A5071331715- Mass Spectrometry Techniques and Applications
- Advanced Chemical Physics Studies
- Spectroscopy and Quantum Chemical Studies
- Quantum, superfluid, helium dynamics
- Protein Structure and Dynamics
- Markov Chains and Monte Carlo Methods
- Research on Leishmaniasis Studies
- Theoretical and Computational Physics
- Computational Drug Discovery Methods
- Machine Learning in Materials Science
- Parasites and Host Interactions
Washington University in St. Louis
2018-2021
Interest in atomically detailed simulations has grown significantly with recent advances computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder their widespread adoption. Namely, how do alternative sampling strategies explore conformational space might this influence predictions generated from the data? Here, we seek to answer these for four commonly used methods: (1) a single long simulation, (2) many short run parallel, (3) adaptive...
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field based upon the model electron density a hydrogen-like atom. This framework used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, polarization, transfer, anisotropic Pauli repulsion, dispersion interactions. Initial parameter values were fit Symmetry Adapted...
Schistosoma mansoni is responsible for virtually all reported cases of schistosomiasis in Latin America and the emergence praziquantel- oxaminiquine-resistant strains makes it urgent to develop new schistosomicide agents. Dihydrofolate reductases (DHFR) from bacteria protozoan parasites are considered validated macromolecular targets this goal, but S. DHFR (SmDHFR) has been largely overlooked. To fill gap knowledge, present work describes optimized conditions carry out thermal shift assays...
Interest in equilibrium-based sampling methods has grown with recent advances computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder widespread adoption. Namely, how do strategies explore conformational space might this influence predictions? Here, we seek to answer these for four commonly used methods: 1) a long simulation, 2) many short simulations, 3) adaptive sampling, 4) FAST. We first develop theoretical framework analytically...
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field based upon the model electron density a hydrogen-like atom. This framework used to derive and parameterize individual terms describing charge penetration damped permanent electrostatics, polarization, transfer, anisotropic Pauli repulsion, dispersion interactions. Initial parameter values were fit Symmetry Adapted...