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REPRESENTATIVE PUBLICATIONS
Research Interests
4
We have pioneered the developmentof many-body methods in quantumchemistry; that is, many-body pertur-bation theory (MBPT, also known asMP) and its infinite-order coupled-clus-ter (CC) generalizations for electron cor-relation to provide predictive solutionsof the Schrödinger equation for mo-lecular structure, spectra, and reac-tions. We have helped to establish thenow well-known paradigm of size-ex-tensive methods [MBPT(2)<M B P T ( 3 ) < C C D < C C S D < C C S D ( T )<CCSDT< CCSDT(Q)< full CI] for con-verging electronic structure results.
Molecular Excited States
Whereas most recent quantum chem-istry has focused on the ground statesof molecules, the problems with ex-cited states are quite interesting andhave proven to be far more difficult formodern quantum chemistry. To ad-dress this problem, we introduced theEOM-CC method and its similarity-transformed analogue, STEOM-CC. Be-cause these approaches are concep-tually single reference, they offer thesame ease of application as is currentlythe case for ground states. STEOM-CC,in particular, is a rigorously correlatedversion that is conceptually like mono-
Coupled-Cluster Approach to Molecular Struc-ture and Spectra: A Step toward PredictiveQuantum Chemistry, R.J. Bartlett, J. Phys. Chem.93, 1697-1708 (featured article) (1989).
Applications of Post-Hartree-Fock Methods: ATutorial, R.J. Bartlett and J.F. Stanton, in Reviewsin Computational Chemistry, Volume V, eds. K.B.Lipkowitz and D.B. Boyd. VCH Publishers, NewYork, pages 65-169 (1994).
Coupled-Cluster Theory: An Overview of Recent De-velopments, R.J. Bartlett in Modern Electronic Struc-ture Theory, Part II, ed. David R. Yarkony. World Scien-tific Publishing Co., Singapore, pgs 1047-1131 (1995).
Ab Initio Density Functional Theory: OEP-MBPT(2) - aNew Orbital-Dependent Correlation Functional, I.Grabowski, S. Hirata, S. Ivanov, and R.J. Bartlett, J.Chem. Phys. 116, 4415-4425 (2002).
Predicted NMR Coupling Constants Across HydrogenBonds: A Fingerprint for Specifying Hydrogen BondType?, J.E. DelBene, S.A. Perera and R.J. Bartlett, Com-munications, J. Am. Chem. Soc., 122, 3560-3561 (2000).
Rodney J.Bartlett
GraduateResearchProfessorChemistry
andPhysics
392-6974
Rm. 2338New Physics
Building
Coupled-ClusterTheory
Ab Initio DFT
Excited States
Hyper-polarizabilities
MetastablePolynitrogen
Molecules
NMR CouplingConstants
Polymers
Non-classical 2-norbornyl cation
excited CI and has similar computationaladvantages. Specifically, we have beenable to present the first ab initio-correlatedstudy of the electronic spectra of free baseporphin that used a polarized basis set.
NMR Coupling Constants
One long-term problem for electronic struc-ture theory has been adequate first-prin-ciples determination of NMR coupling con-stants. EOM-CC provides an approach thatpermits the evaluation of coupling con-
stants. After demonstrating its high accuracy(average error of 3.5 Hz for a wide variety ofdifferent coupling constants), we predictedthe previously unknown coupling constantsfor bridged H in the nonclassical ethyl
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carbocation and determined the constants for thebridged C atom in the nonclassical 2-norbonyl cation,which had resisted experimental determination. Thismolecule has been a focus of the long-term, classicalversus nonclassical, carbocation debate. We now workon the coupling constants across hydrogen bonds inbiological systems, currently a quite hot research area.
Molecules that do not exist but should
We use our predictive quantum chemical techniquesas a “microscope” to “look” for molecules that by elec-tronic considerations should exist, but are not knownexperimentally, primarily because there are morestable forms of the composite atoms. Using high-leveltheory, we have proposed the existence of meta-stable molecules like tetrahedral N4, octahedral N8,N5
-, N6O3, bipentazole, and others. All are found tobe local minima on their potential energy surfaceswith adequate activation barriers to unimolecular dis-sociation to be observ-able. We characterize themolecules by predictingtheir vibrational and elec-tronic spectra for their ex-perimental identification.Verifying our predictions,the first observation of N5- was recently achieved.
Ab Initio DFT
The greatest weakness in density functional theory isthat there is no systematic way to converge to the rightanswer. This is in contrast to ab initio correlated meth-ods like CC/MBPT. To rectify this problem, we have em-barked upon developing the potentials for exchangeand correlation from inverting exact ab initio orbital-de-pendent expressions by functional differentiation withrespect to the density. The first step in this is to introduce“exact exchange” which we have recently done for mol-ecules. This has many consequences, including excep-tional improvement in excitation energies of excitedstates. The next step is to obtain correlation potentialsbased upon orders of MBPT. This alleviates some limi-tations in the current generation of DFT methods andcorrectly describes Van der Waals interations.
Rodney J.Bartlett
Rodney J. BartlettRodney J. Bartlett
Carbon Clusters
The carbon clusters C2-C10, their cations, anions, anddouble anions are fascinating interstellar species.We initiated the current debate about the compara-tive stability of C2n cyclic and linear carbon clustersby finding the cyclic forms (particularly C4, which isnot known experimentally) to be competitive in sta-bility. Because the cyclic forms are singlets and thelinear forms triplets, they cannot generallyinterconvert, so the cyclic forms should be observ-able under the right experimental conditions. Ex-perimental observations of cyclic C6 and C8 haverecently been reported, verifying this hypothesis.Our group’s work also supports experimental find-ings of the existence of gas phase dianions of lin-ear C8 and C10, but disputes the observation of C7
-2.
Electron Correlation inPolymers, Surfaces,
and Crystals
The electronic struc-ture of periodic infinitesystems can be stud-ied with Hartree-Fockand density functionaltheory. However, abinitio correlated meth-ods like MBPT and CCtheory have scarcelybeen applied. As size-
extensive methods, they are the only ab initio corre-lated methods applicable to infinite systems. As inmolecules, it would be highly desirable to have aconverging series of approximations for the elec-tron correlation problem in solids, because the mostinteresting phenomena often depend critically uponcorrelation. We have embarked on the quest, pre-senting thorough studies of MBPT (2) for band struc-ture, band gaps, structure, vibrational spectra, andphotoelectron spectra of polymers. Using such meth-ods, we have been able to resolve discrepanciesamong three experiments for the photoelectronspectra of polyethylene that could not be explainedby Hartree-Fock theory or DFT. We have also recentlyreported the first CCSD results for polymers.
Diagrammatic elements of density matrixin coupled-cluster theory
REPRESENTATIVE PUBLICATIONS
Research Interests
6
Hai-PingCheng
AssociateProfessorPhysics
392-6256
Rm. 2330New Physics
Building
Water Clusters
Particle-Surface
Interactions
Structure and
Dynamics
Molecular
Dynamics
Simulations
Imaging and
Visualization
A Transparent Interface between Classical Mo-lecular Dynamics and the First-Principles Molecu-lar Dynamics, Mao-Hua Du and Hai-Ping Cheng,(in press, IJQC).
Water Clusters: Fascinating Hydrogen-BongNetworks, Solvation Shell Structures, and Pro-ton Motion, Hai-Ping Cheng, J. Phys. Chem.A102, 6201-6204 (1998).
All Quantum Simulations: H3O+ and H5O2
+, Hai-PingCheng, R.N. Barnett and Uzi Landman, Chem. Phys.Lett. 237, 161-170 (1995).
Nano-Modification of Silicon Surface via CoulombExplosion, Hai-Ping Cheng and J.D. Gillaspy, Phys.Rev. B55, 2628-2636 (1997).
Controlled Deposition, Soft Landing, and Glass For-mation in Nanocluster-Surface Collisions, Hai-PingCheng and Uzi Landman, Science 260,1304-1307(1993).
