Kurt Kremer

Max Planck Institute for Polymer Research, Mayence, Rheinland-Pfalz, Germany

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Publications (271)797.3 Total impact

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    ABSTRACT: In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One of the main advantages of such approaches is the computational efficiency gained in the coarse-grained region. In this respect the best coarse-grained system to employ in the low resolution region would be the ideal gas, making intermolecular force calculations in the coarse-grained subdomain redundant. In this case, however, a smooth coupling is challenging due to the high energetic imbalance between typical liquids and a system of non-interacting particles. In the present work, we investigate this approach, using as a test case the most biologically relevant fluid, water. We demonstrate that a successful coupling of water to the ideal gas can be achieved with current adaptive resolution methods, and discuss the issues that remain to be addressed.
    12/2014;
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    ABSTRACT: This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated interactions, attraction between transmembrane proteins, and aggregation in biomembranes leading to large superstructures such as the light harvesting complex of green plants. After a general overview of theoretical considerations and continuum theory of lipid membranes we introduce different options for simulations of biomembrane systems, addressing questions such as: What can be learned from generic models? When is it expedient to go beyond them? And what are the merits and challenges for systematic coarse graining and quasi-atomistic coarse grained models that ensure a certain chemical specificity?
    12/2014;
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    ABSTRACT: Adaptive resolution schemes enable molecular dynamics simulations of liquids and soft matter employing two different resolution levels concurrently in the same setup. These methods are based on a position-dependent interpolation of either forces or potential energy functions. While force-based methods generally lead to non-conservative forces, energy-based ones include undesired force terms proportional to the gradient of the interpolation function. In this work we establish a so far missing bridge between these formalisms making use of the generalized Langevin equation, thereby providing a unifying framework to traditionally juxtaposed approaches to adaptive simulations.
    EPL (Europhysics Letters) 11/2014; 108(3):30007. · 2.27 Impact Factor
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    ABSTRACT: The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea (H-AdResS) allows one to formulate the usual tools of ensembles and statistical mechanics. We present a number of exact and approximate results that provide a statistical mechanics foundation for this simulation method. We also present simulation results that illustrate the theory.
    07/2014;
  • soon to be submitted. 07/2014;
  • in preparation. 07/2014;
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    ABSTRACT: Water and alcohol, such as methanol or ethanol, are miscible and, individually, good solvents for several smart polymers, but this polymer precipitates in water-alcohol mixtures. The intriguing behavior of solvent mixtures that cannot dissolve a given polymer or a given protein, while the same macromolecule dissolves well in each of the cosolvents, is called cononsolvency. It is a widespread phenomenon, relevant for many formulation steps in the physicochemical and pharmaceutical industry, that is usually explained by invoking specific chemical details of the mixtures: as such it has so far eluded any generic explanation. Here, by using a combination of simulations and theory, we present a simple and universal treatment that requires only the preferential interaction of one of the cosolvents with the polymer. The results show striking quantitative agreement with experiments and chemically specific simulations, opening a new perspective towards an operational understanding of macromolecular solubility.
    Nature Communications 07/2014; 5:xxxx. · 10.74 Impact Factor
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    ABSTRACT: A strategy is developed for generating equili-brated high molecular weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains features like hard excluded volume interactions and realistic melt densities. The microscopic representation is mapped onto a model of soft spheres with fluctuating size, where each sphere represents a microscopic subchain with Nb monomers. By varying Nb , a hierarchy of CG representations at different resolutions is obtained. Within this hierarchy, CG configurations equilibrated with Monte Carlo at low resolution are sequentially fine-grained into CG melts described with higher resolution. A Molecular Dynamics scheme is employed to slowly introduce the microscopic details into the latter. All backmapping steps involve only local polymer relaxation; thus, the computational efficiency of the scheme is independent of molecular weight, being just proportional to system size. To demonstrate the robustness of the approach, microscopic configurations containing up to n = 1000 chains with polymerization degrees N = 2000 are generated and equilibration is confirmed by monitoring key structural and conformational properties. The extension to much longer chains or branched polymers is straightforward.
    ACS Macro Lett. 01/2014; 3:198.
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    ABSTRACT: We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational findings in polymer physics related to concentrated, topologically simple (unknotted and unlinked) chains or a system of chains. Second, we review recent experimental discoveries related to genome folding. Understanding in these fields is far from complete, but we show how looking at them in parallel sheds new light on both.
    Reports on Progress in Physics 01/2014; 77(2):022601. · 13.23 Impact Factor
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    ABSTRACT: We outline a method to investigate the role of nuclear quantum effects in liquid water making use of a force field derived from ab initio simulations. Starting from a first-principles molecular dynamics simulation, we obtain an effective force field for bulk liquid water using the force-matching technique. After validating that our effective model reproduces the key structural and dynamic properties of the reference system, we use it to perform path integral simulations to investigate the role played by nuclear quantum effects on bulk water, probing radial distribution functions, vibrational spectra, and hydrogen bond fluctuations. Our approach offers a practical route to derive ab initio quality molecular models to study quantum effects at a low computational cost.
    Journal of Chemical Theory and Computation 01/2014; 10(2):816–824. · 5.39 Impact Factor
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    ABSTRACT: For the example of C60 solutes in toluene, we present the implementation of the adaptive resolutions scheme (AdResS) for molecular simulations into GROMACS. In AdResS a local, typically all-atom cavity is coupled to a surrounding of coarse-grained, simplified molecules. This methodology can not only be used to reduce the CPU time demand of atomistic simulations but also to systematically investigate the relative influence of different interactions on structure formation. For this, we vary the thickness of the all atom layer of toluene around the C60 and analyze the first toluene layers in comparison to a full bulk simulation.
