Related papers: mRNA translation from a unidirectional traffic per…
The totally asymmetric simple exclusion principle (TASEP) is a fundamental model in nonequilibrium statistical mechanics. It describes the stochastic unidirectional movement of particles along a 1D chain of ordered sites. We consider the…
RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the…
Single-file Brownian motion in periodic structures is an important process in nature and technology, which becomes increasingly amenable for experimental investigation under controlled conditions. To explore and understand generic features…
We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular chain and an open chain of sites. The models include a soft version of the simple exclusion principle, that is, as the density…
Deprivation of essential nutrients can have stark consequences for many processes in a cell. We consider amino acid starvation, which can result in bottlenecks in mRNA translation when ribosomes stall due to lack of resources, i.e. tRNAs…
Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and…
During cellular translation, incorporation errors occur. It is the addition of amino acid residues not corresponding to the mRNA code. With an increase in the number of residues in the synthesized molecule, the probability of failure in at…
Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells,…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
Machine translation (MT) is a technique that leverages computers to translate human languages automatically. Nowadays, neural machine translation (NMT) which models direct mapping between source and target languages with deep neural…
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…
Here we generalize our previous model of molecular motors trafficking subdiffusing cargos in viscoelastic cytosol by (i) including mechanochemical coupling between cyclic conformational fluctuations of the motor protein driven by the…
We study the traffic of two types of molecular motors using the two-species symmetric simple exclusion process (ASEP) with periodic boundary conditions and with attachment and detachment of particles. We determine characteristic properties…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Experimental evidences of phenotypic differentiation are given by the presence of bimodal distributions…
We investigate the totally asymmetric simple exclusion process (TASEP) in the presence of a bottleneck, i.e. a sequence of consecutive defect sites with reduced hopping rate. The influence of such a bottleneck on the phase diagram is…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…