My research focuses on the physics ofsystems and phenomena at nano-scale, specifically, properties of clusters,nano-wires, and their interaction withbulk systems. Computer-based mod-eling and simulation methods are themain tools for investigation of suchcomplex systems. The spatial structureand electronic structure are investi-gated using density functional theory.The dynamics of a many-body systemare obtained via numerical solutions ofthe classical, quantum, or coupledclassical-quantum equations of mo-tion. Simulations allow studies of physi-cal and chemical processes with high-resolution in space and time.
One goal of the research is to developa basic understanding of physical andchemical processes in finite-size sys-tems. Clusters and nano-wires exhibitunique properties due to their ultra-
small sizes. Systematic investigations oftheir energetic, structural, dynamic andthermodynamic properties as a function ofsize and their interaction with surfaces andbulk matter, provide insight from the atomicand molecular regime to the condensedphase.
Current Research Activities:
1. Cluster and molecule-surface interaction;Examples include absorption, translation,rotation charge transfer and band struc-tures of C60 on Cu(111) surface.
2. Properties of molecular and nano-wires;Example: Structure and electronics structureof carbon nano-peadpods and effects ofmetallic doping.
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Hai-Ping ChengHai-Ping Cheng
3. Spin-dependent transport properties of layeredFe-FeO-MgO-Fe systems.
4. Proton transfer in water-silica clusters and on wet-ted silica surfaces.
5. Particle surface interactions; Simulation modelshave been developed to study Coulomb explosionsand bond breaking caused by highly charged ion(HCI)-surface interaction. In addition systematic stud-
ies are carried out to in-vestigate C-, Xe-, C20, C60-, Xe55-, and C60,@Xen -Si(111) collisions.
Theoretical Methodologiesand
Numerical Implementations:
1. Classical molecular dynamics (MD) simula-tions; in which the Newtonian equations of mo-t ion of amany-part icle system, interactingthrough pair-wise otentials, three-body poten-tials, and many-body interactions, are solved nu-merically, thus generating the phase-space tra-jectories of equilibrium or non-equilibrium sys-tems.
2. Ab-initio quantum molecular dynamics inthese the classical motion of the ions is evalu-ated on a Born-Oppenheimer potential energysurface obtained by concurrent solution of themany-electron Schrödinger equation (the elec-tronic structure problem is solved using density-functional theory, with the inclusion of gradientcorrections to the exchange-correlation func-tional).
3. All quantum method (AQM); this approachcombines the above ab initio quantum MDmethod with a Feynman path-integral descrip-tion of the ionic degrees of freedom, thus allow-ing investigations of finite temperature proper-ties of systems in which the quantum nature ofthe nuclear degrees of freedom is maintained.
4. Green’s function first-principles/tight-bindingmethods for investigation of finite-bias electronictransport and magnetic spin tunneling in mo-lecular and nano-structured systems.
5. Hybrid QM/CM simulations that allow simu-lations at multi-scale for studies of (H2O)n – silicasurface interactions. The region around the re-action center is treated quantum mechanicallywhile the other parts of the surface are treatedclassically. The interface between QM and CMregions is transparent under stress.
-3 -2 -1 0 1 2
E (ev)
Density of States (top) andstructure (bottom)
of carbon nano-peapodand doped with K atom
0
120
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DO
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ev)
REPRESENTATIVE PUBLICATIONS
Research Interests
8
Wavefunction Phase Space, E. Deumens and Y.Öhrn, J. Chem. Soc., Faraday Trans. 93(5), 1997,919-929.
Time-dependent Theoretical Treatments of the Dy-namics of Electrons and Nuclei in Molecular Sys-tems, E. Deumens, A. Diz, R. Longo and Y. Öhrn,Rev. of Mod. Phys., 66, 917-983 (1994).
Vibrations and Soliton Dynamics of PositivelyCharged Polyacethylene Chains, B. Champagne,
E. Deumens, Y. Öhrn, J. Chem. Phys. 107(14), 5433-5444 (1997).
On Rotational Coherent States in Molecular quan-tum Dynamics, J.A. Morales, E. Deumens, and Y.Öhrn, J. Math. Phys., 40, 766 (1999).
Nonlinear Wave Equation in Dimensions with ExplicitStable Solitary Wave Solutions, E. Deumens and H.Warchall, J. Nonlin. Anal.: Theory, Meth. and Appl.,12, 419-447 (1988).
Teaching Quantum Mechanics, Erik Deumens, Ad-vances in Quantum Chemistry, 35, 21-32 (1999).
My primary interest is in the design andmaintenance of a high performancecomputing environment. The QTP com-puting facility is called the John C. SlaterComputing Laboratory. It was started in1982 by QTP with George Purvis andSam Trickey taking the lead in the archi-tecture and design. The advantages ofa system with an architecture over themore common system that has grownorganically are clearly visible in the QTPcomputing environment.
The goal of the uni-fied system archi-tecture is to pro-vide a consistentand stable envi-ronment for every-one in QTP fromevery desktop.
Two courses wereproduced duringthis effort: one on“Effective Programming in Fortran 77 andFortran 90” (in 1995) and one on “Rulesfor Adequate Parallelization” (in 1998).These have been integrated into onecourse (Spring 2000). The programmingportion of the course introduces mod-ern techniques of software engineering:software source code management
with CVS; building and compilation withmakefiles; managing hardware and op-erating system specific code with prepro-cessors; using a powerful editor likeEmacs; organization, style and conven-tions beyond the language syntax for pro-gramming effectively in any language.The division of the course onparallelization treats distributed memoryand shared memory programming in auniform way and emphasizes a simpleand general programming technique to
deal with coarse-grained object-ori-ented parallel pro-cessing. The prob-lem of fine-grainedparallel processingis considered to besolved byvectorizing compil-ers and superscalararchitectures andno extra program-ming effort is re-quired or useful.
Fine-grained parallel programming lan-guages like the HPF additions to Fortran90 as embodied in the Fortran 95 stan-dard are of minimal use except in rarecases. By focusing on work done by sub-routines on their data, “objects,” bothPOSIX threads programming and MPIprogramming become straightforward.
ErikDeumens
ScientistChemistry &
Physics
QTPComputing
Director
392-6980
Rm 2334New Physics
Building
Computer SystemsArchitecture and
Management
Object OrientedSoftware
Engineering
High PerformanceParallel
Programming
D2124
buddy
D2508
D2124
D2124
D2124zwartC3800
D2124
crunch
D2508
C2924XL
C29241114
xena II
xena III
BayStack
simu
1141
1213
2272
22212250B104B
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Electron Nuclear Dynamics
My second interest is in molecular dynamics in-cluding explicit treatment of electrons and nucleiand their interaction. I have been working on thisproject, called Electron Nuclear Dynamics (END),with Yngve Öhrn. The END approach to moleculardynamics treats the dynamical system of thecoupled nuclear andelectronic degrees offreedom. This allows thedescription of processesat the boundary of elec-tronic structure theoryand molecular dynam-ics such as chargetransfer, electron scat-tering, ionization andelectron capture. Thisproject has been goingon since 1987 and hasso far described a sig-nificant number of sys-tems giving insight intothe time-dependentevolution of molecules.Recently ENDyne wasmodified to be an exten-sion to the popular pro-gramming environmentPython. This greatly in-creases the user’s flex-ibility in manipulatingENDyne data and ac-tions. Currently we areworking on systems thatlose or capture an elec-tron. Work in progressincludes the descriptionof the nuclear degrees of freedom using fully quan-tum mechanical many-body wave functions andmulti-configuration electronic wave functions.
Quantum Theoretical Integrals Package
Another interest is in the development of a compre-hensive library for Computational Chemistry inte-gral evaluation. The QTIP project on integrals was
Erik DeumensErik Deumens
started to provide a bettertoolkit than is available any-where to do the demanding calculations required byEND. The design specifies a set of Integrals Genera-tion Subroutines (IGS) and a set of Linear Algebra Sub-routines (LAS). The IGS create integral patches, the ba-sic object in QTIP. The LAS allow traces, multiplicationsand other basic operations to be done with the patchesand densities and other matrices. These operations
are optimized for modernsuperscalar processors.The object oriented ap-proach allows for efficientparallel processing withequal ease on shared andon distributed memorycomputers. The standardsof POSIX threads and MPImessage passing areused. This project has beengoing on since 1994.
