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1

Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform

Pronk, Sander, Pouya, Iman, Lundborg, Magnus, Rotskoff, Grant, Wesén, Björn, Kasson, Peter M., Lindahl, Erik

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.92 MB

english, 2015

2

Ligand-Gated Ion Channel Opening and Closing Mechanism from Molecular Simulations

Pouya, Iman, Pronk, Sander, Rotskoff, Grant, Kasson, Peter M., Lindahl, Erik

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 42 KB

english, 2013

3

Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation

Dama, James F., Rotskoff, Grant, Parrinello, Michele, Voth, Gregory A.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 954 KB

english, 2014

4

Efficiency and large deviations in time-asymmetric stochastic heat engines

Gingrich, Todd R, Rotskoff, Grant M, Vaikuntanathan, Suriyanarayanan, Geissler, Phillip L

Journal:

New Journal of Physics

Year:

2014

Language:

english

File:

PDF, 910 KB

english, 2014

5

Structural asymmetry in a conserved signaling system that regulates division, replication, and virulence of an intracellular pathogen

Willett, Jonathan W., Herrou, Julien, Briegel, Ariane, Rotskoff, Grant, Crosson, Sean

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.94 MB

english, 2015

6

Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation

Vaikuntanathan, Suriyanarayanan, Rotskoff, Grant, Hudson, Alexander, Geissler, Phillip L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.52 MB

english, 2016

7

Optimal control in nonequilibrium systems: Dynamic Riemannian geometry of the Ising model

Rotskoff, Grant M., Crooks, Gavin E.

Journal:

Physical Review E

Year:

2015

Language:

english

File:

PDF, 2.18 MB

english, 2015

8

Near-optimal protocols in complex nonequilibrium transformations

Gingrich, Todd R., Rotskoff, Grant M., Crooks, Gavin E., Geissler, Phillip L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.02 MB

english, 2016

9

On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water

Sosso, Gabriele Cesare, Caravati, Sebastiano, Rotskoff, Grant, Vaikuntanathan, Suriyanarayan, Hassanali, Ali

Journal:

Journal of Physical Chemistry A

Year:

2017

Language:

english

File:

PDF, 2.47 MB

english, 2017

10

Mapping current fluctuations of stochastic pumps to nonequilibrium steady states

Rotskoff, Grant M.

Journal:

Physical Review E

Year:

2017

Language:

english

File:

PDF, 301 KB

english, 2017

11

Inferring dissipation from current fluctuations

Gingrich, Todd R, Rotskoff, Grant M, Horowitz, Jordan M

Journal:

Journal of Physics A Mathematical and Theoretical

Year:

2017

Language:

english

File:

PDF, 2.33 MB

english, 2017

12

Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems

Rotskoff, Grant M., Crooks, Gavin E., Vanden-Eijnden, Eric

Journal:

Physical Review E

Year:

2017

Language:

english

File:

PDF, 480 KB

english, 2017

13

Robust nonequilibrium pathways to microcompartment assembly

Rotskoff, Grant M., Geissler, Phillip L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

14

Unraveling Kinetically-Driven Mechanisms of Gold Nanocrystal Shape Transformations Using Graphene Liquid Cell Electron Microscopy

Hauwiller, Matthew R., Frechette, Layne B., Jones, Matthew R., Ondry, Justin C., Rotskoff, Grant M., Geissler, Phillip, Alivisatos, A. Paul

Journal:

Year:

2018

Language:

english

File:

PDF, 2.35 MB

english, 2018