Related papers: First-passage probability: a test for DNA Hamilton…
Hybrid systems whose mode dynamics are governed by non-linear ordinary differential equations (ODEs) are often a natural model for biological processes. However such models are difficult to analyze. To address this, we develop a…
We consider a model of "isolation with an initial period of migration" (IIM), where an ancestral population instantaneously split into two descendant populations which exchanged migrants symmetrically at a constant rate for a period of time…
A unification of characteristic mode decomposition for all method-of-moment formulations of field integral equations describing free-space scattering is derived. The work is based on an algebraic link between impedance and transition…
We derive an approximate but explicit formula for the Mean First Passage Time of a random walker between a source and a target node of a directed and weighted network. The formula does not require any matrix inversion, and it takes as only…
The significance of thermal fluctuations on nucleation in structural first-order phase transitions has been examined. The prototype case of martensitic transitions has been experimentally investigated by means of acoustic emission…
We prove that every injective Matrix Product State is the unique ground state of a simple hopping theory. We start by studying the low energy spectrum of parent Hamiltonians of injective Matrix Product States in a particular long range and…
How long a stochastic process survives before leaving a domain depends not only on its intrinsic dynamics but also on how it is observed. Classical first-passage theory assumes continuous monitoring with absorbing boundaries…
In one-dimensional systems, the dynamics of a Brownian particle are governed by the force derived from a potential as well as by diffusion properties. In this work, we obtain the first-passage-time statistics of a Brownian particle driven…
Based on the explicit knowledge of a Hamiltonian of mean force, the classical statistical mechanics and equilibrium thermodynamics of open systems in contact with a thermal environment at arbitrary interaction strength can be formulated.…
The time dependent density matrix of a system with potential barrier is studied using path integrals. The characterization of the initial state, which is assumed to be restricted to one side of the barrier, and the time evolution of the…
We consider the problem of bounding mean first passage times for a class of continuous-time Markov chains that captures stochastic interactions between groups of identical agents. The quantitative analysis of such probabilistic population…
Two known distinct examples of one-dimensional systems which are known to exhibit a phase transition are critically examined: (A) a lattice model with harmonic nearest-neighbor elastic interactions and an on-site Morse potential, and (B)…
The process of fluctuations of trajectory observables of stochastic systems is related to processes with independent increments from the risk theory. The first-passage times of variables of the thermodynamics of trajectories, in particular,…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
We consider a Brownian particle diffusing in a one dimensional interval with absorbing end points. We study the ramifications when such motion is interrupted and restarted from the same initial configuration. We provide a comprehensive…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
Consider a network embedded in the 2D plane, where a particle diffuses along the edges of the network. It is clear that over short length scales a particle moves along a single edge and thus undergoes one-dimensional diffusion. However, on…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
We consider the quantum first detection problem for a particle evolving on a graph under repeated projective measurements with fixed rate $1/\tau$. A general formula for the mean first detected transition time is obtained for a quantum walk…
Nearest-neighbor(NN) free energy parameters for DNA are well studied and reliable values of these parameters exist in the literature. They have been found to be very useful in studying DNA melting and DNA stabilization studies. In this…