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Supercomputing Institute

Biochemistry, Molecular Biology, and Biophysics

Using Nuclear Magnetic Resonance Spectroscopy toUnderstand How Proteins Function

Volume 21, Number 2

Historically, structural biolo-gists have provided de-tailed snapshots of biolog-

ical molecules. Such pictures haveprovided important insights into thephysical and chemical properties ofthe molecules that define our healthand who we are. Much of biologicalfunctioning, however, occurs in thecontext of dynamic complexes andmoving beyond such static snap-shots is expected to have dramaticimplications in our understandingof biological systems.

Research in the laboratory of As-sistant Professor Kylie Walters of theDepartment of Biochemistry, Mole-cular Biology, and Biophysics is fo-cused around providing such dy-namic pictures of how proteins in-

teract with each other. Of specialfocus is the ubiquitin-proteasomepathway, which is well-renownedfor its role in targeted proteindegradation. This system also par-ticipates in transcriptional regula-tion, apoptosis, deoxyribonucleicacid (DNA) repair, immune re-sponse, and cell cycle control. Mal-function of the ubiquitin-protea-some pathway is associated withneurological disorders, inflammato-ry processes, and cancer. Indeed theassociation of this degradation path-way with carcinogenesis has impact-

ed the clinical world, as a specificproteasome inhibitor (Bortezomib)is approved for use in patients withmultiple myeloma.

The Walters lab explores how keycomponents of the ubiquitin-pro-teasome pathway interact to facili-tate diverse cellular events. Towardsthis goal they have provided three-dimensional structures of the ubiq-uitin recognition proteins hHR23a(published in Proceedings of the Na-tional Academy of Sciences, 2003;

Also in This Issue

Investigating Polymer Solubility in Supercritial CO2 . . . . . . . . . .2

Chemical Reaction Rates . . . . . . . .4Bioinformatics: Building Bridges . .6National Advisory Board Visit . . . .8Virtual Laboratory for Earth and

Planetary Materials . . . . . . . . . . .9Integrated Tools for Computational

Chemical Dynamics . . . . . . . . . .9Research Reports . . . . . . . . . . . . .10

Summer 2005 Research Bulletin of the Supercomputing Institute

for Digital Simulation and Advanced Computation

Figure 1: The UBA domain of hHR23a is illustrated (in purple) in a protein com-plex with ubiquitin (in gray).

continued on page 2

Chemistry

Investigating Polymer Solubility in Supercritical Carbon Dioxide

Supercritical carbon dioxide hastremendous potential as a ver-satile, environmentally benign

process solvent because of the acces-sibility of its critical point, the tun-ability of its solvent properties, itshigh abundance, and its low cost.The use of CO2 has been limited,though, because of the difficulty ofdissolving polar and high-molecu-lar-mass compounds in the neat sol-vent. This is despite the fact thatother non-polar solvents with simi-lar pure phase properties, specifical-

ly short alkanes, often exhibit rea-sonable solvating power for polarmolecules that have difficulty beingdissolved in CO2.

The use of surfactants has beenthe primary means for increasing

solubility in CO2. The most successhas been achieved in utilizing blockcopolymer surfactants composed ofa “CO2-philic” block and anotherblock with favorable interactionswith other molecules that would

Figure 1: Structure formula for CARB-PEO copolymers.

UMSI 2003/19) and S5a (Journalof Molecular Biology, 2005; UMSI2005/31 and CB 2005/12). In ad-dition, they have defined how eachof these proteins interacts withubiquitin (published in Biochem-istry, 2003; UMSI 2003/218).Structural work in the Walters labo-ratory is performed in solution byusing nuclear magnetic resonance(NMR) spectroscopy; this technolo-gy is also used to determine the dy-namic properties of biomolecules.S5a and hHR23a have multipleubiquitin binding sites and a sharedinherent flexibility that the Walterslab postulates may aid in bindingpolyubiquitin. Structural work inthe Walters laboratory has led to aworking model of how the outcomeof ubiquitylation is determined incells. In addition it has provided keyinsights into how hHR23 proteinslink members of the ubiquitin-pro-

teasome pathway to regulate thelifespans of other proteins (reviewedin Biochimica and Biophysica Acta,2004; UMSI 2004/248 and CB2004/68).

In a collaboration with AssistantProfessor Duncan Clarke of the De-partment of Genetics, Cell Biology,and Development, the Walters labstudies hHR23 protein function incell cycle progression. HHR23 in-teracts with two other ubiquitin-binding proteins (Ddi1 and Dsk2)and these proteins play an impor-tant role in cell cycle progression.By using NMR spectroscopy, theWalters lab is defining how hHR23proteins interact with Ddi1 andDsk2 and how these interactions af-fect its polyubiquitin binding capa-bilities. This research is expected toreveal cellular mechanisms that haveevolved to preserve genomic stabili-ty and could therefore provide in-

sights towards its improvement. Another focus of Professor Wal-

ters’s laboratory is arylamine N-acetyltransferase (NAT), which theystudy in collaboration with Profes-sor Rick Wagner and Professor PatHanna of the Department of Medi-cinal Chemistry. Humans have twoNAT proteins that function in me-tabolizing various substances, someof which are potential carcinogens.Differences within these two pro-teins exist between individuals,some of which have been connectedby epidemiological studies to an in-creased likelihood of being diag-nosed with urinary bladder cancer.Research in the Walters lab is aimedat revealing how NAT proteinsfunction and how differences thatexist between humans affect theirability to function properly.

This research is supported by theNational Institutes of Health.

