Related papers: Virus-Encoded Ribonucleotide Reductases
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…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
The problem of RNA genomes packaged inside spherical viruses is studied. The viral capsid is modeled as a hollowed sphere. The attraction between RNA molecules and the inner viral capsid is assumed to be non-specific and occurs at the inner…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with…
Reaction constants in traditional Michaelis-Menten type enzyme kinetics are most often determined through a linear Lineweaver-Burk plot. While such a graphical plot is sometimes good to achieve the end, it is always better to go for a few…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
Identifying new viral threats, and developing long term defences against current and future computer viruses, requires an understanding of their behaviour, structure and capabilities. This paper aims to advance this understanding by further…
Block codes are considered for improving the reliability of messages stored in a computer memory with both stuck-at defects and random errors. It is assumed that the side information about the state of the defects is available to the…
Computer viruses have many similarities to biological viruses, and their association may offer new perspectives and new opportunities in the effort to tackle and even eradicate them. Evolutionary game theory has been established as a useful…
This paper investigates how Backdoor Attacks are represented within Vision Transformers (ViTs). By assuming knowledge of the trigger, we identify a specific ``trigger direction'' in the model's activations that corresponds to the internal…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Analysis of the cell population generally provides average information about viral infection in a host whereas the intracellular model captures the individual cellular responses. The primary goal of this study is to comprehensively analyze…
HIV virus replication is a time-related process that includes several stages. Focusing on the core steps, RNA polymerase II transcripts in an early stage pre-mRNA containing regulator proteins (i.e nef,tat,rev,vif,vpr,vpu), which are…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Recurrent neurons, or "simulated" qubits, can store simultaneous true and false with probabilistic behaviors usually reserved for the qubits of quantum physics. Although possible to construct artificially, simulated qubits are intended to…
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for…
Malware evolves over time and antivirus must adapt to such evolution. Hence, it is critical to detect those points in time where malware has evolved so that appropriate countermeasures can be undertaken. In this research, we perform a…