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  • 1.
    Delemotte, Lucie
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics.
    van Keulen, Siri
    Roethlisberger, Ursula
    Gianti, Eleonora
    Carnevale, Vincenzo
    Klein, Michael L.
    Does Proton Conduction in the Voltage-Gated Proton Channel hH(V)1 Involve Grotthus Hopping via Acidic Residues?2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 163A-164AArticle in journal (Other academic)
  • 2. Hilgen, Gerrit
    et al.
    Sorbaro, Martino
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics.
    Pirmoradian, Sahar
    Muthmann, Jens-Oliver
    Kepiro, Ibolya Edit
    Ullo, Simona
    Ramirez, Cesar Juarez
    Encinas, Albert Puente
    Maccione, Alessandro
    Berdondini, Luca
    Murino, Vittorio
    Sona, Diego
    Zanacchi, Francesca Cella
    Sernagor, Evelyne
    Hennig, Matthias Helge
    Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays2017In: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 18, no 10, p. 2521-2532Article in journal (Refereed)
    Abstract [en]

    We present amethod for automated spike sorting for recordings with high-density, large-scale multielectrode arrays. Exploiting the dense sampling of single neurons by multiple electrodes, an efficient, low-dimensional representation of detected spikes consisting of estimated spatial spike locations and dominant spike shape features is exploited for fast and reliable clustering into single units. Millions of events can be sorted in minutes, and the method is parallelized and scales better than quadratically with the number of detected spikes. Performance is demonstrated using recordings with a 4,096-channel array and validated using anatomical imaging, optogenetic stimulation, and model-based quality control. A comparison with semi-automated, shape-based spike sorting exposes significant limitations of conventional methods. Our approach demonstrates that it is feasible to reliably isolate the activity of up to thousands of neurons and that dense, multi-channel probes substantially aid reliable spike sorting.

  • 3. Kimanius, Dari
    et al.
    White, Stephen
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics. Stockholm University, Sweden.
    Kaback, Ronald
    Andersson, Magnus
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics.
    Uptake Dynamics in the LacY Membrane Protein Transporter2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 128A-128AArticle in journal (Other academic)
  • 4.
    Lindahl, Viveca
    et al.
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Villa, Alessandra
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sequence dependency of canonical base pair opening in the DNA double helix2017In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, no 4, article id e1005463Article in journal (Refereed)
    Abstract [en]

    The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.

  • 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. Razavi, Asghar M.
    et al.
    Delemotte, Lucie
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics.
    Berlin, Joshua R.
    Carnevale, Vincenzo
    Voelz, Vincent A.
    Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity2017In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 292, no 30, p. 12412-12423Article in journal (Refereed)
    Abstract [en]

    Na+/K+-ATPase transports Na+ and K+ ions across the cell membrane via an ion-binding site becoming alternatively accessible to the intra- and extracellular milieu by conformational transitions that confer marked changes in ion-binding stoichiometry and selectivity. To probe the mechanism of these changes, we used molecular simulation and free-energy perturbation approaches to identify probable protonation states of Na+- and K+-coordinating residues in E1P and E2P conformations of Na+/K+-ATPase. Analysis of these simulations revealed a molecular mechanism responsible for the change in protonation state: the conformation-dependent binding of an anion (a chloride ion in our simulations) to a previously unrecognized cytoplasmic site in the loop between transmembrane helices 8 and 9, which influences the electrostatic potential of the crucial Na+-coordinating residue Asp(926). This mechanistic model is consistent with experimental observations and provides a molecular-level picture of how E1P to E2P enzyme conformational transitions are coupled to changes in ion-binding stoichiometry and selectivity.

  • 7. Unat, Didem
    et al.
    Dubey, Anshu
    Hoefler, Torsten
    Shalf, John
    Abraham, Mark
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics.
    Bianco, Mauro
    Chamberlain, Bradford L.
    Cledat, Romain
    Edwards, H. Carter
    Finkel, Hal
    Fuerlinger, Karl
    Hannig, Frank
    Jeannot, Emmanuel
    Kamil, Amir
    Keasler, Jeff
    Kelly, Paul H. J.
    Leung, Vitus
    Ltaief, Hatem
    Maruyama, Naoya
    Newburn, Chris J.
    Pericas, Miquel
    Trends in Data Locality Abstractions for HPC Systems2017In: IEEE Transactions on Parallel and Distributed Systems, ISSN 1045-9219, E-ISSN 1558-2183, Vol. 28, no 10, p. 3007-3020Article in journal (Refereed)
    Abstract [en]

    The cost of data movement has always been an important concern in high performance computing (HPC) systems. It has now become the dominant factor in terms of both energy consumption and performance. Support for expression of data locality has been explored in the past, but those efforts have had only modest success in being adopted in HPC applications for various reasons. them However, with the increasing complexity of the memory hierarchy and higher parallelism in emerging HPC systems, locality management has acquired a new urgency. Developers can no longer limit themselves to low-level solutions and ignore the potential for productivity and performance portability obtained by using locality abstractions. Fortunately, the trend emerging in recent literature on the topic alleviates many of the concerns that got in the way of their adoption by application developers. Data locality abstractions are available in the forms of libraries, data structures, languages and runtime systems; a common theme is increasing productivity without sacrificing performance. This paper examines these trends and identifies commonalities that can combine various locality concepts to develop a comprehensive approach to expressing and managing data locality on future large-scale high-performance computing systems.

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