Supercomputing Institute Research Bulletin Summer 20052

Biochemistry, Molecular Biology, and Biophysics

Chemistry

Summer 2005 Supercomputing Institute Research Bulletin 3

otherwise have low solubility inCO2, allowing the efficient use ofCO2 for a variety of processes.CO2-philic polymer blocks contain-ing fluorinated alkyl chains or fluo-roethers have been found to haverelatively high solubility in CO2,but their practical use has been hin-dered by their high production costand low biodegradability. Anotherpromising class of surfactants wasrecently introduced by Eric Beck-man and co-workers at the Univer-sity of Pittsburgh, who demonstrat-ed that carbonate polyether blockcopolymers have high solubility inCO2 at relatively low pressures.

Molecular simulation can providean invaluable tool for the explo-ration of phase equilibria, allowingprediction of coexistence propertiesand determination of the micro-scopic factors that govern themacroscopic observables. But thesimulation of phase equilibria forpolymeric systems using a realisticdescription of the system that accu-rately accounts for the differences inmolecular interactions of differentchemical groups remains a signifi-cant challenge. Another benefit ofmolecular simulation is that oncethe force field has been validatedagainst available experimental data,it can be used to make predictionsfor related systems thereby guidingthe development of improved sepa-ration systems.

Dr. Collin Wick, an NSF Distin-guished International PostdoctoralFellow, Professor Ilja Siepmann,University of Minnesota, and Pro-fessor Doros Theodorou, NationalTechnical University of Athens,have employed a combination ofadvanced simulation techniques

(http://www.chem.umn.edu/groups/siepmann/research/algorithm.html)and the transferable potentials forphase equilibria (TraPPE:http://www.chem.umn.edu/groups/siepmann/research/forcefield.html)force field to investigate the solubili-ties of poly(ethylene oxide) (PEO)and a carbonate poly(ethyleneoxide) (CARB-PEO) copolymer (seeFigure 1) in CO2.

Two separate polymer-CO2 sys-tems were investigated containingeither PEO homopolymer (m=0 andn=11 in Figure 1) orCARB-PEO copolymer(m=2 and n=7, i.e. witha CARB weight fractionof 36%) at a tempera-ture of 335 K and apressure of 16 MPa. TheGibbs ensemble simula-tions utilize two separatesimulation boxes for theCO2-rich and polymer-rich phases containing2000 CO2 moleculesand 40 PEO or CARB-PEO polymer chains.

The Gibbs ensembleMonte Carlo simula-tions yield CO2-richphases with 3.1 ± 0.2and 5.1 ± 0.2 (w/w) forthe PEO and CARB-PEO systems, respective-ly (Figure 2). This agreeswell with the experimen-tal observation that in-troducing carbonyl oxy-gens into polymer chains

results in a higher solubility inCO2. The good agreement for themacroscopic composition observ-ables for these polymers (and smallmolecules, not shown) with CO2provides confidence for the molecu-lar-level analysis presented in thefollowing. The figure shows snap-shots of the CO2-rich phases for theCARB-PEO and PEO systems.Polymer aggregation is only presentfor the CARB-PEO copolymer; aresult that is also supported fromanalysis of polymer segment-poly-

Figure 2: Snapshots of theCO2-rich phases for thePEO system (top) and theCARB-PEO system (bot-tom).

continued on page 4

Chemistry


mer segment radial distributionfunctions and number integrals (notshown).

A detailed analysis of the firstsolvation shell around the carbonyland ether groups points to a muchlarger solvent-accessible surface areafor the carbonyl oxygen. This ex-plains as to why the carbonyl groupenhances solubility over the more

sterically hindered ether oxygen de-spite that the binding enthalpy doesnot discriminate between acetatecarbonyl and ether oxygens. A simi-lar argument might explain the en-hanced solubility of fluorocarbonswhere the fluorine atoms expose alarger surface area for attractive in-teractions with CO2. Of course,other factors also contribute to en-

hanced polymer solubility, amongthose are the strength of the poly-mer-polymer interactions and itsconformational flexibility.

This research was supported bythe National Science Foundationand the Minnesota SupercomputingInstitute.

Quantum Mechanical Reaction Rate Constants forChemical Reactions by Vibrational Configuration Interaction

Vibrational configuration in-teraction is a promisingmethod for representing the

quantum mechanical motions ofmolecules because it offers the pos-sibility of an efficient hierarchicalrepresentation of the potential.This prompts a re-examination ofthe power of time-independentquantum mechanics to solve dy-namical problems, and now, for thefirst time, a converged quantummechanical rate constant has beencalculated for a polyatomic reactionby using time-independent basisfunctions. This work was carriedout by graduate student ArindamChakraborty and Lloyd H. Reyer-son Professor Donald G. Truhlar ofthe Chemistry Department usingthe OH + H2 ! H2O + H reactionas a prototype reaction to demon-strate the method. This applicationis a four-body system, but themethod used here is a generalnonorthogonal spectral method thatis not special to four-body reactions,and the results demonstrate that the

Figure 1. Potential energy contours of the OH + H2 system as a function of the co-ordinates of the bond-forming and bond-breaking modes, with all other degrees offreedom fixed at the saddle point geometry. (The other degrees of freedom are fixedfor the plot, but not—of course—for calculating the rate constant.) The contourspacing is 0.5 eV from 0 to 1 eV, then 1 eV from 1 to 5 eV. A dividing surface pass-ing through the transition state of the reaction was defined such that it separates thereactant region from the product region; this dividing surface is shown as a solid lineinclined at 45° to the axes. The reaction rate over a wide range of temperature(300–1000 K) was calculated by evaluating the net flux of particles across this sur-face from the reactants to the products arrangement. The locations of centers of the2D Gaussian basis functions are shown by solid triangles.

time-independent vibrational con-figuration method can be used forcalculating rate constants for muchlarger reactions than have beentreated up to now.

