MD display: An interactive graphics program for visualization of molecular dynamics trajectories

In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines . state-of-the-art molecular dynamics MD algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystalline environment. Among its unique . features are: i implementation of reversible and symplectic multiple time step . algorithms or r-RESPA, reversible reference system propagation algorithm specifically designed and tuned for biological systems with periodic boundary . conditions; ii availability for simulations with multiple or single time steps of . standard Ewald or smooth particle mesh Ewald SPME for computation of . electrostatic interactions; and iii possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms. Q 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1848)1862, 1997

We developed a new accelerated quantum chemical molecular dynamics program called Colors which can simulate the chemical-mechanical polishing (CMP) processes. It is more than 5,000 times faster than the regular first-principles molecular dynamics program, since it is based on our original tight-binding theory. We employed a SiO2 particle as a polishing material. Two types of silicon surfaces, clean Si(100) and H-terminated Si(100) 2×1, were modeled to clarify the effect of the Si surface structure on the dynamic behaviors of the CMP processes. We paid attention to the bond population of the silicon atom during the CMP processes. The bond population of the silicon atom was decreased by the CMP process on both surfaces, indicating that the electronic state of the silicon wafer became unstable due to the CMP process. It is an interesting finding that the hydrogen atoms were desorbed from the H-terminated Si(100) 2×1 surface. The results indicate that our new program can simulate both the chemical reactions and mechanical polishing processes. To the best of our knowledge, this is the first simulator of the CMP processes on the atomic and electronic levels.

Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.

We have implemented the Martini force field within Lawrence Livermore National Laboratory's molecular dynamics program, ddcMD. The program is extended to a heterogeneous programming model so that it can exploit graphics processing unit (GPU) accelerators. In addition to the Martini force field being ported to the GPU, the entire integration step, including thermostat, barostat, and constraint solver, is ported as well, which speeds up the simulations to 278-fold using one GPU vs one central processing unit (CPU) core. A benchmark study is performed with several test cases, comparing ddcMD and GROMACS Martini simulations. The average performance of ddcMD for a protein-lipid simulation system of 136k particles achieves 1.04 µs/day on one NVIDIA V100 GPU and aggregates 6.19 µs/day on one Summit node with six GPUs. The GPU implementation in ddcMD offloads all computations to the GPU and only requires one CPU core per simulation to manage the inputs and outputs, freeing up remaining CPU resources on the compute node for alternative tasks often required in complex simulation campaigns. The ddcMD code has been made open source and is available on GitHub at https://github.com/LLNL/ddcMD.

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self-consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle-field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD-SCF program profiles, serial MD-SCF and parallel MD-SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs.

In addition to the intended use of graphics processing units (GPU) to accelerate computer games, their potential has become apparent for scientific computations in the recent years. Molecular modeling and molecular design are only few examples of numerous research areas that are significantly benefiting from novel developments of hardware and software platforms. For example, the impact of high computational power of GPUs has been demonstrated in molecular dynamics (MD) simulations or quantum chemical (QC) calculations. Thus far, several MD programs have been adapted to GPU computing, including NAMD/VMD, GROMACS, AMBER, etc. In addition, modeling tools intended for molecular design based on receptor-ligand interactions, such as molecular docking or core hopping protocols have recently been updated for GPU environment. The tremendous increase in the computing power facilitated by the integration of GPUs and the availability of GPU-based systems could accelerate material research on nanoscale. The price/performance ratio of GPU-based systems supports the development of custom-made protocols for efficient modeling of biomolecular systems and nanostructures. GPU-related molecular modeling tools will also accelerate the combined quantum chemical/molecular mechanics (QC/MM) methodologies. An overview of the performance of NVIDIA Tesla GPU-based system built for high-performance and high-throughput computing aimed for biomolecular modeling and nanodesign is presented.

