Interactive Visualization of Molecular Dynamics Simulation Data

Molecular Dynamics Simulations (MD) plays an essential role in the field of computational biology. The simulations produce extensive high-dimensional, spatio-temporal data describ-ing the motion of atoms and molecules. A central challenge in the field is the extraction and visualization of useful behavioral patterns from these simulations. Throughout this thesis, I collaborated with a computational biologist who works on Molecular Dynamics (MD) Simu-lation data. For the sake of exploration, I was provided with a large and complex membrane simulation. I contributed solutions to his data challenges by developing a set of novel visual-ization tools to help him get a better understanding of his simulation data. I employed both scientific and information visualization, and applied concepts of abstraction and dimensions projection in the proposed solutions. The first solution enables the user to interactively fil-ter and highlight dynamic and complex trajectory constituted by motions of molecules. The molecular dynamic trajectories are identified based on path length, edge length, curvature, and normalized curvature, and their combinations. The tool exploits new interactive visual-ization techniques and provides a combination of 2D-3D path rendering in a dual dimension representation to highlight differences arising from the 2D projection on a plane. The sec-ond solution introduces a novel abstract interaction space for Protein-Lipid interaction. The proposed solution addresses the challenge of visualizing complex, time-dependent interactions between protein and lipid molecules. It also proposes a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. I also introduced two abstract level-of-detail (LoD) representations with six levels of detail for lipid molecules and protein interaction. Finally, I proposed a novel framework consisting of four linked views: A time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. The framework exploits abstraction and projection to enable the user to study the molecular interaction and the behavior of the protein-protein interaction and clusters. I introduced a selection of visual designs to convey the behavior of protein-lipid interaction and protein-protein interaction through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, and a projected tiled space is used to present both Protein-Lipid Interaction (PLI) and Protein-Protein Interaction (PPI) at the particle level in a heat-map style visual design. Glyphs are used to represent PPI at the molecular level. I coupled visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately, or together in a unified visual analysis framework

Pre-engineering Spaceflight Validation of Environmental Models and the 2005 HZETRN Simulation Code

The HZETRN code has been identified by NASA for engineering design in the next phase of space exploration highlighting a return to the Moon in preparation for a Mars mission. In response, a new series of algorithms beginning with 2005 HZETRN, will be issued by correcting some prior limitations and improving control of propagated errors along with established code verification processes. Code validation processes will use new/improved low Earth orbit (LEO) environmental models with a recently improved International Space Station (ISS) shield model to validate computational models and procedures using measured data aboard ISS. These validated models will provide a basis for flight-testing the designs of future space vehicles and systems of the Constellation program in the LEO environment

The effect of interplanetary trajectory options on a manned Mars aerobrake configuration

Manned Mars missions originating in low Earth orbit (LEO) in the time frame 2010 to 2025 were analyzed to identify preferred mission opportunities and their associated vehicle and trajectory characteristics. Interplanetary and Mars atmospheric trajectory options were examined under the constraints of an initial manned exploration scenario. Two chemically propelled vehicle options were considered: (1) an all propulsive configuration, and (2) a configuration which employs aerobraking at Earth and Mars with low lift/drag (L/D) shapes. Both the interplanetary trajectory options as well as the Mars atmospheric passage are addressed to provide a coupled trajectory simulation. Direct and Venus swingby interplanetary transfers with a 60 day Mars stopover are considered. The range and variation in both Earth and Mars entry velocity are also defined. Two promising mission strategies emerged from the study: (1) a 1.0 to 2.0 year Venus swingby mission, and (2) a 2.0 to 2.5 year direct mission. Through careful trajectory selection, 11 mission opportunities are identified in which the Mars entry velocity is between 6 and 10 km/sec and Earth entry velocity ranges from 11.5 to 12.5 km/sec. Simulation of the Earth return aerobraking maneuver is not performed. It is shown that a low L/D configuration is not feasible for Mars aerobraking without substantial improvements in the interplanetary navigation system. However, even with an advanced navigation system, entry corridor and aerothermal requirements restrict the number of potential mission opportunities. It is also shown that for a large blunt Mars aerobrake configuration, the effects of radiative heating can be significant at entry velocities as low as 6.2 km/sec and will grow to dominate the aerothermal environment at entry velocities above 8.5 km/sec. Despite the additional system complexity associated with an aerobraking vehicle, the use of aerobraking was shown to significantly lower the required initial LEO weight. In comparison with an all propulsive mission, savings between 19 and 59 percent were obtained depending upon launch date

Research Report 2011

Introduction From the Chairperson Atomic and Molecular Physics Condensed Matter Physics Nuclear Physics Physics Education Research and Public Lectures at WMU Personnel January 1- December 31, 201