Mathematical,Physical
andPhilosophical
Foundations ofQuantum Mechanics
My hobby is the math-ematical, physical andphilosophical foundationsof Quantum Mechanics (inthat order). After studyingthe mathematical treatisesof Von Neumann, Jauch,Piron, and Omnès relatedto defining and exploring anew logic on which to base
Quantum Mechanics, I have come to the conclusionthat this is not the way to go. I now believe that Quan-tum Mechanics has a foundation that is natural andclear to explain and contains physical principles. Themathematics may be advanced, but is not as outland-ish as for example the quantum logic is. The ideas ofdecoherence that gained prominence in the 80’s arepromising. I would like to carry out a numerical simu-lation that shows decoherence in a realistic systemand investigate the dependence on the system size.
Erik Deumens and Ryan Chancey withsome of the many cables used for Xena II
REPRESENTATIVE PUBLICATIONS
Research Interests
10
Algebraic and Diagrammatic Methods in Many-Fermion Theory, F.E. Harris, H.J. Monkhorst, andD.L. Freeman, Oxford University Press (1992).
Light-Cone Hamiltonian in Quantum Chemistry:Gaussian Basis Representation for QuantumElectrodynamics, V.G. Koures and F.E. Harris, Int.J. Quantum Chem. S29, 277-282 (1995).
Analytic Evaluation for Three-Electron Integrals withSlater Wave Functions,” F.E. Harris, Phys. Rev. A 55,1820-1831 (1997).
Ewald Summations in Systems with Two-DimensionalPeriodicity, F.E. Harris, Int. J. Quantum Chem. 68,385-404 (1998).
Analytical Evaluation of Two-Center STO Electron Re-pulsion Integrals via Ellipsoidal Expansion, F.E. Har-ris, Int. J. Quantum Chem. 88, 701-734 (2002).
Frank E.Harris
Resident AdjunctProfessorChemistry
846-3143
Rm 2328New Physics
Building
Few-body Systems
Complex ScalingMethods
Periodic Systems
FragmentationSimulations
Computer-AidedFormula Generation
My current research focuses on:
(1) Few-body nonadiabatic systems,
(2) Complex scaling methods for re- active atom-atom and atom-ion scattering, and
(3) Electronic structures and static or dynamic properties of periodic systems.
Unusual “Molecules”
Environments containing unstableparticles and antiparticles provide op-portunities for the creation of unusualmolecular species, of which some in-teresting examples are
e + e - (denoted Ps),e- e + e - (Ps -), ande - e + e- e + (Ps2).
There are also a large number of two,three, and four-body systems involvingvarious mesons. These systems all havein common the feature that particles ofopposite sign of charge have compa-rable masses. Some of these exotic spe-cies may form as precursors to annihi-lation reactions, and a knowledge oftheir wavefunctions will be a componentin the calculations of annihilation rates.
The few-body systems under consider-ation cannot be well-treated by theschemes that have been so successfulfor conventional atoms and molecules.Those schemes rely on the separationof slow, heavy-particle motion from thatof the faster, lighter particles, with afixed-nuclei (adiabatic) calculation anexcellent approximation. Moreover, anindependent-particle description of thelight particles (electrons) is often quitesatisfactory, as the electrons correlatemore strongly with the nuclear positionsthan with those of other electrons. In theabsence of these simplifying features,there seems no alternative to usingwavefunctions containing all the inter-particle distances. This approach waspioneered by Hylleraas (for the Heatom), but progress has lagged be-cause the mathematical analyses in-volved have turned out to be quite diffi-cult.
Our present work stems out of the ana-lytical formulas we have developed forevaluating, for four-body problems, allthe integrals that arise in energy calcu-lations using exponentials in all the in-terparticle distances. We are develop-ing practical methods of calculation withthese functions, and are in the processof studying ground and excited boundstates of Ps2 and other systems.
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Frank E. HarrisFrank E. Harris
Atomic Scattering
An interesting approach to atomic scattering pro-cesses involves a search for singularities when theelectronic energy is computed for complex values ofthe interatomic distance. It would be desirable to ex-tend previous successes (by Solov’ev, Krstic, and oth-ers) for processes containing a single “active” elec-tron to those in which the states of several electronschange in a significant way (i.e. shake-up processes,multiple ionization). To do so requires the extensionof diatomic molecular-orbital methods to accommo-date the complex scaling in a numerically stable fash-ion. We are presently studying model problems togain more insight as to the mathematical approachesto be used.
Simulations
My undergraduate student has had a lot of fun car-rying out classical dynamics simulations of suface-impact fragmentation of buckmin-sterfullerene (C60)and other cage molecules. The observed fragmen-tation patterns fit nicely with scaling laws developedfor larger objects, including meteorites.
Computer Algebra
Another theme among my research interests hasbeen the use of symbol manipulation programs(“computer algebra”) to develop computationallyuseful formulas for physical quantities when pen-cil-and-paper mathematics leads to unmanage-able complexity. Part of our effort in this directionhas involved computer programming to manipu-late unconventional mathematical objects such asthe Feynman diagrams which represent contribu-tions to many-body perturbation theory. We haveused this approach to verify the correctness ofsome formulas arising in a discrete light-conequantization formulation of quantum electrody-namics, and have shown how similar techniquescan generate coupled-cluster equations such asthose found in our book Algebraic and Diagram-matic Methods in Many-Fermion Theory.
Periodic Systems
In collaboration with Professor Joseph Delhalle ofFacultés Universitaires Notre Dame de la Paix inNamur, Belgium, we are learning how to make first-principles descriptions of arrays of molecules thatare periodic in two of the three spatial dimensions(“2D” periodicity) as models for surface systems. Theperiodicity presents both opportunities and chal-lenges: electrostatic forces die off with distance suf-ficiently slowly that it is impractical just to add theircontributions at a point from all the charged par-ticles that are close enough to matter. On the otherhand, if we can determine the forces acting at apoint, we will then also know the forces (and result-ant energies) associated with the infinitude of simi-lar points in the periodic system.
Using the Gaussian functions now popular formolecular calculations, we have obtainedworking formulas for the forces and energiesassociated with infinite lattices of such func-tions in surface systems, complementing ear-lier work by Delhalle and his students on one-dimensional arrays of such functions (useful inmodels for polymer chains).C
60 after collision with the wall
REPRESENTATIVE PUBLICATIONS
Research Interests
12
Research in my group focuses on theo-retical studies of time-dependent laser-matter interactions. Advances in lasertechnology over the past few years havecreated a unique opportunity to studymatter at its most fundamental level. La-ser pulses can now be pro-duced on the time, lengthand energy scales ofatomic, molecularand elec-tronic mo-tion. This en-ables directinves t iga-tions ofc h e m i c a lsystems as theyare reacting, and offersthe possibility to move beyondthe passive observation of ma-terials to the active control ofthem.
Several projects are currentlyunderway in my group. Theyare described briefly below.
Dendrimers
In collaboration with Wilfredo Ortiz andAdrian Roitberg, we are considering thedynamics and control of molecules in
exotic environments. We are currently con-centrating on dendrimers, which have theunique ability to serve as light-harvestingsystems, without loss of vibrational energy.Specially designed dendrimers may createselective environments in which novel pho-tochemistry can be achieved.
To date, we have performed molecular dy-namics studies of the time-
dependent structures ofthese systems. We
have found thatcomparativelyrare events, inwhich terminal
units of thedenrimer wrap
around to the core, maydominate the electron trans-
fer rate. We have instituted a col-laboration with Valeria Kleiman, anultrafast phenomena experimentalist atUF, to investigate the energy transfer pro-cesses in a variety of dendritic systems.
