Computational Research Needs for Alternative and Renewable Energy

1
Computational Research Needs for Alternative and
Renewable Energy Natural and Artificial
Photosynthesis Victor S. Batista Department of
Chemistry, Yale University, New Haven, CT
06520-8107

• NSF CHE-0345984
• NSF ECCS-0725118
• NIH 2R01-GM043278-14
• DOE DE-FG02-07ER15909
• US-Israel BSF
• NSF ECS-0404191
• Research Corporation Innovation Award RI0702
• ACS PRF-37789-G6
• Sloan Fellowship
• Camillie Dreyfus Teacher Scholar Award

Funding
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• Natural Photosynthetic Systems
• McEvoy et. al. Photosynthesis Fundamental
  Aspects to Global Perspectives vol. 1, (D. Bruce
  and A. van der Est, ed.) Allen Press Inc.,
  Lawrence, Kansas, p. 278-280 (2005).
• Sproviero et. al. Photochem. Photobiol. 4,
  940-949 (2005).
• Sproviero et. al. J. Inorg. Biochem. 100, 786-800
  (2006).
• Sproviero et. al. J. Chem. Theor. Comput.
  41119-1134 (2006).
• Sproviero et. al. Curr. Op. Struct. Biol.
  17173-180 (2007).
• Sproviero et. al. Coord. Chem. Rev. 252395-415
  (2008)
• Sproviero et. al. J. Am. Chem. Soc. 1303428-3442
  (2008)
• Sproviero et. al. Phil. Trans. Royal Soc. London
  B 3631149-1156 (2008)
• Sproviero et. al. Photosynth. Res., in press
  (2008)
• Sproviero et. al. J. Am. Chem. Soc. 130
  6728-6730 (2008).
• Gascon et. al. Photosynthesis. Energy from the
  Sun. Eds. J. F. Allen, E. Gantt, J.H. Golbeck and
  B. Osmond, p. 363-368, Springer Publishers, New
  York (2008).
• Artificial Systems
• L.G.C. Rego, L. F. Santos and V. S. Batista, Ann.
  Rev. Phys. Chem. in press (2008)
• L.G.C. Rego, S.G. Abuabara and V. S. Batista, J.
  Mod. Optics 542817-2627 (2007)
• S.G. Abuabara, L.G.C. Rego and V. S. Batista, J.
  Mod. Optics 53, 2519-2532 (2006)
• S.G. Abuabara, L.G.C. Rego and V.S. Batista, J.
  Am. Chem. Soc. 122, 18234 (2005)
• L.G.C. Rego, S.G. Abuabara and V.S. Batista,
  Quant. Inform. Comput. 5, 318 (2005)

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COLLABORATORS
Enrique R. Batista, Los Alamos Natl Lab, USA.
Jean Luc-Bredás, Georgia Inst. Tech., USA.
David Britt, University of California, Davis,
USA. Doug Bruce, Brock University, Canada.
Gary W. Brudvig, Yale University, USA. Paul
Brumer, University of Toronto, Canada. Robert H.
Crabtree, Yale University, USA. Niels Damrauer,
Univ. of Colorado, Boulder, USA. Holger Dau,
Freie Universität Berlin, Germany. José A.
Gascon, University of Connecticut, USA. Victor
Guallar, Barcelona Supercomput. Center, Spain.
Marilyn Gunner, City College of New York, USA.
Michael F. Herman, Tulane University, USA.
Casey Hynes, University of Colorado, Boulder,
USA. Daniel Laria, University of Buenos Aires,
Argentina. Kevin Leung, Sandia National
Laboratories, USA. Tim Lian, Emory University,
USA. J. Patrick Loria, Yale University, USA.
Krishna C. Mandal, EIC Lab. Inc, USA. James P.
McEvoy, Regis University, USA.
Latika Menon, Northeastern University, USA.
William H. Miller, Univ. California, Berkeley,
USA. Erik T.J. Nibbering, Max-Born Institut,
Berlin, Germany. Lou Noodleman, The Scripps Res.
Inst., USA. Ehud Pines, Univ. Negev, Beer-Sheva,
Israel. Tijana Rajh, Argonne National Lab, IL,
USA. Luis G.C. Rego, Univ. Federal S. Catarina,
Brazil. Susan B. Rempe, Sandia Natl
Laboratories, USA. Charles A. Schmuttenmaer,
Yale University, USA. Per Siegbahn, Stockholm
University, Sweden. Scott Strobel, Yale
University, USA. Ann Valentine, Yale University,
USA. Yinghua Wu, Georgia Inst. of Technology,
USA.
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Photo Courtesy of Michael Newcomer
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Woodford and Phillips wells, Tarr Farm, 1861 From
Pennsylvania Historical Museum Commission,
Drake Well Museum Collection, Titusville, PA
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Production of Greenhouse Gas
Drake Well, 1859
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http//climate.yale.edu/test/
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DOE CRNARE Report
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A viable solution to alternative and renewable
energy
Hydrogen Production by Solar Water-Splitting
H2O(l) O2 (g) 4H (aq)
4e- 4H(aq) 4e- H2 (g)
H-Storage
catalyst
catalyst
catalyst
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Kok Cycle S-state Cycle of Photosynthetic Water
Oxidation
Joliot, P. Barbieri, G. Chabaud, R. Photochem.
Photobiol. (1969) 10 309-329. Kok, B. Forbush,
B. and McGloin, M., Photochem. Photobiol. (1970)
11 457-475.