Spectral Analysis of the Chandra Comet Survey

We present results of the analysis of cometary X-ray spectra with an extended version of our charge exchange emission model (Bodewits et al. 2006). We have applied this model to the sample of 8 comets thus far observed with the Chandra X-ray observatory and ACIS spectrometer in the 300-1000 eV range. The surveyed comets are C/1999 S4 (LINEAR), C/1999 T1 (McNaught-Hartley), C/2000 WM1 (LINEAR), 153P/2002 (Ikeya-Zhang), 2P/2003 (Encke), C/2001 Q4 (NEAT), 9P/2005 (Tempel 1) and 73P/2006-B (Schwassmann-Wachmann 3) and the observations include a broad variety of comets, solar wind environments and observational conditions. The interaction model is based on state selective, velocity dependent charge exchange cross sections and is used to explore how cometary X-ray emission depend on cometary, observational and solar wind characteristics. It is further demonstrated that cometary X-ray spectra mainly reflect the state of the local solar wind. The current sample of Chandra observations was fit using the constrains of the charge exchange model, and relative solar wind abundances were derived from the X-ray spectra. Our analysis showed that spectral differences can be ascribed to different solar wind states, as such identifying comets interacting with (I) fast, cold wind, (II), slow, warm wind and (III) disturbed, fast, hot winds associated with interplanetary coronal mass ejections. We furthermore predict the existence of a fourth spectral class, associated with the cool, fast high latitude wind.Comment: 16 pages, 16 figures, and 7 Tables; accepted A&A (Due to space limits, this version has lower resolution jpeg images.

Space-time multiresolution approach to atomistic visualization

Time-varying three-dimensional positional atomistic data are rich in spatial and temporal information. The problem is to understand them. This work offers multiple approaches that enable such understanding. An interactive atomistic visualization system is developed integrating complex analyses with visualization to present the data on space-time multiresolution basis facilitating the information extraction and generate understanding. This work also shows the usefulness of such an integrated approach. The information obtained from the analyses represents the system at multiple length and time scales. Radial distribution function (RDF) provides a complete average spatial map of the distribution of the atoms in the system which is probed to explore the system at different length scales. Coordination environments and cluster structures are visualized to look at the short range structures. Rings are visualized to understand the medium range structure. Displacement data and covariance matrices are visualized to understand the dynamical behaviors. Combinations of rendering techniques including animation, color map, sphere, polygonal and ellipsoid representations, pathlines and glyphs are used during the visualization process. The three-dimensional atomic configurations are reproduced accurately during rendering because of their physical significance while attributes such as coordination number, coordination stability and atomic species lack direct physical relevance and provide additional flexibilities in rendering. The performance results show interactive frame rates are achievable for systems consisting upto a thousand atoms. Such systems are typical of the systems simulated using first principles molecular dynamics simulations. The effectiveness and the usefulness of this work are justified for complex material systems using silicate and oxide liquids for visual analyses. The exploratory approach taken here has not been reported anywhere else before. The major contributions of this works are: 1. A new approach to the atomistic visualization advocating a formal integration of data analyses into the visualization system to improve the effectiveness and also present an implementation of the exploratory atomistic visualization system with integrated spatio-temporal analytical techniques. 2. The modeling of coordination environments, stability of the coordination environments, clusters, ring structures and diffusion for individual atoms. 3. The use of the visualization system for visual analysis of various liquid mineral systems of geophysical relevance

Studying protein-ligand interactions using a Monte Carlo procedure

[eng] Biomolecular simulations have been widely used in the study of protein-ligand interactions; comprehending the mechanisms involved in the prediction of binding affinities would have a significant repercussion in the pharmaceutical industry. Notwithstanding the intrinsic difficulty of sampling the phase space, hardware and methodological developments make computer simulations a promising candidate in the resolution of biophysically relevant problems. In this context, the objective of the thesis is the development of a protocol that permits studying protein-ligand interactions, in view to be applied in drug discovery pipelines. The author contributed to the rewriting PELE, our Monte Carlo sampling procedure, using good practices of software development. These involved testing, improving the readability, modularity, encapsulation, maintenance and version control, just to name a few. Importantly, the recoding resulted in a competitive cutting-edge software that is able to integrate new algorithms and platforms, such as new force fields or a graphical user interface, while being reliable and efficient. The rest of the thesis is built upon this development. At this point, we established a protocol of unbiased all-atom simulations using PELE, often combined with Markov (state) Models (MSM) to characterize the energy landscape exploration. In the thesis, we have shown that PELE is a suitable tool to map complex mechanisms in an accurate and efficient manner. For example, we successfully conducted studies of ligand migration in prolyl oligopeptidases and nuclear hormone receptors (NHRs). Using PELE, we could map the ligand migration and binding pathway in such complex systems in less than 48 hours. On the other hand, with this technique we often run batches of 100s of simulations to reduce the wall-clock time. MSM is a useful technique to join these independent simulations in a unique statistical model, as individual trajectories only need to characterize the energy landscape locally, and the global characterization can be extracted from the model. We successfully applied the combination of these two methodologies to quantify binding mechanisms and estimate the binding free energy in systems involving NHRs and tyorsinases. However, this technique represents a significant computational effort. To reduce the computational load, we developed a new methodology to overcome the sampling limitations caused by the ruggedness of the energy landscape. In particular, we used a procedure of iterative simulations with adaptive spawning points based on reinforcement learning ideas. This permits sampling binding mechanisms at a fraction of the cost, and represents a speedup of an order of magnitude in complex systems. Importantly, we show in a proof-of-concept that it can be used to estimate absolute binding free energies. Overall, we hope that the methodologies presented herein help streamline the drug design process.[spa] Las simulaciones biomoleculares se han usado ampliamente en el estudio de interacciones proteína-ligando. Comprender los mecanismos involucrados en la predicción de afinidades de unión tiene una gran repercusión en la industria farmacéutica. A pesar de las dificultades intrínsecas en el muestreo del espacio de fases, mejoras de hardware y metodológicas hacen de las simulaciones por ordenador un candidato prometedor en la resolución de problemas biofísicos con alta relevancia. En este contexto, el objetivo de la tesis es el desarrollo de un protocolo que introduce un estudio más eficiente de las interacciones proteína-ligando, con vistas a diseminar PELE, un procedimiento de muestreo de Monte Carlo, en el diseño de fármacos. Nuestro principal foco ha sido sobrepasar las limitaciones de muestreo causadas por la rugosidad del paisaje de energías, aplicando nuestro protocolo para hacer analsis detallados a nivel atomístico en receptores nucleares de hormonas, receptores acoplados a proteínas G, tirosinasas y prolil oligopeptidasas, en colaboración con una compañía farmacéutica y de varios laboratorios experimentales. Con todo ello, esperamos que las metodologías presentadas en esta tesis ayuden a mejorar el diseño de fármacos