Control in Rydberg Wave Packets
A second project, in collaboration with KenSchafer (Dept. of Physics, LSU) and CorneliuManescu, concerns the production and de-tection of sculpted wave packets in Rydbergatoms. When an atom is placed in a staticDC field, the angular momentum quantum
Theoretical Study of the UV-Induced Desorptionof Molecular Oxygen from the Reduced TiO2 (110)surface, Maria Pilar de Lara-Castells and JeffreyL. Krause, Journal of Chemical Physics 118, 5098-5104 (2003).
Controlling THz Emission from Quantum Wells,Kevin L. Shuford and Jeffrey L. Krause, Journalof Physical Chemistry, A 106, 10818-10824 (2002).
Adiabatic Passage in Quantum Wells Via DC Fields,Kevin L. Shuford and Jeffrey L. Krause, Journal ofPhysics D, Applied Physics 36, 439-445 (2003).
Control of THz Emission from Stark Wave Packets,Jeffrey L. Krause and Kenneth J. Schafer, Journal ofPhysical Chemistry 103, 10118-10125 (1998).
Control of Non-Franck-Condon Transitions: Lightinga Dark State, Vladimir S. Malinovsky and Jeffrey L.Krause, Chemical Physics, 267, 47-57 (2001).
Jeffrey L.Krause
Associate ProfessorChemistry& Physics
Associate DirectorQTP
392-6971
Rm 2332New Physics
Building
Quantum Control
Time-DependentMethods
Ultrafast LaserFields
Wave Packets
Quantum Dynamics
13
number, l, is spoiled. As the DC field increases, thel states split in energy. To understand the effects ofthis symmetry breaking, we are examining the en-ergy and angular-resolved photoelectron spectraproduced by ionizing selected Stark states with half-cycle, THz pulses. Half-cycle pulses act as an impul-sive kick of the electron into the continuum. We findthat the photoelectron spectra vary considerably de-pending on which Stark state is ionized, and in whichdirection it is kicked.
Molecules on Surfaces
In collaboration with Maria Pilar de Lara Castells,we are studying the dynamics and photochemistryof molecules adsorbed on semiconductor surfaces.We are using high-level quantum chemistry meth-ods to determine the structure and energetics of theadsorption process. As a first example, we have ana-
lyzed the electronic structure of a molecule of oxygenadsorbed on a TiO2 surface. The oxygen adsorbs atdefect sites in two different geometries and three spinmultiplicities. We are currently comparing our resultswith experiments. Future work will consider the dy-namics of the desorption process, and investigate thepossibility that shaped laser pulses can be used to
Jeffrey L. KrauseJeffrey L. Krauseperform selective des-
orption of co-adsorbedspecies.
Control of Molecules with Light
We are currently extending our studies of laser-mat-ter interactions to systems of chemical and biologi-cal interest. In collaboration with Vladimir Mali-novsky, we are investigating electronic populationtransfer in diatomic molecules. We have developeda model based on time-dependent, laser-inducedpotentials to explain existing experimental data,and to make predictions for new experiments. Inparticular, we have shown that pairs of intense,ultrafast pulses can be used to invert populationfrom the ground state of a molecule to a desiredfinal state using intense, ultrafast pulses to createand then delicately modify the light-induced poten-tials on which the dynamics occur. As an example,
we showed that electronicpopulation in the sodiumdimer can be inverted to a“dark” final state. An analy-sis of the structure of thetime-dependent, light-in-duced potentials reveals thedetailed mechanism of thepopulation dynamics.
Control in Semiconductors
Another project, in collabo-ration with Kevin Shuford, in-volves the dynamics ofcharge carriers in semicon-ductor heterostructures. Ourinitial work considered theasymmetric double quan-tum well. We have recentlyextended our method to
study control of wave packets and THz emissionin superlattices. We find that pairs of pulses canamplify or suppress the wave packet density, andhence the intensity of the emitted radiation. Alter-natively, shaped DC fields can be used to steer awave packet adiabatically to a desired location ata chosen time.
3o2 o2-
Ti3+
REPRESENTATIVE PUBLICATIONS
Research Interests
14
Our research deals with theoretical andcomputational aspects of molecular andmaterials sciences, with emphasis on theunified treatment of physical and chemi-cal kinetics using quantum molecular dy-namics. It includes collisionalphenomena in the gas phaseand at solid surfaces, andphenomena induced by the in-teraction of molecular systemswith light. Our aim is to providea fundamental approach tomolecular dynamics, in whichelectronic and nuclear motionsare consistently coupled to ac-count for quantal effects. We usequantum and statistical mechanics,mathematical, as well as computationalmethods, to describe time-dependentphenomena in both simple and complexmolecular systems.
First-Principles Quantum Dynamics
Modern experimental techniques provideinformation on molecular phenomenawhich last femtoseconds and extend overnanometers. This brings up theoreticalchallenges best considered with time-de-pendent density matrix methods whichcombine quantum and statistical descrip-tions, and can be applied to small mol-ecules as well as to extended molecularsystems. One of our objectives is to de-
velop a first-principles quantum dynamics ofmolecular interactions, and to apply it to thefemtosecond dynamics and spectra of elec-tronic rearrangement in the gas phase andat solid surfaces. It is based on a density ma-trix approach which combines time-depen-dent many-electron theory and eikonal meth-
ods for many-atom systems. Thistheory aims to provide new in-sight, concepts and predictivecomputational tools to deal withcollision-induced and photoin-duced electronic transitions. Itscomputational implementation
generates electronic potential en-ergies and their couplings, and tran-
sition dipoles as needed in studies ofdynamical phenomena. This is signifi-
cant to chemical kinetics because, justas stationary MO theory has done for mo-
lecular properties, it provides both concep-tual insight and quantitative results.
State-to-State Transition Probabilities
A related objective is to develop computa-tional methods and to program algorithms tocalculate state-to-state transition probabilitiesand time-evolving properties for electronic en-ergy and charge transfer, orbital polarization,and spin-orbit recoupling. The methods in-volve using basis sets of static and travelingatomic functions in time-dependent molecu-lar orbitals, effective interatomic potentials fornuclear motions, and pseudopotentials for theelectronic cores of atoms. Calculations requirethe numerical solutions of coupled differen-
The Calculation of Electron Transfer Probabili-ties in Slow Ion-Metal Surface Collisions, D.A.Micha and E.Q. Feng, Computer Phys. Comm.90, 242-258 (1994), special issue on Gas-Sur-face Dynamics, eds. E. Vilallonga and H. Rabitz.
Time-Dependent Many-Electron Treatment ofElectronic Energy and Charge Transfer in AtomicCollisions (Feature Article), D.A. Micha, J. Phys.Chem. 103, 7662-7574 (1999).
A Time-Dependent Many Electron Approach to
Slow Ion-Atom Collisions for Systems with SeveralActive Electrons, K. Runge and D.A. Micha, Phys.Rev. A, 62, 022703.1-9 (2000).
Spectral Line Shapes in Dissipative Systems: Mol-ecules Adsorbed on Metal Surfaces, S. Miret-Artes,D.A. Micha, and D. Beksic, J. Chem. Phys. 114,4690-95 (2001).
Nonlinear Optical Response and Yield in theFemtosecond Photodesorption of CO from theCu(001) Surface: a Density Matrix Treatment, D.A.Micha, A. Santana, and A. Salam, J. Chem. Phys.116, 5173-85 (2002).
David A.Micha
ProfessorChemistry and
Physics
392-6977
Rm 2318New Physics
Building
QuantumMolecular Dynamics
Electronic Energy andCharge Transfer
SurfaceDynamics
Photo-InducedDynamics
Few- and Many-BodyCollision Theory
Time-DependentMany-Electron
Theory
Density MatrixTheory
15
tial equations in the time variable for functions withquite different time scales, the efficient propagationof electronic density matrices and nuclearwavepackets or trajectory bundles in several vari-ables, and integration over initial conditions to obtainvalues of observables.
