Related papers: What can one learn from two-state single molecule …
We apply the large-deviation method to study trajectories in dissipative quantum systems. We show that in the long time limit the statistics of quantum jumps can be understood from thermodynamic arguments by exploiting the analogy between…
A wide range of physical problems can be described by randomly-oriented linear trajectories, including any system of objects, organisms, particles, or rays that follow a linear path. Dependent upon the particular random variables that…
We consider stochastic motion of a particle on a cyclic graph with arbitrarily periodic time dependent kinetic rates. We demonstrate duality relations for statistics of currents in this model and in its continuous version of a diffusion in…
We study simple models of intermittency, involving switching between two states, within the dynamical large-deviation formalism. Singularities appear in the formalism when switching is cooperative, or when its basic timescale diverges. In…
Time-dependent correlation functions of (unstable) particles undergoing biased or unbiased diffusion, coagulation and annihilation are calculated. This is achieved by similarity transformations between different stochastic models and…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Fluctuation in fluorescence emission of immobilized single molecule is typically ascribed to the chromophore's intrinsic structural conformations and the influence of local environmental factors. Despite extensive research over several…
In this paper, I consider the issue of how two mathematical models of modern physics, the variational principles and the quantum path integral formalism, relate to reality. I assume that the observed phenomena are consistent with the…
It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with…
With recent advances in sensing and tracking technology, trajectory data is becoming increasingly pervasive and analysis of trajectory data is becoming exceedingly important. A fundamental problem in analyzing trajectory data is that of…
We theoretically investigate the flow of the atomic excitations in a driven chiral-coupled atomic chain with nonreciprocal decay channels. This one-dimensional system allows infinite-range dipole-dipole interaction, and enables directional…
Steep slope streams show large fluctuations of sediment discharge across several time scales. These fluctuations may be inherent to the internal dynamics of the sediment transport process. A probabilistic framework thus seems appropriate to…
We explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Single cell responses are shaped by the geometry of signaling kinetic trajectories carved in a multidimensional space spanned by signaling protein abundances. It is however challenging to assay large number (>3) of signaling species in…
We consider continuous time random walks (CTRW) for open systems that exchange energy and matter with multiple reservoirs. Each waiting time distribution (WTD) for times between steps is characterized by a positive parameter a, which is set…
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…
In the absence of directional motion it is often hard to recognize athermal fluctuations. Probability currents provide such a measure in terms of the rate at which they enclose area in the reduced phase space. We measure this area enclosing…
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…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…