The OH + H2 system has six vi-brational degrees of freedom. Nor-mal mode analysis at the saddlepoint geometry gives frequencies of3675, 2439, 1191, 690, 573 and1210 cm-1 for modes 1 to 6, re-spectively. Modes two and six arethe two stretch modes that activelyparticipate in the bond-forming andbond-breaking process. These tworeactive modes were representedusing two-dimensional (2D) distrib-uted Gaussian functions, and the re-maining four spectator modes wererepresented by harmonic oscillatorbasis functions. The six-dimensional(6D) basis was formed by taking adirect product between 243 2D dis-tributed Gaussian functions and 18four-dimensional harmonic oscilla-tor functions, resulting in 4374nonorthogonal 6D basis functionsfor the vibrational configuration in-teraction expansion. The centers ofthe 243 distributed Gaussian func-tions used in the present calcula-tions are shown in Figure 1. Thegeneralized eigenvalues and eigen-vectors of the Hamiltonian wereused to compute the quantum me-chanical flux through a hypersurfacedividing reactants from productsand the corresponding flux autocor-relation function, which, along withthe rotational partition function ofthe transition state and the reactantpartition function, was used to cal-culate the rate constant. Figure 2shows the flux autocorrelation func-tion and its time integral at 300 K.The computed thermal rate con-

stants are in good agreement withthe earlier results obtained by Gold-field and Gray using time-depend-ent wave packet calculations. Overthe temperature range of 300–1000K, the mean unsigned deviationfrom the time-dependent wavepacket calculations is only 2%.

The present calculation hasopened doors for reaction rate cal-culations for larger polyatomic sys-tems like C2H6 + H ! C2H5 +H2. A global potential energy sur-face for this reaction has been creat-ed, also involving collaboration withresearch associate Hai Lin and grad-uate student Yan Zhao, by a newcombined valence bond–molecularmechanics method, and functionsare being optimized to form an effi-cient vibrational basis. The C2H6 +

H reaction has 21 vibrational de-grees of freedom, and one of thechallenging aspects of this project isthe computation of the matrix ele-ments of the Hamiltonian operator.Each matrix element involves a 21-dimensional integral over all thenormal mode coordinates, and a di-rect evaluation of such integralsusing Gauss-Hermite quadrature iscomputationally prohibitive. Toovercome this computational bottle-neck, the researchers will use the hi-erarchical expansion of the potentialoperator, which has been shown (incollaborative work with Bowmanand Carter) to be very efficient forbound-state calculations. This workis supported by the National Sci-ence Foundation.

Chemistry


Figure 2. Flux autocorrelation function (a) and its time integral (b) as functions oftime for the OH + H2 reaction at 300 K, as calculated by time-independent quan-tum mechanics.


The Fourth Annual Bioinfor-matics: Building BridgesSymposium was held at the

Digital Technology Center on April14 and 15, 2005. This was the firsttime that this annual event has ex-tended to two full days. The sympo-sium includes participants from aca-demics, industry, and non-profit in-stitutions, with expertise in comput-er science; physics; math; statistics;molecular, cellular and developmen-tal biology; biochemistry and bio-physics; animal science; ecology,evolution, and behavior; and thehealth sciences. The tutorials andpresentations were Webcast live viaUNITE.

The first day of the symposiumwas mostly dedicated to tutorials(see sidebar, page 7). The final eventof the day was a talk, co-sponsoredby the Graduate Program in HealthInformatics and the BiotechnologyInstitute, by Timothy Griffin of theDepartment of Biochemistry, Mole-cular Biology, and Biophysics. Thispresentation discussed computation-al methods and bioinformatics in

proteomic stud-ies.

Over 120 peo-ple attended thesecond day of thesymposium. Inthe morning,Keith A. Bagger-ly, University ofTexas, discussedproteomics, ovar-ian cancer, andexperimental de-sign; DanielBoley, Universityof Minnesota,talked about recent developments oflinear algebra for bioinformatics;and Christine Elsik, Texas A&MUniversity, gave a presentation onbioinformatics for cattle and honey-bees. In the afternoon, Yang Da,University of Minnesota, talkedabout the detection of epistatic ef-fects of complex traits; KevinKarplus, University of California,Santa Cruz, presented his work onprotein folding by computer; andWei Pan, University of Minnesota,

discussed integra-tive analysis ofmultiple types ofgenomic data.

Besides formaltalks, the sympo-sium included 15poster presenta-tions. Contribu-tors included re-searchers from theUniversity ofMinnesota, the

University of St.

Thomas, IBM, St. Olaf College,and Certusoft. There were also fourexhibits from organizations at theUniversity of Minnesota, includingthe Graduate Program in Bioinfor-matics, the Supercomputing Insti-tute, the Cancer Center, and theCenter for Computational Ge-nomics and Bioinformatics.

For the first time, IBM Life Sci-ences donated a prize for bestposter. Flora Fan, a graduate studentin the Microbiology, Immunology,and Cancer Biology program, wonthe award for her poster, “Transla-tional Effeciency is Linked to Spe-cific mRNA Elements DuringApoptotic Rescue.” The coauthorsfor this poster were Cavan Reilly,Biostatistics, and Peter Bitterman,Medicine.

Cosponsors included the Divi-sion of Health Informatics, theGraduate Faculty in Bioinformatics,the Graduate School, the Super-computing Institute, the DigitalTechnology Center, the AcademicHealth Center, the College of Agri-

Events, Symposia, and Meetings

Bioinformatics: Building Bridges

Left to right: Scott Fahrenkrug, University of Minnesota (seat-ed); David Fan, University of Minnesota; Christine Elsik, TexasA&M University; Daniel Boley, University of Minnesota

Cristian Domnisoru, University of St. Thomas, explains hisposter to symposium attendees.


cultural, Food, and EnvironmentalSciences, the College of BiologicalSciences, IBM, the Institute ofTechnology, SGI, Medtronic, andCertusoft.

