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      Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

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          Abstract

          We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV) 4 are used to examine peptide aggregation in different environments, in water, and at the water–octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.

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          Rapid planetesimal formation in turbulent circumstellar discs

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

            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.
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              Why do ultrasoft repulsive particles cluster and crystallize? Analytical results from density functional theory

              We demonstrate the accuracy of the hypernetted chain closure and of the mean-field approximation for the calculation of the fluid-state properties of systems interacting by means of bounded and positive-definite pair potentials with oscillating Fourier transforms. Subsequently, we prove the validity of a bilinear, random-phase density functional for arbitrary inhomogeneous phases of the same systems. On the basis of this functional, we calculate analytically the freezing parameters of the latter. We demonstrate explicitly that the stable crystals feature a lattice constant that is independent of density and whose value is dictated by the position of the negative minimum of the Fourier transform of the pair potential. This property is equivalent with the existence of clusters, whose population scales proportionally to the density. We establish that regardless of the form of the interaction potential and of the location on the freezing line, all cluster crystals have a universal Lindemann ratio L = 0.189 at freezing. We further make an explicit link between the aforementioned density functional and the harmonic theory of crystals. This allows us to establish an equivalence between the emergence of clusters and the existence of negative Fourier components of the interaction potential. Finally, we make a connection between the class of models at hand and the system of infinite-dimensional hard spheres, when the limits of interaction steepness and space dimension are both taken to infinity in a particularly described fashion.
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                Author and article information

                Journal
                J Chem Theory Comput
                J Chem Theory Comput
                ct
                jctcce
                Journal of Chemical Theory and Computation
                American Chemical Society
                1549-9618
                1549-9626
                26 March 2012
                08 May 2012
                : 8
                : 5
                : 1774-1785
                Affiliations
                []Department of Biological Sciences and Institute for Biocomplexity and Informatics, simpleUniversity of Calgary , Calgary, Alberta, Canada
                []Molecular Structure and Function, Hospital for Sick Children and Department of Biochemistry, simpleUniversity of Toronto , Toronto, Ontario, Canada
                Author notes
                Article
                10.1021/ct200876v
                3348680
                22582033
                Copyright © 2012 American Chemical Society

                This is an open-access article distributed under the ACS AuthorChoice Terms & Conditions. Any use of this article, must conform to the terms of that license which are available at http://pubs.acs.org.

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                ct200876v
                ct-2011-00876v

                Computational chemistry & Modeling

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