    Journal of Chemical Theory and Computation 12/2013; 8(2):398. · 5.39 Impact Factor
  • The Journal of Chemical Physics 12/2013; 139(21):217102. · 3.12 Impact Factor
  • Debashish Mukherji, Kurt Kremer
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    ABSTRACT: Conformational transitions of (bio)macromolecules in aqueous mixtures are intimately linked to local concentration fluctuations of different solvent components. Though computer simulations are ideally suited to investigate such phenomena, in conventional setups the excess of one cosolvent close to the solute leads to depletion elsewhere, requiring very large simulations domain to avoid system size effects. We, here, propose an approach to overcome this depletion effect, which combines the Adaptive Resolution Scheme (AdResS) with a Metropolis particle exchange criterion. In AdResS, a small all-atom region, containing the solute, is coupled to a coarse-grained reservoir, where the particle exchange is performed. The particle exchange would be almost impossible had they been performed in an all-atom setup of a dense molecular liquid. We apply this approach to the reentrant collapse and swelling transition of poly(N-isopropylacrylamide) in aqueous methanol mixtures and demonstrate the role of the delicate interplay of the different intermolecular interactions.
    Macromolecules 11/2013; 46:9158. · 5.93 Impact Factor
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    ABSTRACT: We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water–water and water–ion interactions in the coarse-grained model are derived using structure-based coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced by our adaptive resolution method. Our multiscale approach, which is general and can be used for any classical non-polarizable force-field and/or types of ions, will significantly speed up biomolecular simulation involving aqueous salt.
    New Journal of Physics 10/2013; 15:105007. · 3.67 Impact Factor
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    ABSTRACT: Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The nonmatching properties of high- and low-resolution models, however, lead to thermodynamic imbalances between the system's subdomains. Such inhomogeneities can be healed by appropriate compensation forces, whose calculation requires nontrivial iterative procedures. In this work we employ the recently developed Hamiltonian adaptive resolution simulation method to perform Monte Carlo simulations of a binary mixture, and propose an efficient scheme, based on Kirkwood thermodynamic integration, to regulate the thermodynamic balance of multicomponent systems.
    Physical Review Letters 08/2013; 111(6):060601. · 7.73 Impact Factor
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    ABSTRACT: We develop a generic coarse-grained model for describing liquid crystalline ordering of polymeric semiconductors on mesoscopic scales, using poly(3-hexylthiophene) (P3HT) as a test system. The bonded interactions are obtained by Boltzmann-inverting the distributions of coarse-grained degrees of freedom resulting from a canonical sampling of an atomistic chain in Θ-solvent conditions. The nonbonded interactions are given by soft anisotropic potentials, representing the combined effects of anisotropic π–π interactions and entropic repulsion of side chains. We demonstrate that the model can describe uniaxial and biaxial nematic mesophases, reproduces the experimentally observed effect of molecular weight on phase behavior, and predicts Frank elastic constants typical for polymeric liquid crystals. We investigate charge transport properties of the biaxial nematic phase by analyzing the length distribution of conjugated segments and the internal energetic landscape for hole transport. Results show how conjugation defects tend to localize near chain ends and how long-range orientational correlations lead to a spatially correlated, non-Gaussian density of states.
    Macromolecules 07/2013; 46(14):5762–5774. · 5.93 Impact Factor
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    ABSTRACT: We investigate translocation mechanisms in smectic A liquid crystals (LCs) by a realistic, coarse-grained model of a LC compound comprising a stiff azobenzene core with flexible tails. We observe that the molecules can permeate from one smectic layer to the next via two different mechanisms, with and without significant reorientation, the former being facilitated through transverse interlayer intermediates. This is possible due to the intrinsic flexibility of the molecules. The two processes lead to characteristic signatures in the Van Hove self-correlation function, which can also be observed experimentally.
    Physical Review E 07/2013; 88(1-1):010502. · 2.31 Impact Factor
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    ABSTRACT: Binary blends of polystyrene with oligostyrene are perfectly miscible (χ=0) yet dynamically heterogeneous. This is evidenced by independent probing of the dipole relaxation perpendicular to the backbone by dielectric spectroscopy and molecular dynamics. The self-concentration model with a single intramolecular length scale qualitatively describes the slower segmental dynamics. A quantitative comparison based on MD, however, requires a composition-dependent length scale. The pertinent dynamic length scale that best describes the slow segmental dynamics in miscible blends relates to both intra- and intermolecular contributions.
    Physical Review Letters 04/2013; 110(16):165701. · 7.73 Impact Factor
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    ABSTRACT: The redesigned Extensible Simulation Package for Research on Soft matter systems (ESPResSo++) is a free, open-source, parallelized, object-oriented simulation package designed to perform many-particle simulations, principally molecular dynamics and Monte Carlo, of condensed soft matter systems. In addition to the standard simulation methods found in well-established packages, ESPResSo++ provides the ability to perform Adaptive Resolution Scheme (AdResS) simulations which are multiscale simulations of molecular systems where the level of resolution of each molecule can change on-the-fly. With the main design objective being extensibility, the software features a highly modular C++ kernel that is coupled to a Python user interface. This makes it easy to add new algorithms, setup a simulation, perform online analysis, use complex workflows and steer a simulation. The extreme flexibility of the software allows for the study of a wide range of systems. The modular structure enables scientists to use ESPResSo++ as a research platform for their own methodological developments, which at the same time allows the software to grow and acquire the most modern methods. ESPResSo++ is targeted for a broad range of architectures and is licensed under the GNU General Public License.
    Computer Physics Communications 04/2013; 184:1129-1149} publisher={Elsevier. · 2.41 Impact Factor
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    ABSTRACT: Adaptive resolution schemes allow the simulation of a molecular fluid treating simultaneously different subregions of the system at different levels of resolution. In this work we present a new scheme formulated in terms of a global Hamiltonian. Within this approach equilibrium states corresponding to well defined statistical ensembles can be generated making use of all standard Molecular Dynamics or Monte Carlo methods. Models at different resolutions can thus be coupled, and thermodynamic equilibrium can be modulated keeping each region at desired pressure or density without disrupting the Hamiltonian framework.
    Physical Review Letters 03/2013; 110(10):108301. · 7.73 Impact Factor