Atom-Atom Interactions
We are interested particularly in atomic and molecu-lar orbital changes over time, with and without con-current electron transfer. For atom-atom interactions,questions of interest areu How do electronic energy, charge distributions,and orbital polarization change with time during col-lisions or dissociation?u How does the coupling of the spin and orbital an-gular momenta of electrons change over time duringcollisions?u How do electrons in transient states emit or absorblight?
Condensed Matter Phenomena
As one deals with larger systems, such as moleculesadsorbed on solid surfaces, ions interacting with sur-faces, or electroni-cally excited mol-ecules evolving incomplexes, impor-tant questions are:u How is electron lo-calization affectedover time by the dy-namics of the me-dium?u What is themechanism of cou-pling between local-ized electronic rear-rangement andcharge polarizationof a driven medium?u How does this cou-pling change the in-teratomic potentials and transition dipoles in the re-arrangement region?u When does the medium dynamics lead to devia-tions from the Franck-Condon process?
Ongoing Research
Studies presently being carried out with graduatestudent assistants, post-doctoral research associ-ates and visiting scientists are as follows:
u Electronic energy, charge transfer, and light emis-sion in collisions of ions with atoms and with solidsurfaces, using eikonal methods and time-depen-dent Hartree-Fock electronic states.u Time-resolved spectra of atoms and moleculesin media (clusters and solid surfaces) using time-dependent many-electron theory.u Femtosecond dynamics of photodesorption ofdiatomics from metal surfaces by visible and UVpulses, using density matrix methods and calcu-lated potential energy functions and transition di-poles.u Computational methods for solving the Liouville-von Neumann equation for the density operator in-cluding dissipation, for integration of differentialequations for fast and slow degrees of freedom (the“relax-and-drive” method), and for generation ofelectron integrals in time-dependent many-electroncalculations.u Computer visualization and animation of molecu-
lar interactionsincluding ani-mation of thetemporal evolu-tion of bothnuclear motionsand electronicdensities usingnuclear trajecto-ries andisocontours ofelectronic den-sities.
u Animation ofelectronic tran-sitions and elec-tron transfer ob-tained fromtime-dependent
molecular orbitals.u Animation of light emission in collisions of ionsinvolving electronic rearrangement and the relatedtransient dipoles.
David A. MichaDavid A. Micha
REPRESENTATIVE PUBLICATIONS
Research Interests
16
Colliding Beam Fusion Reactor (CBFR)
u Research and development of asystem of colliding hydrogen and bo-ron-11 beams within a Field ReversedConfiguration (FRC) of a cylindrical, ro-tating plasma with magnetic selectiveself-confine-ment; Extrac-tion of energywith Direct En-ergy Conver-sion (DEC) atover 80% effi-ciency, solu-tion of Vlasovand Fokker-Planck equa-tions.
PolymerSuperconduc-
tivity
u Joint experimental/theoreticalsearch for the proper electronic andgeometric conditions of conductivepolymers for superconductivity likely tooccur. development of the many-bodytools in order to quantify the (super)conductive states.
Ab Initio Electronic Band Calculations
Starting from accurate Hartreewavefunctions and energies, and includingexchange and RPA-level correlation withGreen’s function techniques. Extensive useof momentum and Fourier transform meth-ods deal with conditional convergence prob-lems and the Hartree Fock pathologies.
Non-AdiabaticMolecular Physics
& MolecularCoupled Cluster
Method
Further develop-ment and imple-mentation of theM o l e c u l a rCoupled-Clustermethod; chemicalphysics without theBorn- Oppenhe-imer approxima-tion. Time-Depen-
dent formulation for scattering and half-colli-sions (many-body wavepacket dynamics).
A central theme to my research group effort isthe intimate interplay between careful math-ematical treatment and accurate, systematiccalculations.
On Special points for Brillouin Zone Integrations,H.J. Monkhorst and J.D. Pack, Phys. Rev. B 13,5188 (1976).
Atomic and Molecular Correlation Energies withExplicitly Correlated Gaussian Geminals. V. Car-tesian Gaussian Geminals and the Neon Atom,K. Wenzel, K. Szalewicz, J.G. Zabolitzky, B.Jeziorski, and H.J. Monkhorst, J.Chem. Phys. 85,3964 (1986).
Chemical Physics without the Born-Oppenheimer Approximation: the MolecularCoupled-Cluster Method, H.J. Monkhorst, Phys.Rev. A 36, 1544 (1987).
Colliding Beam Fusion Reactor, N. Rostoker, M.Binderbauer, and H.J. Monkhorst, Science 278,1419 (1997).
Direct Energy Conversion for Aneutronic FusionReactors with FIeld Reversed Configuration Plas-mas, H.J. Monkhorst and N. Rostoker, Proceed-ings, AAAS Meeting, 2002, Boston, MA.
HendrikMonkhorst
ProfessorPhysics
and Chemistry
392-1597
Rm 2320New Physics
Building
Colliding BeamFusion Reactor
Polymer (Super)Conductivity
Electrons in Ex-tended Systems
Non-adiabaticMolecular Physics
Coupled ClusterMethod
Artist’s conception of 2-50 MWColliding Beam Reactors & Support
Equipment
17
Design and Development of the Colliding BeamFusion Reactor (CBFR)
In collaboration with Norman Rostoker, from UC atIrvine, we have designed a novel type of fusion reac-tor, the Colliding Beam Fusion Reactor (CBFR). It usesprotons (p) and boron-11 (11B) for fuel. Fusion reactionsproduce only three helium-4 (4He) nuclei, and nearly9 million eV energy. Central to the design is the use ofa so-called Field Reversed Configuration (FRC) plasma.It has a cylindrical shape, rotates fast about its axisinside a solenoidal magnet, and thus produces a mag-netic field that closes upon itself: a kind of self-con-finement of fuel nuclei is established, with all confinedparticles flowing in the same direction. Protons rotatefast, with an energy of about 1 MeV, and 11B can goslow such that the protons “rear-end” the 11B with anenergy at which the fusion cross section is highest.
We have found that plasma parameters can be setsuch that essentially all injected p and 11B undergofusion to 4He products, and lots of kinetic energy.These ions readily escapethe FRC plasma, and areguided into so-called Di-rect Energy Converter(DEC) devices. These de-vices turn their kinetic en-ergy directly into electric-ity (no boiling of water, nosteam, no turbine, smallthermal inefficiencies).
Several advantages result:abundant fuel supply, verylittle radioactivity, no dan-ger of run-away reactionsor explosions, scalability ofsize and output power,easier engineering andmaintainability.
A multifaceted study is underway to establish the fullfeasibility of the design. Most of the large-scale cal-culations, theory development and nuclear polariza-tion (to enhance the fusion reactivity) are centered inQTP, University of Nebraska, Lincoln, and UC Irvine’sPhysics Department. Experiments and engineeringstudies are being conducted at a start-up company,Tri Alpha Energy, Inc., in Foothill Ranch, California.
Hendrik J. MonkhorstHendrik J. Monkhorst
(Super) ConductingPolymers
Together with various experimentalists we havebeen trying to implement certain theoretical rulesfor polymers to satisfy so that they (1) can be ex-pected to conduct: (2) can be possible supercon-ductors. Several proposals for polymers to besynthesized have been made, and some are be-ing studied experimentally. There are severalhighly conducting polymers, with a few super-conductors that satisfy these rules. We hope tofind polymers that are strong enough to be madeinto wires.
Molecular Coupled Cluster Method
Laser spectroscopies of molecules and attemptsat quantum control ofchemical reactions callfor a very sophisticatedtreatment of the nuclearas well as electronic dy-namics of molecules.This means that the tra-dit ional Born-Oppenheimer style, po-tential-energy-surfacedriven descriptions ofthe molecular proper-t ies are rather inad-equate. Instead, elec-trons and nuclei shouldbe described at thesame quantum-dy-namical footing.
The coupled-clustermethodology is ideal for this, allowing a physi-cal picture for the various truncations and ap-proximations needed to make calculations prac-tical. Currently work is underway to compute theintegrals arising from the use of basis sets thatare quite different from those used in traditionalquantum chemical applications of the coupled-cluster method.
