Elsje Pienaar

Partially-functional exhausted CD8+ T cells can contribute to short-term viral suppression: a computational prediction for children with perinatal HIV

The paper uses a computational model to predict how T cell exhaustion affects viral control in children with perinatal HIV, finding that exhausted CD8+ T cells can contribute to short-term viral suppression.

Timing matters in Macrophage / CD4+ T cell interactions: An agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals

This paper develops an agent-based model to simulate immune responses to Mycobacterium tuberculosis infection, showing that early macrophage-CD4+ T cell interactions in latent TB infection reduce bacterial load through TNF and IFNγ mechanisms.

Local traveling waves of cytosolic calcium elicited by defense signals or wounding are propagated by distinct mechanisms

The paper quantifies Ca2+ wave propagation in Arabidopsis cells in response to MAMPs and wounding, showing distinct mechanisms for each.

Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma

The paper uses agent-based simulations to show that 3D spheroid structures and cell movement enhance bacterial control in tuberculosis granuloma models.

Impact of Ebola virus nucleoprotein on VP40 virus-like particle production: a computational approach

This study uses computational methods to show that NP enhances VP40 VLP production by stabilizing filaments and accelerating budding, with optimal timing and expression ratios.

Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly

This paper evaluates the effect of fendiline on EBOV VP40 filament assembly using a computational model, finding it may temporarily increase VLP production but generally reduces it.

Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load

In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models

This paper introduces an agent-based model to simulate and compare traditional and spheroid in vitro tuberculosis infection models, showing heterogeneous outputs and predictive capabilities.

Chemokine Signaling Caused by Mycobacterium avium Biofilms in the Lung Airway Increases Bacterial Loads by Spatially Diverting Macrophages

This study uses a computational model to show that MAC biofilms spatially divert macrophages, increasing bacterial loads through chemokine-driven chemotaxis and repeated exposure.

Mechanisms of phosphatidylserine influence on viral production: a computational model of Ebola virus matrix protein assembly

This study uses a computational model to investigate how phosphatidylserine influences VP40 matrix protein assembly in Ebola virus, showing PS affects filament growth and assembly steps.

The Role of Biofilms, Bacterial Phenotypes, and Innate Immune Response in Mycobacterium avium Colonization to Infection

This paper develops a 3D agent-based model to simulate early MAC infection dynamics, showing how biofilms and immune responses influence bacterial colonization and infection outcomes.

Mathematical modeling of N-803 treatment in SIV-infected non-human primates

This paper uses mathematical models to analyze N-803 treatment in SIV-infected macaques, showing immune regulation and viral escape contribute to viral rebound after treatment interruption.

Iterative community-driven development of a SARS-CoV-2 tissue simulator

Open-source agent-based PhysiCell model of SARS-CoV-2 infection in lung epithelium; version 5 clears virus in about 6 days in simulation, and delayed T cell arrival increases epithelial loss.