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Generative adversarial models with convolutional neural network (CNN) backbones have recently been established as state-of-the-art in numerous medical image synthesis tasks. However, CNNs are designed to perform local processing with…
The in vitro transcription reaction (IVT) is of growing importance for the manufacture of RNA vaccines and therapeutics. While the kinetics of the microscopic steps of this reaction (promoter binding, initiation, and elongation) are well…
A big class of viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and ss RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ss RNA in the…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral…
Antibodies are essential proteins responsible for immune responses in organisms, capable of specifically recognizing antigen molecules of pathogens. Recent advances in generative models have significantly enhanced rational antibody design.…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
Directed motion up a concentration gradient is crucial for the survival and maintenance of numerous biological systems, such as sperms moving towards an egg during fertilization or ciliates moving towards a food source. In these systems,…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
While RNA technologies hold immense therapeutic potential in a range of applications from vaccination to gene editing, the broad implementation of these technologies is hindered by the challenge of delivering these agents effectively. Lipid…
Much of the work on modeling the spread of viral infections utilized partial differential equa- tions. Traveling-wave solutions to these PDEs are typically concentrated on velocities and their dependence on the various parameters. Most of…
Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively…
The use of ad-hoc engineered viruses in the fight against tumours is one of the greatest ideas in cancer therapeutics within the last three decades. Together with other strategies such as immunotherapies, nanoparticles and adjunct…
Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
In randomized controlled trials (RCTs) of infectious disease interventions, it is well recognized that unmeasured individual heterogeneity at baseline can induce selection bias over time, thereby complicating the interpretation of the…
Heterogeneous treatment effects can be very important in the analysis of randomized clinical trials. Heightened risks or enhanced benefits may exist for particular subsets of study subjects. When the heterogeneous treatment effects are…
We examine two models for hepatitis C viral (HCV) dynamics, one for monotherapy with interferon (IFN) and the other for combination therapy with IFN and ribavirin. Optimal therapy for both the models is determined using the steepest…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Due to the persistence of latently infected CD4$^+$ T cells, achieving a functional cure for HIV-1 remains a significant challenge since the viruses are able to evade immune clearance, which in turn enables post-treatment viral rebound.…