Related papers: mRNA translation from a unidirectional traffic per…
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,…
The number of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy model to study the trade-off between the ribosomal supply and the…
It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNAs or ceRNAs) that could prove to be crucial for…
We introduce a model of a totally asymmetric simple exclusion process (TASEP) on a tree network where the aggregate hopping rate is constant from level to level. With this choice for hopping rates the model shows the same phase diagram as…
Cell migration is essential for regulating many biological processes in physiological or pathological conditions, including embryonic development and cancer invasion. In vitro and in silico studies suggest that collective cell migration is…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
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…
Adherent cells exert traction forces on to their environment, which allows them to migrate, to maintain tissue integrity, and to form complex multicellular structures. This traction can be measured in a perturbation-free manner with…
The conventional paradigm in speech translation starts with a speech recognition step to generate transcripts, followed by a translation step with the automatic transcripts as input. To address various shortcomings of this paradigm, recent…
Human-translated text displays distinct features from naturally written text in the same language. This phenomena, known as translationese, has been argued to confound the machine translation (MT) evaluation. Yet, we find that existing work…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Nuclear pore complexes are constantly confronted by large fluxes of macromolecules and macromolecular complexes that need to get into and out of the nucleus. Such bi-directional traffic occurring in a narrow channel can easily lead to…
Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic and optical properties. At the single-molecule level, two major complementary ways to explore these…
Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying…
Intracellular transport of DNA carriers is a fundamental step of gene delivery. We present here a theoretical approach to study generically a single virus or DNA particle trafficking in a cell cytoplasm. Cellular trafficking has been…
We present here a detailed description of the model of ran-driven nuclear transduction in living cells to be published elswere. The mathematical model presented is the first to account for the active transport of molecules along the…
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription…
We propose a modification to the study of site-wise dynamically disordered totally asymmetric simple exclusion process (TASEP). Motivated by the process of gene transcription, a study in ref. \cite{waclaw2019totally} introduced an extension…
Several important biological processes are initiated by the binding of a protein to a specific site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for searching its specific binding site on the DNA has been…
Existing multilingual machine translation approaches mainly focus on English-centric directions, while the non-English directions still lag behind. In this work, we aim to build a many-to-many translation system with an emphasis on the…