of DNA with histone and proposed an octamer-rotation model to describe the process of nucleosome formation. Nucleosome disruption under stretching was also…

Coherent control of OH-free radicals interacting with the spin-triplet state of a DNA molecule is investigated. A model Hamiltonian for molecular spin singlet-triplet resonance is developed. We illustrate that the spin-triplet state in DNA…

Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…