Publication Stats

8k Citations
797.30 Total Impact Points

Institutions

  • 1996–2014
    • Max Planck Institute for Polymer Research
      Mayence, Rheinland-Pfalz, Germany
  • 2011
    • National Institute of Chemistry
      Lubliano, Ljubljana, Slovenia
  • 2008–2010
    • Rice University
      • • Department of Chemical and Biomolecular Engineering
      • • Department of Chemistry
      Houston, TX, United States
  • 2009
    • CUNY Graduate Center
      New York City, New York, United States
  • 2008–2009
    • Universidad Autónoma de Madrid
      • Department of Condensed Matter Physics
      Madrid, Madrid, Spain
  • 2007–2008
    • Imperial College London
      • Department of Physics
      London, ENG, United Kingdom
    • Northeast Institute of Geography and Agroecology
      • State Key Laboratory of Polymer Physics and Chemistry
      Beijing, Beijing Shi, China
  • 1990–2007
    • Forschungszentrum Jülich
      Jülich, North Rhine-Westphalia, Germany
  • 2005
    • Max Planck Society
      München, Bavaria, Germany
  • 2000
    • University of New Mexico
      • Center for Micro-Engineered Materials
      Albuquerque, NM, United States
  • 1988–1998
    • Johannes Gutenberg-Universität Mainz
      • Institute of Physics
      Mainz, Rhineland-Palatinate, Germany