68 citations · 218 across the 6 of their papers we have counts for
7 papers
A deep-learning view of chemical space designed to facilitate drug discovery
Paul Maragakis, Hunter Nisonoff, Brian Cole +1
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a gi…
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise
Paul Maragakis, Felix Ritort, Carlos Bustamante +2
The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to non-equilibrium measurements of the work. These relations extend to single-molecule…
Multiscale model of electronic behavior and localization in stretched dry DNA
Ryan Barnett, Paul Maragakis, Ari Turner +2
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopi…
Optimal estimates of free energies from multi-state nonequilibrium work data
Paul Maragakis, Martin Spichty, Martin Karplus
We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward…
Electronic structure of overstretched DNA
Paul Maragakis, Ryan Lee Barnett, Efthimios Kaxiras +2
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition…
HARES: an efficient method for first-principles electronic structure calculations of complex systems
U. V. Waghmare, Hanchul Kim, I. J. Park +3
We discuss our new implementation of the Real-space Electronic Structure method for studying the atomic and electronic structure of infinite periodic as well as finite systems, bas…