Publications List

This page collects relevant publications on some of the methods which have been used in the ExTASY project, as well as new work by the project team.

Project Outputs

  • Leimkuhler, B. and Matthews, C. (2016), "Efficient molecular dynamics using geodesic integration and solvent-solute splitting" Proceedings of the Royal Society A, 472 doi:10.1098/rspa.2016.0138
  • Balasubramanian, V., Bethune, I., Shkurti, A., Breitmoser, E., Hruska, E., Clementi, C., Laughton, C. and Jha, S. (2016), "ExTASY: Scalable and Flexible Coupling of MD Simulations and Advanced Sampling Techniques" arXiv:1606.00093
  • Santcroos, M., Castain, R., Merzky, A., Bethune, I. and Jha, S. (2016), "Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot" Cray User Group 2016, Online proceedings
  • Shkurti, A., Goni, R., Andrio, P., Breitmoser, E., Bethune, I., Orozco, M. and Laughton, C. (2016), "pyPcazip: a PCA-based Toolkit for Compression and Analysis of Molecular Simulation Data" SoftwareX. doi:10.1016/j.softx.2016.04.002
  • Balasubramanian, V., Treikalis, A., Weidner, O. and Jha, S. (2016), "Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks" arXiv:1602.00678
  • Bethune, I., Breitmoser, E., Collis, A.B.K., Gobbo, G. and Leimkuhler, B.J. (2015), "Interfacing novel integrators and existing Molecular Dynamics codes with the MIST library" Producing High Performance and Sustainable Software for Molecular Simulation Workshop, Supercomputing 2015. Preprint
  • Boninsegna, L., Gobbo, G., Noe, F. and Clementi, C. (2015), "Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps" Journal of Chemical Theory and Computation 11 (12). doi:10.1021/acs.jctc.5b00749
  • Gobbo, G and Leimkuhler, B. (2015), "Extended Hamiltonian approach to continuous tempering." Phys. Rev. E 91, 061301(R). doi:10.1103/PhysRevE.91.061301
  • Preto, J. and Clementi, C. (2014), "Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics" Physical Chemistry Chemical Physics 16. doi:10.1039/C3CP54520B


  • Zheng, W., Rohrdanz, M. A. and Clementi, C. (2013), "Rapid exploration of configuration space with diffusion-map-directed molecular dynamics", The Journal of Physical Chemistry B 117 (42). doi:10.1021/jp401911h
  • Laughton, C. A., Orozco, M. and Vranken, W. (2009), "COCO: A simple tool to enrich the representation of conformational variability in NMR structures." Proteins, 75: 206–216. doi:10.1002/prot.22235