Poster and exhibit abstracts,speaker information, and other in-formation about this symposiumcan be found at:

http://www.binf.umn.edu/bisymp05/


Bioinformatics Symposium Tutorials

Bioinformatics ProgrammingZheng Jin Tu, Supercomputing Institute

Microarray Technology and Software ToolsWayne Xu, Supercomputing Institute

BLAST for BeginnersCarlos Sosa, IBMZheng Jin Tu, Supercomputing Institute

Literature Resources for BioinformaticsKevin Messner, University Libraries

Introduction to Homology ModelingYuk Sham, Supercomputing Institute

Biology for BioinformaticsBetsy Martinez-Vaz, Biochemistry, Molecular Biology,

and Biophysics

Top left: Keith Baggerly, M. D. Anderson Cancer Center, discusseshis presentation with Helen Slayton, University of St. Thomas.Middle left: John Carlis and Scott Fahrenkrug (both University ofMinnesota) during a break.Bottom left: Carlos Sosa, IBM, explains his poster to Rick Ross,3M Company.Above: Flora Fan, University of Minnesota, receives her award forBest Poster from Carlos Sosa, IBM.

photo by Marni Anderson-Brown, Digital Technology Center

photo by Brian Hanson, Digital Technology Center


The Supercomputing Insti-tute’s National AdvisoryBoard met with Institute

senior staff and researchers on May9, 2005. The National AdvisoryBoard’s charge is to assist the Insti-tute with its strategic planningprocess to ensure that it stays at theforefront of supercomputing in theUnited States. They provided rec-ommendations about the Institute’sstrategic plan and input regardingnew initiatives and directions in su-percomputing.

Members of the board include:Dr. Albert F. Wagner, Argonne Na-tional Laboratory, chair; Dr. RobertJernigan, Iowa State University; Dr.David Keyes, Columbia University;and Dr. Daniel Reed, University ofNorth Carolina at Chapel Hill.

The Board met with various In-stitute committees during the day,including the MSI Planning Com-mittee, the Basic Sciences and Com-puting Laboratory Executive andSteering Committees, the Grid andBlueGene Computing Committee,

the Computational Genetics Labo-ratory Executive and Steering Com-mittees, the Supercomputing Re-sources Peer Review Panel, and theResearch Scholarship Peer ReviewPanel.

Members of the Board also metwith Institute of Technology DeanSteven Crouch and Digital Technol-ogy Center Director AndrewOdlyzko, and they received a tourof the Basic Sciences and Comput-ing Laboratory.


National Advisory Board Visit

Top, left to right: Daniel Reed, University of North Carolina, Chapel Hill; Albert Wagner, Argonne National Labo-ratory; David Keyes, Columbia University; Robert Jernigan, Iowa State UniversityBottom left: Daniel Reed, Robert Jernigan, and Albert Wagner talk during a break.Bottom right: Vivek Kapur, University of Minnesota, talks with David Keyes.


Supercomputing Institute Programs

The Virtual Laboratory forEarth and Planetary Materi-als (VLab), a new initiative

funded by the National ScienceFoundation and hosted by the Su-percomputing Institute, is an inter-disciplinary consortium dedicatedto the development and promotionof the theory of planetary materials.Institutions involved in this consor-tium include:

• University of Minnesota • State University of New

York–Stony Brook • Florida State University • Louisiana State University • Indiana State University • University of California–Santa

Monica • DEMOCRITOS Modeling

Center, Trieste, Italy

• Daresbury Laboratory, UnitedKingdom

• University College London,United Kingdom (ES, Physics)

Research at VLab is motivatedand informed by central questionsin Earth and planetary sciences.They pose specific challenges to ma-terials theory and to computationalmethodologies. The emergence ofnovel capabilities is leading to thedevelopment of grand-challengecomputational projects in the studyof these materials. Projects for thenear future include those that: haveovercome fundamental theoreticaldifficulties; address properties otherthan those that have been addressedso far; and involve simulations thatare larger by orders of magnitudethan those that are currently thenorm.

Grand-challenge problems focuson building highly realistic modelstaking into account physical andchemical variations in the system.These studies require massive num-bers of computations and generatehuge amounts of data that cannotbe analyzed by conventional means.This will also require new methodsand tools for collaborative inter-lab-oratory work.

The VLab sponsors interns eachsummer that participate in the Su-percomputing Institute’s annual Un-dergraduate Internship Program.Other outreach activities includeworkshops and tutorials. Further in-formation about the VLab canfound at their Web site:

www.vlab.msi.umn.edu

Virtual Laboratory for Earth and Planetary Materials

Integrated Tools for Computational Chemical Dynamics

The University of MinnesotaSupercomputing Instituteand Chemistry Depart-

ment, in association with PacificNorthwest National Laboratory, re-cently received a grant from the Of-fice of Naval Research to fund a Re-search Tools Design Consortium forComputational Chemistry; thisproject is entitled, “Integrated Toolsfor Computational Chemical Dy-namics.” The goal of this project isto develop more powerful simula-tion methods and incorporate theminto a user-friendly high-throughputintegrated software suite for chemi-cal dynamics.

