Related papers: Stochastic simulation of binary annihilation react…
One of the most important problems in system identification and statistics is how to estimate the unknown parameters of a given model. Optimization methods and specialized procedures, such as Empirical Minimization (EM) can be used in case…
We apply the operator approach to a stochastic system belonging to a class of death-birth processes, which we introduce utilizing the master equation approach. By employing Doi- Peliti formalism we recast the master equation in the form of…
A new algorithm, "HiER-leap", is derived which improves on the computational properties of the ER-leap algorithm for exact accelerated simulation of stochastic chemical kinetics. Unlike ER-leap, HiER-leap utilizes a hierarchical or…
We propose and test improvements to state-of-the-art techniques of Bayeasian statistical inference based on pseudolikelihood maximization with $\ell_1$ regularization and with decimation. In particular, we present a method to determine the…
Stereoselective reactions (both chemical and enzymatic reactions) have been essential for origin of life, evolution, human biology and medicine. Since late 1960s, there have been numerous successes in the exciting new frontier of asymmetric…
Electron Transfer (ET) reactions are modeled by the dynamics of a quantum two-level system (representing the electronic state) coupled to a thermalized bath of classical harmonic oscillators (representing the nuclei degrees of freedom).…
A variety of phenomena in nuclear and high energy physics seemingly do not satisfy the basic hypothesis for possible stationary states to be of the type covered by Boltzmann-Gibbs (BG) statistical mechanics. More specifically, the system…
Motivation: Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortu-nately, in all but simplest models the resulting discrete…
The ability of implementing quantum operations plays fundamental role in manipulating quantum systems. Creation and annihilation operators which transform a quantum state to another by adding or subtracting a particle are crucial of…
In Bhattacharya et al. (Science Advances, 2020), a set of chemical reactions involved in the dynamics of actin waves in cells was studied. Both at the microscopic level, where the individual chemical reactions are directly modelled using…
We study the two-species diffusion-annihilation process, $A+B\rightarrow$ \O, on the fully-connected lattice. Probability distributions for the number of particles and the reaction time are obtained for a finite-size system using a master…
Molecular dynamics simulation is used to study the time-scales involved in the homogeneous melting of a superheated crystal. The interaction model used is an embedded-atom model for Fe developed in previous work, and the melting process is…
Biochemical reaction networks are an amalgamation of reactions where each reaction represents the interaction of different species. Generally, these networks exhibit a multi-scale behavior caused by the high variability in reaction rates…
Simulating the time-evolution of quantum mechanical systems is BQP-hard and expected to be one of the foremost applications of quantum computers. We consider classical algorithms for the approximation of Hamiltonian dynamics using…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Steady state is an essential concept in reaction networks. Its stability reflects fundamental characteristics of several biological phenomena such as cellular signal transduction and gene expression. Because biochemical reactions occur at…
The exact solution for a system with two-particle annihilation and decoagulation has been studied. The spectrum of the Hamiltonian of the system is found. It is shown that the steady state is two-fold degenerate. The average number density…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
In this work, we consider systems that are subjected to intermittent instabilities due to external stochastic excitation. These intermittent instabilities, though rare, have a large impact on the probabilistic response of the system and…
Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be…