Related papers: Polysomally Protected Viruses
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic…
Machine learning based malware detection techniques rely on grayscale images of malware and tends to classify malware based on the distribution of textures in graycale images. Albeit the advancement and promising results shown by machine…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to…
Malicious software is abundant in a world of innumerable computer users, who are constantly faced with these threats from various sources like the internet, local networks and portable drives. Malware is potentially low to high risk and can…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
Memory isolation is a critical property for system reliability, security, and safety. We demonstrate RowPress, a DRAM read disturbance phenomenon different from the well-known RowHammer. RowPress induces bitflips by keeping a DRAM row open…
Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive N-terminal tails. We explore the role…