T
Thomas J. Lane
Researcher at SLAC National Accelerator Laboratory
Publications - 128
Citations - 7198
Thomas J. Lane is an academic researcher from SLAC National Accelerator Laboratory. The author has contributed to research in topics: Femtosecond & Pyronaridine. The author has an hindex of 30, co-authored 117 publications receiving 4972 citations. Previous affiliations of Thomas J. Lane include University of Cambridge & University of North Carolina at Greensboro.
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Journal ArticleDOI
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
Robert T. McGibbon,Kyle A. Beauchamp,Matthew P. Harrigan,Christoph Klein,Jason M. Swails,Carlos X. Hernández,Christian R. Schwantes,Lee-Ping Wang,Thomas J. Lane,Vijay S. Pande +9 more
TL;DR: MDTraj is a modern, lightweight, and fast software package for analyzing MD simulations that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
Journal ArticleDOI
OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation
Peter Eastman,Mark S. Friedrichs,John D. Chodera,Randall J. Radmer,Christopher M. Bruns,Joy P. Ku,Kyle A. Beauchamp,Thomas J. Lane,Lee-Ping Wang,Diwakar Shukla,Tony Tye,Mike Houston,Timo Stich,Christoph Klein,Michael R. Shirts,Vijay S. Pande +15 more
TL;DR: OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures that was designed to be extensible, so new hardware architectures can be accommodated and new functionality can be easily added.
Journal ArticleDOI
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.
Kyle A. Beauchamp,Gregory R. Bowman,Thomas J. Lane,Lutz Maibaum,Imran S. Haque,Vijay S. Pande +5 more
TL;DR: An improved protocol for constructing Markov State Models from molecular dynamics simulations is described, which leads to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems.
Journal ArticleDOI
To milliseconds and beyond: challenges in the simulation of protein folding.
TL;DR: Recent progress in MD simulation techniques is reviewed and how the vast datasets generated by such techniques present new challenges for analysis is shown, including reaction coordinate and Markov state model methods.
Journal ArticleDOI
Structure of photosystem II and substrate binding at room temperature
Iris D. Young,Mohamed Ibrahim,Ruchira Chatterjee,Sheraz Gul,Franklin D. Fuller,Sergey Koroidov,Aaron S. Brewster,Rosalie Tran,Roberto Alonso-Mori,Thomas Kroll,Tara Michels-Clark,Hartawan Laksmono,Raymond G. Sierra,Claudiu A. Stan,Rana Hussein,Miao Zhang,Lacey Douthit,Markus Kubin,Casper de Lichtenberg,Long Vo Pham,Håkan Nilsson,Mun Hon Cheah,Dmitriy Shevela,Claudio Saracini,Mackenzie A. Bean,Ina Seuffert,Dimosthenis Sokaras,Tsu-Chien Weng,Ernest Pastor,Clemens Weninger,Thomas Fransson,Louise Lassalle,Philipp Bräuer,Pierre Aller,P. T. Docker,Babak Andi,Allen M. Orville,James M. Glownia,Silke Nelson,Marcin Sikorski,Diling Zhu,Mark S. Hunter,Thomas J. Lane,Andrew Aquila,Jason E. Koglin,Joseph Robinson,Mengning Liang,Sébastien Boutet,Artem Y. Lyubimov,Artem Y. Lyubimov,Monarin Uervirojnangkoorn,Monarin Uervirojnangkoorn,Nigel W. Moriarty,Dorothee Liebschner,Pavel V. Afonine,David G. Waterman,Gwyndaf Evans,Philippe Wernet,Holger Dobbek,William I. Weis,Axel T. Brunger,Petrus H. Zwart,Paul D. Adams,Paul D. Adams,Athina Zouni,Johannes Messinger,Johannes Messinger,Uwe Bergmann,Nicholas K. Sauter,Jan Kern,Jan Kern,Vittal K. Yachandra,Junko Yano +72 more
TL;DR: Ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states, and this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.