A5000071820- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Nanopore and Nanochannel Transport Studies
- Microfluidic and Capillary Electrophoresis Applications
- Computational Drug Discovery Methods
New York University
2023
Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem systematically determining proper reaction coordinate (RC) specific process terms set putative can be achieved using committor analysis (CA). Identifying essential degrees freedom that govern such CA remains elusive because high...
Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated dynamics (TAMD)/driven-adiabatic free energy (d-AFED), unified (UFED), and sliced (TASS), uses an extended formalism to achieve quick exploration conformational space. These powerful, as they enhance the a large number CVs simultaneously compared other techniques. Extended...
Collective variable (CV)-based enhanced sampling tech- niques are widely used today for accelerating barrier- crossing events in molecular simulations. A class of these methods, which includes Temperature Accelerated Molecu- lar Dynamics (TAMD)/driven-Adiabatic Free Energy Dy- namics (d-AFED), Unified (UFED), and Sliced Sampling (TASS), use a unique extended formalism to achieve quick explo- ration conformational space. These techniques pow- erful, as they permit the simultaneous large...