Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

1999


J.A. Nairn. “Fracture Mechanics of Composites with Residual Stresses, Traction-Loaded Cracks, and Imperfect Interfaces,” In European Structural Integrity Society: Fracture of Polymers, Composites and Adhesives, Vol. 27, pp. 111--121. 1999.
DOI: 10.1016/S1566-1369(00)80012-6

ABSTRACT

By partitioning the total stresses in a damaged composite into either mechanical and residual stresses or into initial and pertubation stresses, it was possible to derive several exact results for the energy release rate due to crack growth. These general results automatically include the effects of residual stresses, traction-loaded cracks, and imperfect interfaces. By considering approximate solutions based on admissible stress states and admissible strain states, it was possible to derive rigorous upper and lower bounds to the energy release rate for crack growth. Two examples of using these equations are mode I fracture in adhesive double cantilever beam specimens and analysis of microcracking in composite laminates.

Keywords: Fracture Mechanics, Energy Release Rate, Residual Stresses, Adhesive Fracture, Matrix Microcracking



J. Nash, P. Dew, M. Berzins. “Using SADTs to Support Irregular Computational Problems,” In International Symposium on Parallel Architectures, Algorithms, and Networks, IEEE Computer Society, Los Alamitos, CA, USA pp. 338--344. 1999.
ISSN: 1087-4089
DOI: 10.1109/ISPAN.1999.778961



J. Nash, M. Berzins, P. Selwood. “A Structured SADT Approach to the Support of a Parallel Adaptive 3D CFD Code,” In Euro-Par'99 Parallel Processing, Springer Nature, pp. 651--658. 1999.
DOI: 10.1007/3-540-48311-x_91



E.M. Nurgat, M. Berzins, L.E. Scales. “Solving EHL Problems Using Iterative Multigrid and Homotopy Methods,” In ASME Journal of Tribology, Vol. 121, pp. 28--34. January, 1999.



S.G. Parker, M. Parker, Y. Livnat, P.P. Sloan, C.D. Hansen, P. Shirley. “Interactive Ray Tracing for Volume Visualization,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 5, No. 3, pp. 238--250. July-September, 1999.



S.G. Parker, P. Shirley, Y. Livnat, C.D. Hansen, P.-P. Sloan, M. Parker. “Interacting with Gigabyte Volume Datasets on the Origin 2000,” In The 41st Annual Cray User's Group Conference, 1999.



S.G. Parker, W. Martin, P.-P. Sloan, P. Shirley, B. Smits, C.D. Hansen. “Interactive Ray Tracing,” In Symposium on Interactive 3D Graphics: Interactive 3D, pp. 119--126. April 26-28, 1999.



J.D. Peterson, S. Vyazovkin, C.A. Wight. “Kinetic Study of Stabilizing Effect of Oxygen on Thermal Degradation of Poly(methyl methacrylate),” In Journal of Physical Chemistry, B, Vol. 103, No. 38, pp. 8087--8092. August, 1999.
DOI: 10.1021/jp991582d

ABSTRACT

The thermal degradation of poly(methyl methacrylate) (PMMA) has been studied in both pure nitrogen and oxygen-containing atmospheres. The presence of oxygen increases the initial decomposition temperature by 70 °C. The stabilizing effect of oxygen may be explained by forming thermally stable radical species that suppress unzipping of the polymer. This assumption is supported by the experimental fact that introduction of NO into gaseous atmosphere increases the initial decomposition temperature by more than 100 °C. The model-free isoconversional method has been used to determine the dependence of the effective activation energy on the extent of degradation. The initial stages of the process show a dramatic difference in the activation energies that were found to be 60 and 220 kJ mol-1 for respective degradations in nitrogen and air.



