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We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally,…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
We examine the dynamics of the translation stage of cellular protein production, in which ribosomes move uni-directionally along mRNA strands building an amino acid chain as they go. We describe the system using a timed event graph - a…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…
Molecular communication (MC) allows nanomachines to communicate and cooperate with each other in a fluid environment. The diffusion-based MC is popular but is easily constrained by the transmit distance due to the severe attenuation of…
Dense image correspondence is central to many applications, such as visual odometry, 3D reconstruction, object association, and re-identification. Historically, dense correspondence has been tackled separately for wide-baseline scenarios…
Diffusion and flow models have become the dominant paradigm for generative modeling on Riemannian manifolds, with successful applications in protein backbone generation and DNA sequence design. However, these methods require tens to…
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…
We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…
Molecular Communication (MC) is an important nanoscale communication paradigm, which is employed for the interconnection of the nanomachines (NMs) to form nanonetworks. A transmitter NM (TN) sends the information symbols by emitting…
In diffusion-based molecular communication, information transport is governed by diffusion through a fluid medium. The achievable data rates for these channels are very low compared to the radio-based communication system, since diffusion…
Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA…
Factorization machines (FM) are a popular model class to learn pairwise interactions by a low-rank approximation. Different from existing FM-based approaches which use a fixed rank for all features, this paper proposes a Rank-Aware FM…
We propose Pullback Flow Matching (PFM), a novel framework for generative modeling on data manifolds. Unlike existing methods that assume or learn restrictive closed-form manifold mappings for training Riemannian Flow Matching (RFM) models,…
Recently, Flow Matching models have pushed the boundaries of high-fidelity data generation across a wide range of domains. It typically employs a single large network to learn the entire generative trajectory from noise to data. Despite…
Ultrafast and accurate physical layer models are essential for designing, optimizing and managing ultra-wideband optical transmission systems. We present a closed-form GN/EGN model, named Polynomial Closed-Form Model (PCFM), improving…
Accurate and real-time radio map (RM) generation is crucial for next-generation wireless systems, yet diffusion-based approaches often suffer from large model sizes, slow iterative denoising, and high inference latency, which hinder…
One-dimensional non-equilibrium models of particles subjected to a coagulation-diffusion process are important in understanding non-equilibrium dynamics, and fluctuation-dissipation relation. We consider in this paper transport properties…