Artist’s conception of a power stationwith a
colliding beam fusion reactor
REPRESENTATIVE PUBLICATIONS
Research Interests
18
u Development of rigorous,computationally tractable theory ofmolecular energetics and dynamics.
u Development of explicitly time-de-pendent theory beyond the adiabaticapproximation for the study of molecu-lar reactive processes.
u Application of such methods to thestudy of elementary chemical reac-tions involving charge transfer, en-ergy transfer, and rearrangements aswell as ion-atom and ion moleculecollisions at higher energies to studyenergy loss, and projectile chargestates.
u Application of such theory to the in-teraction of molecular systems withexternal fields, such as intense laserfields.
u Development and application ofpropagator methods to the study ofmolecular spectroscopy and the un-derstanding of optical and conduc-tion properties of polymeric systems.
Modern experimental techniques us-ing laser technology permit the studyof molecular reactive processes, viatime-lapse photography as the reac-tants make their way towards prod-ucts. Theoretical methods in the time
domain that can help to interpret suchexperiments have been developed in myresearch group under the name ElectronNuclear Dynam ics (END) (see Reviews ofModern Physics, 66, 917-983 (1994)). TheEND theory treats electrons and nucleifully dynamically accounting for the ef-fects of nonadiabatic coupling terms. Thelowest level of approximation can becharacterized as Time-Dependent Har-tree-Fock with dynamically moving nucleiand is implemented in the program sys-tem ENDyne. This level of theory has beenapplied to a large number of reactive pro-cesses at collision energies ranging fromfractions of an eV to tens of keV with re-markable success.
Some of the publications containing re-sults from such calculations are J. Chem.Phys. 96, 6820 (1992); Chem. Phys. Lett.220, 305 (1994); Chem. Phys. Lett. 233,392 (1995); Nucl. Instr. Meth. B 96, 633(1995); J. Chem. Phys. 103, 9968 (1995);Int. J. Quantum Chem. 58, 583 (1996); J.Chem. Phys. 107, 6146 (1997); Chem.Phys. Lett. 279, 241 (1997); Phys. Rev. A61, 032719 (2000). Further developmentof the END theory is underway in order tobring the treatment of electronic andnuclear dynamics to a higher level oftheory (see J. Math. Phys. 32, 1166 (1991);J. Math. Phys. 35, 1139 (1994); J. Chem.Soc. Faraday Trans. 93, 919 (1997); J.Math. Phys. 40, 766 (1999)).
Time-dependent Theoretical Treatments of theDynamics of Electrons and Nuclei in MolecularSystems, E. Deumens, A. Diz, R. Longo, and Y.Öhrn, Reviews of Modern Physics, 66, 917-983(1994).
Phase Space Approach to the Dynamics of Mo-lecular Systems, E. Deumens and Y. Öhrn J.Chem. Soc. Faraday Trans. 93, 919 (1997) .
Charge Exchange and Threshold Effects in the
Energy Loss of Slow Projectiles, R. Cabrera-Trujillo,J.R. Sabin, Y. Öhrn, E. Deumens. Phys. Rev. Lett., 845300 (2000)
Electron Nuclear Dynamics, Y. Öhrn and E. Deumens,in Effects of Electronic Degenerate States on NuclearDynamics Processes, Adv. Chem. Phys., Vol 124, 323-353 (Eds. Michael Baer and Gerd D. Billing) Wiley &Sons, New York, 2002).
Elements of Molecular Symmetry, Y. Öhrn,(Wiley&Sons, New York, 2000).
N. YngveÖhrn
ProfessorChemistry
and Physics
392-6979
Rm 2312New Physics
Building
Electron NuclearDynamics
Time-DependentDynamics
END
ENDyne
Propagator
Electron Transfer
19
Experimental studies of processes at the molecu-lar level involve using probes of various kinds, suchas photons, charged or neutral particles to interactwith the target system and measuring the changeof state and the associated probability for such achange in the target or the probe. Propagators [seePropagators in Quantum Chemistry (AcademicPress, London 1973)] are ideally suited for theoreti-cal interpretation of such experiments. They are ex-plicitly time-or equivalently frequency-dependentfunctions (or rather distributions) that satisfy equa-tions of motion which can be solved at well-definedlevels of approximation.
Electron Nuclear Dynamics
The electron nuclear dynamics (END) theory hasbeen developed in close collaboration with ErikDeumens, a group of talented graduate students,and postdoctoral associates over the past fourteenyears. This is an explicitly time-dependent approachto molecular processes. The END theory is generaland can beapplied atvarious well-defined levelsof approxima-tion. The ENDequations ared e v e l o p e dfrom thequantum me-chanical ac-tion employ-ing the time-d e p e n d e n tvariational principle and they approximate the time-dependent Schrödinger equation. The level of ap-proximation is defined by the choice ofwavefunction form for the participating electrons,atomic nuclei and, of course, the choice of basis.Beyond those choices there are no further approxi-mations such as restricted nuclear geometries, ne-glect of nonadiabatic coupling terms, etc., com-monly found in other approaches.
The END equations take the form of coupled first-order differential equations in time, and the dynami-cal variables whose time evolution is governed by
these equations arethe wavefunction pa-rameters such as mo-lecular orbital coefficients, nuclear average posi-tions, and nuclear average momenta. In this man-ner, electronic and nuclear dynamics are treatedsimultaneously and fully coupled.
This level of END theory has been applied to a num-ber of gas phase molecular reactive processes withgreat success and actually performs better at en-ergies well above thermal than do more estab-lished dynamics on potential energy surfaces.
From the point of view of fundamental theory, el-ementary chemical reactions are simply the de-tailed dynamics of the participating electrons andnuclei. Electrons and atomic nuclei are the “el-ementary particles” of chemistry and their dynam-ics under the influence of mutual Coulombicforces and possibly other terms (such as spin-or-bit coupling) is governed by the time-dependentSchrödinger equation. Spectroscopic and dy-
namic mo-lecular pro-cesses areby their verynature inti-mately con-nected withstates thatevolve intime, i.e. nots ta t ionarystates. Obvi-ously evolv-ing states
can be expressed in terms of stationary states,but clearly such pointwise determined Born-Oppenheimer electronic states only have the roleof a basis, and could be replaced by another ba-sis set which might be easier to produce.
The END approach takes this point of view, andby dealing with the simultaneous dynamics ofelectrons and nuclei, does not force the reactiondynamics to follow a predetermined potential en-ergy surface, but is governed by the instanta-neous forces derived from the full quantum me-chanical Hamiltonian of the system.
N. Yngve Öhrn
N. Yngve ÖhrnN. Yngve Öhrn
H+4 C2H
6, 10 eV: Time = 1800
EnDyne
REPRESENTATIVE PUBLICATIONS
Research Interests
20
My main interest relates to the model-ing of biomolecules. The complexity oftheir behavior and their obvious impor-tance for life makes them fascinatingsystems to study.The questionsone can ask arealmost limitless,and the recentsequencing ofthe human ge-nome will bringthe research inbiophysics evenmore to the fore-front. I am par-ticularly inter-ested in the ener-getics and dy-namics of pep-tides, proteinsand nucleic ac-ids, as well as inthe computa-tional aspects ofenzyme reactionmodeling.
Folding: how do they do that?
A simple combinatorial argument canshow that peptides and proteins can-not possibly fold by visiting every pos-
All Atom Structure Prediction and Folding Simula-
tions of a Stable Protein, Carlos L. Simmerling,
Bentley Strockbine, and Adrian E. Roitberg, Jour-
nal of the American Chemical Society, 124 (38),
11258 -11259 (2002).
Solvent-Induced Symmetry Breaking of Nitrate Ion
in Aqueous Clusters: A QM/MM Study, Mariano
C. González Lebrero, Damián E. Bikiel, M. Dolores
Elola, Darío A. Estrin, and Adrian E. Roitberg. Jour-
nal of Chemical Physics, 117(6), 2718-2722 (2002).