Introduction In order to sustain the current production capacity of crude oil in Western Ganada, enhanced oil recovery (EOR) techniques such as utilizing carbon dioxide (CO2) must be used. According to Saskatchewan Department of Energy and Mines, a large amount of crude oil worth multi-billion of dollars can be recovered using these techniques. At, the same time, a large amount of carbon dioxide (CO2) is, being produced by industrial plants in the region. This, tremendous quantity of carbon dioxide is discharged into the atmosphere and could be causing an enhanced greenhouse effect nd global warming. To overcome the CO2 emission problem, here is great interest to capture the carbon dioxide and utilize it as a flooding agent for EOR processes. The concept of recovering O2 and utilizing it as an EOR flooding agent or chemical feedstock will provide two important benefits. First, we can market the captured O2 as a commodity chemical which would generate revenue. Second, we will be able to reduce CO2 emissions to the atmosphere and help alleviate a serious environmental problem, at minimum cost. The ultimate goal of this research and development program is to develop better and more effective CO2 separation processes which can be used to recover CO2 from industrial sources such as fossil fuel fired power stations, coal gasification plants and hydrogen production units for EOR applications at the lowest possible apital and operating costs. Research Facilities and Personnel We have initiated a research program on high efficiency separation process technologies for carbon dioxide removal from industrial sources at the Process Systems Laboratory, University of Regina since 1991. We have acquired and built a number of pieces of research apparatus, equipment and pilot plants over the past five years. These include three pilot plant units for testing high efficiency gas treating systems which consists of different sizes of absorption and regeneration towers packed with a variety of high performance packings. The pilot plants are also equipped with microprocessor-based infrared gas analysers, state-of-the-art gas chromatograph units and a high speed digital data logging system. We are in the process of acquiring an ion chromatographysystem and a GC/MS mass detector for comprehensive analysis of solvent compositions and their activities. In addition, a number of embrane reactors have been constructed which can be used as very high capacity absorbers, as well numerous pieces of research apparatus have been built for solvent absorption capacity testing, corrosion studies and gas/liquid diffusivity determination. In terms of computer applications, our laboratory now is well equipped with and has access to high performance computing facilities. including three high speed Pentium work-stations (each has 64 MB memory and 2.5 GB Hard Drive), a number of 486 PCs, a Silicon Graphics work station (32 MB memory. 1 GB Hard ive) and a very large Silicon Graphics Server (12 of 150 Mhz processor, 1 GB memory, 22 GB Hard Drive). These computing facilities are also equipped with state-of-the-art real time intelligent systems development tools such as G2, GDA, NeurOn-Line, COMDALEIX and COMDALE/C, as well as advanced computeraided process engineering simulators including ASPEN.

Heterogeneous clusters that include accelerators have become more common in the realm of high performance computing because of the high GFlop/s rates such clusters are capable of achieving. However, heterogeneous clusters are typically considered hard to program as they usually require programmers to interleave architecture-specific code within application code. We have extended the Charm++ programming model and runtime system to support heterogeneous clusters (with host cores that differ in their architecture) that include accelerators. We are currently focusing on clusters that include commodity processors, Cell processors, and Larrabee devices. When our extensions are used to develop code, the resulting code is portable between various homogeneous and heterogeneous clusters that may or may not include accelerators. Using a simple example molecular dynamics (MD) code, we demonstrate our programming model extensions and runtime system modifications on a heterogeneous cluster comprised of Xeon and Cell processors. Even though there is no architecture-specific code in the example MD program, it is able to successfully make use of three core types, each with a different ISA (Xeon, PPE, SPE), three SIMD instruction extensions (SSE, AltiVec/VMX and the SPE's SIMD instructions), and two memory models (cache hierarchies and scratchpad memories) in a single execution. Our programming model extensions abstract away hardware complexities while our runtime system modifications automatically adjust application data to account for architectural differences between the various cores.

: As outlined in the original proposal, FEO intends to determine how effectively a neural network coupled to a multiple aperture vision system (MAVS) can be applied to the tracking task. Over the course of the contract FEO will perform seven (7) experimental simulations to evaluate the proposed tracking systems' performance. The October 15, 1992 report discussed the modeling of the first three (3) configurations. The following report discusses the results of the implementation of these first three experiments on the Silicon Graphics IRIS Indigo workstation. Additionally, FEO has completed the optical modeling of experiments four through seven and completed the C++ coding of experiments four and five. FEO has enclosed a DAT tape containing executable code and source code for experiments 1 through 3. The programs can be loaded onto a Silicon Graphics workstation using the tar tape facility. A description of the operation of each program is provided below. Once begun, operation of the executable programs is self-explanatory.

