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

2007


F. Zhang, C. Goodlett, E. Hancock, G. Gerig. “Probabilistic White Matter Fiber Tracking using Particle Filtering,” In Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), Lecture Notes in Computer Science, Vol. 4791, pp. 144--151. November, 2007.



H.R. Zhang, E.G. Eddings, A.F. Sarofim. “Combustion Reactions of Paraffin Components in Liquid Transportation Fuels Using Generic Rates,” In Combustion Science and Technology, Vol. 179, No. 1-2, pp. 61--89. 2007.
DOI: 10.1080/00102200600805975

ABSTRACT

The approach of mechanism generation is the accepted one of assigning generic rates to reactions in the same class. The procedure has been successfully applied to higher paraffins that include detailed sub-models of n-hexane, cyclohexane, n-heptane, n-decane, n-dodecane, and n-hexadecane and semi-detailed sub-models of iso-octane and methyl cyclohexane, in addition to reactions of aromatic formation and oxidation. Comparison between predictions and experimental data were found to be satisfactory for n-heptane, iso-octane, n-decane and gasoline premixed flames. The mechanism was also able to reproduce the measured concentrations for a n-hexadecane experiment in a jet stirred reactor. The numerical accuracy in predicting the flame structures of soot precursors, including acetylene and benzene, is one of the major foci of this study. The predicted maximum concentrations of acetylene and benzene are within 20% for most flames in this study.



H.R. Zhang, E.G. Eddings, A.F. Sarofim. “Olefin Chemistry in a Premixed N-Heptane Flame,” In Energy and Fuels, Vol. 21, No. 2, pp. 677--685. 2007.
DOI: 10.1021/ef060195h

ABSTRACT

Three different n-heptane mechanisms were used to simulate a fuel-rich normal heptane premixed flame in order to identify major reaction pathways for olefin formation and consumption and areas of uncertainties of these reactions. Olefins are formed mainly via β-scission and hydrogen abstraction, and smaller olefins are sometimes formed by combination of allylic radicals and H/CH3 radicals. Olefins are consumed by direct decomposition, radical-addition, and hydrogen-abstraction reactions. Isomerization between alkyl radicals plays an important role in olefin formation and in determining olefin species distribution. Peroxy radicals contribute to the olefin formation in the low-temperature region, but further studies are needed to resolve many uncertainties. Simulation results using the Pitsch, LLNL, and Utah heptane mechanisms were compared to experimental concentration profiles of selected species, and the uncertainties in the olefin chemistry thus identified are discussed. The discrepancies in the computed concentrations of most olefin species are usually due to the combined effects of uncertainties in the kinetics of β-scission and isomerization reactions. Resolving these uncertainties in n-heptane combustion chemistry is critical for building practical mechanisms for the larger paraffins that are major components of liquid aviation and diesel transportation fuels. In addition, olefin chemistry is critical to any combustion mechanisms that focus on the soot formation, because products of olefin decomposition such as C3Hx and C4Hx species are well-known precursors for the formation of the first aromatic ring.



H.R. Zhang, E.G. Eddings, A.F. Sarofim, C.K. Westbrook. “Mechanism Reduction and Generation Using Analysis of Major Fuel Consumption Pathways for n-Heptane in Premixed and Diffusion Flames,” In Energy and Fuels, Vol. 21, No. 4, pp. 1967--1976. 2007.
DOI: 10.1021/ef060092z

ABSTRACT

Reaction pathway analyses were conducted for three mechanisms (designated as the Pitsch, Utah, and Lawrence Livermore National Lab) for a normal heptane premixed flame (Φ = 1.9) and a normal heptane opposed diffusion flame, in order to identify the relative importance of the major fuel consumption pathways in the two flame classes. In premixed flames, hydrogen abstraction is found to be the major fuel consumption route although it is surpassed by thermal decomposition when the flame temperature exceeds 1400 - 1500 K. At the higher temperatures, however, little fuel remains in a premixed flame so that thermal decomposition provides a minor pathway for overall fuel decomposition. The principal abstractor is the hydrogen radical in all three mechanisms with the hydroxyl radical having a secondary role. In opposed diffusion flames, thermal decomposition competes with hydrogen abstraction in providing the major pathway for fuel consumption. Thermal decomposition becomes important when a large fraction of the fuel reaches the high-temperature zone in a flame. By understanding the relative importance of competing fuel consumption pathways, mechanisms can be tailored to each specific application by eliminating or lumping insignificant reactions. The results obtained in this study for n-heptane may be used to guide the reduction of existing mechanisms for a particular application or the generation of mechanisms for the combustion of larger paraffins that are major components of liquid aviation and transportation fuels.



