Related papers: Power series method for solving TASEP-based models…
A totally asymmetric exclusion process on a ring with $\nu$ non-conserved internal degrees of freedom, where particles hop forward with a rate that depends on their internal state, has been studied. We show, using a mapping of the model to…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
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…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…
The mRNA optimization is critical for therapeutic and biotechnological applications, since sequence features directly govern protein expression levels and efficacy. However, current methods face significant challenges in simultaneously…
A system consisting of two parallel coupled channels where particles in one of them follow the rules of totally asymmetric exclusion processes (TASEP) and in another one move as in symmetric simple exclusion processes (SSEP) is investigated…
We consider the one-dimensional totally asymmetric simple exclusion model (TASEP model) with open boundary conditions and present the analytical computations leading to the exact formula for distance clearance distribution, i.e. probability…
We introduce an $n$-species totally asymmetric zero range process ($n$-TAZRP) on one-dimensional periodic lattice with $L$ sites. It is a continuous time Markov process in which $n$ species of particles hop to the adjacent site only in one…
The TASEP (totally asymmetric simple exclusion process) is a basic model for an one-dimensional interacting particle system with non-reversible dynamics. Despite the simplicity of the model it shows a very rich and interesting behaviour. In…
Understanding how stochastic gene expression is regulated in biological systems using snapshots of single-cell transcripts requires state-of-the-art methods of computational analysis and statistical inference. A Bayesian approach to…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
Nonsense-mediated mRNA decay (NMD) is a critical post-transcriptional surveillance mechanism that degrades transcripts with premature termination codons, safeguarding transcriptome integrity and shaping disease phenotypes. However,…
Deep learning, particularly with the advancement of Large Language Models, has transformed biomolecular modeling, with protein language models such as ESM inspiring emerging RNA language models such as RiNALMo. Recent work has begun…
We calculate the spectral gap of the Markov matrix of the totally asymmetric simple exclusion process (TASEP) on a ring of L sites with N particles. Our derivation is simple and self-contained and extends a previous calculation that was…
Transcription of the genetic message encoded chemically in the sequence of the DNA template is carried out by a molecular machine called RNA polymerase (RNAP). Backward or forward slippage of the nascent RNA with respect to the DNA template…
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…
Motivation: The mapping of RNA-seq reads to their transcripts of origin is a fundamental task in transcript expression estimation and differential expression scoring. Where ambiguities in mapping exist due to transcripts sharing sequence,…
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged…