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Project C8: Numerical approximation of high-dimensional Fokker-Planck equations Stochastic processes driven by Brownian motion, which play a fundamental role in soft matter physics, can also be described by associated deterministic Fokker-Planck equations for probability distributions, where the dimensionality of the space on which this equation is posed increases linearly with respect to the number of particles. The aim of this project is to develop numerical solution methods for such high-dimensional problems that allow for the efficient extraction of quantities of interest, which typically take the form of certain integrals with respect to the computed distributions. In the high-dimensional case, beyond the basic numerical feasibility, a central issue is to ensure the accuracy of the computed solutions by suitable a posteriori error control. The initial focus of the project, which started during the second funding period, was on the development of numerical methods. On the one hand, we considered adaptive low-rank […]

Project G: Central soft matter simulation platform The goals of project G in the second funding phase of the TRR 146 have been the implementation of new methods of general interest into the molecular dynamics simulation environment ESPResSo++ Guzman et al. (2019), which can be used as foundation for research projects inside the TRR 146, and the optimization of ESPResSo++ to efficiently use modern HPC resources and therefore to become performance competitive with state-of-the-art MD environments like LAMMPS. Project G has been successful integrating new simulation methods by coupling ESPResSo++ with the ScaFaCos library Hofmann et al. (2018), Arnold et al. (2013) to provide fast parallelized long-range interaction algorithm (e.g. P3M / multipolar P3M), developing and implementing a new approach for Lees-Edwards boundary conditions to provide a fast parallel implementation of shear boundary conditions. The performance optimization of the ESPResSo++ environment included to change the memory layout to benefit from […]

Project B4: Equilibrium and non-equilibrium processes in open systems via adaptive resolution simulations Computational soft matter constitutes a major application area for simulations, with extraordinary conceptual and practical relevance. Due to the systems’ intrinsic complexity, a considerable effort in this area has focused on investigating somewhat idealised models, e.g., consisting of a few essential molecular species in explicit or implicit solvent. In reality, even the simplest experimentally relevant systems, such as (bio)macromolecules in aqueous mixtures and nanochannels, are far more complex, involving many interacting species, evolving under open-boundary and non-equilibrium conditions. Increasing the complexity and detail of the computational model for these systems poses a significant challenge. Indeed, the interplay of interactions and processes spanning a wide range of length and time scales requires a multiscale approach, including methods resolving quantum, classical, coarse-grained and continuum degrees of resolution. However, it is often the case that a high-resolution method is only […]

Project A7: Dynamical coarse-graining for non-equilibrium steady states with stochastic dynamics Preserving dynamic information such as diffusion coefficients and transition rates in coarse-grained models is a persistent challenge in multi-scale simulations. This task becomes even more daunting when the original microscopic dynamics breaks detailed balance, corresponding to the system being driven away from thermal equilibrium. The aim of this project is to develop a comprehensive computational method to coarse-grain models from atomistic resolution to a few discrete states while preserving the statistics of the energetic exchange with their environment. In complex macro and biomolecules, these discrete states are identified with long-lived molecular conformations. In the second funding period, we are addressing the question how to model transitions that go beyond simple conformational transitions and involve a chemical transformation. To this end, we study a molecular rotor that is driven by light and performs asymmetric photoisomerization steps to achieve directional rotation. […]

Project A8: Roberto – Improved dynamics in hybrid particle-field molecular dynamics simulations of polymers We pursue one of the approaches to generate coarse-grained polymer models with correct dynamical properties. If such models can be made predictive for, say, polymer melt viscosities and other rheological characteristics they will make their important contribution toward, e.g., energy-efficient plastics processing or mechanical recycling of plastics waste. In funding period 2 (FP2), we have developed and implemented the Roberto method, a combination of hybrid-particle-field (hPF) molecular dynamics and slip-springs. The hPF method by itself is computationally fast, yet it allows coarse-grained or even atomistic accuracy for the base models. It performs excellent for static polymer properties, but provides a qualitatively wrong molecular mobility. As the field treatment of intermolecular interactions makes them effectively soft-core, atoms can superpose, and polymer chains can cut through one another. The artificial dynamics is remedied by the slip-springs, which restore […]