Adrian E.Roitberg
Assistant ScientistChemistry
392-6972
Rm 2336New Physics
Building
Biomolecularmodeling
Molecular Dynamics
Protein Folding
Quantum/classicaltreatment of
enzymatic reactions
MolecularElectronics
sible energy minimum available to them.There is simply not enough time to do it thatway; it would take then billions of years, andthey manage to do it in seconds. This
means thatbiomolecules aremuch more cleverthan us in their choiceof techniques. Under-standing how they doit is the so-called theprotein-folding prob-lem.
We are designingnew methodologiesto study this problemefficiently. Our currentmethods make use ofclusters of commoditycomputers that areused to run multiplesimulations of folding,starting from confor-mations belonging tounfolded ensembles.We monitor each in-
dependent trajectory until they reach a pre-determined folded state. This way we canhave single folding event and ensemble av-eraged (over the trajectories) information.We can then relate to experimental foldingrates for medium size systems, while keep-ing detailed atomic information of the fold-ing mechanisms.
A Theoretical Study of the Chorismate Mutase Catalyzed
Claisen Rearrangement Reaction, Sharon E. Worthington,
Adrian E. Roitberg, and Morris Krauss, Journal of Physical
Chemistry B, 105, 7087-7095 (2001).
The Electronic Spectrum of the Prephenate Di-Anion. An
Experimental and Theoretical (MD/QM) Comparison,
Adrian E. Roitberg, Sharon Worthington, Marcia J. Holden,
Martin P. Mayhew, and Morris Krauss, Journal of the
American Chemical Society, 122, 7312-7316,(2000).
Molecular Wire Conductance: Electrostatic Potential Spatial
Effects, Vladimiro Mujica, Adrian E. Roitberg, and Mark A.
Ratner, Journal of Chemical Physics, 112, 6834-6839 (2000).
21
involved in Chagas’sDisease, an endemicillness in SouthAmerica.
Quantum/Classical Methods for Small Molecules
A different line of research in my group involvesthe study of solvent effects in structure, dynam-ics, and spectroscopy of small molecules. Clas-sical mechanics has the advantage of comput-ing some aspects of the dynamics of a systemvery efficiently and accurately, while being un-able to describe properties that involved purelyquantum mechanical effects. We are developing
methods and simula-tions that mix these twotechniques, using themselectively to answerdifferent questions. Wehave published somework on the calculationof UV/Visible absorp-tion spectra on theprephenate anion us-ing these methods.Classical molecular dy-namics was employedto sample the confor-mational space in themolecule ground statein relevant long time
scales, while quantum mechanical methodswere used to compute vertical excitation ener-gies as well as intensities.
Current Work
Current work involves the dynamics of the NO3anion in water. One would expect this moleculeto have a symmetric geometry with the 3 N-Obonds being of equal length. This is not thecase. Our simulations using density functionaltheory for the dynamics of the anion and clas-sical mechanics for the solvent show that themolecule prefers to break symmetry, creatinga dipole moment and hence increasing its sol-vation energy.
Conformational Searches
We are developing new methodologies to deal withsampling and conformational search problems en-countered in classical molecular dynamics simula-tions. We would like first to understand how far a pro-tein could move in its conformational space at a giventemperature and within a given time scale. We arealso working on methods that would allow enhanc-ing sampling for sections of a system of interest with-out spending valuable computational time simulat-ing uninteresting parts. We call this method “LocallyEnhanced Sampling,” or LES. We are using some ofthese techniques to investigate conformational pref-erences of some neuropeptides being currently in-vestigated in the Univer-sity of Florida Brain Insti-tute, in collaboration withProf. Art Edison.
Quantum/ClassicalMethods for Enzymatic
Reactions
Chemical reactions cata-lyzed by biomoleculeshave been subjected tofantastic experimentalscrutiny. Theory is nowcatching up with new de-velopments and is ex-pected to provide de-tailed information about the mechanisms. Enzymeactive sites provide a solvation shell around the re-actants and products that is different from regularsolvents, mostly because it is structured and very in-homogeneous. We are modeling the reactants andthe residues in the active site that actively participatein the reaction with true quantum mechanical meth-ods. The rest of the active site is modeled with Effec-tive Fragments Potentials that appropriately mimic theelectrostatics and repulsion terms that one would ex-pect from quantum mechanics, but at a very smallfraction of the cost. We have already applied thismethodology to the Claisen rearrangement catalyzedby the enzyme Chorismate Mutase from B.Subtilis. Alocal collaboration with Prof. Nicole Horenstein in theChemistry Department will focus on the quantum/classical modeling of reactions catalyzed by enzymes
Adrian RoitbergAdrian Roitberg
REPRESENTATIVE PUBLICATIONS
Research Interests
22
Consider a beam of swift ions, from, forexample, an accelerator, cosmic rays, ora reactor. When the particles passthrough matter, they interact with it, typi-cally losing energy and causing somedamage in the target system. Such inter-action is not always undesirable, as thisis the method used to fabricate many mi-croelectronicdevices, runnuclear reac-tors, and to treatvarious tumorswithout re-course to theknife. In othercases, the inter-action leads tointerference incommunica-tions, singleevent upset fail-ures in comput-ers, and radia-tion sickness inliving things. The details of the mecha-nism of the interaction of massive particleradiation with matter are thus of interest.The understanding of these mechanismsand prediction of their effects on materi-als provides the unifying theme of my re-search.
When a beam of particles with ener-gies of the order of several hundreds
of kev/amu impinges on a material (see Fig.1), the particle undergoes collisions and isslowed by transferring its kinetic energy totarget electrons with the consequence ofcausing excitation, ionization, fragmenta-tion, and defect formation in the target. Theenergy distribution in the beam is conse-quently shifted to lower energy (the energyloss or stopping power) and is broadened(the straggling). We study these processes
at energies from afew eV to tens ofMeV/amu.
Some of the prob-lems of present con-cern are sketchedbelow.
u As the basic pro-cess in stoppingproblems is the colli-sion of a projectilewith the electrons ofthe target atoms,namely an ion/targetcollision, we can
study energy transfer using the methodsof collision theory. We have chosen Elec-tron Nuclear Dynamics (END), developedby Deumens and Öhrn here at the QTP, asthe vehicle for this study. The method doesnot place any restrictions on the projectiletrajectories, does not require any choiceof open channels, allows for excitation,ionization, and fragmentation of both pro-jectile and target, and although not pres-
Trajectory and Molecular Binding Effects inStopping Cross section for Hydrogen Beamson H2, R. Cabrera-Trujillo, Y. Öhrn, E. Deu-mens, and J.R. Sabin, J. Chem. Phys. 116,2783-2793 (2002).
Molecular Target and Projectile Angular Scat-tering Effects in Stopping Power and ChargeExchange at Low to Intermediate ProjectileEnergies, R. Cabrera-Trujillo, Y. Öhrn, J.R.Sabin, and E. Deumens, Phys. Rev. A 65,
024901-(4 pages) (2002).
Shape Dependent Molecular Polarizabilities, S.P.Apell, J.R. Sabin and S.B. Trickey, Int. J. QuantumChem. 86, 35-39 (2002).
Stopping Cross Section and Charge ExchangeStudy on the He+ 6Ne System, R. Cabrera-Trujillo,J.R. Sabin, E. Deumens and Y. Öhrn, AIP Proceed-ings, CP576, 3-6 (2001)
Effects of Confinement on Mean Excitation Energy,P.B. Sabin and J.R. Sabin, Int. J. Quantum Chem.82, 277-281 (2001).
John R.Sabin
ProfessorPhysics andChemistry
Director ofInformationResources &
TechnologicalPrograms (CLAS)
392-1599
Rm 2316New Physics
Building
Energy-Deposition
Stopping Power
Anisotropy
Magnetic Fields
E-dE
straggling
Inte
nsity
stopping
Energy
Z±q2
v
E
v-dv
6| dx |7
23
ently implemented, allows even for quantum me-chanical nuclei. Using this method, we have calcu-lated deflection functions, total differential cross sec-tions, energy loss, and the stopping cross sectionsfor several projectile/target systems.
