Related papers: Sequence Dependence of Self-Interacting Random Cha…
We study the thermodynamic properties of a microscopic model of coupled oscillators that exhibits a dynamical phase transition from a desynchronized to a synchronized phase. We consider two different configurations for the thermodynamic…
Recent advances have shown that introducing dependency interactions between two superconducting networks can trigger abrupt, hysteretic normal-superconductor phase transitions. In this study, we demonstrate that such behavior can also arise…
Existing sequence prediction methods are mostly concerned with time-independent sequences, in which the actual time span between events is irrelevant and the distance between events is simply the difference between their order positions in…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
We analyze random networks that change over time. First we analyze a dynamic Erdos-Renyi model, whose edges change over time. We describe its stationary distribution, its convergence thereto, and the SI contact process on the network, which…
We introduce a model of a preferential attachment based random graph which extends the family of models in which condensation phenomena can occur. Each vertex has an associated uniform random variable which we call its location. Our model…
This paper introduces a novel methodology that utilizes latency to unveil time-series dependence patterns. A customized statistical test detects memory dependence in event sequences by analyzing their inter-event time distributions.…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
A class of exclusion processes in which particles perform history-dependent random walks is introduced, stimulated by dynamic phenomena in some biological and artificial systems. The particles locally interact with the underlying substrate…
We study the time evolution of the R\'enyi entanglement entropies following a quantum quench in a two-dimensional (2D) free-fermion system. By employing dimensional reduction, we effectively transform the 2D problem into decoupled chains, a…
Irreversible random sequential deposition of interacting particles is widely used to model aggregation phenomena in physical, chemical, and biophysical systems. We show that in one dimension the exact time dependent solution of such…
The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in…
We investigate the behavior of colloidal suspensions with different volume fractions confined between parallel walls under a range of steady shears. We model the particles using molecular dynamics (MD) with full hydrodynamic interactions…
We consider a random graph model evolving in discrete time-steps that is based on 3-interactions among vertices. Triangles, edges and vertices have different weights; objects with larger weight are more likely to participate in future…
We study the nonequilibrium dynamics of a one-dimensional topological Kondo insulator, modelled by a $p$-wave Anderson lattice model, following a quantum quench of the on-site interaction strength. Our goal is to examine how the quench…
Random walks and related spatial stochastic models have been used in a range of application areas including animal and plant ecology, infectious disease epidemiology, developmental biology, wound healing, and oncology. Classical random walk…
Critical behavior of the contact process is studied in annealed scale-free networks by mapping it on the random walk problem. We obtain the analytic results for the critical scaling, using the event-driven dynamics approach. These results…