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

2000


N. Touheed, P. Selwood, P.K. Jimack, M. Berzins. “A Comparison of Some Dynamic Load Balancing Algorithms for a Parallel Adaptive Flow Solver,” In Parallel Computing, Vol. 26, No. 12, pp. 1535--1554. 2000.



X. Tricoche, G. Scheuermann, H. Hagen. “Higher Order Singularities in Piecewise Linear Vector Fields,” In The Mathematics of Surfaces IX, Springer, London, pp. 99--113. 2000.



X. Tricoche, G. Scheuermann, H. Hagen. “A Topology Simplification Method for 2D Vector Fields,” In Proceedings of IEEE Visualization 2000, pp. 359--366. 2000.



T.N. Truong. “Reaction Class Transition State Theory: Hydrogen Abstraction Reactions by Hydrogen Atoms as Test Cases,” In Journal of Chemical Physics, Vol. 113, No. 12, pp. 4957-4964. 2000.
DOI: 10.1063/1.1287839

ABSTRACT

We present a new method called Reaction Class Transition State Theory (RC-TST) for estimating thermal rate constants of a large number of reactions in a class. This method is based on the transition state theory framework within the reaction class approach. Thermal rate constants of a given reaction in a class relative to those of its principal reaction can be efficiently predicted from only its differential barrier height and reaction energy. Such requirements are much less than what is needed by the conventional TST method. Furthermore, we have shown that the differential energetic information can be calculated at a relatively low level of theory. No frequency calculation beyond those of the principal reaction is required for this theory. The new theory was applied to a number of hydrogen abstraction reactions. Excellent agreement with experimental data shows that the RC-TST method can be very useful in design of fundamental kinetic models of complex reactions.



T.N. Truong, D.K. Maity, T.-T.T. Truong. “A combined reaction class approach with integrated molecular orbital+molecular orbital (IMOMO) methodology: A practical tool for kinetic modeling,” In Journal of Chemical Physics, Vol. 112, No. 1, pp. 24--30. 2000.
DOI: 10.1063/1.480558

ABSTRACT

We present a new practical computational methodology for predicting thermal rate constants of reactions involving large molecules or a large number of elementary reactions in the same class. This methodology combines the integrated molecular orbital+molecular orbital (IMOMO) approach with our recently proposed reaction class models for tunneling. With the new methodology, we show that it is possible to significantly reduce the computational cost by several orders of magnitude while compromising the accuracy in the predicted rate constants by less than 40% over a wide range of temperatures. Another important result is that the computational cost increases only slightly as the system size increases.



D.C. Van Essen, H.A. Drury, S. Joshi, M. Miller. “Functional and Structural Mapping of Human Cerebral Cortex: Solutions are in the Surfaces,” In Adv Neurol, Vol. 84, pp. 23--34. 2000.



S. Vyazovkin, C.A. Wight. “Estimating Realistic Confidence Intervals for the Activation Energy Determined from Thermoanalytical Measurements,” In Analytical Chemistry, Vol. 72, No. 14, pp. 3171--3175. June, 2000.
DOI: 10.1021/ac000210u

ABSTRACT

A statistical procedure is proposed for estimating realistic confidence intervals for the activation energy determined by using an advanced isoconversional method. Nine sets of five thermogravimetric measurements have been produced for the process of gassification of ammonium nitrate at five different heating rates. Independent estimates of the confidence intervals for the activation energy have been obtained from these data sets. Agreement with these independent estimates demonstrates that the proposed statistical procedure is capable of adequately estimating the actual uncertainty in the activation energy determined from a small number of measurements. The resulting averaged relative errors in the activation energy were found to be 26, 21, and 17% for three, four, and five heating rate estimates, respectively.



D.M. Weinstein, L. Zhukov, G. Potts. “Localization of Multiple Deep Epileptic Sources in a Realistic Head Model via Independent Component Analysis,” School of Computing Technical Report, No. UUCS-2000-004, University of Utah, February, 2000.



D.M. Weinstein, L. Zhukov, C.R. Johnson. “Lead-Field Bases for EEG Source Imaging,” In Annal. Biomed. Eng., Vol. 28, No. 9, pp. 1059--1065. Sep, 2000.



D. Weinstein. “Scanline Surfacing: Building Separating Surfaces from Planar Contours,” In Proceeding of IEEE Visualization 2000, pp. 283--289. 2000.



