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Quantitative Fitness Analysis (QFA) is a high-throughput experimental and computational methodology for measuring the growth of microbial populations. QFA screens can be used to compare the health of cell populations with and without a…
Microswimmers such as E. Coli bacteria accumulate and exhibit an intriguing dynamics near walls, governed by hydrodynamic and steric interactions. Insight into the underlying mechanisms and predominant interactions demand a detailed…
Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It…
We present a model for host-parasite dynamics which incorporates both vertical and horizontal transmission as well as spatial structure. Our model consists of stacked contact processes (CP), where the dynamics of the host is a simple CP on…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Immune cells learn about their antigenic targets using tactile sense: during recognition, a highly organized yet dynamic motif, named immunological synapse, forms between immune cells and antigen-presenting cells (APCs). Via synapses,…
The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using…
Gastrulation, namely cell internalization, is a significant milestone during the development of metazoans from worm to human, which generates multiple embryonic layers with distinct cell fates and spatial organizations. Although many…
In this work, we apply a phase-field modeling framework to elucidate the interplay between nucleation and kinetics in the dynamic evolution of twinning interfaces. The key feature of this phase-field approach is the ability to transparently…
After more than 6 million deaths worldwide, the ongoing vaccination to conquer the COVID-19 disease is now competing with the emergence of increasingly contagious mutations, repeatedly supplanting earlier strains. Following the near-absence…
Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes: the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia DNA to the host genome is common. We…
Viral kinetics have been extensively studied in the past through the use of spatially homogeneous ordinary differential equations describing the time evolution of the diseased state. However, spatial characteristics such as localized…
A central feature of vertebrate immune response is affinity maturation, wherein antibody-producing B cells undergo evolutionary selection in microanatomical structures called germinal centers, which form in secondary lymphoid organs upon…
The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this…
This paper investigates the effects of vaccination on the dynamics of infectious disease, which is spreading in a population concurrently with awareness. The model considers contributions to the overall awareness from a global information…
In this paper, Wolbachia infection in a bisexual and diploid population with a fixed cytoplasmic incompatibility rate $w$ and maternal transmission rate $d$ is studied as an evolution algebra. As the cytoplasmic incompatibility (CI) of the…
Infectious diseases that incorporate pre-symptomatic transmission are challenging to monitor, model, predict and contain. We address this scenario by studying a variant of a stochastic susceptible-exposed-infected-recovered model on…
Many animals in their natural habitat exhibit collective motion and form complex patterns to tackle environmental difficulties. Several physical and biological factors, such as animal motility, population densities, and chemical cues, play…
The goal of this study is to develop a computational model of the progression of changes in mitochondrial phenotype resulting from infection with pathogenic mycobacteria. This ultimately will enable a large-scale virulence screen of mutant…