Related papers: Error probability amplification in cellular transl…
Cells measure concentrations of external ligands by capturing ligand molecules with cell surface receptors. The numbers of molecules captured by different receptors co-vary because they depend on the same extrinsic ligand fluctuations.…
Recently, several groups have used error-prone polymerase chain reactions to construct mutant libraries containing up to 27 nucleotide mutations per gene on average, and reported a striking observation: although retention of protein…
Translation is an important stage in gene expression. During this stage, macro-molecules called ribosomes travel along the mRNA strand linking amino-acids together in a specific order to create a functioning protein. An important question…
The study of functional genomics--particularly in non-model organisms has been dramatically improved over the last few years by use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally…
Paper [1] derived the probability density function (PDF) of a sum of products of two correlated complex Gaussian zero-mean random variables (RVs) that has been applied to calculate the error probabilities of a \emph{M}-ary phase shift…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
Error and erasure exponents for the broadcast channel with degraded message sets are analyzed. The focus of our error probability analysis is on the main receiver where, nominally, both messages are to be decoded. A two-step decoding…
Matrices resulting from the discretization of a kernel function, e.g., in the context of integral equations or sampling probability distributions, can frequently be approximated by interpolation. In order to improve the efficiency, a…
A key challenge in Molecular Communications (MC) is low data transmission rates, which can be addressed by channel multiplexing techniques. One way to achieve channel multiplexing in MC is to leverage the diversity of different molecule…
DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\it polymerase} catalyzing the elongation of a new DNA molecule by adding a…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…
In this paper, a simple memory limited transmitter for molecular communication is proposed, in which information is encoded in the diffusion rate of the molecules. Taking advantage of memory, the proposed transmitter reduces the ISI problem…
Exponential error bounds achievable by universal coding and decoding are derived for frame-asynchronous discrete memoryless %asynchronous multiple access channels with two senders, via the method of subtypes, a refinement of the method of…
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 present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with…
Modern computer architectures support low-precision arithmetic, which present opportunities for the adoption of mixed-precision algorithms to achieve high computational throughput and reduce energy consumption. As a growing number of…
Agarwal et al. gave an closed-form expression for write amplification in NAND flash memory by finding the probability of a page being valid over the whole flash memory. This paper gives an improved analytic expression for write…
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…