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Daoulas K.C.,Max Planck Institute for Polymer Research | Daoulas K.C.,Heidelberg Innovation | Ruhle V.,Max Planck Institute for Polymer Research | Ruhle V.,University of Cambridge | Kremer K.,Max Planck Institute for Polymer Research
Journal of Physics Condensed Matter | Year: 2012

We develop a hybrid Monte Carlo approach for modelling nematic liquid crystals of homopolymer melts. The polymer architecture is described with a discrete worm-like chain model. A quadratic density functional accounts for the limited compressibility of the liquid, while an additional quadratic functional of the local orientation tensor of the segments captures the nematic ordering. The approach can efficiently address large systems parametrized according to volumetric and conformational properties, representative of real polymeric materials. The results of the simulations regarding the influence of the molecular weight on the isotropic-nematic transition are compared to predictions from a Landau-de Gennes free energy expansion. The formation of the nematic phase is addressed within Rouse-like dynamics, realized using the current model. © 2012 IOP Publishing Ltd. Source

Zhang G.,Max Planck Institute for Polymer Research | Moreira L.A.,Max Planck Institute for Polymer Research | Stuehn T.,Max Planck Institute for Polymer Research | Daoulas K.C.,Max Planck Institute for Polymer Research | And 2 more authors.
ACS Macro Letters | Year: 2014

A strategy is developed for generating equilibrated 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. © 2014 American Chemical Society. Source

Volkamer A.,Heidelberg Innovation | Rarey M.,University of Hamburg
Future Medicinal Chemistry | Year: 2014

The amount of known protein structures is continuously growing, exhibited in over 95,000 3D structures freely available via the PDB. Over the last decade, pharmaceutical research has sparked interest in computationally extracting information from this large data pool, resulting in a homology-driven knowledge transfer from annotated to new structures. Studying protein structures with respect to understanding and modulating their functional behavior means analyzing their centers of action. Therefore, the detection and description of potential binding sites on the protein surface is a major step towards protein classification and assessment. Subsequently, these representations can be incorporated to compare proteins, and to predict their druggability or function. Especially in the context of target identification and polypharmacology, automated tools for large-scale target comparisons are highly needed. In this article, developments for automated structure-based target assessment are reviewed and remaining challenges as well as future perspectives are discussed. © 2014 Future Science Ltd. Source

Muller M.,University of Gottingen | Daoulas K.Ch.,University of Gottingen | Daoulas K.Ch.,Max Planck Institute for Polymer Research | Daoulas K.Ch.,Heidelberg Innovation
Physical Review Letters | Year: 2011

The difficulty to study intrinsically slow collective processes by computer simulation of particle models stems from multiple disparate time scales (e.g., stiff bonded interactions versus soft nonbonded interactions). Continuum models, which describe the system by collective variables rather than the coordinates of the individual molecular constituents, often do not suffer from this time-scale problem because the stiff microscopic degrees of freedom have been integrated out. We propose to concurrently couple these two descriptions by a heterogeneous multiscale method. We illustrate the technique by studying the Lifshitz-Slyozov coarsening mechanism in a binary polymer blend using a soft coarse-grained particle model and a Landau-Ginzburg-de Gennes free energy functional, respectively. A speedup of up to two orders of magnitudes is achieved. © 2011 American Physical Society. Source

Daoulas K.C.,Max Planck Institute for Polymer Research | Daoulas K.C.,Heidelberg Innovation | Muller M.,University of Gottingen
Soft Matter | Year: 2013

The prospects of compressible Self-Consistent Field (SCF) theory schemes for describing structures in amphiphilic membranes are illustrated by considering the thermodynamic stability of hourglass-shaped, hydrophobic connections (stalks) between apposed bilayers. The membranes are represented by a coarse-grained, solvent-free model. We represent the chain architecture by a Gaussian-thread representation of the chain architecture and capture the non-bonded interactions with a functional, which is of third-order in the densities of the hydrophilic and the hydrophobic segments. Using a three dimensional real-space scheme, we study the thermodynamic stability of the stalk with respect to two planar apposing bilayers as a function of membrane tension and molecular asymmetry. The structure and thermodynamics predicted by SCF theory agree very well with particle-based simulations, which include fluctuations. We discuss how the longer-range perturbations of the membrane induced by the stalk can affect thermodynamic properties. This journal is © The Royal Society of Chemistry 2013. Source

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