Figure 2 shows the results of calculations of the simplecase of He colliding with a Neon atom. The total dif-ferential cross section as a function of scattering angleis shown along with a comparison with available ex-perimental data.
u In the higher projectile energy regime, the energyloss can be described in the First Born Approxima-tion by calculating the generalized oscillator strengthdistribution of the target material. We use the polar-ization propagator scheme to calculate the propermatrix elements for excitations of the target using adiscrete representation of the continuum. Thescheme allows us to study the differences in energyloss for different orientations of a target molecule withrespect to the beam or for molecular targets in dif-ferent physical environments.
u Sometimes it is not necessary to predict energyloss properties accurately, but it is sufficient to deter-mine trends as the parameters of the problem arechanged. For example, one might be interested inhow the stopping anisotropy changes as a molecu-lar target gets long and thin as opposed to short andfat. Such predictions can be very useful in designingmaterials with special properties. In order to predictsuch trends, we have developed a back-of-the-en-
John R. SabinJohn R. Sabin
velope scheme wheremolecular targets arerepresented as sharpboundaried, jellium ellipsoids with the physical di-mensions of the molecule under study (see Fig.3).
Although such a scheme is extremely crude, it hasallowed quite useful predictions of molecular prop-erties as a function of molecular geometry.
Check Fig.4 for a measure of the anisotropy in thestopping cross section of several molecules as com-pared to accurate calculations.
u Other problems under consideration include col-lisions of swift ions with surfaces, clusters, and largemolecules.
REPRESENTATIVE PUBLICATIONS
Research Interests
24
Samuel B.Trickey
ProfessorPhysics andChemistry
Director QTP
392-1597
Rm 2324New Physics
Building
Density FunctionalTheory
Multi-Scale Simula-tions
Ultra-Thin Films
Periodic SystemAlgorithms
Research in my group focuses on
u Development and implementa-tion of robust algorithms for pre-dictive simulations of materials,particularly ordered systems.
u Predictive calculation of struc-tures and properties of crystalsand ordered ultrathin films de-rived from them, including quan-tum size effects, surface ener-gies, fracture-related quantities,high-pressure response, andmagnetic effects.
u Fundamentals of Density FunctionalTheory (DFT)
Algorithms for Ordered Systems
Under a new NSF ITR award, we be-gan a top-to-bottom rebuild of theGaussian orbital, fitting-functionmethodology for periodic sys-tems embodied in theBoettger-Trickey code GTOFF.Modern, object oriented pro-gramming and contemporarycomputer languages (C++,F90, Python) will be used toreimplement the fitting meth-odology (including our unique
fit-to-fit of exchange-correlationquantities to the fitted density), gen-eralized Ewald summations, mixeddirect and reciprocal space tech-niques, and Douglas-Kroll-Hessrelativistic methodologies that aremain features of GTOFF. Ashley
Alford is the primary worker on thiseffort.
A major review article about theprinciple algorithmic features of
GTOFF was written this year and is toappear in “Computational MaterialsScience”, a volume of “Theoreticaland Computational Chemistry” ed-ited by J. Leszczynski. The aim of theproject is to have a code that is veryclean and systematic so as to en-able addition of new physics aswell as be readily maintainable.The new physics on which we areconcentrating is Current DensityFunctional Theory. Initial studies are
nearly complete. Wuming Zhu isdoing his Ph.D. thesis on this topic,
after completing notablework on pair potentials forSilica and on the Benoit et al.approximate DFT scheme.
The work on GTOFF contin-ues to be in close collabora-tion with Dr. JonathanBoettger (Los Alamos Na-tional Lab).
Methods and Implementation of Robust,Highprecision Gaussian Basis DFT Calculationsfor Periodic Systems: the GTOFF Code, S.B.Trickey, J.A. Alford, and J.C. Boettger, in Theo-retical and Computational Chemistry vol. 8 of“Computational Materials Science”, J.Leszczynski ed.(Elsevier) in press.
Tests of Perturbative DFT Total Energy EstimatesImplemented in a Gaussian Basis, Wuming Zhuand S.B. Trickey, Int. J. Quantum Chem. [in press]
Deformation and Fracture of SiO2 Nanorod, Ting Zhu,Ju Li, Sidney Yip, R.J. Bartlett, S.B. Trickey and, N.H.de Leeuw, Molecular Simulations [in press]
Challenges and State of the Art in Simulation ofChemoMechanical Processes, S.B. Trickey and P.A.Deymier, in Chemical Mechanical Planarization IV R.L.Opila, C. ReidsemaSimpson, K.B. Sundaram, and S.Seal eds (The Electrochemical Society, Pennington N.J.2001) 3 17.
State Energy Functionals and Variational Equations inDensity Functional Theory, B. Weiner and S.B. Trickey,J. Molec. Struct. (Theochem) 501-02, 6583 (2000).
Figure: 144 atomnanorod at
T = 100 K, justbefore tensile
failure.
25
Samuel B. TrickeySamuel B. Trickey
Predictive Calculations of Material Properties
We continue to study the problem of purely theoreti-cal parameterization of the classical potentials usedin multiscale molecular dynamics simulation ofchemo-mechanical processes. Our focus is simula-tions of fracture in silica. The goal is to understandand manage the information transfer across theq u a n t u mmechanicalMDinterface. Wecontinued tostruggle withthe results ofmassive calcu-lations ona l p h a q u a r t z(using GTOFF)and on theH6Si2O7 andH4SiO4 mol-ecules. The cru-cial finding isthat the mixedtheory and ex-periment ap-proach to po-tential fittingfound in the lit-erature is notconsistent withthe potentialsthat actuallyemerge from fittingto a purely compu-tational data base.Yet a purely com-putational embed-ding of the quan-tum mechanical region in a region of classical po-tentials is inevitable in any multi-scale simulation ofa chemo-mechanical process. We are now consid-ering how to incorporate the QM information into “re-active” potentials.
Recently I resumed the study of lattice-dependence ofthe electronic magnetic moment in 3d transition metalultra-thin films. These exhibit many very different spin-ordering behaviors as a function of lattice spacing. After
completing the isolatedmonolayers, I will studythe extent to which anepitaxial insulatingsubstrate alters (or even suppresses) those behav-iors.
Fundamentals of Density Functional Theory
I continue towork, as timeallows, on fun-damentals ofDensity Func-tional Theorywith Prof. BrianWeiner (PennState). Our re-cent focus hasbeen on Den-sity MatrixF u n c t i o n a lTheory, specifi-cally in rela-tionship withour construc-tive approachto DFT ex-change- cor-r e l a t i o nfunct ionals .We have for-mulated con-
strained searchDFT in terms of fi-ber bundles andtransformationson them. The ap-proach is valid forb o t h
timedependent and time-independent DFT. Since thetransformations that search intrabundle andinterbundle can be approximated systematically interms of any familiar trial wave function (HartreeFock,AGP, single CI, etc.), we have a systematic way ofbuilding functionals that correspond to what, in thejargon of quantum chemists, is a specified “level” oftheory. Recently we have attempted to extend thisapproach to density-matrix functional theory, whichturns out to be a challenging problem.
Stress-strain curves for the 144 atom nanorod atT = 1K with two classical potentials.
Stre
ss [G
Pa]
60
50
40
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10
0
-10
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-50-0.1 -0.05 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35
TTAM
BKS
BKS
TTAM
Strain
Chuck Frazier & David Colburn
Neil Sullivan &David Micha
Jack Sabin &Neil Sullivan
Chuck Frazier, David Colburn,& Neil Sullivan experiencingthe Immersadesk
RECEPTION AND OPEN HOUSE FOR THE NEWEST XENA ACQUISITION
Sam Trickey
Henk Monkhorst, Jack Sabin,Erik Deumens, Frank Harris,& Yngve Öhrn
Yngve Öhrn & David Colburn
Dave Richardson, Chris Stanton,& Yngve Öhrn