Recent advances in computerpower and algorithms have madepossible accurate calculations ofmany chemical properties for bothequilibria and kinetics. Nonetheless,applications to complex chemicalsystems, such as reactive processes inthe condensed phase, remain prob-lematic due to the lack of a seamlessintegration of computational meth-ods that allow modern quantumelectronic structure calculations tobe performed with state-of-the-artmethods for electronic structure,chemical thermodynamics, and re-active dynamics. These problems areoften exacerbated by invalidatedmethods, non-modular and non-

portable computer codes, and inad-equate documentation that drasti-cally limit software reliability,throughput, and ease of use. Thegoal of the consortium is to developan integrated software suite thatcombines electronic structure pack-ages with dynamics codes and effi-cient sampling algorithms for con-densed-phase modeling problems,including thermochemical kineticsand rate constants, photochemistryand spectroscopy, and chemical andphase equilibria.

Further information can befound at the Web site:

comp.chem.umn.edu/itccd

Research Reports


Aerospace Engineeringand Mechanics

2005/15, February 2005Direct Numerical Simulation ofTurbulent Jets in CrossflowS. Muppidi and K. Mahesh

2005/55, May 2005Numerical Study of the SteadyState Uniform Flow Past a Rotat-ing CylinderJ. C. Padrino and D. D. Joseph

2005/56, May 2005Migration of a Sphere in TubeFlowB. H. Yang, J. Wang, D. D.Joseph, H. H. Hu, T-W. Pan,and R. Glowinski

2005/81, May 2005Stress Induced Cavitation for theStreaming Motion of a ViscousLiquid Past a SphereJ. C. Padrino, D. D. Joseph,T. Funada, and J. Wang

Astronomy

2005/16, February 2005MHD Simulations of Relic RadioBubbles in ClustersT. W. Jones and D. S. De Young

Biochemstry, MolecularBiology, and Biophysics

2005/28, April 2005Phospholamban Pentamer Quater-nary Conformation Determined byIn-Gel Fluorescence AnisotropyS. L. Robia, N. C. Flohr, andD. D. Thomas

2005/31, April 2005Structure of S5a Bound to Mo-noubiquitin Provides a Model forPolyubiquitin Recognition Q. Wang, P. Young, and K. J.Walters

2005/39, April 2005Organelle and TranslocatableForms of Glyoxysomal Malate De-hydrogenase—The Effect of the N-terminal PresequenceB. Cox, M. M. Chit, T. Weaver,C. Gietl, J. Bailey, E. Bell, andL. Banaszak

2005/69, May 2005Subtilisin-Catalyzed Resolution ofN-Acyl ArylsulfinamidesC. K. Savile, V. P. Magloire, andR. J. Kazlauskas

2005/71, May 2005Molecular Basis of PerhydrolaseActivity in Serine HydrolasesP. Bernhardt, K. Hult, and R. J.Kazlauskas

2005/89, June 2005Unexpected Subtilisin-CatalyzedHydrolysis of a Sulfinamide Bondin Preference to a CarboxamideBond in N-Acyl SulfinamidesP. F. Mugford, V. P. Magloire,and R. J.Kazlauskas

Biomedical Engineering

2005/24, March 2005Deterministic Material-Based Av-eraging Theory Model of CollagenGel MicromechanicsP. L. Chandran and V. H. Baro-cas

Biostatistics

2005/21, February 2005Model Selection For Clustered Re-current Event Data Using NestedGamma Frailty ModelsX. Zhi, L. E. Eberly, and P. M.Grambsch

Chemical Engineeringand Materials Science

2005/12, February 2005Accurate Hybrid Stochastic Simu-lation of a System of CoupledChemical or Biochemical ReactionsH. Salis and Y. Kaznessis

2005/13, February 2005Protegrin Structure-Activity Rela-tionships: Using Homology Modelsof Synthetic Sequences to Deter-mine Structural CharacteristicsImportant for ActivityN. Ostberg and Y. Kaznessis

2005/27, April 2005The Orthorhombic Fddd Networkin Triblock and Diblock Copoly-mer MeltsC. A. Tyler and D. C. Morse

2005/29, April 2005Computing Charge Densities WithPartially Reorthogonalized LanczosC. Bekas, Y. Saad, M. L. Tiago,and J. R. Chelikowsky

2005/45, April 2005Molecular Dynamics Simulationsof Helical Antimicrobial Peptidesin SDS Micelles: What Do PointMutations Achieve? H. Khandelia and Y. N. Kaznes-sis

2005/44, April 2005Physicochemical and Residue Con-servation Calculations to Improvethe Ranking of Protein-ProteinDocking SolutionsY. Duan, B. V. B. Reddy, andY. N. Kaznessis

2005/60, May 2005Spherical-Tip Indentation of Vis-coelastic MaterialL. Cheng, X. Xia, L. E. Scriven,and W. W. Gerberich

2005/76, May 2005Ab Initio Simulations of Non-Sto-ichiometric Cd[x]Te[1-x] LiquidsE. Ko, M. Alemany, J. J. Derby,and J. R. Chelikowsky

Names of University of Minnesota principal investigators appear in bold type.