Reconciliation of essential process parameters for an enhanced predictability of Arctic stratospheric ozone loss and its climate interactions

Significant reductions in stratospheric ozone occur inside the polar vortices each spring when chlorine radicals produced by heterogeneous reactions on cold particle surfaces in winter destroy ozone mainly in two catalytic cycles, the ClO dimer cycle and the ClO/BrO cycle. Chlorofluorocarbons (CFCs), which are responsible for most of the chlorine currently present in the stratosphere, have been banned by the Montreal Protocol and its amendments, and the ozone layer is predicted to recover to 1980 levels within the next few decades. During the same period, however, climate change is expected to alter the temperature, circulation patterns and chemical composition in the stratosphere, and possible geo-engineering ventures to mitigate climate change may lead to additional changes. To realistically predict the response of the ozone layer to such influences requires the correct representation of all relevant processes. The European project RECONCILE has comprehensively addressed remaining questions in the context of polar ozone depletion, with the objective to quantify the rates of some of the most relevant, yet still uncertain physical and chemical processes. To this end RECONCILE used a broad approach of laboratory experiments, two field missions in the Arctic winter 2009/10 employing the high altitude research aircraft M55-Geophysica and an extensive match ozone sonde campaign, as well as microphysical and chemical transport modelling and data assimilation. Some of the main outcomes of RECONCILE are as follows: (1) vortex meteorology: the 2009/10 Arctic winter was unusually cold at stratospheric levels during the six-week period from mid-December 2009 until the end of January 2010, with reduced transport and mixing across the polar vortex edge; polar vortex stability and how it is influenced by dynamic processes in the troposphere has led to unprecedented, synoptic-scale stratospheric regions with temperatures below the frost point; in these regions stratospheric ice clouds have been observed, extending over >106km2 during more than 3 weeks. (2) Particle microphysics: heterogeneous nucleation of nitric acid trihydrate (NAT) particles in the absence of ice has been unambiguously demonstrated; conversely, the synoptic scale ice clouds also appear to nucleate heterogeneously; a variety of possible heterogeneous nuclei has been characterised by chemical analysis of the non-volatile fraction of the background aerosol; substantial formation of solid particles and denitrification via their sedimentation has been observed and model parameterizations have been improved. (3) Chemistry: strong evidence has been found for significant chlorine activation not only on polar stratospheric clouds (PSCs) but also on cold binary aerosol; laboratory experiments and field data on the ClOOCl photolysis rate and other kinetic parameters have been shown to be consistent with an adequate degree of certainty; no evidence has been found that would support the existence of yet unknown chemical mechanisms making a significant contribution to polar ozone loss. (4) Global modelling: results from process studies have been implemented in a prognostic chemistry climate model (CCM); simulations with improved parameterisations of processes relevant for polar ozone depletion are evaluated against satellite data and other long term records using data assimilation and detrended fluctuation analysis. Finally, measurements and process studies within RECONCILE were also applied to the winter 2010/11, when special meteorological conditions led to the highest chemical ozone loss ever observed in the Arctic. In addition to quantifying the 2010/11 ozone loss and to understand its causes including possible connections to climate change, its impacts were addressed, such as changes in surface ultraviolet (UV) radiation in the densely populated northern mid-latitudes