Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower computational overheads and longer timescales with respect to atom- istic level models. However, their acceleration on parallel architectures such as Graphic Processing Units (GPU) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specic optimizations for CG models, such as dedicated data structures to handle dierent bead type interac- tions, obtaining a maximum speed-up of 14 on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three dierent GPU architectures as case studie

Enhancing performance of ionic liquid property prediction with molecular dynamics.

Molecular dynamics have been used to predict thermodynamic and transport properties of eight room-temperature ionic liquids. Simulation parameters including box size and van der Waals cutoffs were varied. The density, heat capacity, and self-diffusion coefficients of the ionic liquids were computed and compared to experimental data and to previously published simulations. Predicted properties were generally close to their experimentally observed values. It was determined that the prediction of ionic liquid properties via molecular dynamics simulations could be accelerated several-fold by using less stringent integration parameters and smaller simulation sizes. The properties of density and heat capacity did not change significantly even with the least computationally expensive parameters tested, whereas diffusion coefficients were impacted by smaller box sizes. These results indicate that several important properties of ionic liquids can be predicted much more quickly than previously thought, thus improving large-scale computational screening of ionic liquids and other novel solvents.[JW1] [JW1]Andrew informed me this will have to be trimmed to 150 words. So I reduced its size

The NASA SBIR product catalog

The purpose of this catalog is to assist small business firms in making the community aware of products emerging from their efforts in the Small Business Innovation Research (SBIR) program. It contains descriptions of some products that have advanced into Phase 3 and others that are identified as prospective products. Both lists of products in this catalog are based on information supplied by NASA SBIR contractors in responding to an invitation to be represented in this document. Generally, all products suggested by the small firms were included in order to meet the goals of information exchange for SBIR results. Of the 444 SBIR contractors NASA queried, 137 provided information on 219 products. The catalog presents the product information in the technology areas listed in the table of contents. Within each area, the products are listed in alphabetical order by product name and are given identifying numbers. Also included is an alphabetical listing of the companies that have products described. This listing cross-references the product list and provides information on the business activity of each firm. In addition, there are three indexes: one a list of firms by states, one that lists the products according to NASA Centers that managed the SBIR projects, and one that lists the products by the relevant Technical Topics utilized in NASA's annual program solicitation under which each SBIR project was selected

NASA SBIR abstracts of 1991 phase 1 projects

The objectives of 301 projects placed under contract by the Small Business Innovation Research (SBIR) program of the National Aeronautics and Space Administration (NASA) are described. These projects were selected competitively from among proposals submitted to NASA in response to the 1991 SBIR Program Solicitation. The basic document consists of edited, non-proprietary abstracts of the winning proposals submitted by small businesses. The abstracts are presented under the 15 technical topics within which Phase 1 proposals were solicited. Each project was assigned a sequential identifying number from 001 to 301, in order of its appearance in the body of the report. Appendixes to provide additional information about the SBIR program and permit cross-reference of the 1991 Phase 1 projects by company name, location by state, principal investigator, NASA Field Center responsible for management of each project, and NASA contract number are included

Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful computational method for fundamental research in science branches such as biology, chemistry, biomedicine and physics over the past 60 years. Powered by rapidly advanced supercomputing technologies in recent decades, MD has entered the engineering domain as a first-principle predictive method for material properties, physicochemical processes, and even as a design tool. Such developments have far-reaching consequences, and are covered for the first time in the present paper, with a focus on MD for combustion and energy systems encompassing topics like gas/liquid/solid fuel oxidation, pyrolysis, catalytic combustion, heterogeneous combustion, electrochemistry, nanoparticle synthesis, heat transfer, phase change, and fluid mechanics. First, the theoretical framework of the MD methodology is described systemically, covering both classical and reactive MD. The emphasis is on the development of the reactive force field (ReaxFF) MD, which enables chemical reactions to be simulated within the MD framework, utilizing quantum chemistry calculations and/or experimental data for the force field training. Second, details of the numerical methods, boundary conditions, post-processing and computational costs of MD simulations are provided. This is followed by a critical review of selected applications of classical and reactive MD methods in combustion and energy systems. It is demonstrated that the ReaxFF MD has been successfully deployed to gain fundamental insights into pyrolysis and/or oxidation of gas/liquid/solid fuels, revealing detailed energy changes and chemical pathways. Moreover, the complex physico-chemical dynamic processes in catalytic reactions, soot formation, and flame synthesis of nanoparticles are made plainly visible from an atomistic perspective. Flow, heat transfer and phase change phenomena are also scrutinized by MD simulations. Unprecedented details of nanoscale processes such as droplet collision, fuel droplet evaporation, and CO2 capture and storage under subcritical and supercritical conditions are examined at the atomic level. Finally, the outlook for atomistic simulations of combustion and energy systems is discussed in the context of emerging computing platforms, machine learning and multiscale modelling

Heterogeneous oxidation of multi-component aqueous organic aerosols: The effect of transport phenomena and reaction compartment on reaction kinetics.