Research Reports


2005/85, May 2005Suppression of Flow Oscillations ina Vertical Bridgman CrystalGrowth SystemP. Sonda, A. Yeckel, J. J. Derby,and P. Daoutidis

2005/96, June 2005Efficient Computation of the Cou-pling Matrix in Time-DependentDensity Functional TheoryE. Lorin de la Grandmaison,S. B. Gowda, Y. Saad, M. L.Tiago, and J. R. Chelikowsky

Chemistry

2005/11, February 2005An Efficient Linear-Scaling EwaldMethod for Long-Range Electrosta-tic Interactions in CombinedQM/MM CalculationsK. Nam, J. Gao, and D. M.York

2005/20, February 2005Hydrogen Atom Transfers in B12EnzymesR. Banerjee, D. G. Truhlar,A. Dybala-Defratyka, andP. Paneth

2005/22, February 2005Many-Body Tight-Binding Modelfor Aluminum NanoparticlesG. Staszewska, P. Staszewski,N. E. Schultz, and D. G. Truh-lar

2005/30, April 2005High-Order DiscretizationSchemes for Biochemical Applica-tions of Boundary Element Solva-tion and Variational ElectrostaticProjection MethodsB. A. Gregersen and D. M. York

2005/33, April 2005Oligomeric Rods of Alkyl- and Hy-dridogallium ImidesB. L. Kormos, J. A. Jegier, P. C.Ewbank, U. Pernisz, V. G.Young, Jr., C. J. Cramer, andW. L. Gladfelter

2005/34, April 2005Density-Functional Theory andHybrid Density-Functional TheoryContinuum Solvation Models forAqueous and Organic Solvents:Universal SM5.43 and SM5.43RSolvation Models for Any Fractionof Hartree-Fock ExchangeJ. D. Thompson, C. J. Cramer,and D. G. Truhlar

2005/35, April 2005The Enthalpies of Formation of o-,m-, and p-Benzoquinone: Gas-Phase Ion Energetics, CombustionCalorimetry, and QuantumChemical Computations Com-binedA. Fattahi, S. R. Kass, J. F. Lieb-man, M. A. R. Matos, M. S. Mi-randa, and V. M. F. Morais

2005/40, April 2005Potential of Mean Force Calcula-tion for the Proton and HydrideTransfer Reactions Catalyzed byMedium Chain Acyl-CoA Dehy-drogenase: The Effect of Mutationson Enzyme CatalysisS. Bhattacharyya, S. Ma, D. G.Truhlar, M. T. Stankovich, andJ. Gao

2005/48, May 2005The Nature of Iodine OxygenBonds in Hypervalent 10-I-3 Io-dine CompoundsP. Kiprof

2005/87, June 2005Measuring the Change in the In-termolecular Raman Spectrumduring Dipolar SolvationD. F. Underwood and D. A.Blank

2005/97, June 2005Simulating Vapor-Liquid Nucle-ation of Water: A Combined His-togram-Reweighting and Aggrega-tion-Volume-Bias Monte Carlo In-vestigation for Fixed-Charge andPolarizable ModelsB. Chen, J. I. Siepmann, andM. L. Klein

2005/98, June 2005Pressure Dependence of the Vapor-Liquid-Liquid Phase Behavior inTernary Mixtures Consisting of n-Alkanes, n-Perfluoroalkanes, andCarbon DioxideL. Zhang and J. I. Siepmann

2005/99, June 2005Vapor-Liquid and Vapor-SolidPhase Equilibria and United-Atom Benzene Models Near TheirTriple Points: The Importance ofQuadrupolar InteractionsX. S. Zhao, B. Chen, S. Kara-borni, and J. I. Siepmann

2005/100, June 2005Elucidating the Vibrational Spec-tra of Hydrogen-Bonded Aggregatesin Solution: Electronic StructureCalculations With Implicit Solventand First-Principles Molecular Dy-namics Simulations With ExplicitSolvent for 1-Hexanol in n-Hexa-neJ. M. Stubbs and J. I. Siepmann

Civil Engineering

2005/1, January 2005Floodplain Morphometry Extrac-tion from a High Resolution Digi-tal Elevation Model: A Simple Al-gorithm for Regional AnalysisStudiesB. A. Dodov and E. Foufoula-Georgiou

2005/3, January 2005A Dynamic Similarity SubgridModel for Chemical Transforma-tions in Large Eddy Simulation ofthe Atmospheric Boundary LayerJ. F. Vinuesa and F. Porté-Agel

2005/4, January 2005Scale-Dependent Dynamic Modelsfor LES: Surface Heterogeneity Ef-fectsR. Stoll and F. Porté-Agel

2005/51, May 2005Sounding of Finite Solid Bodies ByWay of Topological DerivativeB. B. Guzina and M. Bonnet

Research Reports



2005/64, May 2005A Methodology for Merging Mul-tisensor Precipitation EstimatesBased on Expectation-Maximiza-tion and Scale Recursive Estima-tionR. Gupta, V. Venugopal, andE. Foufoula-Georgiou

2005/84, May 2005Fluvial Processes and StreamflowVariability: Interplay in the Scale-Frequency Continuum and Impli-cations for ScalingB. Dodov and E. Foufoula-Georgiou

2005/94, June 2005Solute Transfer Into a SedimentLayer Under a Standing WaterWave: Numerical Solution of the2-D Advection/Diffusion Equationand Derivation of a 1-D Disper-sion CoefficientQ. Qian, V. Voller, and H. G.Stefan

Computer Scienceand Engineering

2005/9, February 2005Adapting Distributed ScientificApplications to Run-Time Net-work ConditionsM. Sosonkina

2005/25, March 2005Maximizing Semantic Relatednessto Perform Word Sense Disam-biguationT. Pedersen, S. Banerjee, andS. Patwardhan E

2005/29, April 2005Computing Charge Densities WithPartially Reorthogonalized LanczosC. Bekas, Y. Saad, M. L. Tiago,and J. R. Chelikowsky

2005/36, April 2005Multi-Objective Hypergraph Par-titioning Algorithms for Cut andMaximum Subdomain DegreeMinimizationN. Selvakkumaran andG. Karypis

2005/37, April 2005Frequent Sub-Structure-Based Ap-proaches for Classifying ChemicalCompoundsM. Deshpande, M. Kuramochi,N. Wale, and G. Karypis

