Related papers: Exact solution of the Bernoulli matching model of …
For the Bernoulli Matching model of sequence alignment problem we apply the Bethe ansatz technique via an exact mapping to the 5--vertex model on a square lattice. Considering the terrace--like representation of the sequence alignment…
Finding analytically the statistics of the longest common subsequence (LCS) of a pair of random sequences drawn from c alphabets is a challenging problem in computational evolutionary biology. We present exact asymptotic results for the…
Consider the extreme value of a Bernoulli random walk on the one-dimensional integer lattice, with reflection at 0, over a finite discrete time interval. Only the asymmetric (biased) case is discussed. Asymptotic mean/variance results are…
Exact density profiles in the steady state of the one-dimensional fully asymmetric simple exclusion process on semi-infinite chains are obtained in the case of forward-ordered sequential dynamics by taking the thermodynamic limit in our…
We consider the totally asymmetric exclusion process in discrete time with generalized updating rules. We introduce a control parameter into the interaction between particles. Two particular values of the parameter correspond to known…
Using the Bethe ansatz, we obtain the exact solution of the master equation for the totally asymmetric exclusion process on an infinite one-dimensional lattice. We derive explicit expressions for the conditional probabilities P(x_1, ...…
An exact mapping is established between sequence alignment, one of the most commonly used tools of computational biology, and the asymmetric exclusion process, one of the few exactly solvable models of nonequilibrium physics. The…
We study the sequence alignment problem and its independent version, the discrete Hammersley process with an exploration penalty. We obtain rigorous upper bounds for the number of optimality regions in both models near the soft edge. At…
This elementary treatment first summarizes extreme values of a Bernoulli random walk on the one-dimensional integer lattice over a finite discrete time interval. Both the symmetric (unbiased) and asymmetric (biased) cases are discussed.…
We consider the totally asymmetric exclusion process in discrete time with the parallel update. Constructing an appropriate transformation of the evolution operator, we reduce the problem to that solvable by the Bethe ansatz. The…
The relaxation dynamics of the one-dimensional totally asymmetric simple exclusion process on a ring is considered in the case of step initial condition. Analyzing the time evolution of the local particle densities and currents by the Bethe…
The asymmetric exclusion process on a ring in one-dimension is considered with a single defect particle. The steady state has previously been solved by a matrix product method. Here we use the Bethe ansatz to solve exactly for the long time…
Using the Bethe ansatz we obtain the determinant expression for the time dependent transition probabilities in the totally asymmetric exclusion process with parallel update on a ring. Developing a method of summation over the roots of Bethe…
We investigate the stationary state of Symmetric and Totally Asymmetric Simple Exclusion Processes with local resetting, on a one-dimensional lattice with periodic boundary conditions, using mean-field approximations, which appear to be…
The most general one dimensional reaction-diffusion model with nearest-neighbor interactions, which is exactly-solvable through the empty interval method, has been introduced. Assuming translationally-invariant initial conditions, the…
We study the long time asymptotics of the relaxation dynamics of the totally asymmetric simple exclusion process on a ring. Evaluating the asymptotic amplitudes of the local currents by the algebraic Bethe ansatz method, we find the…
We define a family of asymmetric processes for particles on a one-dimensional lattice, depending on a continuous parameter $\lambda \in [0,1] $, interpolating between the completely asymmetric processes [1] (for $\lambda =1$) and the n=1…
We consider the symmetric exclusion process on the $d$-dimensional lattice with translational invariant and ergodic initial data. It is then known that as $t$ diverges the distribution of the process at time $t$ converges to a Bernoulli…
By an extension of the Bethe ansatz method used by Gwa and Spohn, we obtain an exact expression for the large deviation function of the time averaged current for the fully asymmetric exclusion process in a ring containing $N$ sites and $p$…
We study dropout regularization in continuous-time models through the lens of random-batch methods -- a family of stochastic sampling schemes originally devised to reduce the computational cost of interacting particle systems. We construct…