Accelerated Molecular Dynamics for the Exascale

A range of specialized Molecular Dynamics (MD) methods have been developed in order to overcome the challenge of reaching longer timescales in systems that evolve through sequences of rare events. In this talk, we consider Parallel Trajectory Splicing (ParSplice) which works by generating large number of MD trajectory segments in parallel in such a way that they can later be assembled into a single statistically correct state-to-state trajectory, enabling parallel speedups up to N, the number of parallel workers. The prospect of strong-scaling MD is extremely enticing given the continuously increasing scale of available computational resources: on current peta-scale platforms N can be in the hundreds of thousands, which opens the door to MD-accurate millisecond-long atomistic simulations; extending such a capability into the exascale era could be transformative.In practice, however, the ability for ParSplice to scale increasingly relies on predicting where the trajectory will be found in the future. With this insight in mind, we develop a maximum likelihood transition model that is updated on the fly and make use of an uncertainty-driven estimator to approximate the optimal distribution of trajectory segments to be generated next. In addition, we investigate resource optimization schemes designed to fully utilize computational resources in order to generate the maximum expected throughput

Modelling thin film growth in the Ti-Ag system

With the aim to model the surface growth of Ti-Ag system over realistic time scales, two interatomic potential mixing rules for the Ti-Ag system were first investigated based on the embedded-atom method (EAM) elemental potentials. First principles calculations were performed using SIESTA for various configurations of the Ti-Ag system to see which model best fitted the ab initio results. The results showed that the surface energies, es- pecially that of Ti, were not well fitted by either model and the surface binding energies differed from the ab initio calculations. As a result, the modified embedded-atom method (MEAM) was investigated. In contrast to the other models, surface energies for pure Ti calculated by MEAM were in good agreement with the experimental data and the ab initio results. The MEAM mixing rule was used to investigate Ag adatoms on Ti and Ti adatoms on Ag. The results showed good agreement with SIESTA after parameter optimisation. Simulations of thin film growth in the Ag-Ti system are presented using an adaptive kinetic Monte Carlo method (AKMC). For the growth of Ti on Ag (100) and Ag (111) surfaces, the Ti adatoms prefer to exchange with the original surface layer atoms creating a mixed Ag/Ti surface. On a silver substrate, up to four mixed layers need to be formed before a pure Ti layer is obtained when the deposition energy is less than 20 eV. Conversely, the simulations of Ag on the Ti (0001) plane showed that the Ag adatoms repel each other on the Ti basal plane, before a complete first layer of Ag was obtained in a face-centred cubic structure. The implementations of a super-basin method within the adaptive ki- netic Monte Carlo method has allowed the simulation of 0.4s of surface growth on the Ag substrates. This work also compared two long time scale dynamics methods, namely AKMC and Parallel Trajectory Splicing (ParSplice) simulations. For these two configurations are considered on the Ag (111) substrate. The transitions and the associated energy barriers are identical for single atom diffusion but the diffusion rates differ. In the case of an adatom on an island, a super-basin system was created. The exit transitions found by a transition search algorithm and ParSplice were again the same whilst the mean exit time differed by a factor of two due to inaccurate prefactor calculations. The distribution of basin-exit times is also examined which obeys an exponential distribution

Computational Methods in Biomolecules:Study of Hydrophilic Interactions in Protein Folding & Constant-pH Molecular Simulation of pH Sensitive Lipid MORC16

Water molecules play a significant role in biological process and are directly involved with bio-molecules and organic compounds and ions. Recent research has focused on the thermal dynamics and kinetics of water molecules in solution, including experimental (infrared spectroscopy and Raman spectroscopy) and computational (Quantum Mechanics and Molecular Dynamics) approaches. The reason that water molecules are so unique, why they have such a profound influence on bio-activity, why water molecules show some anomalies compared to other small molecules, and where and how water molecules exert their influence on solutes are some of the areas under study. We studied some properties of hydrogen bond networks, and the relationship of these properties with solutes in water. Molecular dynamics simulation, followed by an analysis of “water bridges”, which represent protein-water interaction have been carried out on folded and unfolded proteins. Results suggest that the formation of transient water bridges within a certain distance helps to consolidate the protein, possibly in transition states, and may help further guide the correct folding of proteins from these transition states. This is supporting evidence that a hydrophilic interaction is the driving force of protein folding. Biological membranes are complex structures formed mostly by lipids and proteins. For this reason the lipid bilayer has received much attention, through computation and experimental studies in recent years. In this dissertation, we report results of a newly designed pH sensitive lipid MORC16, through all-atom and coarse-grained models. The results did not yield a MORC16 amphiphile which flips its conformation in response to protonation. This may be due to imperfect force field parameters for this lipid, an imperfect protonation definition, or formation of hydrogen bond does not responsible for conformation flip in our models. Despite this, some insights for future work were obtained

Perspectives of Nuclear Physics in Europe: NuPECC Long Range Plan 2010

The goal of this European Science Foundation Forward Look into the future of Nuclear Physics is to bring together the entire Nuclear Physics community in Europe to formulate a coherent plan of the best way to develop the field in the coming decade and beyond.<p></p> The primary aim of Nuclear Physics is to understand the origin, evolution, structure and phases of strongly interacting matter, which constitutes nearly 100% of the visible matter in the universe. This is an immensely important and challenging task that requires the concerted effort of scientists working in both theory and experiment, funding agencies, politicians and the public.<p></p> Nuclear Physics projects are often “big science”, which implies large investments and long lead times. They need careful forward planning and strong support from policy makers. This Forward Look provides an excellent tool to achieve this. It represents the outcome of detailed scrutiny by Europe’s leading experts and will help focus the views of the scientific community on the most promising directions in the field and create the basis for funding agencies to provide adequate support.<p></p> The current NuPECC Long Range Plan 2010 “Perspectives of Nuclear Physics in Europe” resulted from consultation with close to 6 000 scientists and engineers over a period of approximately one year. Its detailed recommendations are presented on the following pages. For the interested public, a short summary brochure has been produced to accompany the Forward Look.<p></p&gt

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Climate Change and Sea Level Rise Projections for Boston

While the broad outlines of how climate change would impact Boston have been known for some time, it is only recently that we have developed a more definitive understanding of what lies ahead. That understanding was advanced considerably with the publication of Climate Change and Sea Level Rise Projections for Boston by the Boston Research Advisory Group (BRAG).The BRAG report is the first major product of "Climate Ready Boston," a project led by the City of Boston in partnership with the Green Ribbon Commission and funded in part by the Barr Foundation. The BRAG team includes 20 leading experts from the region's major universities on subjects ranging from sea level rise to temperature extremes. University of Massachusetts Boston professors Ellen Douglas and Paul Kirshen headed the research.The BRAG report validates earlier studies, concluding Boston will get hotter, wetter, and saltier in the decades ahead (see figures below). But the group has produced a much more definitive set of projections than existed previously, especially for the problem of sea level rise. BRAG also concluded that some of the effects of climate change will come sooner than expected, accelerating the urgency of planning and action