D.M. Weinstein, L. Zhukov, C.R. Johnson. “An Inverse EEG Problem Solving Environment and its Applications to EEG Source Localization,” In NeuroImage (suppl.), pp. 921. 2000.



M. Weiler, R. Westermann, C.D. Hansen, K. Zimmerman, T. Ertl. “Level-Of-Detail Volume Rendering via 3D Textures,” In Proceeding of IEEE Volume Visualization 2000, SLC, Utah, pp. 7--13. October, 2000.



D.M. Weinstein, L. Zhukov, C.R. Johnson, S.G. Parker, R. Van Uitert, R.S. MacLeod, C.D. Hansen. “Interactive Source Imaging with BioPSE,” In Chicago 2000 World Congress on Medical Physics and Biomedical Engineering, Chicago, IL., Note: Refereed abstract., July, 2000.



D.M. Weinstein, P. Krysl, C.R. Johnson. “The BioPSE Inverse EEG Modeling Pipeline,” In ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.



R. Westermann, C.R. Johnson, T. Ertl. “A Level-Set Method for Flow Visualization,” In Proceeding of IEEE Visualization 2000, IEEE Computer Society, Salt Lake City pp. 147--154. 2000.



S. Zhang, T.N. Truong. “Direct ab initio Dynamics Studies of N+H2NH+H Reaction,” In Journal of Chemical Physics, Vol. 113, No. 15, pp. 6149--6153. 2000.
DOI: 10.1063/1.1308544

ABSTRACT

Kinetics of the N+H2↔NH+Hreaction have been studied using a direct ab initio dynamics method. Potential energy surface for low electronic states have been explored at the QCISD/cc-pVDZ level of theory. We found the ground-statereaction is N(4S)+H2→NH(3Σ)+H. Thermal rate constants for this reaction were calculated using the microcanonical variational transition state theory.Reaction path information was calculated at the QCISD/cc-pVDZ level of theory. Energies along the minimum energy path (MEP) were then refined at the QCISD(TQ)/cc-pVTZ level of theory. The forward and reverse barriers of the ground-statereaction are predicted to be 29.60 and 0.53 kcal/mol, respectively. The calculated rate constants for both forward and reverse reactions are in good agreement with available experimental data. They can be expressed as k(T)=2.33×1014 exp(-30.83 (kcal/mol)/RT) cm3 mol−1 s−1 for the forward reaction and k(T)=5.55×108T1.44 exp(−0.78(kcal/mol)/RT) cm3 mol−1 s−1 for the reverse reaction in the temperature range 400–2500 K.



S. Zhang, T.N. Truong. “Thermal Rate Constants of the NO2 fission reaction of Gas Phase a-HMX: A Direct Ab Initio Dynamics Study,” In Journal of Physical Chemistry, A, Vol. 104, pp. 7304--7307. 2000.
DOI: 10.1021/jp001419e

ABSTRACT

The NO2 fission reaction of gas phase α-HMX has been studied using a direct ab initio method within the framework of microcanonical variational transition state theory (μVT). The potential energy calculations were calculated using the hybrid nonlocal B3LYP density functional theory with the cc-pVDZ basis set. The calculated results show that the potential energy of breaking the axial NO2 groups is lower than that of breaking the equatorial NO2 groups. No traditional transition state was found along the reaction path. Microcanonical rate constants calculation shows the variational transition state varies from 2.0 to 3.5 Å of the breaking N−N bond length as a function of the excess energy. The μVT method was used for thermal rate constants calculation over a temperature range from 250 to 2000 K. The fitted Arrhenius expression from the calculated data is k(T) = 1.66 × 1015 exp(−18748K/T) s-1, which is in good agreement with the experimental data at low temperatures.



L. Zhukov, D. Weinstein, C.R. Johnson. “Statistical Analysis For FEM EEG Source Localization in Realistic Head Models,” School of Computing Technical Report, No. UUCS-2000-003, University of Utah, February, 2000.



L. Zhukov, D.M. Weinstein, C.R. Johnson. “Reciprocity Basis for EEG Source Imaging,” In NeuroImage (suppl.), pp. 598. 2000.



L. Zhukov, D. Weinstein, C.R. Johnson. “Independent Component Analysis for EEG Source Localization in Realistic Head Models,” In IEEE Engineering in Medicine and Biology, Vol. 19, No. 3, pp. 87--96. 2000.