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We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…
We reexamine basic aspects of a nonequilibrium steady state in the Kondo problem for a quantum dot under a bias voltage using a reduced density matrix, which is obtained in the Fock space by integrating out one of the two conduction…
Maxwell-Stefan systems describing the dynamics of the molar concentrations of a gas mixture with an arbitrary number of components are analyzed in a bounded domain under isobaric, isothermal conditions. The systems consist of mass balance…
We study nonlinear dynamics of superposition of quantum wavepackets in various systems such as Kerr medium, Morse oscillator and bosonic Josephson junction. The prime reason behind this study is to find out how the superposition of states…
This paper considers random graph approach to simulate irreversible step-growth polymerization. We study generalization of approach developed by Kryven~I. by introducing different types of bonds each with its own weight representing…
Predicting monomer reactivity ratios is crucial for controlling monomer sequence distribution in copolymers and their properties. Traditional experimental methods of determining reactivity ratios are time-consuming and resource-intensive,…
In this paper we study multivariate kinetic-type equations in a general setup, which includes in particular the spatially homogeneous Boltzmann equation with Maxwellian molecules, both with elastic and inelastic collisions. Using a…
Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that…
A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above…
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…
Large-scale dynamic inverse problems are often ill-posed due to model complexity and the high dimensionality of the unknown parameters. Regularization is commonly employed to mitigate ill-posedness by incorporating prior information and…
We present a detailed study of the non-Markovian two-state system dynamics for the regime of incoherent quantum tunneling. Using perturbation theory in the system tunneling amplitude $\Delta$, and in the limit of strong system-bath…
We consider continuous--time Markov kinetics with a finite number of states and a given positive equilibrium distribution P*. For an arbitrary probability distribution $P$ we study the possible right hand sides, dP/dt, of the Kolmogorov…
Conserved quantities increasingly underpin the inference of physical models. Recently new conserved quantities have been found in this context, that currently lack an interpretation. Here, we show that irreversible reactions in CRNs and…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
We propose and theoretically study an experiment designed to measure short time polymer reaction kinetics in melts or dilute solutions. The photolysis of groups centrally located along chain backbones, one group per chain, creates pairs of…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…