J.D. Peterson, S. Vyazovkin, C.A. Wight. “Stabilizing Effect of Oxygen on Thermal Degradation of Poly(methyl methacrylate),” In Macromolecular Rapid Communications, Vol. 20, No. 9, pp. 480--483. September, 1999.
DOI: 10.1002/(SICI)1521-3927(19990901)20:93.0.CO;2-7

ABSTRACT

The thermal degradation of poly(methyl methacrylate) has been studied under nitrogen and air. The presence of oxygen increases the initial decomposition temperature by 70 degrees C. The stabilizing effect of oxygen is explained by the formation of thermally stable radical species that suppress unzipping of the polymer. This assumption is supported by the experimental fact that introduction of NO into the gaseous atmosphere increases the initial decomposition temperature by more than 100 degrees C.



M. Richards, N.A. Waanders, J.A. Weiss, V. Bhatia, L.E. Senunas, M.B. Schaffler, S.A. Goldstein, J.A. Goulet. “Reduced Gap Strains Induce Changes in Bone Regeneration During Distraction,” In Journal of Biomechanical Engineering, Vol. 121, pp. 348--355. 1999.



G. Scheuermann, X. Tricoche, H. Hagen. “C1-Interpolation for Vector Field Topology Visualization,” In Proceeding IEEE Visualization 1999, pp. 271--278. 1999.



P. Selwood, M. Berzins. “Portable Parallel Adaptation of Unstructured Tetrahedral Meshes,” In Concurrency, Vol. 11, No. 13, pp. 1--22. 1999.



P.P. Sloan, C.D. Hansen. “Parallel Lumigraph Reconstruction,” In Parallel Visualization and Graphics Symposium 1999, pp. 7--14. October, 1999.



G.D. Smith, R. Bharadwaj. “Quantum Chemistry Based Force Field for Simulations of HMX,” In Journal of Physical Chemistry, B, Vol. 103, No. 18, pp. 3570--3575. April, 1999.
DOI: 10.1021/jp984599p

ABSTRACT

The molecular geometries and conformational energies of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 1,3-dimethyl-1,3-dinitro methyldiamine (DDMD) and have been determined from high-level quantum chemistry calculations and have been used in parametrizing a classical potential function for simulations of HMX. Geometry optimizations for HMX and DDMD and rotational energy barrier searches for DDMD were performed at the B3LYP/6-311G** level, with subsequent single-point energy calculations at the MP2/6-311G** level. Four unique low-energy conformers were found for HMX, two whose conformational geometries correspond closely to those found in HMX polymorphs from crystallographic studies and two additional, lower energy conformers that are not seen in the crystalline phases. For DDMD, three unique low-energy conformers, and the rotational energy barriers between them, were located. In parametrizing the classical potential function for HMX, nonbonded repulsion/dispersion parameters, valence parameters, and parameters describing nitro group rotation and out-of-plane distortion at the amine nitrogen were taken from our previous studies of dimethylnitramine. Polar effects in HMX and DDMD were represented by sets of partial atomic charges that reproduce the electrostatic potential and dipole moments for the low-energy conformers of these molecules as determined from the quantum chemistry wave functions. Parameters describing conformational energetics for the C−N−C−N dihedrals were determined by fitting the classical potential function to reproduce relative conformational energies in HMX as found from quantum chemistry. The resulting potential was found to give a good representation of the conformer geometries and relative conformer energies in HMX and a reasonable description of the low-energy conformers and rotational energy barriers in DDMD.



G.D. Smith, W. Paul, M. Monkenbusch, L. Willner, D. Richter, X.H. Qiu, M.D. Ediger. “Molecular Dynamics of a 1,4-Polybutadiene Melt. Comparison of Experiment and Simulation,” In Macromolecules, Vol. 32, No. 26, pp. 8857--8865. November, 1999.
DOI: 10.1021/ma991130z

