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Disk space, input/output (I/O) speed, and data-transfer bandwidth present a major bottleneck in large-scale molecular dynamics simulations, which require storing positions and velocities of multimillion atoms. A data compression algorithm is designed for scalable I/O of molecular dynamics data. The algorithm uses octree indexing and sorts atoms accordingly… (More)

For realistic modeling of materials, a molecular-dynamics (MD) algorithm is developed based on multiresolutions in both space and time. Materials of interest are characterized by the long-range Coulomb, steric and charge-dipole interactions as well as three-body covalent potentials. The long-range Coulomb interaction is computed with the fast multipole… (More)

- Ashish K Sharma, Aiichiro Nakano, +7 authors Andy Haas
- Presence
- 2002

We have developed a visualization system, named Atomsviewer, to render a billion atoms from the results of a molecular dynamics simulation. This system uses a hierarchical view frustum culling algorithm based on the octree data structure to efciently remove atoms that are outside of the eld of view. A novel occlusion culling algorithm, using a probability… (More)

- Liu Peng, Richard Seymour, +7 authors Chap C. Wong
- 2009 IEEE International Symposium on Parallel…
- 2009

Stencil computation (SC) is of critical importance for broad scientific and engineering applications. However, it is a challenge to optimize complex, high-order SC on emerging clusters of multicore processors. We have developed a hierarchical SC parallelization framework that combines: (1) spatial decomposition based on message passing; (2) multithreading… (More)

- Amit Choubey, Rajiv K. Kalia, Noah Malmstadt, Aiichiro Nakano, Priya Vashishta
- Biophysical journal
- 2013

Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes and controlling intracellular transport and signal transduction. Using an all-atom molecular dynamics approach, we study the process of CHOL interleaflet transport (flip-flop) in a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer over a time period of 15 μs. We… (More)

- Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta
- Computer Physics Communications
- 2008

A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principlesbased reactive force fields (ReaxFF) describe chemical reactions. Environment-dependent bond orders associated with atomic pairs and their derivatives are reused extensively with the aid of linked-list cells to minimize… (More)

- Aiichiro Nakano, Martina E. Bachlechner, +7 authors Anupam Madhukar
- IEEE Computational Science and Engineering
- 1998

Materials and devices with microstructures on the nanometer scale are revolutionizing technology, but until recently simulation at this scale has been problematic. Developments in parallel computing are now allowing atomistic simulation using multiresolution algorithms, such as fast multipole methods. With these algorithms, researchers may soon be able to… (More)

A hybrid quantum mechanical/molecular dynamics simulation scheme is developed, in which a quantum mechanical system described by the density functional theory on real-space multigrids is embedded in a classical system of atoms interacting via an empirical interatomic potential. Handshake atoms coupling the quantum and the classical systems are treated by a… (More)

- Ken-ichi Nomura, Rajiv K. Kalia, +6 authors Nichols A. Romero
- SC
- 2014

We enabled an unprecedented scale of quantum molecular dynamics simulations through algorithmic innovations. A new lean divide-and-conquer density functional theory algorithm significantly reduces the prefactor of the <i>O</i>(<i>N</i>) computational cost based on complexity and error analyses. A globally scalable and locally fast solver hybridizes a global… (More)

- Liu Peng, Manaschai Kunaseth, +5 authors Priya Vashishta
- The Journal of Supercomputing
- 2011

We have developed a scalable hierarchical parallelization scheme for molecular dynamics (MD) simulation on multicore clusters. The scheme explores multilevel parallelism combining: (1) Internode parallelism using spatial decomposition via message passing; (2) intercore parallelism using cellular decomposition via multithreading employing a master/worker… (More)