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Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
We connect two different generalizations of Boltzmann's kinetic theory by requiring the same stationary solution. Non-extensive statistics can be produced by either using corresponding collision rates nonlinear in the one-particle densities…
We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
We establish that mass conserving single terminal-linkage networks of chemical reactions admit positive steady states regardless of network deficiency and the choice of reaction rate constants. This result holds for closed systems without…
Experimental mechanisms that yield the growth of homochiral copolymers over their heterochiral counterparts have been advocated by Lahav and co-workers. These chiral amplification mechanisms proceed through racemic {\beta}-sheet-controlled…
We derive a closed equation of motion for the current density of an inhomogeneous quantum many-body system under the assumption that the time-dependent wave function can be described as a geometric deformation of the ground-state wave…
The method of 'coupling from the past' permits exact sampling from the invariant distribution of a Markov chain on a finite state space. The coupling is successful whenever the stochastic dynamics are such that there is coalescence of all…
The existence of stationary distributions in a multicomponent Boltzmann equation using a non-additive kinetic energy composition rule for binary collisions is discussed. It is found that detailed balance is not achieved when -- in contrast…
We propose a model for chiral polymerisation and investigate its symmetric and asymmetric solutions. The model has a source species which decays into left- and right-handed types of monomer, each of which can polymerise to form homochiral…
The Koopman operator provides a linear perspective on non-linear dynamics by focusing on the evolution of observables in an invariant subspace. Observables of interest are typically linearly reconstructed from the Koopman eigenfunctions.…
A wide class of ``counting'' problems have been studied in Computer Science. Three typical examples are the estimation of - (i) the permanent of an $n\times n$ 0-1 matrix, (ii) the partition function of certain $n-$ particle Statistical…
A kinetic equation is derived for the phase density of a system of point particles, generating a system of integro-differential equations for distribution functions that have a deterministic meaning. The derivation took into account the…
To determine the effect of nonradiative excitation energy transfer on the fluorescence of a rigid multicomponent solution, a new analytical method was developed by treating this transfer as a time-resolved Markov chain (TRMC). In the TRMC…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
We use molecular dynamics simulations to study the static properties of a single linear multiblock copolymer chain under poor solvent conditions varying the block length $N$, the number of blocks $n$, and the solvent quality by variation of…
A model for the coherent output coupler of the Bose-Einstein condensed atoms from a trap in the recent MIT experiment (Phys. Rev. Lett., 78 (1997) 582) is established with a simple many-boson system of two states with linear coupling. Its…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
Thomas's necessary conditions for the existence of multiple steady states in gene networks have been proved by Soul\'e with high generality for dynamical systems defined by differential equations. When applied to (protein) reaction networks…
We consider stochastic and open quantum systems with a finite number of states, where a stochastic transition between two specific states is monitored by a detector. The long-time counting statistics of the observed realizations of the…