H.R. Zhang, L.K. Huynh, N. Kungwan, Z. Yang, S. Zhang. “Combustion modeling and kinetic rate calculations for a stoichiometric cyclohexane flame. 1. Major reaction pathways,” In Journal of Physical Chemistry, A, Vol. 111, No. 19, pp. 4102--4115. 2007.
DOI: 10.1021/jp068237q
PubMed ID: 17388269

ABSTRACT

The Utah Surrogate Mechanism was extended in order to model a stoichiometric premixed cyclohexane flame (P = 30 Torr). Generic rates were assigned to reaction classes of hydrogen abstraction, beta scission, and isomerization, and the resulting mechanism was found to be adequate in describing the combustion chemistry of cyclohexane. Satisfactory results were obtained in comparison with the experimental data of oxygen, major products and important intermediates, which include major soot precursors of C2-C5 unsaturated species. Measured concentrations of immediate products of fuel decomposition were also successfully reproduced. For example, the maximum concentrations of benzene and 1,3-butadiene, two major fuel decomposition products via competing pathways, were predicted within 10% of the measured values. Ring-opening reactions compete with those of cascading dehydrogenation for the decomposition of the conjugate cyclohexyl radical. The major ring-opening pathways produce 1-buten-4-yl radical, molecular ethylene, and 1,3-butadiene. The butadiene species is formed via beta scission after a 1-4 internal hydrogen migration of 1-hexen-6-yl radical. Cascading dehydrogenation also makes an important contribution to the fuel decomposition and provides the exclusive formation pathway of benzene. Benzene formation routes via combination of C2-C4 hydrocarbon fragments were found to be insignificant under current flame conditions, inferred by the later concentration peak of fulvene, in comparison with benzene, because the analogous species series for benzene formation via dehydrogenation was found to be precursors with regard to parent species of fulvene.



H.R. Zhang, Z. Yang, E.G. Eddings, A.F. Sarofim. “Pollutant Formation in Premixed and Diffusion Flames of Paraffinic Fuels Using the Reduced Utah Surrogate Mechanisms,” In American Chemical Society, Division of Fuel Chemistry, Vol. 52, No. 1, pp. 144--147. 2007.

ABSTRACT

Normal heptane, isooctane and cyclohexane have been the most interested surrogate components for liquid transportation and aviation fuels, due to their roles as indicative fuels for octane number and the representative compounds for normal, iso and cyclo-paraffins. Methodologies of mechanism generation for these representative fuel fractions have been discussed in detail in literature. The basics of fuel consumption in flames have been discussed by Vovelle1, Ranzi2, Zhang3 and coworkers, among others. Ranzi et al.2 presented a lumping technique that was also discussed in detail in an earlier study3 and used for generation of reaction mechanisms that can be used to model flames of liquid fuels. The lumping approach is an effective reduction technique for models of large aliphatic fuels. Reaction pathway analysis presents another reduction technique that was used to reduce a complete kinetic set to smaller models. Doute et al.4 reduced a n-decane model by removing less important reaction routes systematically and still obtained satisfactory agreement between the experimental data and predicted results. Bollig et al.5 proposed a reduced n-heptane mechanism and modeled a diffusion flame with the emphasis on pollutant-related intermediates. The mechanism was further reduced using another technique with the assumption of partial equilibrium for intermediates. There are many important applications that need reduced kinetic mechanism, especially in those that require expensive computations but are less demanding in kinetic details. For example, only a few dozen reactions can be comfortably acquired in aerodynamic applications. In this study, the detailed Utah Surrogate Mechanisms of about 1200 reactions and 210 species3 will be reduced by a combined technique. The resultant mechanism will be used to simulate premixed and counter-flow diffusion flames of normal heptane, iso-octane and cyclo-hexane fuels. And the pollutant formation of soot precursors, e.g. benzene and acetylene, will be investigated for the three common surrogate components.



H.R. Zhang, E.G. Eddings, A.F. Sarofim. “Criteria for Selection of Components for Surrogate of Natural Gas and Transportation Fuels,” In Proceedings of the Combustion Institute, Vol. 31, No. 1, pp. 401--409. January, 2007.
DOI: 10.1016/j.proci.2006.08.001