Maurotoxin (MTX) and HsTx1 are two scorpion toxins belonging to the alpha-KTx6 structural family. These 34-residue toxins, cross-linked by four disulfide bridges, share 59% sequence identity and fold along the classical alpha/beta scaffold. Despite these structural similarities, they fully differ in their pharmacological profiles. MTX is highly active on small (SK) and intermediate (IK) conductance Ca(2+)-activated (K(+)) channels and on voltage-gated Kv1.2 channel, whereas HsTx1 potently blocks voltage-gated Kv1.1 and Kv1.3 channels only. Here, we designed and chemically produced MTX-HsTx1, a chimera of both toxins that contains the N-terminal helical region of MTX (sequence 1-16) and the C-terminal beta-sheet region of HsTx1 (sequence 17-34). The three-dimensional structure of the peptide in solution was solved by (1)H NMR. MTX-HsTx1 displays the activity of MTX on SK channel, whereas it exhibits the pharmacological profile of HsTx1 on Kv1.1, Kv1.2, Kv1.3, and IK channels. These data demonstrate that the helical region of MTX exerts a key role in SK channel recognition, whereas the beta-sheet region of HsTx1 is crucial for activity on all other channel types tested.

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems, from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of future massively parallel processing systems for modest-sized problems in the range of 50,000 atoms and the communication requirements needed to achieve 30 to 40% efficiency on MPPs. We analyzed a scalable benchmark molecular dynamics program executing on the Intel Touchstone Deleta parallelized with an interaction decomposition method. Using a validated analytical performance model of the code, we determined that for an MPP with a four-dimensional mesh topology and 400 MHz processors the communication startup time must be at most 90 clock cycles and the network bandwidth must be at least 2.3 GB/s. This configuration results in 30 to 40% efficiency of the MPP for a problem with 50,000 atoms executing on 50,000 processors. >

Huwentoxin-X (HWTX-X) is a novel peptide toxin, purified from the venom of the spider Ornithoctonus huwena. It comprises 28 amino acid residues including six cysteine residues as disulfide bridges linked in the pattern of I-IV, II-V, and III-VI. Its cDNA, determined by rapid amplification of 3' and 5' cDNA ends, encodes a 65-residue prepropeptide. HWTX-X shares low sequence homology with omega-conotoxins GVIA and MVIIA, two well known blockers of N-type Ca2+ channels. Nevertheless, whole cell studies indicate that it can block N-type Ca2+ channels in rat dorsal root ganglion cells (IC50 40 nm) and the blockage by HWTX-X is completely reversible. The rank order of specificity for N-type Ca2+ channels is GVIA approximately HWTX-X > MVIIA. In contrast to GVIA and MVIIA, HWTX-X had no detectable effect on the twitch response of rat vas deferens to low frequency electrical stimulation, indicating that HWTX-X has different selectivity for isoforms of N-type Ca2+ channels, compared with GVIA or MVIIA. A comparison of the structures of HWTX-X and GVIA reveals that they not only adopt a common structural motif (inhibitor cystine knot), but also have a similar functional motif, a binding surface formed by the critical residue Tyr, and several basic residues. However, the dissimilarities of their binding surfaces provide some insights into their different selectivities for isoforms of N-type Ca2+ channels.

Direct numerical simulations of quartz particles, given a turbulent stationary velocity field, are per formed in "real time" on a Silicon Graphics work station. Interaction of the surrounding flozu on spherical particles is taken into account by a modi fied version of the Basset-Boussinesq-Oseen equa tion, including nonlinear resistance. Boundary con ditions (walls) are modeled with the use of reflection laws. Interactions between particles are neglected. The velocity field has been pre-computed with the k—∈ model over different geometries. Second-order accuracy numerical implementation and error esti mation are discussed. Impacts on s urfaces are ac counted for by means of direction and kinetic energy of incident particles. The areas with the highest probability of damage are then mapped. Real-time high-quality interactive graphics are an important aspect of this useful numerical tool.

Confocal Laser Scanning Microscopy and 3-D Reconstructions of Neuronal Structures in Human Brain Cortex

Non-equilibrium molecular simulation studies on gas separation by microporous membranes using dual ensemble molecular simulation techniques