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The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
Molecular spintronics is made possible by the coupling between electronic configuration and magnetic po- larization of the molecules. For control and application of the individual molecular states it is necessary to both read and write…
We present a quantitative analysis of recent data on the kinetics of ATP hydrolysis, which has presented a puzzle regarding the load dependence of the Michaelis constant. Within the framework of coarse grained two-state ratchet models, our…
Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in time. A periodically changing allocation of the protein budget…
The quasi-steady-state approximation is widely used to develop simplified deterministic or stochastic models of enzyme catalyzed reactions. In deterministic models, the quasi-steady-state approximation can be mathematically justified from…
This paper presents a methodology of controlling the resonance energy exchange in mechanical system consisting of two weakly coupled magnetic pendulums interacting with the magnetic field generated by coils placed underneath. It is shown…
We examine the impact of the intrinsic molecular reorganization energy on switching in two-state quantum-dot cellular automata (QCA) cells. Switching a bit involves an electron transferring between charge centers within the molecule. This…
On-demand control of molecular actions is essential for realizing single-molecule functional devices. Such a control can be achieved by manipulating interactions between individual molecules and their nanoscale environment. In this study,…
A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
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…
We study the quantum dynamics of an optomechanical setup comprising two optical modes and one mechanical mode. We show that the same system can undergo a Dicke-Hepp-Lieb superradiant type phase transition. We found that the coupling between…
We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical…
We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a…
This paper describes a very general approach to the calculation of the Zeeman splitting effect produced by an external magnetic field on the rotational levels of diatomic molecules. The method is valid for arbitrary values of the total…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
Single-molecule F\"orster Resonance Energy Transfer (smFRET) is ideally suited to resolve the dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly…
We perform molecular dynamics simulations on an interacting electron gas confined to a cylindrical surface and subject to a radial magnetic field and the field of the positive background. In order to study the system at lowest energy states…
Microscopic biological systems operate far from equilibrium, are subject to strong fluctuations, and are composed of many coupled components with interactions varying in nature and strength. Researchers are actively investigating the…
This work is devoted to quantifying how periodic perturbation can change the rate of metastable transition in stochastic mechanical systems with weak noises. A closed-form explicit expression for approximating the rate change is provided,…