Related papers: Ribosome collisions and Translation efficiency: Op…
RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…
The ribosome ensures translational accuracy by monitoring codon-anticodon interactions at the A site decoding center. However, the mechanism by which conserved nucleotide A1493 contributes to this process remains controversial. To address…
Totally asymmetric simple exclusion process (TASEP) was originally introduced as a model for the traffic-like collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motor-like forward stepping of…
We study the performance of random linear network coding for time division duplexing channels with Poisson arrivals. We model the system as a bulk-service queue with variable bulk size. A full characterization for random linear network…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
Data on stopping in intermediate-energy central heavy-ion collisions are analyzed following transport theory based on the Boltzmann equation. In consequence, values of nuclear shear viscosity are inferred. The inferred values are…
Transport of molecules across membrane channels is investigated theoretically using exactly solvable discrete stochastic site-binding models. It is shown that the interaction potential between molecules and the channel has a strong effect…
Despite the absence of a membrane-enclosed nucleus, the bacterial DNA is typically condensed into a compact body - the nucleoid. This compaction influences the localization and dynamics of many cellular processes including transcription,…
The migratory dynamics of cells in physiological processes, ranging from wound healing to cancer metastasis, rely on contact-mediated cell-cell interactions. These interactions play a key role in shaping the stochastic trajectories of…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
Molecular communication between biological entities is a new paradigm in communications. Recently, we studied molecular communication between two nodes formed from synthetic bacteria. Due to high randomness in behavior of bacteria, we used…
Classical translation models constrain the space of possible outputs by selecting a subset of translation rules based on the input sentence. Recent work on improving the efficiency of neural translation models adopted a similar strategy by…
A new channel coding approach was proposed in [1] for random multiple access communication over the discrete-time memoryless channel. The coding approach allows users to choose their communication rates independently without sharing the…
With the emergence of large model-based agents, widely adopted transformer-based architectures inevitably produce excessively long token embeddings for transmission, which may result in high bandwidth overhead, increased power consumption…
We analyze a simple network where a source and a receiver are connected by a line of erasure channels of different reliabilities. Recent prior work has shown that random linear network coding can achieve the min-cut capacity and therefore…
Interesting theoretical problems of target search or threshold crossing, formally known as {\it first passage}, often arise in both diffusive transport problems as well as problems of chemical reaction kinetics. We study three systems…
Automatic speech translation is sensitive to speech recognition errors, but in a multilingual scenario, the same content may be available in various languages via simultaneous interpreting, dubbing or subtitling. In this paper, we…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
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…