Kurt Kremer

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

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Publications (294)926.01 Total impact

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    ABSTRACT: The correct interplay of interactions between protein, pigment and lipid molecules is highly relevant for our understanding of the association behavior of the light harvesting complex (LHCII) of green plants. To cover the relevant time and length scales in this multicomponent system, a multi-scale simulation ansatz is employed that subsequently uses a classical all atomistic (AA) model to derive a suitable coarse grained (CG) model which can be backmapped into the AA resolutions, aiming for a seamless conversion between two scales. Such an approach requires a faithful description of not only the protein and lipid components, but also the interaction functions for the indispensable pigment molecules, chlorophyll b and chlorophyll a (referred to as chl b/chl a). In this paper we develop a CG model for chl b and chl a in a dipalmitoylphosphatidyl choline (DPPC) bilayer system. The structural properties and the distribution behavior of chl within the lipid bilayer in the CG simulations are consistent with those of atomistic reference simulations. The non-bonded potentials are parameterized such that they fit to the thermodynamics based MARTINI force-field for the lipid bilayer and the protein. The CG simulation shows chl aggregation in the lipid bilayer which is supported by fluorescence quenching experiments. It is shown that the derived chl model is well suited for CG simulations of stable, structurally-consistent, trimeric LHCII and can in the future be used to study their large scale aggregation behavior.
    Physical Chemistry Chemical Physics 07/2015; DOI:10.1039/C5CP01140J · 4.20 Impact Factor
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    ABSTRACT: Mesoscale behavior of polymers is frequently described by universal laws. This physical property motivates us to propose a new modeling concept, grouping polymers into classes with a common long-wavelength representation. In the same class, samples of different materials can be generated from this representation, encoded in a single library system. We focus on homopolymer melts, grouped according to the invariant degree of polymerization. They are described with a bead-spring model, varying chain stiffness and density to mimic chemical diversity. In a renormalization group-like fashion, library samples provide a universal blob-based description, hierarchically backmapped to create configurations of other class-members. Thus, large systems with experimentally relevant invariant degree of polymerizations (so far accessible only on very coarse-grained level) can be microscopically described. Equilibration is verified comparing conformations and melt structure with smaller scale conventional simulations.
    The Journal of Chemical Physics 06/2015; 142(22):221102. DOI:10.1063/1.4922538 · 3.12 Impact Factor
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    ABSTRACT: Back Cover: Predicting the hierarchic structure and charge transport properties of polymeric semiconductors requires simulation techniques that describe mesoscale order while preserving atomistic details. Shown is the hierarchy of coarse-grained models-from plate-based to atomistic-used for predictions and sequential refinement of large-scale morphologies. Further details can be found in the article by P. Gemünden, C. Poelking, K. Kremer,* K. Daoulas,* and D. Andrienko* on page 1047. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Macromolecular Rapid Communications 06/2015; 36(11). DOI:10.1002/marc.201570046 · 4.61 Impact Factor
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    ABSTRACT: Topological constraints due to chain connectivity and uncrossability greatly impact the long time dynamics and rheology of high molecular weight polymer melts. Computer simulations to study properties of such melts are very advantageous, since perfect control of molecular conformation and melt morphology is available. We present a methodology to prepare well-equilibrated polymer melts which only requires local relaxation. The approach efficiently leads to equilibrated ensembles of bead-spring polymer melts of 1 000 chains of up to 2 000 beads, which correspond to 24 (fully flexible) and 45 entanglement lengths (semi-flexible chains). Entanglements are identified by a primitive path analysis and a master curve of the entanglement lengths for different chain and persistence lengths is presented.
    Macromolecular Theory and Simulations 06/2015; DOI:10.1002/mats.201500013 · 1.79 Impact Factor
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    ABSTRACT: A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.
    The Journal of Chemical Physics 05/2015; 142(19):195101. DOI:10.1063/1.4921347 · 3.12 Impact Factor
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    ABSTRACT: In computer simulations, quantum delocalization of atomic nuclei can be modeled making use of the Path Integral (PI) formulation of quantum statistical mechanics. This approach, however, comes with a large computational cost. By restricting the PI modeling to a small region of space, this cost can be significantly reduced. In the present work we derive a Hamiltonian formulation for a bottom-up, theoretically solid simulation protocol that allows molecules to change their resolution from quantum-mechanical to classical and vice versa on the fly, while freely diffusing across the system. This approach renders possible simulations of quantum systems at constant chemical potential. The validity of the proposed scheme is demonstrated by means of simulations of low temperature parahydrogen. Potential future applications include simulations of biomolecules, membranes, and interfaces.
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    ABSTRACT: Crystallisation of liquid solutions is of uttermost importance in a wide variety of processes in materials, atmospheric and food science. Depending on the type and concentration of solutes the freezing point shifts, thus allowing control on the thermodynamics of complex fluids. Here we investigate the basic principles of solute-induced freezing point depression by computing the melting temperature of a Lennard-Jones fluid with low concentrations of solutes, by means of equilibrium molecular dynamics simulations. The effect of solvophilic and weakly solvophobic solutes at low concentrations is analysed, scanning systematically the size and the concentration. We identify the range of parameters that produce deviations from the linear dependence of the freezing point on the molal concentration of solutes, expected for ideal solutions. Our simulations allow us also to link the shifts in coexistence temperature to the microscopic structure of the solutions.
    Molecular Physics 04/2015; DOI:10.1080/00268976.2015.1029029 · 1.64 Impact Factor
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    ABSTRACT: A multiscale simulation scheme, which incorporates both long-range conformational disorder and local molecular ordering, is proposed for predicting large-scale morphologies and charge transport properties of polymeric semiconductors. Using poly(3-hexylthiophene) as an example, it is illustrated how the energy landscape and its spatial correlations evolve with increasing degree of structural order in mesophases with amorphous, uniaxial, and biaxial nematic ordering. It is shown that the formation of low-lying energy states in more ordered systems is mostly due to larger (on average) conjugation lengths and not due to electrostatic interactions. The proposed scheme is general and can be applied to a wide range of polymeric organic materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Macromolecular Rapid Communications 03/2015; 36(11). DOI:10.1002/marc.201400725 · 4.61 Impact Factor
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    ABSTRACT: Smart polymers are a modern class of polymeric materials that often exhibit unpredictable behavior in mixtures of solvents. One such phenomenon is co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and competing good solvents, for a given polymer, are mixed together. As a result, the same polymer collapses into a compact globule within intermediate mixing ratios. More interestingly, polymer collapses when the solvent quality remains good and even gets increasingly better by the addition of the better cosolvent. This is a puzzling phenomenon that is driven by strong local concentration fluctuations. Because of the discrete particle based nature of the interactions, Flory-Huggins type mean field arguments become unsuitable. In this work, we extend the analysis of the co-non-solvency effect presented earlier [Nature Communications 5, 4882 (2014)]. We explain why co-non-solvency is a generic phenomenon that can be understood by the thermodynamic treatment of the competitive displacement of (co)solvent components. This competition can result in a polymer collapse upon improvement of the solvent quality. Specific chemical details are not required to understand these complex conformational transitions. Therefore, a broad range of polymers are expected to exhibit similar reentrant coil-globule-coil transitions in competing good solvents.
    The Journal of Chemical Physics 02/2015; 142(11). DOI:10.1063/1.4914870 · 3.12 Impact Factor
  • Soft Matter 01/2015; DOI:10.1039/C5SM01772F · 4.15 Impact Factor
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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.
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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?
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    ABSTRACT: Atomistic molecular dynamics simulations of a chemically realistic model of atactic short-chain polystyrene between gold surfaces (111) and positron annihilation lifetime spectroscopy experiments on similar polystyrene thin films on gold were performed. Results from both approaches show that the free volume voids in the film have a slightly smaller average size than in bulk polystyrene. In agreement to that the existence of an interphase of higher density at the polymer–solid substrate interface is shown both by the simulation as well as in the experiment. The average shape of the voids is similar in the bulk and the film.
    Macromolecules 12/2014; 47(23):8459-8465. DOI:10.1021/ma501747j · 5.93 Impact Factor
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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. DOI:10.1209/0295-5075/108/30007 · 2.27 Impact Factor
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    ABSTRACT: In the last few decades, computer simulations have become a fundamental tool in the field of soft matter science, allowing researchers to investigate the properties of a large variety of systems. Nonetheless, even the most powerful computational resources presently available are, in general, sufficient to simulate complex biomolecules only for a few nanoseconds. This limitation is often circumvented by using coarse-grained models, in which only a subset of the system's degrees of freedom is retained; for an effective and insightful use of these simplified models; however, an appropriate parametrization of the interactions is of fundamental importance. Additionally, in many cases the removal of fine-grained details in a specific, small region of the system would destroy relevant features; such cases can be treated using dual-resolution simulation methods, where a subregion of the system is described with high resolution, and a coarse-grained representation is employed in the rest of the simulation domain. In this review we discuss the basic notions of coarse-graining theory, presenting the most common methodologies employed to build low-resolution descriptions of a system and putting particular emphasis on their similarities and differences. The AdResS and H-AdResS adaptive resolution simulation schemes are reported as examples of dual-resolution approaches, especially focusing in particular on their theoretical background.
    Entropy 08/2014; 16(8):4199-4245. DOI:10.3390/e16084199 · 1.56 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.
    The Journal of Chemical Physics 07/2014; 142(6). DOI:10.1063/1.4907006 · 3.12 Impact Factor
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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. DOI:10.1038/ncomms5882 · 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 Letters 01/2014; 3(2):198. DOI:10.1021/mz5000015 · 5.24 Impact Factor

