Related papers: Protocols for copying and proofreading in template…
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by…
In this paper, we propose a novel transfer learning approach called multi-modal cascade model with feature transfer for polymer property prediction.Polymers are characterized by a composite of data in several different formats, including…
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential…
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
Random sequential adsorption (RSA) of polymer, modeled as a chain of identical spheres, is systematically studied. In order to control precisely anisotropy and number of degrees of freedom, two different kinds of polymers are used. In the…
We illustrate the use of tools (asymptotic theories of standard error quantification using appropriate statistical models, bootstrapping, model comparison techniques) in addition to sensitivity that may be employed to determine the…
Transcription is a key process in gene expression, in which RNA polymerases produce a complementary RNA copy from a DNA template. RNA polymerization is frequently interrupted by backtracking, a process in which polymerases perform a random…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
Language model approaches have recently been integrated into binary analysis tasks, such as function similarity detection and function signature recovery. These models typically employ a two-stage training process: pre-training via Masked…
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…
We propose and analyze a process that extracts useful work from a single active particle maintained at constant temperature in a harmonic potential by measuring the relative sign of the self-propulsion and the confining force and then…
Differential replication through copying refers to the process of replicating the decision behavior of a machine learning model using another model that possesses enhanced features and attributes. This process is relevant when external…
Block-sparse regularization is already well-known in active thermal imaging and is used for multiple measurement based inverse problems. The main bottleneck of this method is the choice of regularization parameters which differs for each…
We use the term protocol coding to denote the communication strategies in which information is encoded through the actions taken by a certain communication protocol. In this work we investigate strategies for protocol coding via…
We present a novel approach to efficiently learn a simultaneous translation model with coupled programmer-interpreter policies. First, wepresent an algorithmic oracle to produce oracle READ/WRITE actions for training bilingual…
Polymer composite materials require softening to reduce their glass transition temperature and improve processability. To this end, plasticizers, which are small organic molecules, are added to the polymer matrix. The miscibility of these…
This paper describes a method for the automatic inference of structural transfer rules to be used in a shallow-transfer machine translation (MT) system from small parallel corpora. The structural transfer rules are based on alignment…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…