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  • 1. Facey, Jody-Ann
    et al.
    Venner, Laura
    Hyde, Michael
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Howard, Rebecca
    Polar substitutions in the ion-conducting pore of GLIC alter gating and alcohol modulation2014In: The FASEB Journal, ISSN 0892-6638, E-ISSN 1530-6860, Vol. 28, no 1, p. 1061.9-Article in journal (Other academic)
  • 2. Heusser, Stephanie A.
    et al.
    Howard, Rebecca J.
    Pouya, Iman
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Klement, Göran
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Borghese, Cecilia
    Harris, R. Adron
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholms universitet.
    A Single Mutation in GLIC Reveals Both the Potentiating and the Inhibitory Nature of Propofol2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 3, p. 456A-456AArticle in journal (Other academic)
  • 3. Klement, Goran
    et al.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Yoluk, Özge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Howard, Rebecca
    Lindahl, Erik
    Ligand-Gated Ion Channel Gating Kinetics and the Opening/Closing Mechanism are Sensitive to Mutations Altering the Hydrophobicity of the Ion Conduction Pore2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 343A-343AArticle in journal (Other academic)
  • 4. Larsson, Per
    et al.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding2014In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 54, no 8-9, p. 1274-1285Article, review/survey (Refereed)
    Abstract [en]

    Simulations of biological macromolecules have evolved tremendously since the discoveries of the 1970s. The field has moved from simple simulations in vacuo on picosecond scales to milliseconds of accurate sampling of large proteins, and it has become a standard tool in biochemistry and biophysics, rather than a dedicated theoretical one. This is partly due to increasing computational power, but it would not have been possible without huge research efforts invested in new algorithms and software. Here, we illustrate some of this development, both past and future challenges, and in particular, discuss how the recent introduction of modern ensemble methods is breaking the trend of ever-longer simulations to instead focus on throughput and sampling. This has not only helped simulations become much more accurate, but it provides statistical error estimates, which are critical, as simulations are increasingly used to predict properties that have not yet been measured experimentally.

  • 5.
    Pouya, Iman
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pronk, Sander
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundborg, M.
    Lindahl, Erik R.
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling2017In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 71, p. 18-31Article in journal (Refereed)
    Abstract [en]

    Compute-intensive applications have gradually changed focus from massively parallel supercomputers to capacity as a resource obtained on-demand. This is particularly true for the large-scale adoption of cloud computing and MapReduce in industry, while it has been difficult for traditional high-performance computing (HPC) usage in scientific and engineering computing to exploit this type of resources. However, with the strong trend of increasing parallelism rather than faster processors, a growing number of applications target parallelism already on the algorithm level with loosely coupled approaches based on sampling and ensembles. While these cannot trivially be formulated as MapReduce, they are highly amenable to throughput computing. There are many general and powerful frameworks, but in particular for sampling-based algorithms in scientific computing there are some clear advantages from having a platform and scheduler that are highly aware of the underlying physical problem. Here, we present how these challenges are addressed with combinations of dataflow programming, peer-to-peer techniques and peer-to-peer networks in the Copernicus platform. This allows automation of sampling-focused workflows, task generation, dependency tracking, and not least distributing these to a diverse set of compute resources ranging from supercomputers to clouds and distributed computing (across firewalls and fragile networks). Workflows are defined from modules using existing programs, which makes them reusable without programming requirements. The system achieves resiliency by handling node failures transparently with minimal loss of computing time due to checkpointing, and a single server can manage hundreds of thousands of cores e.g. for computational chemistry applications.

  • 6.
    Pouya, Iman
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Pronk, Sander
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Rotskoff, Grant
    Kasson, Peter M.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Ligand-Gated Ion Channel Opening and Closing Mechanism from Molecular Simulations2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 271A-271AArticle in journal (Other academic)
  • 7.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Larsson, Per
    Stockholm University.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Bowman, Gregory
    Haque, Imran
    Beauchamp, Kyle
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Pande, Vijay
    Kasson, Peter
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Copernicus: A new paradigm for parallel adaptive molecular dynamics2011In: Proceedings of 2011 SC - International Conference for High Performance Computing, Networking, Storage and Analysis, 2011, p. 60-Conference paper (Refereed)
    Abstract [en]

    Biomolecular simulation is a core application on supercomputers, but it is exceptionally difficult to achieve the strong scaling necessary to reach biologically relevant timescales. Here, we present a new paradigm for parallel adaptive molecular dynamics and a publicly available implementation: Copernicus. This framework combines performance-leading molecular dynamics parallelized on three levels (SIMD, threads, and message-passing) with kinetic clustering, statistical model building and real-time result monitoring. Copernicus enables execution as single parallel jobs with automatic resource allocation. Even for a small protein such as villin (9,864 atoms), Copernicus exhibits near-linear strong scaling from 1 to 5,376 AMD cores. Starting from extended chains we observe structures 0.6 Å from the native state within 30h, and achieve sufficient sampling to predict the native state without a priori knowledge after 80-90h. To match Copernicus'efficiency, a classical simulation would have to exceed 50 microseconds per day, currently infeasible even with custom hardware designed for simulations.

  • 8.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundborg, Magnus
    Rotskoff, Grant
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wesén, Björn
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kasson, Peter M.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 6, p. 2600-2608Article in journal (Refereed)
    Abstract [en]

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide mote processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  • 9. Voigt, T. B.
    et al.
    Heusser, S.
    KTH.
    Klement, Göran
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Mola, A. R.
    Ruel, T. M. D.
    Trudell, J. R.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Howard, R. J.
    Physicochemical determinants of alcohol binding in a model ligand-gated ion channel2015In: Alcohol and Alcoholism, ISSN 0735-0414, E-ISSN 1464-3502, Vol. 50Article in journal (Other academic)
  • 10.
    Yoluk, Ozge
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Heusser, Stephanie
    Stockholm Univ, Biochem & Biophys, S-10691 Stockholm, Sweden..
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics.
    Howard, Rebecca
    Skidmore Coll, Chem, Saratoga Springs, Sweden..
    Klement, Göran
    Stockholm Univ, Biochem & Biophys, S-10691 Stockholm, Sweden..
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. Stockholm Univ, Biochem & Biophys, S-10691 Stockholm, SwedenStockholm Univ, Biochem & Biophys, S-10691 Stockholm, Sweden.
    Opening and Selectivity of the Glic Ligand-Gated Ion Channel can be Tuned by Mutation of Hydrophobic Residues in the Pore2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 431A-431AArticle in journal (Other academic)
1 - 10 of 10
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