Between the scales: water from different perspectives

In der vorliegenden Arbeit werden verschiedene Wassermodelle in sogenannten Multiskalen-Computersimulationen mit zwei Auflösungen untersucht, in atomistischer Auflösung und in einer vergröberten Auflösung, die als "coarse-grained" bezeichnet wird. In der atomistischen Auflösung wird ein Wassermolekül, entsprechend seiner chemischen Struktur, durch drei Atome beschrieben, im Gegensatz dazu wird ein Molekül in der coarse-grained Auflösung durch eine Kugel dargestellt.rnrnDie coarse-grained Modelle, die in dieser Arbeit vorgestellt werden, werden mit verschiedenen coarse-graining Methoden entwickelt. Hierbei kommen hauptsächlich die "iterative Boltzmann Inversion" und die "iterative Monte Carlo Inversion" zum Einsatz. Beides sind struktur-basierte Ansätze, die darauf abzielen bestimmte strukturelle Eigenschaften, wie etwa die Paarverteilungsfunktionen, des zugrundeliegenden atomistischen Systems zu reproduzieren. Zur automatisierten Anwendung dieser Methoden wurde das Softwarepaket "Versatile Object-oriented Toolkit for Coarse-Graining Applications" (VOTCA) entwickelt.rnrnEs wird untersucht, in welchem Maße coarse-grained Modelle mehrere Eigenschaftenrndes zugrundeliegenden atomistischen Modells gleichzeitig reproduzieren können, z.B. thermodynamische Eigenschaften wie Druck und Kompressibilität oder strukturelle Eigenschaften, die nicht zur Modellbildung verwendet wurden, z.B. das tetraedrische Packungsverhalten, welches für viele spezielle Eigenschaft von Wasser verantwortlich ist.rnrnMit Hilfe des "Adaptive Resolution Schemes" werden beide Auflösungen in einer Simulation kombiniert. Dabei profitiert man von den Vorteilen beider Modelle:rnVon der detaillierten Darstellung eines räumlich kleinen Bereichs in atomistischer Auflösung und von der rechnerischen Effizienz des coarse-grained Modells, die den Bereich simulierbarer Zeit- und Längenskalen vergrössert.rnrnIn diesen Simulationen kann der Einfluss des Wasserstoffbrückenbindungsnetzwerks auf die Hydration von Fullerenen untersucht werden. Es zeigt sich, dass die Struktur der Wassermoleküle an der Oberfläche hauptsächlich von der Art der Wechselwirkung zwischen dem Fulleren und Wasser und weniger von dem Wasserstoffbrückenbindungsnetzwerk dominiert wird.rnWater is one of the most frequently studied fluids on earth. In this thesis, water was investigated at two resolutions using multi-scale computer simulation techniques. First, the atomistic and coarse-grained resolutions were studied separately. In the atomistic resolution, a~water molecule is described chemically by three atoms, while in the coarse-grained case, a~molecule is modeled by a~sphere.rnrnIn this work, various coarse-grained models have been developed using different coarse-graining techniques, mainly iterative Boltzmann inversion and iterative inverse Monte Carlo, which are structure-based approaches that aim to reproduce distributions, such as the pair distribution functions, of the atomistic model. In this context the Versatile Object-oriented Toolkit for Coarse-graining applications (VOTCA) was developed.rnrnIt was studied to which extent the coarse-grained models can simultaneously reproduce several properties of the underlying atomistic model, such as thermodynamic properties like pressure and compressibility or structural properties, which have not been used in the coarse-graining process, e.g. the tetrahedral packing behavior, which is responsible for many special properties of water.rnrnSubsequently, these two resolutions were combined using the adaptive resolution scheme, which combines the advantage of atomistic details in a~small cavity of high resolution with the computational efficiency of the coarse-grained model in order to access larger time and length scales. In this scheme, the introduced coarse-grained models were used to study the influence of the hydrogen bonds on the hydration of small fullerenes. It was found that the interface structure is more dependent on the nature of the interaction between the solute and water molecules than on the presence of the hydrogen bond network.r

Ligand-protein interactions in lysozyme investigated through a dual-resolution model

A fully atomistic modelling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and it a posteriori analysis. This difficulty can be overcome with the use of multi-resolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes, computationally expensive atomistic detail is crucial in the modelling of the active site in order to capture e.g. the chemically subtle process of ligand binding. In contrast, important yet more collective properties of the remainder of the protein can be reproduced with a coarser description. In the present work, we demonstrate the effectiveness of this approach through the calculation of the binding free energy of hen egg white lysozyme (HEWL) with the inhibitor di-N-acetylchitotriose. Particular attention is posed to the impact of the mapping, i.e. the selection of atomistic and coarse-grained residues, on the binding free energy. It is shown that, in spite of small variations of the binding free energy with respect to the active site resolution, the separate contributions coming from different energetic terms (such as electrostatic and van der Waals interactions) manifest a stronger dependence on the mapping, thus pointing to the existence of an optimal level of intermediate resolution

From Classical to Quantum and Back: Hamiltonian Adaptive Resolution Path Integral, Ring Polymer, and Centroid Molecular Dynamics

Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, such as ring polymer and centroid molecular dynamics, which allow the approximate calculation of both quantum statistical and quantum dynamical properties. To this end, we derive a new integration algorithm which also makes use of multiple time-stepping. The scheme is validated via adaptive classical--path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins

Zn二次電池負極におけるZn析出成長のマルチスケールシミュレーション及び実験的解析

早大学位記番号:新9147早稲田大

Uncoupling System and Environment Simulation Cells for Fast-Scaling Modeling of Complex Continuum Embeddings

Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all atomistic simulations. However, some challenges with the implementation of these models in plane-wave simulation packages still persists, especially when the goal is to simulate complex and heterogeneous environments. Among these challenges is the computational cost associated with large heterogeneous environments, which in plane-wave simulations has a direct effect on the basis-set size and, as a result, on the cost of the electronic structure calculation. Moreover, the use of periodic simulation cells are not well-suited for modeling systems embedded in semi-infinite media, which is often the case in continuum solvation models. To address these challenges, we present the implementation of a double-cell formalism, in which the simulation cell used for the continuum environment is uncoupled from the one used for the electronic-structure simulation of the quantum-mechanical system. This allows for a larger simulation cell to be used for the environment, without significantly increasing computational time. In this work, we show how the double-cell formalism can be used as an effective PBC correction scheme for non-periodic and partially periodic systems. The accuracy of the double-cell formalism is tested using representative examples with different dimensionalities, both in vacuum and in a continuum dielectric environment. Fast convergence and good speedups are observed for all the simulation setups, provided the quantum-mechanical simulation cell is chosen to completely fit the electronic density of the system