2005/38, April 2005Clustering in Life SciencesY. Zhao and G. Karypis

2005/42, April 2005Filtered Conjugate Residual-TypeAlgorithms With ApplicationsY. Saad

2005/57, May 2005Discovery of Patterns in Earth Sci-ence Data Using Data MiningP. Zhang, M. Steinbach,V. Kumar, S. Shekhar, P.-N. Tan,S. Klooster, and C. Potter

2005/67, May 2005Intrusion Detection: A SurveyA. Lazarevic, V. Kumar, andJ. Srivastava

2005/68, May 2005The MINDS–Minnesota IntrusionDetection SystemL. Ertöz, E. Eilertson, A. Lazare-vic, P.-N. Tan, V. Kumar, J. Sri-vastava, and P. Dokas

2005/72, May 2005RBA: An Integrated Frameworkfor Regression Based on AssociationRulesA. Ozgur, P.-N. Tan, andV. Kumar

2005/73, May 2005A Framework for Discovering Co-location Patterns in Data SetsWith Extended Spatial ObjectsH. Xiong, S. Shekhar, Y. Huang,V. Kumar, X. Ma, and J. S. Yoo

2005/74, May 2005HICAP: Hierarchical ClusteringWith Pattern PreservationH. Xiong, M. Steinbach, P.-N.Tan, and V. Kumar

2005/80, May 2005Resolving Ambiguities in Biomed-ical Text With Unsupervised Clus-tering ApproachesG. Savova, T. Pedersen, A. Pu-randare, and A. Kulkarni

2005/82, May 2005An Estimator for the Diagonal of aMatrixC. Bekas, E. Kokiopoulou, andY. Saad

2005/96, June 2005Efficient Computation of the Cou-pling Matrix in Time-DependentDensity Functional TheoryE. Lorin de la Grandmaison,S. B. Gowda, Y. Saad, M. L.Tiago, and J. R. Chelikowsky

Electrical and Computer Engineering

2005/2, January 2005The Applicability of AdaptiveControl Theory to QoS Design:Limitations and SolutionsK. Wu, D. J. Lilja, and H. Bai

2005/32, April 2005Fast Computation of the Tempera-ture Distribution in VLSI ChipsUsing the Discrete Cosine Trans-form and Table Look-upY. Zhan and S. S. Sapatnekar

2005/46, May 2005Exchange Coupled CompositeMedia for Perpendicular MagneticRecordingR. H. Victora and X. Shen

2005/54, May 2005Microarchitecture-Aware Floor-planning Using a Statistical De-sign of Experiments ApproachV. Nookala, Y. Chen, D. J. Lilja,and S. S. Sapatnekar

Research Reports


Geology and Geophysics

2005/5, January 2005Visualization and Analysis ofMulti-Terabyte GeophysicalDatasets in an Interactive SettingWith Remote Webcam CapabilitiesB. J. Kadlec, D. A. Yuen, andG. Erlebacher

2005/6, January 2005A Grid Framework for Visualiza-tion Services in the Earth SciencesG. Erlebacher, D. A. Yuen, E. F.Bollig, M. Pierce, and S. Pal-lickara

2005/7, January 2005Quartz Rheology and Short-Timescale Crustal InstabilitiesK. Regenauer-Lieb and D. A.Yuen

2005/10, February 2005Simulated Tomographic Imagery ofCold Hydrous Upper-MantlePlumes in the Mantle WedgeT. V. Gerya, J. A. D. Connolly,D. A. Yuen, W. Gorzcyk, andA. M. Capel

2005/43, April 2005Tradeoffs in Chemical and Ther-mal Variations in the Post-Per-ovskite Phase Transition: MixedPhase Regions in the Deep LowerMantleF. J. Spera, D. A. Yuen, andG. Giles

2005/50, May 2005Efficient Adjoint Sensitivity Analy-sis for Flow and Transport in theEarth’s Crust and MantleC. A. Hier Majumder, B. J.Travis, E. Bélanger, G. Richard,A. P. Vincent, and D. A. Yuen

2005/70, May 2005River Systems With Complex Net-work Topology Modeled With Fineand Coarse Grained Cellular Au-tomataP. Topa, W. Dzwinel, and D. A.Yuen

Mathematics

2005/14, February 2005An Equation-Free ComputationalApproach for Extracting Popula-tion-Level Behavior from Individ-ual-Based Models of BiologicalDispersalR. Erban, I. G. Kevrekidis, andH. G. Othmer

2005/52, May 2005Existence of Energy Minimizers forMagnetostrictive MaterialsP. Rybka and M. Luskin

2005/93, June 2005On the Calculation of Maass CuspFormsD. A. Hejhal

Mechanical Engineering

2005/18, February 2005Numerical Simulation of FlowField and Heat Transfer of Stream-lined Cylinders in CrossflowZ. Li, J. Davidson, and S. Man-tell

2005/19, February 2005Friction Drag Resulting From theSimultaneous Imposed Motions ofa Freestream and Its BoundingSurfaceJ. P. Abraham and E. M. Spar-row

2005/53, May 2005Atmospheric Pressure Glow Dis-charge Initiation From a SingleElectron AvalancheP. Zhang and U. Kortshagen

2005/58, May 2005A Novel Nonlinearly Explicit Sec-ond-Order Accurate L-StableMethodology for Finite Deforma-tion: Hypoelastic/Hypoelasto-Plas-tic Structural Dynamics ProblemsX. Zhou, D. Sha, and K. K.Tamma

2005/59, May 2005A New Unified Theory UnderlyingTime Dependent Linear First-Order Systems: A Prelude to Algo-rithms by DesignX. Zhou and K. K. Tamma

