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Alphafold2 Modeling And Molecular Dynamics Simulations Of The Conformational Ensembles For The Sars-Cov-2 Spike Omicron Jn.1, Kp.2 And Kp.3 Variants: Mutational Profiling Of Binding Energetics Reveals Epistatic Drivers Of The Ace2 Affinity And Escape Hotspots Of Antibody Resistance, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker
Alphafold2 Modeling And Molecular Dynamics Simulations Of The Conformational Ensembles For The Sars-Cov-2 Spike Omicron Jn.1, Kp.2 And Kp.3 Variants: Mutational Profiling Of Binding Energetics Reveals Epistatic Drivers Of The Ace2 Affinity And Escape Hotspots Of Antibody Resistance, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
AlphaFold2-based atomistic predictions of structures and conformational ensembles of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the most dominant Omicron variants JN.1, KP.1, KP.2 and KP.3 to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and computations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. The results suggested the existence of epistatic interactions between convergent mutational sites at L455, F456, Q493 positions that protect and restore …
Md Simulations Of Collision Effects For A Strongly Coupled Plasma, Jawon Jo
Md Simulations Of Collision Effects For A Strongly Coupled Plasma, Jawon Jo
All Graduate Theses and Dissertations, Fall 2023 to Present
Studying strongly coupled plasmas can be effectively accomplished using molecular dynamics (MD) simulations. We have developed an advanced MD simulation code that can analyze plasmas with various coupling parameters. This code employs a spherically symmetric cut-off Coulomb force verified through convergence tests by modulating the cut-off and minimum force ranges. Additionally, it incorporates a new algorithm for optimizing the initial positions of particles at a given temperature. This method maintains the temperature constant and the velocity distribution unchanged. As a result, we eliminate the unphysical initial rises and oscillations in temperature that a random distribution of positions causes. The code …
Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens
Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens
Chemistry and Chemical Biology ETDs
Protein Interacting with C Kinase-1 (PICK1) is a scaffolding protein that offers a promising solution to support individuals suffering from substance use disorders. While many efforts have been put towards identifying small-molecule drugs with the potential to target PICK1 and ultimately support individuals suffering from the effects of substance use disorders, all efforts have so far fallen short. The purpose of this work is to use computational tools to assist the design of a small-molecule inhibitor of PICK1 while also advancing the knowledge of its biological functions. This work provides information that is currently missing the field by (1) revealing …
Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust
Assessing Interatomic Potentials For Molecular Dynamics Simulation Of Soybean Oil Pyrolysis, Tanner Garrett Rust
MSU Graduate Theses
The world today relies on hydrocarbon combustion for many reasons, including its high energy density that provides ease of transportation. However, hydrocarbons sourced from fossil fuels are not expected to last forever. Biodiesel, a renewable alternative, has many attractive benefits but comes with other downsides. Biodiesel can gel in cold environments and may leave residue in an engine. Pyrolysis of biodiesel has shown promise in addressing these common detriments. Inducing pyrolysis on biodiesel feedstock (commonly soybean oil in the USA) would be an attractive option presuming it continues to produce fossil fuel analogs similar to biodiesel pyrolysis. Herein, Langevin molecular …