相关论文: Dynamics and energetics of a molecular zipper unde…
We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an…
We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states)…
A two-dimensional half-filled lattice gas model with nearest-neighbor attractive interaction is studied where particles are coupled to two thermal baths at different temperatures $T_1$ and $T_2$. The hopping of particles is governed by the…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and…
A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…
A non-equilibrium steady state can be characterized by a nonzero but stationary flux driven by a static external force. Under a weak external force, the drift velocity is difficult to detect because the drift motion is feeble and submerged…
Self-propelling active matter relies on the conversion of energy from the undirected, nanoscopic scale to directed, macroscopic motion. One of the challenges in the design of synthetic active matter lies in the control of dynamic states, or…
We propose a new method for simulating electron dynamics in open quantum systems out of equilibrium, using a finite atomistic model. The proposed method is motivated by the intuitive and practical nature of the driven Liouville von-Neumann…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
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)…
Kittel's 1D model represents a natural DNA with two strands as a (molecular) zipper, which may separated as the temperature is varied. We define multidimensional version of this model on a Cayley tree and study the set of Gibbs measures. We…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Transport of molecular motors, stimulated by interactions with specific links between consecutive binding sites (called ``bridges''), is investigated theoretically by analyzing discrete-state stochastic ``burnt-bridge'' models. When an…
The collective dynamics of $N$ weakly coupled processive molecular motors are considered theoretically. We show, using a discrete lattice model, that the velocity-force curves strongly depend on the effective dynamic interactions between…
The molecular conductors [M(tmdt)$_2$] (M=Ni, Pt) consisting of single molecular species are investigated with $^{13}$C NMR and $^1$H NMR. The temperature dependences of $^{13}$C NMR shift and relaxation rate provide microscopic evidences…
A hopping model for molecular motors is presented consisting of a state with asymmetric hopping rates with period 2 and a state with uniform hopping rates. State changes lead to a stationary unidirectional current of a particle. The current…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
We study a LiCs strongly-interacting molecular gas loaded into an one-dimensional optical lattice at quarter filling. The molecules are in the lowest electronic and vibrational state, $X^{1}\Sigma$ ($\nu=0$). Due to the large intermolecular…