The surface-bulk partitioning of small organic molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80-Å cubic water box containing series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water-bulk were examined at a molecular-level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars and amides leads to the migration of the molecule toward the interface. Within the first 2 nm from the water surface, surface-active solutes lose their rotational freedom and adopt a preferred orientation with the alkyl group pointing toward the surface. The different packing within the interface leads to different solvation shell structures and enhanced interaction between the organic molecules and absorbed OH radicals. The simulations provide quantitative information about the dimension, composition, and organization of the air-water interface as well as about the non-reactive interaction of the OH radicals with the organic solutes. It reveals that the enhanced reactivity of surface-active molecules is due to increased concentrations, preferred orientation, and decreased solvation near the air-water surface. The results are important to explain how heterogeneous oxidation mechanisms and kinetics within interfaces may differ from those of the bulk. An atmospheric pressure flow-tube reactor coupled with offline GC-MS analysis techniques was used to determine the kinetics of the OH-initiated oxidation of equimolar aqueous organic aerosol. Saccharides (glucose and MGP) and amides (propionamide, urea, and acetamide), were chosen as model molecules because of their partitioning properties, availability in the atmosphere, and the important role they play in atmospheric chemistry. The decay rates of the solutes (saccharides and amides) were determined by measuring the loss in signal of solutes in the particle phase as a function of OH exposure (time-integrated total concentration of OH radical). The reactivity of MGP towards OH radicals was shown to be higher in the presence of urea (a surface in-active molecule) than when in the presence of propionamide (a surface in-active molecule). The decreases in MGP reactivity was shown by the change in rate coefficients from 1.2(±0.1) x 10-11 cm-3 s-1 in the urea-MGP particles to 4.7(±0.3) x 10-12 cm-3 s-1 in the propionamide-MGP particles. These findings highlight the importance of surface interactions over bulk interactions in determining the reaction rate of reactive species in aqueous aerosols. The change in particle size with change in chemical composition was also demonstrated

Laboratory directed research development annual report. Fiscal year 1996

This document comprises Pacific Northwest National Laboratory`s report for Fiscal Year 1996 on research and development programs. The document contains 161 project summaries in 16 areas of research and development. The 16 areas of research and development reported on are: atmospheric sciences, biotechnology, chemical instrumentation and analysis, computer and information science, ecological science, electronics and sensors, health protection and dosimetry, hydrological and geologic sciences, marine sciences, materials science and engineering, molecular science, process science and engineering, risk and safety analysis, socio-technical systems analysis, statistics and applied mathematics, and thermal and energy systems. In addition, this report provides an overview of the research and development program, program management, program funding, and Fiscal Year 1997 projects

Vibrational Probe and Methods Development for Studying the Ultrafast Dynamics of Preferential Solvation of Biomolecules by 2D-IR.

Over the last decade two-dimensional infrared spectroscopy (2D-IR) has emerged as a powerful method for the investigation of biological samples and their dynamics. Through the implementation of state of the art signal processing methods we have demonstrated a significant, 20-fold, reduction in the acquisition time of traditional 2D-IR spectra. This new technique, utilizing compressed sensing, compliments our previously developed RASD method, allowing for the rapid acquisition of complete 2D-IR spectra as opposed to dynamical information at a single excitation-detection frequency pair. Additionally we have realized the first biocompatible, modular, metal-carbonyl probes for 2D-IR utilizing benzyl-chromium tribarbonyls. This has enabled ultrafast 2D-IR investigations of lipids and preferential solvation in solutions and at site-specific locations within enzyme scaffolds. In aqueous solutions we find that preferential solvation by a polar cosolvent causes a slowdown of the observed dynamics sensed by our probes. From modeling our system this slowdown is found to be consistent with arising from the slow, ca. 8 ps, exchange dynamics between the polar co-solute and water in the vicinity of our probe. This interpretation of preferential solvation in solution is further able to describe the observed dynamical differences found at the protein-solvent interface in a model system. By studying a series of protein mutants we find, spectroscopically and through simulations, that interactions between the side chains and the solution are sufficient to modulate the degree of preferential solvation and therefore dynamics, within specific sites of the protein. This information provides a foundation on how to modulate of the diffusion of substrates and products into and out-of the active sites of enzymes, through directed mutation of their protein sequence. The diffusional motion of the solvent and substrates is often the rate-limiting step in enzymatic catalysis. By controlling the local solvation dynamics of enzymes, sequence mutations offer a method to fine-tune the dynamics of enzymes. The ability to characterize the site-specific solvation dynamics of enzymes in response to primary structure mutations, positions 2D-IR and our chromium tricarbonyl probes as powerful tools for understanding protein and enzyme dynamics. This provides insight into controlling the catalytic rate of enzymes through directed mutation.PhDBiophysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111440/1/josefd_1.pd