N. M. Dixit

Disentangling competitive and cooperative components of the interactions between microbial species

The paper disentangles competitive and cooperative interactions between microbial species using a new methodology, revealing that net interactions are composed of positive and negative components that can cancel each other.

Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection

This study uses mathematical modeling of SIV-infected macaques to show that early CD8 T-cell suppressive capacity predicts natural control of infection.

Molecular Dynamics Simulations Show How Antibodies May Rescue HIV-1 Mutants Incapable of Infecting Host Cells

The paper uses molecular dynamics simulations to show how antibodies can rescue HIV-1 mutants that cannot infect host cells by restoring the native gp41 conformation.

An evolutionary paradigm favoring crosstalk between bacterial two-component signaling systems

This paper proposes an evolutionary paradigm where crosstalk between bacterial two-component signaling systems can be advantageous in programmed environments, supported by simulations and data from Mycobacterium tuberculosis.

Modelling how the altered usage of cell entry pathways by the SARS-CoV-2 Omicron variant may affect the efficacy and synergy of TMPRSS2 and Cathepsin B/L inhibitors

Mechanistic Insights into the Effects of Key Mutations on SARS-CoV-2 RBD-ACE2 Binding

This study examines how key mutations in SARS-CoV-2 RBD affect binding to ACE2 using molecular dynamics simulations and free energy calculations, finding increased binding affinities in mutated variants.

Early exposure to broadly neutralizing antibodies may trigger a dynamical switch from progressive disease to lasting control of SHIV infection

This paper models the effects of early bNAb therapy on HIV-1 infection dynamics in macaques, showing it can trigger a switch from progressive disease to lasting viremic control through pleiotropic immune effects.

Concerted interactions between multiple gp41 trimers and the target cell lipidome may be required for HIV-1 entry

This study uses molecular dynamics simulations to show that multiple gp41 trimers and host cell lipidomes are required for efficient HIV-1 membrane fusion.

Pre-existing resistant proviruses can compromise maintenance of remission by VRC01 in chronic HIV-1 infection

The paper develops a mathematical model to explain VRC01 failure in HIV-1 patients by simulating pre-existing resistant proviruses reactivating during therapy.

A dynamical motif comprising the interactions between antigens and CD8 T cells may underlie the outcomes of viral infections

The paper identifies a dynamical motif of antigen-CD8 T cell interactions that determines outcomes of viral infections and explains various experimental observations.