Related papers: mRNA translation from a unidirectional traffic per…
We investigate the following question for machine translation (MT): can we develop a single universal MT model to serve as the common seed and obtain derivative and improved models on arbitrary language pairs? We propose mRASP, an approach…
This work applies the methods of signal processing and the concepts of control system design to model the maintenance and modulation of reading frame in the process of protein synthesis. The model shows how translational speed can modulate…
We investigate the totally asymmetric simple exclusion process (TASEP) in the presence of obstacles that dynamically bind and unbind from the lattice. The model is motivated by biological processes such as transcription in the presence of…
RNA molecules follow a succession of enzyme-mediated processing steps from transcription until maturation. The participating enzymes, for example the spliceosome for mRNAs and Drosha and Dicer for microRNAs, are also produced in the cell…
In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a nucleoid near the cell center, while ribosomes$-$molecular complexes that translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the poles. We study…
It is increasingly common to encounter data from dynamic processes captured by static cross-sectional measurements over time, particularly in biomedical settings. Recent attempts to model individual trajectories from this data use optimal…
All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Cell migration, which can be significantly affected by intracellular signaling pathways (ICSP) and extracellular matrix (ECM), plays a crucial role in many physiological and pathological processes. The efficiency of cell migration, which is…
The totally asymmetric simple exclusion process (TASEP) is a basic model of statistical mechanics that has found numerous applications. We consider the case of TASEP with a finite chain where particles may enter from the left and leave to…
Motivated by recent experiments on an antibiotic resistance gene, we investigate genetic interactions between synonymous mutations in the framework of exclusion models of translation. We show that the range of possible interactions is…
Recent genome and transcriptome sequencing projects have unveiled a plethora of highly structured RNA molecules as central mediators of cellular function. Single molecule Forster Resonance Energy Transfer (smFRET) is a powerful tool for…
We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice represents a DNA strand while each of the particles that hop on…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
The asymmetric simple exclusion process (ASEP) is an important model from statistical physics describing particles that hop randomly from one site to the next along an ordered lattice of sites, but only if the next site is empty. ASEP has…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
The totally asymmetric simple exclusion process (TASEP), which describes the stochastic dynamics of interacting particles on a lattice, has been actively studied over the past several decades and applied to model important biological…
Cell migration, which is strictly regulated by intracellular and extracellular cues, is crucial for normal physiological processes and the progression of certain diseases. However, there is a lack of an efficient approach to analyze…
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first…