ABSTRACT

We have made detailed comparison of the local and chain dynamics of a melt of 1,4-polybutadiene (PBD) as determined from experiment and molecular dynamics simulation at 353 K. The PBD was found to have a random microstructure consisting of 40% cis, 50% trans, and 10% 1,2-vinyl units with a number-average degree of polymerization 〈Xn〉 = 25.4. Local (conformational) dynamics were studied via measurements of the 13C NMR spin−lattice relaxation time T1 and the nuclear Overhauser enhancement (NOE) at a proton resonance of 300 MHz for 12 distinguishable nuclei. Chain dynamics were studied on time scales up to 22 ns via neutron spin−echo (NSE) spectroscopy with momentum transfers ranging from q = 0.05 to 0.30 Å-1. Molecular dynamics simulations of a 100 carbon (Xn = 25) PBD random copolymer of 50% trans and 50% cis units employing a quantum chemistry-based united atom potential function were performed at 353 K. The T1 and NOE values obtained from simulation, as well as the center of mass diffusion coefficient and dynamic structure factor, were found to be in qualitative agreement with experiment. However, comparison of T1 and NOE values for the various distinguishable resonances revealed that the local dynamics of the simulated chains were systematically too fast, whereas comparison with the center of mass diffusion coefficient revealed a similar trend in the chain dynamics. To improve agreement with experiment, (1) the chain length was increased to match the experimental Mz, (2) vinyl units groups were included in the chain microstructure, and (3) rotational energy barriers were increased by 0.4 kcal/mol in order to reduce the rate of conformational transitions. With these changes, dynamic properties from simulation were found to differ 20-30% or less from experiment, comparable to the agreement seen in previous simulations of polyethylene using a quantum chemistry-based united atom potential.



P. Sutton, C.D. Hansen. “Isosurface Extraction in Time-varying Fields Using a Temporal Branch-on-Need Tree (T-BON),” In IEEE Visualization 1999, pp. 147--153. Oct, 1999.



T. Tasdizen, J.-P. Tarel, D. B. Cooper. “Algebraic curves that work better,” In Proceedings. 1999 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 1999.
DOI: 10.1109/cvpr.1999.784605



A. Tomlin, S. Ghorai, G. Hart, M. Berzins. “3D adaptive unstructured meshes for air pollution modelling,” In Environmental Management and Health, Vol. 10, No. 4, pp. 267-275. 1999.
DOI: 10.1108/09566169910276238



T.N. Truong, W.T. Duncan, M. Tirtowidjojo. “A Reaction Class Approach for Modeling Gas Phase Reaction Rates,” In Physical Chemistry Chemical Physics, Vol. 1, No. 6, pp. 1061-1065. 1999.
DOI: 10.1039/A808438F

ABSTRACT

We present a series of new tunneling models based on a reaction class approach. Reaction class consists of all reactions that have the same reactive moiety. One can expect that reactions in the same class share similarities in the shape of the potential energy surfaces along the reaction path. By exploring such similarities, we propose to use reaction path information from the parent (smallest) reaction in calculations of tunneling contributions of larger reactions in the class. This significantly reduces the computational cost while maintaining the accuracy of the model.



T.N. Truong, T.-T.T. Truong. “A Reaction Class Approach with the Integrated Molecular Orbital + Molecular Orbital (IMOMO) Methodology,” In Chemical Physics Letters, Vol. 314, No. 5-6, pp. 529--533. 1999.
DOI: 10.1016/S0009-2614(99)01188-4

ABSTRACT

We investigate the use of the reaction-class approach within the integrated molecular + molecular orbital (IMOMO) methodology for improving energetic information of chemical reactions. We have tested this approach using two classes of hydrogen abstraction reactions. One is abstraction from saturated hydrocarbons and the other from unsaturated hydrocarbons. For saturated hydrocarbon systems, this approach yields average unsign errors of the order of 1 kcal/mol in the reaction energy and about 0.2 kcal/mol in the barrier height. The errors are larger in the unsaturated hydrocarbon systems and are of the order of 2 kcal/mol. Analysis of the performance shows that this approach provides a practical and cost-effective tool for studying reactions involving large molecules.