Related papers: Error probability amplification in cellular transl…
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…
Whole transcriptome sequencing is increasingly being used as a functional genomics tool to study non- model organisms. However, when the reference transcriptome used to calculate differential expression is incomplete, significant error in…
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…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Despite strong performance in many sequence-to-sequence tasks, autoregressive models trained with maximum likelihood estimation suffer from exposure bias, i.e. the discrepancy between the ground-truth prefixes used during training and the…
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which…
The paper elucidates, with an analytic example, a subtle mistake in the application of the extended likelihood method to the problem of determining the fractions of pure samples in a mixed sample from the shape of the distribution of a…
Molecular Communication (MC) architectures suffer from molecular build-up in the channel if they do not have appropriate reuptake mechanisms. The molecular build-up either leads to intersymbol interference (ISI) or reduces the transmission…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
We derive a sphere-packing error exponent for coded transmission over discrete memoryless channels with a fixed decoding metric. By studying the error probability of the code over an auxiliary channel, we find a lower bound to the…
When it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling…
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…
The sufficient condition of entanglement enhanced classical capacity is given for Pauli memory channel with arbitrary channel parameters. In some special case the condition is also necessary but fail to be necessary in general. The theory…
The standard approach to incorporate linguistic information to neural machine translation systems consists in maintaining separate vocabularies for each of the annotated features to be incorporated (e.g. POS tags, dependency relation…
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…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
In this note, we consider the problem of estimating multinomial cell probabilities under the entropy loss when side information in aggregated data is available. We use the Jeffreys prior to obtain Bayes estimators. It is shown that by…
Translation is the cellular process in which ribosomes make proteins from information encoded on messenger RNA (mRNA). We model translation with an exclusion process taking into account the experimentally determined, non-exponential,…
Recent experiments have shown that stochastic effects exerted at the level of translation contribute a substantial portion of the variation in abundance of proteins expressed at moderate to high levels. This study analyzes translational…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…