ABSTRACT

The present paper addressed the production of soot precursors, acetylene, benzene and higher aromatics, by the paraffinic (n-, iso-, and cyclo-) and aromatic components in fuels. To this end, a normal heptane mechanism compiled from sub-models in the literature was extended to large normal-, iso-, and cyclo-paraffins by assigning generic rates to reactions involving paraffins, olefins, and alkyl radicals in the same reaction class. Lumping was used to develop other semi-detailed sub-models. The resulting mechanism for components of complex fuels (named the Utah Surrogate Mechanism) includes detailed sub-models of n-butane, n-hexane, n-heptane, n-decane, n-dodecane, n-tetradecane and n-hexadecane, and semi-detailed sub-models of i-butane, i-pentane, n-pentane, 2,4-dimethyl pentane, i-octane, 2,2,3,3-tetramethyl butane, cyclohexane, methyl cyclohexane, tetralin, 2-methyl 1-butene, 3-methyl 2-pentene and aromatics. Generic rates of reaction classes were found adequate to generate reaction mechanisms of large paraffinic components. The predicted maximum concentrations of the fuel, oxidizer, and inert species, major products and important combustion intermediates, which include critical radicals and soot precursors, were in good agreement with the experimental data of three premixed flames of composite fuels under various conditions. The relative importance in benzene formation of each component in the kerosene surrogate was found to follow the trend aromatics > cyclo-paraffins > iso-paraffins > normal-paraffins. In contrast, acetylene formation is not that sensitive to the fuel chemical structure. Therefore, in formulation of surrogate fuels, attention should be focused on selecting components that will yield benzene concentrations comparable to those produced by the fuel, with the assurance that the acetylene concentration will also be well approximated.


2006


G. Adluru, E.V.R. DiBella, R.T. Whitaker. “Automatic Segmentation of Cardiac Short Axis Slices in Perfusion MRI,” In Proceedings of The 2006 IEEE International Symposium on Biomedical Imaging, pp. 133--136. 2006.



G. Adluru, E.V.R. DiBella. “Segmentation Based Registration of Myocardium in Cardiac Perfusion Images,” In Proceedings of The 14th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM), Vol. 14, pp. 1223. 2006.



G. Adluru, E.V.R. DiBella, M.C. Schabel. “Model-Based Registration for Dynamic Cardiac Perfusion MRI,” In Journal of Magnetic Resonance Imaging, Vol. 24, No. 5, Wiley Subscription Services, Inc., A Wiley Company, pp. 1062--1070. 2006.
DOI: 10.1002/jmri.20756



I. Altintas, O. Barney, Z. Cheng, T. Critchlow, B. Ludaescher, S.G. Parker, A. Shoshani, M. Vouk. “Accelerating the Scientific Exploration Process with Scientific Workflows,” In J. Phys. : Conf. Ser., Vol. 46, pp. 468--478. 2006.



O. Alter. “Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data,” In Proceedings of the National Academy of Sciences, Vol. 103, No. 44, Proceedings of the National Academy of Sciences, pp. 16063--16064. October, 2006.
DOI: 10.1073/pnas.0607650103



O. Alter, G. H. Golub. “Singular Value Decomposition of Genome-Scale mRNA Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band Broadening,” In Proceedings of the National Academy of Sciences, Vol. 103, No. 32, Proceedings of the National Academy of Sciences, pp. 11828--11833. July, 2006.
DOI: 10.1073/pnas.0604756103



E.W. Anderson, S.P. Callahan, G.T.Y. Chen, J. Freire, E. Santos, C.E. Scheidegger, C.T. Silva, H.T. Vo. “Visualization in Radiation Oncology: Towards Replacing the Laboratory Notebook,” SCI Institute Technical Report, No. UUSCI-2006-017, University of Utah, 2006.



A.E. Anderson, B.J. Ellis, J.A. Weiss. “Verification, Validation and Sensitivity Studies in Computational Biomechanics,” In Computer Methods in Biomechanics and Biomedical Engineering, pp. (in press). 2006.



R. Armstrong, G. Kumfert, L.C. McInnes, S.G. Parker, B. Allan, M. Sottile, T. Epperly, T. Dahlgren. “The CCA Component Model for High-Performance Scientific Computing,” In Concurrency and Computation: Practice & Experience, Vol. 18, No. 2, John Wiley and Sons Ltd., Chichester, UK pp. 215--229. 2006.
ISSN: 1532-0626



G.A. Ateshian, B.J. Ellis, J.A. Weiss. “Equivalence Between Instantaneous Biphasic and Incompressible Elastic Material Response,” In Journal of Biomechanical Engineering, pp. (in press). November, 2006.



L. Atty, N. Holzschuch, M. Lapierre, J.-M. Hasenfratz, C.D. Hansen, F.X. Sillion. “Soft Shadow Maps: Efficient Sampling of Light Source Visibility,” In Computer Graphics Forum, Vol. 25, No. 4, pp. 725--741. 2006.



S.P. Awate, T. Tasdizen, N. Foster, R.T. Whitaker. “Adaptive, Nonparametric Markov Modeling for Unsupervised, MRI Brain-Tissue Classification,” SCI Institute Technical Report, No. UUSCI-2006-008, University of Utah, 2006.



S.P. Awate, T. Tasdizen, R.T. Whitaker. “Unsupervised Texture Segmentation with Nonparametric Neighborhood Statistics,” In Proceedings of The European Conference on Computer Vision (ECCV) 2006 Springer, Lecture Notes in Computer Science, pp. 494--507. 2006.