Related papers: Therapeutic Interfering Particles Exploiting Viral…
RNA viruses exist in large intra-host populations which display great genotypic and phenotypic diversity. We analyze a model of viral competition between two different viral strains infecting a constantly replenished cell pool, in which we…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
Therapeutic antibody candidates often require extensive engineering to improve key functional and developability properties before clinical development. This can be achieved through iterative design, where starting molecules are optimized…
This paper analyzes a simplified model of viral infection and evolution using the 'grand canonical ensemble' and formalisms from statistical mechanics and thermodynamics to enumerate all possible viruses and to derive thermodynamic…
Deep learning models have shown remarkable success in dermatological image analysis, offering potential for automated skin disease diagnosis. Previously, convolutional neural network(CNN) based architectures have achieved immense popularity…
We consider the mutual interactions, via cytokine exchanges, among helper lymphocytes, B lymphocytes and killer lymphocytes, and we model them as a unique system by means of a tripartite network. Each part includes all the different clones…
Extreme enrichment of the human immunodeficiency virus (HIV-1) RNA genome for the purine A parallels the mild purine-loading of the RNAs of most organisms. This should militate against loop-loop "kissing" interactions between the structured…
The effectiveness of biochemical antivirals are vulnerable to mutations, motivating physical approaches. Recent experiments with ultrasound reveal viral disruption at MHz frequencies, yet the mechanism remains unclear. We model viruses as…
Crystalline films offer various physical properties based on the modulation of their thicknesses and atomic structures. The layer-by-layer assembly of atomically thin crystals provides powerful means to arbitrarily design films at the…
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
In this paper, a mathematical analysis of the global dynamics of a viral infection model in vivo is carried out. We study the dynamics of a hepatitis C virus (HCV) model, under therapy, that considers both extracellular and intracellular…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which…
Oncolytic virotherapy is an experimental cancer treatment that uses genetically engineered viruses to target and kill cancer cells. One major limitation of this treatment is that virus particles are rapidly cleared by the immune system,…
Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are…
The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop…
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of…
Viral spread on large graphs has many real-life applications such as malware propagation in computer networks and rumor (or misinformation) spread in Twitter-like online social networks. Although viral spread on large graphs has been…
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…