Engineering topics
Gnanakaran, Sandrasegaram
Publications and source records attributed to Gnanakaran, Sandrasegaram.
Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations
We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.
Quantification of heterogeneity in human CD8 + T cell responses to vaccine antigens: an HLA-guided perspective
Vaccines have historically played a pivotal role in controlling epidemics. Effective vaccines for viruses causing significant human disease, e.g., Ebola, Lassa fever, or Crimean Congo hemorrhagic fever virus, would be invaluable to public health strategies and counter-measure development missions. Here, we propose coverage metrics to quantify vaccine-induced CD8 + T cell-mediated immune protection, as well as metrics to characterize immuno-dominant epitopes, in light of human genetic heterogeneity and viral evolution. Proof-of-principle of our approach and methods are demonstrated for Ebola virus, SARS-CoV-2, and Burkholderia pseudomallei (vaccine) proteins.
Modeling Infection on a Molecular Level: Human Immunodeficiency Virus and Arenaviruses
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