A model of the innate immune response to SARS-CoV-2 in the alveolar epithelium.

We present a differential equation model of the innate immune response to SARS-CoV-2 within the alveolar epithelium. Critical determinants of the viral dynamics and host response, including type I and type II alveolar epithelial cells, interferons, chemokines, toxins and innate immune cells, are included. We estimate model parameters, compute the within-host basic reproductive number, and study the impacts of therapies, prophylactics, and host/pathogen variability on the course of the infection.

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

A practical approach for computing the active site of the ribonucleoside hydrolase of E. coli encoded by rihC.

We predict the potential active and catalytic sites, the transition state and how it is stabilized, and the mechanism of rihC ribonucleoside hydrolase of E. coli. Our approach is based on well-known primary sequence analysis techniques.

Dynamics of prostate cancer stem cells with diffusion and organism response.

We develop a systems based model for prostate cancer, as a sub-system of the organism. We accomplish this in two stages. We first start with a general ODE that includes organism response terms.

Soliton/exciton transport in proteins.

The study of electron/proton transport in alpha-helix sections of proteins have illustrated the existence of soliton-like mechanisms. Recently, Ciblis and Cosic extended investigation to the existence of possible like soliton-type mechanisms in other parts of the protein. They used Quantum Hamiltonian analysis to investigate.