Related papers: Modeling Translation in Protein Synthesis with TAS…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The Totally Asymmetric Simple Exclusion Process (TASEP) is a non-equilibrium particle model on a finite one-dimensional lattice with open boundaries. In our earlier paper, we obtained a determinantal formula that computes the steady state…
We present explicit formulas for total crossing events in the multi-species asymmetric exclusion process ($r$-ASEP) with underlying $U_q(\widehat{\mathfrak{sl}}_{r+1})$ symmetry. In the case of the two-species TASEP these can be derived…
We study the one-dimensional asymmetric simple exclusion process (ASEP) with open boundary conditions. Particles are injected and ejected at both boundaries. It is clarified that the steady state of the model is intimately related to the…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We study a totally asymmetric simple exclusion process (TASEP) with one defect site, hopping rate $q<1$, near the system boundary. Regarding our system as a pair of uniform TASEP's coupled through the defect, we study various methods to…
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential…
We consider all totally asymmetric simple exclusion processes (TASEPs) whose transition probabilities are given in the Sch\"utz-type formulas and which jump with homogeneous rates. We show that the multi-point distribution of particle…
We introduce a family of layer to layer transfer matrices in a three-dimensional (3D) lattice model which can be viewed as partition functions of the $q$-oscillator valued six-vertex model on $m \times n$ square lattice. By invoking the…
We obtain the exact solution of the facilitated totally asymmetric simple exclusion process (F-TASEP) in 1D. The model is closely related to the conserved lattice gas (CLG) model and to some cellular automaton traffic models. In the F-TASEP…
The resources in a cell are finite, which implies that the various components of the cell must compete for resources. One such resource is the ribosomes used during translation to create proteins. Motivated by this example, we explore this…
The discrete-time version of totally asymmetric simple-exclusion process (TASEP) on a finite one-dimensional lattice is studied with the periodic boundary condition. Each particle at a site hops to the next site with probability $0 \leq p…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
Many integrable stochastic particle systems in one space dimension (such as TASEP - totally asymmetric simple exclusion process - and its various deformations, with a notable exception of ASEP) remain integrable when we equip each particle…
We investigate the current properties in the totally asymmetric simple exclusion process (TASEP) on a quenched random energy landscape. In low- and high-density regimes, the properties are characterized by single-particle dynamics. In the…
The TASEP is a paradigmatic model of out-of-equilibrium statistical physics, for which many quantities have been computed, either exactly or by approximate methods. In this work we study two new kinds of observables that have some relevance…
In the totally asymmetric simple exclusion process (TASEP) two processes arise in the large time limit: the Airy_1 and Airy_2 processes. The Airy_2 process is an universal limit process occurring also in other models: in a stochastic growth…
Motor proteins are key players in intracellular transport processes and biological motion. Theoretical modeling of these systems has been achieved by the use of step processes on one-dimensional lattices. After a comprehensive introduction…