Publication Stats

12k Citations
926.01 Total Impact Points

Institutions

  • 1996–2015
    • Max Planck Institute for Polymer Research
      Mayence, Rheinland-Pfalz, Germany
  • 2011
    • Carnegie Mellon University
      • Department of Chemistry
      Pittsburgh, Pennsylvania, United States
  • 2009
    • Technical University Darmstadt
      • Center of Smart Interfaces (CSI)
      Darmstadt, Hesse, Germany
    • CUNY Graduate Center
      New York City, New York, United States
  • 2007
    • Ruhr-Universität Bochum
      • Theoretical Chemistry
      Bochum, North Rhine-Westphalia, Germany
    • Rice University
      • Department of Chemistry
      Houston, Texas, United States
  • 1990–2007
    • Forschungszentrum Jülich
      Jülich, North Rhine-Westphalia, Germany
  • 1995
    • University of California, Santa Barbara
      Santa Barbara, California, United States
  • 1991
    • Forschungsinstitut Futtermitteltechik der IFF
      Brunswyck, Lower Saxony, Germany
  • 1987–1991
    • Johannes Gutenberg-Universität Mainz
      • Institute of Physics
      Mayence, Rheinland-Pfalz, Germany
  • 1981
    • University of Cologne
      • Institute for Theoretical Physics
      Köln, North Rhine-Westphalia, Germany