2005/61, May 2005A Compressible Finite Volume For-mulation for Large Eddy Simula-tion of Turbulent Pipe Flows atLow Mach Number in CartesianCoordinatesX. Xu, J. S. Lee, and R. H.Pletcher

2005/62, May 2005Large Eddy Simulation of Turbu-lent Boundary Layers Subjected toFree-Stream TurbulenceK. Liu and R. H. Pletcher

2005/63, May 2005A Computational Analysis of theRadiative and Convective ProcessesWhich Take Place in a Preheat-ed/Non-Preheated OvenE. M. Sparrow and J. P. Abra-ham

2005/65, May 2005Design, Analysis, and Synthesis ofGeneralized Single Step SingleSolve and Optimal Algorithms forStructural DynamicsX. Zhou and K. K. Tamma

2005/66, May 2005Transient Algorithms for HeatTransfer: General Developmentsand Approaches for TheoreticallyGenerating Nth-Order Time Accu-rate Operators Including Practical-ly Useful Second-Order FormsK. K. Tamma, X. Zhou, andD. Sha

2005/79, May 2005Nanoparticle Coagulation via aNavier-Stokes/Nodal Methodology:Evolution of the Particle FieldS. C. Garrick, K. E. J. Lehtinen,and M. R. Zachariah

2005/86, May 2005Universal Solutions for the Stream-wise Variation of the Temperatureof a Moving Sheet in the Presenceof a Moving FluidE. M. Sparrow and J. P. Abra-ham

2005/88, June 2005Design and Relative Stability ofMulticomponent NanowiresT. Dumitrica, V. Barone,M. Hua, and B. I. Yakobson

Research Reports



2005/95, June 2005Natural Convective Flow andHeat Transfer in a Collector Stor-age With an Immersed Heat Ex-changer: Numerical StudyY. Su and J. H. Davidson

Neuroscience

2005/8, February 2005The Expression and Function ofMTG/ETO Family Proteins Dur-ing NeurogenesisN. Koyano-Nakagawa andC. Kintner

Operations andManagement Science

2005/49, May 2005Model Discrimination-AnotherPerspective on Model-Robust De-signsB. A. Jones, W. Li, C. J. Nacht-sheim, and K. Q. Ye

Pharmaceutics

2005/23, March 2005Measurement of Process-DependentMaterial Properties of Pharmaceu-tical Solids by NanoindentationX. Liao and T. S. Wiedmann

2005/41, April 2005Effect of Supersaturation on theCrystallization of PhenylbutazonePolymorphsS. Datta and D. J. W. Grant

2005/78, May 2005Mechanochromism of PiroxicamAccompanied by IntermolecularProton Transfer Probed by Spectro-scopic Methods and Solid-PhaseChangesA. R. Sheth, J. W. Lubach, E. J.Munson, F. X. Muller, andD. J. W. Grant

Pharmacology

2005/26, April 2005Chronic Administration of StatinsAlters Multiple Gene ExpressionPatterns in Mouse Cerebral CortexL. N. Johnson-Anuna, G. P. Eck-ert, J. H. Keller, U. Igbavboa,C. Franke, T. Fechner, M. Schu-bert-Zsilavecz, M. Karas, W. E.Müller, and W. G. Wood

Physics

2005/17, February 2005Local Density of States and OrderParameter Configurations in Lay-ered Ferromagnet-SuperconductorStructuresK. Halterman and O. T. Valls

2005/75, May 2005Two-Dimensional Super Yang-Mills Theory Investigated with Im-proved ResolutionJ. R. Hiller, S. Pinsky, N. Sal-wen, and U. Trittmann

2005/77, May 2005Binding Energies of HydrogenMolecules to Isoreticular Metal-Organic Framework MaterialsT. Sagara, J. Klassen, J. Ortony,and E. Ganz

2005/83, May 2005Phase Diagram of the Vortex Sys-tem in Layered SuperconductorsWith Strong Columnar PinningC. Dasgupta and O. T. Valls

2005/91, June 2005Under-Knotted and Over-KnottedPolymers: 1. Unrestricted LoopsN. T. Moore, R. C. Lua, andA. Y. Grosberg

2005/92, June 2005Under-Knotted and Over-KnottedPolymers: 2. Compact Self-Avoid-ing LoopsR. C. Lua, N. T. Moore, andA. Y. Grosberg

2005/101, June 2005Phonon Mediated Helium AtomTransmission Through SuperfluidHelium FourK. A. Lidke, A. Wynveen,N. Baisch, C. Koay, C. F. Giese,and J. W. Halley

2005/102, June 2005Mechanisms of Lithium Transportin Amorphous Polyethylene OxideY. Duan, J. W. Halley, L. Cur-tiss, and P. Redfern

2005/103, June 2005Self Consistent Tight BindingStudy of Low-Index Titanium Sur-facesS. Erdin and J. W. Halley

2005/104, June 2005Application of Self ConsistentTight Binding Method to theStudy of Anatase NanocrystalsJ. W. Halley, S. Erdin, Y. Lin,and P. Zapol

2005/105, June 2005Helium-Vapor Dynamics: CanBEC Be Produced in a MovingFrame Without ConfinementJ. W. Halley, Y. Lutyshyn, andA. Wynveen

Physiology

2005/47, May 2005Magnetosphere-Ionosphere Cou-pling by Alfvén Waves: BeyondCurrent ContinuityR. L. Lysak and Y. Song

Veterinary andBiomedical Sciences

2005/90, June 2005Regulation of Apoptotic Pathwaysin Bovine "/# T CellsM. Deng, J. Liu, C. N. Pelak,C. A. Lancto, and M. S. Abra-hamsen

Research Reports


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