Related papers: Polysomally Protected Viruses
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
Standardized file formats play a key role in the development and use of computer software. However, it is possible to abuse standardized file formats by creating a file that is valid in multiple file formats. The resulting polyglot (many…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
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…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
This paper develops and analyzes optimization models for rapid detection of viruses in large contact networks. In the model, a virus spreads in a stochastic manner over an undirected connected graph, under various assumptions on the spread…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
Protecting sensitive program content is a critical issue in various situations, ranging from legitimate use cases to unethical contexts. Obfuscation is one of the most used techniques to ensure such protection. Consequently, attackers must…
The continued evolution and diversity of malware constitutes a major threat in modern systems. It is well proven that security defenses currently available are ineffective to mitigate the skills and imagination of cyber-criminals…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding…
Ransomware is considered as a significant threat for most enterprises since the past few years. In scenarios wherein users can access all files on a shared server, one infected host can lock the access to all shared files. We propose a tool…
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…