Related papers: mRNA translation from a unidirectional traffic per…
Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
Recent studies have revealed a number of pathologies of neural machine translation (NMT) systems. Hypotheses explaining these mostly suggest there is something fundamentally wrong with NMT as a model or its training algorithm, maximum…
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…
As part of a larger project on optimal learning conditions in neural machine translation, we investigate characteristic training phases of translation engines. All our experiments are carried out using OpenNMT-Py: the pre-processing step is…
In the past decades microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
Smooth transportation has drawn the attention of many researchers and practitioners in several fields. In the present paper, we propose a modified model of a totally asymmetric simple exclusion process (TASEP), which includes multiple…
miRNAs serve as crucial post-transcriptional regulators in various essential cell fate decision. However, the contribution of the mRNA-miRNA mutual regulation to bistability is not fully understood. Here, we built a set of mathematical…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
Intracellular transport of large cargoes, such as organelles, vesicles or large proteins, is a complex dynamical process that involves the interplay of ATP-consuming molecular motors, cytoskeleton filaments and the viscoelastic cytoplasm.…
Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing…
Machine translation is a popular test bed for research in neural sequence-to-sequence models but despite much recent research, there is still a lack of understanding of these models. Practitioners report performance degradation with large…
The totally asymmetric simple exclusion process (TASEP) is a paradigmatic stochastic model for non-equilibrium physics, and has been successfully applied to describe active transport of molecular motors along cytoskeletal filaments.…
Modeling the dynamics of cellular differentiation is fundamental to advancing the understanding and treatment of diseases associated with this process, such as cancer. With the rapid growth of single-cell datasets, this has also become a…
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
Several theoretical models based on totally asymmetric simple exclusion process (TASEP) have been extensively utilized to study various non-equilibrium transport phenomena. Inspired by the the role of microtubule-transported vesicles in…
The quality of machine translation is rapidly evolving. Today one can find several machine translation systems on the web that provide reasonable translations, although the systems are not perfect. In some specific domains, the quality may…
Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…