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Träfflista för sökning "WFRF:(Berk M.) ;pers:(Hess Berk)"

Sökning: WFRF:(Berk M.) > Hess Berk

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1.
  • Ghiringhelli, Luca M, et al. (författare)
  • Competing adsorption between hydrated peptides and water onto metal surfaces : from electronic to conformational properties
  • 2008
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 130:40, s. 13460-13464
  • Tidskriftsartikel (refereegranskat)abstract
    • Inorganic-(bio)organic interfaces are of central importance in many fields of current research. Theoretical and computational tools face the difficult problem of the different time and length scales that are involved and linked in a nontrivial way. In this work, a recently proposed hierarchical quantum-classical scale-bridging approach is further developed to study large flexible molecules. The approach is then applied to study the adsorption of oligopeptides on a hydrophilic Pt(111) surface under complete wetting conditions. We examine histidine sequences, which are well known for their binding affinity to metal surfaces. Based on a comparison with phenylalanine, which binds as strong as histidine under high vacuum conditions but, as we show, has no surface affinity under wet conditions, we illustrate the mediating effects of near-surface water molecules. These contribute significantly to the mechanism and strength of peptide binding. In addition to providing physical-chemical insights in the mechanism of surface binding, our computational approach provides future opportunities for surface-specific sequence design.
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2.
  • Kasson, Peter M., et al. (författare)
  • Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions
  • 2013
  • Ingår i: Chemistry and Physics of Lipids. - : Elsevier BV. - 0009-3084 .- 1873-2941. ; 169, s. 106-112
  • Tidskriftsartikel (refereegranskat)abstract
    • Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations.
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3.
  • Lundborg, M., et al. (författare)
  • The accelerated weight histogram method for alchemical free energy calculations
  • 2021
  • Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 154:20
  • Tidskriftsartikel (refereegranskat)abstract
    • The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.
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4.
  • Pronk, Sander, et al. (författare)
  • GROMACS 4.5 : a high-throughput and highly parallel open source molecular simulation toolkit
  • 2013
  • Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 29:7, s. 845-854
  • Tidskriftsartikel (refereegranskat)abstract
    • Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
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  • Resultat 1-5 av 5

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