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.

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.

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.

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.

Stochastic simulations show how passive immunization can influence the germinal centre reaction and optimize host humoral responses

This paper uses stochastic simulations to show that passive immunization can bias germinal centre selection towards high-affinity B cells, optimizing host humoral responses through a quality-quantity trade-off.