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Project C4 (Completed): Coarse-graining frequency-dependent phenomena and memory in colloidal systems Electrostatic interactions can strongly influence the behavior of macromolecular systems. A particular challenge for their prediction is the accurate, albeit computationally tractable, handling of the influence of water dipoles on the potentials. To address this challenge, we develop an efficient and accurate numerical framework for nonlocal electrostatics of large molecular systems. An improved understanding of the influence of water structure on electrostatics has far-reaching applications: the results of the project can, in principle, be used wherever implicit water models are desired, but where a simple structureless continuum is insufficiently accurate. This project has ended in June 2018.

Project C5: Adaptive hybrid multiscale simulations of soft matter fluids We develop and analyse efficient, hybrid multiscale methods that bridge the continuum-particle gap by combining a discontinuous Galerkin method for the macroscopic model with molecular dynamics. In the second funding period we have focused on the description of non-Newtonian fluids, particularly polymer melts, in sim- ple and complex geometries as well as on theoretical convergence analysis of numerical schemes taking multiscale effects into account. Building on these results we will study the flow behaviour of polymer mixtures and develop methods to separate polymers with similar molecular masses based on differences in rheological properties (WP1). Applying a probabilistic concept of solutions, we will extend our convergence analysis to these non-Newtonian systems (WP3) and investigate effects of uncertainty with machine learning techniques (WP4). In the final funding period, we would also like to expand the scope of our project to a novel, […]

Project C6 (Completed): Linking hydrodynamics and microscopic models of wet active matter with anisotropic particles The goal of this project is to develop a systematic, quantitative coarse-graining approach for a class of inherently non-equilibrium systems, namely suspensions of self-propelled particles. We link particle based models with effective hydrodynamic models within a multiscale framework based on sequential coupling and parameter passing. To this end, we combine microscopic Stokesian dynamics simulations with a mesoscopic kinetic model coupled to the macroscopic Stokes equation, and, in a second step, derive an effective hydrodynamic description in terms of particle density, polarization and nematic order parameter profiles. The multiscale scheme is applied to systems of self-propelled rod-like magnetic colloids suspended in a fluid. This is motivated by recent experiments on magnetotactic bacteria, which have shown that the interplay of internal drive (self-propulsion, mutual interactions) and external drive (magnetic field, oxygen gradient) in these systems leads to […]

Project C7: Dense active suspensions in the chaotic regime Active matter has become a quickly evolving field spanning from biology and physics to chemistry and engineering. Its defining property is the directed motion—translational, rotational, or both—of its constituents. This directed motion requires the steady input of free energy. Freed from the constraints of thermal equilibrium, active matter exhibits a wide range of novel phenomena; on the level of its single constituents up to emergent many-body collective and dynamic behavior. Extensively studied have been the aggregation of active particles into clusters, swarms, and other highly collective and dynamics states; but also spontaneous flow states where sufficiently high activity triggers the transition from a quiescent to a flowing fluid. At high densities, chaotic behavior has been reported in suspensions of bacteria and in numerical simulations. The aim of this project is to develop a comprehensive multiscale framework that bridges the properties of […]

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 B2: Many-body effects and optimized mapping schemes for systematic coarse-graining The first goal of the B2 project is to provide the consortium with a platform for systematic coarse-graining via the open-source software package “Versatile Object-oriented Toolkit for Coarse-graining Applications” (VOTCA). Projects requiring swift parameterizations of coarse-grained models have already benefited from using this toolkit. The second goal is the development of coarse-grained potentials that capture more accurately many-body effects, by going beyond standard pair-wise interactions. To this end, we develop and test various coarse-graining strategies based on short-range three-body, local-density-dependent, and local-conformation-dependent potentials. Further, we devise optimized mapping schemes for coarse-grained representations using machine-learning techniques: In the previous funding period, we trained artificial neural networks for structural coarse-graining, and kernel-based methods to develop a general model for three-body potentials. Building upon our previous research, we will advance our coarse-graining strategies to better reproduce conformational details and dynamics, and also […]

Project B3: Coarse-graining of solvent effects in force-probe molecular dynamics simulations The study of the conformational kinetics of biomolecules and supramolecular complexes using molecular simulations often is complicated by the fact that these processes are very slow. Various simulation techniques have been developed in order to resolve this issue. One very efficient way to investigate the atomistic details of conformational changes is provided by force-probe molecular dynamics (FPMD) simulations. In the most common realization of this technique, one end of the (supra)molecular system under consideration is fixed in space and the other end is pulled apart with a constant velocity via the application of a harmonic potential. From the distributions of the forces needed to unfold the system important information regarding the kinetics and the thermodynamics of the relevant conformational rearrangements can be obtained via a statistical analysis. The direct comparison to the results of experimental realizations of force spectroscopy […]

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 B5: Multi-resolution methods including quantum chemistry, force fields, and hybrid particle-field schemes Multiscaling techniques that involve a quantum-chemical treatment of the electronic structure for the part with the highest resolution are promising computational tools. They are particularly useful for dealing with problems involving large systems like enzymes, membranes, polymers, etc., where, for example, chemical reactions take place. Having completed in the previous funding period of the TRR (i.e., the first funding period of this project) a corresponding QM/MM implementation that allows to include high-accuracy quantum-chemical methods from either coupled-cluster (CC) theory (i.e., CCSD, CCSD(T), etc.) or of multiconfigurational nature (i.e., CASSCF), we intend to complete the envisioned QM/MM/CG/hPF implementation that extends the QM/MM approach to coarse-grained (CG) treatments. In particular, we plan on using hybrid particle-field (hPF) theory based on its Hamiltonian reformulation, where the latter has been accomplished in the first funding period of this project. This reformulation […]