17,086 research outputs found
Parallelization of a Code for the Simulation of Self-gravitating Systems in Astrophysics. Preliminary Speed-up Results
We have preliminary results on the parallelization of a Tree-Code for
evaluating gravitational forces in N-body astrophysical systems. For our Cray
T3D/CRAFT implementation, we have obtained an encouraging speed-up behavior,
which reaches a value of 37 with 64 processor elements (PEs). According to the
Amdahl'law, this means that about 99% of the code is actually parallelized. The
speed-up tests regarded the evaluation of the forces among N = 130,369
particles distributed scaling the actual distribution of a sample of galaxies
seen in the Northern sky hemisphere. Parallelization of the time integration of
the trajectories, which has not yet been taken into account, is both easier to
implement and not as fundamental.Comment: 14 pages LaTeX + 1 EPS figure + 2 EPS colour figures, epsf.sty and
aasms4.sty included; to be published in Science & Supercomputing at CINECA,
Report 1997 (Bologna, Italy
AlSub: Fully Parallel and Modular Subdivision
In recent years, mesh subdivision---the process of forging smooth free-form
surfaces from coarse polygonal meshes---has become an indispensable production
instrument. Although subdivision performance is crucial during simulation,
animation and rendering, state-of-the-art approaches still rely on serial
implementations for complex parts of the subdivision process. Therefore, they
often fail to harness the power of modern parallel devices, like the graphics
processing unit (GPU), for large parts of the algorithm and must resort to
time-consuming serial preprocessing. In this paper, we show that a complete
parallelization of the subdivision process for modern architectures is
possible. Building on sparse matrix linear algebra, we show how to structure
the complete subdivision process into a sequence of algebra operations. By
restructuring and grouping these operations, we adapt the process for different
use cases, such as regular subdivision of dynamic meshes, uniform subdivision
for immutable topology, and feature-adaptive subdivision for efficient
rendering of animated models. As the same machinery is used for all use cases,
identical subdivision results are achieved in all parts of the production
pipeline. As a second contribution, we show how these linear algebra
formulations can effectively be translated into efficient GPU kernels. Applying
our strategies to , Loop and Catmull-Clark subdivision shows
significant speedups of our approach compared to state-of-the-art solutions,
while we completely avoid serial preprocessing.Comment: Changed structure Added content Improved description
Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB
The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for
the dissemination of structural data from single-particle reconstructions of
supramolecular protein assemblies including motors, chaperones, cytoskeletal
assemblies, and viral capsids. While the static structure of these assemblies
provides essential insight into their biological function, their conformational
dynamics and mechanics provide additional important information regarding the
mechanism of their biological function. Here, we present an unsupervised
computational framework to analyze and store for public access the
conformational dynamics of supramolecular protein assemblies deposited in the
EMDB. Conformational dynamics are analyzed using normal mode analysis in the
finite element framework, which is used to compute equilibrium thermal
fluctuations, cross-correlations in molecular motions, and strain energy
distributions for 452 of the 681 entries stored in the EMDB at present. Results
for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and
GroEL are presented in detail and validated with all-atom based models. The
conformational dynamics of protein assemblies in the EMDB may be useful in the
interpretation of their biological function, as well as in the classification
and refinement of EM-based structures.Comment: Associated online data bank available at:
http://lcbb.mit.edu/~em-nmdb
A real-time proximity querying algorithm for haptic-based molecular docking
Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware
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