Quantitative Biology
Computing the rate of evolution in spatially structured populations is difficult. A key quantity is the fixation time of a single mutant with relative reproduction rate $r$ which invades a population of residents. We say that the fixation…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
Fragment-based drug design is a promising strategy leveraging the binding of small chemical moieties that can efficiently guide drug discovery. The initial step of fragment identification remains challenging, as fragments often bind weakly…
Digital pathology has emerged as a transformative approach to tissue analysis, offering unprecedented opportunities for objective, quantitative assessment of histopathological features. However, the complexity of implementing artificial…
The scarcity of experimental protein-ligand complexes poses a significant challenge for training robust deep learning models for molecular docking. Given the prohibitive cost and time constraints associated with experimental structure…
Cancer is a complex sequence of disease conditions progressing gradually with generalized loss of growth control. It continues to be one of the biggest global health problems, and its etiology has given rise to a huge array of treatment…
The Gillespie algorithm and its extensions are commonly used for the simulation of chemical reaction networks. A limitation of these algorithms is that they have to process and update the system after every reaction, requiring significant…
Protein design has the potential to revolutionize biotechnology and medicine. While most efforts have focused on proteins with well-defined structures, increased recognition of the functional significance of intrinsically disordered…
Summary: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies,…
Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. Among them, RNA-binding antiterminator proteins play a major role…
This paper investigates a behavioral-feedback SIR model in which the infection rate adapts dynamically based on the fractions of susceptible and infected individuals. We introduce an invariant of motion and we characterize the peak of…
Reproducibility of computational research is critical for ensuring transparency, reliability and reusability. Challenges with computational reproducibility have been documented in several fields, but healthcare discrete-event simulation…
We derive a charge conserving phase space cable equation for the propagating action potential, expressing ionic, capacitive and axoplasmic currents as functions of membrane potential. The new equation prediction of ionic current crossing…
The macroscopic (population-level) dynamics of chemotactic cell movement -- arising from underlying microscopic (individual-based) models -- are often described by parabolic partial differential equations (PDEs) governing the…
This study presents a mathematical model formulated as a system of first-order non-linear ordinary differential equations, aimed at examining the effects of different factors, classified as local and systemic factors on a wound healing…
Epidemic control frequently relies on adjusting interventions based on prevalence. But designing such policies is a highly non-trivial problem due to uncertain intervention effects, costs and the difficulty of quantifying key transmission…
Background: Outdoor navigation poses significant challenges for people with blindness or low vision, yet the role of gaze behavior in supporting mobility remains underexplored. Fully sighted individuals typically adopt consistent scanning…
PF708 teriparatide, manufactured by Alvogen, was approved through the 505(B)(2) application after the expiration of Forteo market exclusivity in October 2019. The 505(B)(2) application allows safety and efficacy information to come from…
Moving animal groups consist of many distinct individuals but can operate and function as one unit when performing different tasks. Effectively evading unexpected predator attacks is one primary task for many moving groups. The current…
Tumor-immune interactions are shaped by both antigenic heterogeneity and stochastic perturbations in the tumor microenvironment, yet the mathematical mechanisms underlying immune phase transitions remain poorly understood. We propose a…