Related papers: Optimal Translation Along a Circular mRNA
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…
Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
Translation of proteins is a fundamental part of gene expression that is mediated by ribosomes. As ribosomes significantly contribute to both cellular mass and energy consumption, achieving efficient management of the ribosome population is…
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or…
Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using…
Protein translation is one of the most important processes in cell life but, despite being well understood biochemically, the implications of its intrinsic stochastic nature have not been fully elucidated. In this paper we develop a…
Magnetic Resonance Fingerprinting (MRF) leverages transient-state signal dynamics generated by the tunable acquisition parameters, making the design of an optimal, robust sequence a complex, high-dimensional sequential decision problem,…
In the recent paper of Valleriani {\it et al} [Phys. Rev. E {\bf 83}, 042903 (2011)], a simple model for describing the translation of messenger RNA (mRNA) by ribosomes is presented, and an expression of the translational ratio $r$, defined…
Individual mRNAs are translated by multiple ribosomes that initiate translation with a few seconds interval. The ribosome speed is codon dependant, and ribosome queuing has been suggested to explain specific data for translation of some…
We propose a novel decoding approach for neural machine translation (NMT) based on continuous optimisation. We convert decoding - basically a discrete optimization problem - into a continuous optimization problem. The resulting constrained…
Multilingual neural machine translation (MNMT) learns to translate multiple language pairs with a single model, potentially improving both the accuracy and the memory-efficiency of deployed models. However, the heavy data imbalance between…
We introduce an optimal transport-based model for learning a metric tensor from cross-sectional samples of evolving probability measures on a common Riemannian manifold. We neurally parametrize the metric as a spatially-varying matrix field…
One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to…
Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here we study the kinetics of translation at molecular level through a stochastic simulation model. The model…
Multi-modal Magnetic Resonance Imaging (MRI) translation leverages information from source MRI sequences to generate target modalities, enabling comprehensive diagnosis while overcoming the limitations of acquiring all sequences. While…
Transformers have achieved great success in effectively processing sequential data such as text. Their architecture consisting of several attention and feedforward blocks can model relations between elements of a sequence in parallel…
In 802.11 systems, Rate Adaptation (RA) is a fundamental mechanism allowing transmitters to adapt the coding and modulation scheme as well as the MIMO transmission mode to the radio channel conditions, and in turn, to learn and track the…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
In training deep learning networks, the optimizer and related learning rate are often used without much thought or with minimal tuning, even though it is crucial in ensuring a fast convergence to a good quality minimum of the loss function…