For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
21
views
40
references
 Top references
cited by
17
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      224
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: not found

      Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.

          Related collections

          Most cited references40

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Rapid planetesimal formation in turbulent circumstellar discs

          Anders Johansen, Jeffrey S. Oishi, Mordecai-Mark Mac Low … (2007)
          The initial stages of planet formation in circumstellar gas discs proceed via dust grains that collide and build up larger and larger bodies (Safronov 1969). How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem (Dominik et al. 2007): boulders stick together poorly (Benz 2000), and spiral into the protostar in a few hundred orbits due to a head wind from the slower rotating gas (Weidenschilling 1977). Gravitational collapse of the solid component has been suggested to overcome this barrier (Safronov 1969, Goldreich & Ward 1973, Youdin & Shu 2002). Even low levels of turbulence, however, inhibit sedimentation of solids to a sufficiently dense midplane layer (Weidenschilling & Cuzzi 1993, Dominik et al. 2007), but turbulence must be present to explain observed gas accretion in protostellar discs (Hartmann 1998). Here we report the discovery of efficient gravitational collapse of boulders in locally overdense regions in the midplane. The boulders concentrate initially in transient high pressures in the turbulent gas (Johansen, Klahr, & Henning 2006), and these concentrations are augmented a further order of magnitude by a streaming instability (Youdin & Goodman 2005, Johansen, Henning, & Klahr 2006, Johansen & Youdin 2007) driven by the relative flow of gas and solids. We find that gravitationally bound clusters form with masses comparable to dwarf planets and containing a distribution of boulder sizes. Gravitational collapse happens much faster than radial drift, offering a possible path to planetesimal formation in accreting circumstellar discs.
          Article 0 comments Cited 2503 times – based on 0 reviews
          Preprint
               Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            The Dicke Quantum Phase Transition with a Superfluid Gas in an Optical Cavity

            Ferdinand Brennecke, Tilman Esslinger, Christine Guerlin … (2009)
            A phase transition describes the sudden change of state in a physical system, such as the transition between a fluid and a solid. Quantum gases provide the opportunity to establish a direct link between experiment and generic models which capture the underlying physics. A fundamental concept to describe the collective matter-light interaction is the Dicke model which has been predicted to show an intriguing quantum phase transition. Here we realize the Dicke quantum phase transition in an open system formed by a Bose-Einstein condensate coupled to an optical cavity, and observe the emergence of a self-organized supersolid phase. The phase transition is driven by infinitely long-ranged interactions between the condensed atoms. These are induced by two-photon processes involving the cavity mode and a pump field. We show that the phase transition is described by the Dicke Hamiltonian, including counter-rotating coupling terms, and that the supersolid phase is associated with a spontaneously broken spatial symmetry. The boundary of the phase transition is mapped out in quantitative agreement with the Dicke model. The work opens the field of quantum gases with long-ranged interactions, and provides access to novel quantum phases.
            Article 0 comments Cited 1675 times – based on 0 reviews
            Preprint
                 Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Versatile Photocatalytic Systems for H2 Generation in Water Based on an Efficient DuBois-Type Nickel Catalyst

              Manuela Groß, Anna Reynal, James R. Durrant … (2013)
              The generation of renewable H2 through an efficient photochemical route requires photoinduced electron transfer (ET) from a light harvester to an efficient electrocatalyst in water. Here, we report on a molecular H2 evolution catalyst (NiP) with a DuBois-type [Ni(P2 R′N2 R″)2]2+ core (P2 R′N2 R″ = bis(1,5-R′-diphospha-3,7-R″-diazacyclooctane), which contains an outer coordination sphere with phosphonic acid groups. The latter functionality allows for good solubility in water and immobilization on metal oxide semiconductors. Electrochemical studies confirm that NiP is a highly active electrocatalyst in aqueous electrolyte solution (overpotential of approximately 200 mV at pH 4.5 with a Faradaic yield of 85 ± 4%). Photocatalytic experiments and investigations on the ET kinetics were carried out in combination with a phosphonated Ru(II) tris(bipyridine) dye (RuP) in homogeneous and heterogeneous environments. Time-resolved luminescence and transient absorption spectroscopy studies confirmed that directed ET from RuP to NiP occurs efficiently in all systems on the nano- to microsecond time scale, through three distinct routes: reductive quenching of RuP in solution or on the surface of ZrO2 (“on particle” system) or oxidative quenching of RuP when the compounds were immobilized on TiO2 (“through particle” system). Our studies show that NiP can be used in a purely aqueous solution and on a semiconductor surface with a high degree of versatility. A high TOF of 460 ± 60 h–1 with a TON of 723 ± 171 for photocatalytic H2 generation with a molecular Ni catalyst in water and a photon-to-H2 quantum yield of approximately 10% were achieved for the homogeneous system.
              Article 0 comments Cited 448 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): J Chem Theory Comput
                Journal ID (iso-abbrev): J Chem Theory Comput
                Journal ID (publisher-id): ct
                Journal ID (coden): jctcce
                Title: Journal of Chemical Theory and Computation
                Publisher: American Chemical Society
                ISSN (Print): 1549-9618
                ISSN (Electronic): 1549-9626
                Publication date (Electronic): 13 January 2015
                Publication date (Print): 10 February 2015
                Volume: 11
                Issue: 2
                Pages: 780-787
                Affiliations
                [† ]Department of Chemistry and Molecular Biology, University of Gothenburg , SE-405 30 Gothenburg, Sweden
                [‡ ]Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , SE-751 05 Uppsala, Sweden
                Author notes
                [* ]E-mail: spoel@ 123456xray.bmc.uu.se (D. van der Spoel).
                [* ]E-mail: westenho@ 123456chem.gu.se (S. Westenhoff).
                Article
                DOI: 10.1021/ct5009735
                PMC ID: 4325560
                PubMed ID: 25688181
                SO-VID: 1a142aa6-aa51-47d7-bada-35cf93565f46
                Copyright © Copyright © 2015 American Chemical Society
                License:

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                History
                Date received : 31 October 2014
                Categories
                Subject: Article
                Custom metadata
                document-id-old-9 ct5009735
                document-id-new-14 ct-2014-009735
                ccc-price

                ScienceOpen disciplines: Computational chemistry & Modeling
                Data availability:
                ScienceOpen disciplines: Computational chemistry & Modeling

                Comments

                Comment on this article

                scite_

                Similar content224

                See all similar

                Cited by17

                See all cited by