Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach which is a combination of an heterogeneity sensitive spatial domain decomposition with an \textit{a priori} rearrangement of subdomain-walls. Within this approach, the theoretical modeling and scaling-laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid.Comment: 14 pages, 12 figure

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

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

Atmospheric characterization of Proxima b by coupling the Sphere high-contrast imager to the Espresso spectrograph

Context. The temperate Earth-mass planet Proxima b is the closest exoplanet to Earth and represents what may be our best ever opportunity to search for life outside the Solar System. Aims. We aim at directly detecting Proxima b and characterizing its atmosphere by spatially resolving the planet and obtaining high-resolution reflected-light spectra. Methods. We propose to develop a coupling interface between the SPHERE high-contrast imager and the new ESPRESSO spectrograph, both installed at ESO VLT. The angular separation of 37 mas between Proxima b and its host star requires the use of visible wavelengths to spatially resolve the planet on a 8.2-m telescope. At an estimated planet-to-star contrast of ~10^-7 in reflected light, Proxima b is extremely challenging to detect with SPHERE alone. However, the combination of a ~10^3-10^4 contrast enhancement from SPHERE to the high spectral resolution of ESPRESSO can reveal the planetary spectral features and disentangle them from the stellar ones. Results. We find that significant but realistic upgrades to SPHERE and ESPRESSO would enable a 5-sigma detection of the planet and yield a measurement of its true mass and albedo in 20-40 nights of telescope time, assuming an Earth-like atmospheric composition. Moreover, it will be possible to probe the O2 bands at 627, 686 and 760 nm, the water vapour band at 717 nm, and the methane band at 715 nm. In particular, a 3.6-sigma detection of O2 could be made in about 60 nights of telescope time. Those would need to be spread over 3 years considering optimal observability conditions for the planet. Conclusions. The very existence of Proxima b and the SPHERE-ESPRESSO synergy represent a unique opportunity to detect biosignatures on an exoplanet in the near future. It is also a crucial pathfinder experiment for the development of Extremely Large Telescopes and their instruments (abridged).Comment: 16 pages, 7 figures, revised version accepted to A&

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions

Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations

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