• Current understanding of the mechanism of
  photosynthetic water oxidation.
• The start of the quest for the chemical nature
  of intermediates (structure,
• oxidation states and substrate water
  bonding).

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Photosystem II Structural Model

• Cyanobacteria
• Algae
• Higher plants

P680Pheo hu P680Pheo-
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Breakthroughs in X-ray Diffraction Models of
Photosystem II
Ferreira, K. N. et al Science 2004, 303,
1831-1838. X-ray structure at 3.5 Å
resolution Biesiadka, J. et al Phys. Chem. Chem.
Phys. 2004, 6, 4733-4736. X-ray structure at 3.2
Å resolution Loll, B. et al Nature 2005, 438,
1040-1044 X-ray structure at 3.0 Å resolution
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An outstanding challenge Oxygen Evolving Complex
Phys.Chem. Chem. Phys. (2004) 64781-4792

• (A) 3.8 Å resolution Zouni, A. et. al. Nature
  (2001) 409739-743.
• (B) 3.6 Å resolution Kamiya, N. and Shen, J.R.,
  PNAS USA (2003) 10098-103.
• (C) 3.5 Å resolution Ferreira, K.N. et. al.
  Science (2004) 3031831-1838.
• (D) 3.2 Å resolution Biesiadka, J. et al. Phys.
  Chem. Chem. Phys. (2004) 64733-4736.
• (E) 3.0 Å resolution Loll, B. et. al. Nature
  (2005) 4381040-1044.

RADIATION DAMAGE caused by exposure to high dosis
of x-rays during data collection. J. Yano, J.
Kern, K. D. Irrgang, M. J. Latimer, U. Bergmann,
P. Glatzel, Y. Pushkar, J. Biesiadka, B. Loll, K.
Sauer, J. Messinger, A. Zouni, and V. K.
Yachandra. Natl. Acad. Sci. U. S. A.,
1021204712052, 2005. STRUCTURAL DISORDER Even
at the highest available resolution of 3.2-3.0 Å
Biesadka, J. et. al. Phys. Chem. Chem. Phys.
(2004) 64733 Nature (2005) 438 1040 the
nuclear geometry of the Mn complex itself remains
invisible since the coordinate error can be as
high as 1 Å and individual Mn ions can hardly be
assigned.
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Jim Barbers Model Ferreira et al. Science
(2004) 3031831-1838
Ca
Mn
The coordinates of the Mn atoms were chosen
consistently with the observed dual-lobe
electronic density to have Mn-Mn distances of
about 2.7 Å and 3.3 Å length as reported by XAS
studies see, e.g., George, G.N. Prince, R.C.
and Cramer, S.P. Science (1989) 243789-791 and
the cuboidal structure with a dangling Mn
suggested by EPR and ENDOR data Peloquin, J.M.
Campbell, K.A.Eandall, D.W.Evanchik,
M.A.Pecoraro, V.L.Amstrong, W.A.Britt, R.D. J.
Am. Chem. Soc. (2000) 12210926-10942.
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QM/MM Models of the Oxygen Evolving Complex of
Photosystem II

• Construct chemically sensible QM/MM models of
  the OEC, explicitly including the perturbational
  influence of the surrounding protein environment,
  by using empirical structural models as
  initial-guess configurations based on XRD data
  and oxidation states based on EPR.
• Investigate changes in structural and electronic
  properties of the OEC along the catalytic cycle
  of water oxidation in order to provide insight
  into the mechanism of photosynthetic water
  oxidation as well as first-principle
  interpretations of high-resolution experimental
  data, including FTIR, XAS and EPR/ENDOR as well
  as XRD, MS measurements and mutagenesis studies.

• McEvoy et. al. Photosynthesis Fundamental
  Aspects to Global Perspectives vol. 1, (D. Bruce
  and A. van der Est, ed.) Allen Press Inc.,
  Lawrence, Kansas, p. 278-280 (2005).
• Sproviero et. al. Photochem. Photobiol. 4,
  940-949 (2005).
• Sproviero et. al. J. Inorg. Biochem. 100, 786-800
  (2006).
• Sproviero et. al. J. Chem. Theor. Comput.
  41119-1134 (2006).
• Sproviero et. al. Curr. Op. Struct. Biol.
  17173-180 (2007).
• Sproviero et. al. Coord. Chem. Rev. 252395-415
  (2008)
• Sproviero et. al. J. Am. Chem. Soc. 1303428-3442
  (2008)
• Sproviero et. al. Phil. Trans. Royal Soc. London
  B 3631149-1156 (2008)
• Sproviero et. al. Photosynth. Res., in press
  (2008)
• Sproviero et. al. J. Am. Chem. Soc. 130
  6728-6730 (2008).
• Gascon et. al. Photosynthesis. Energy from the
  Sun. Eds. J. F. Allen, E. Gantt, J.H. Golbeck and
  B. Osmond, p. 363-368, Springer Publishers, New
  York (2008).

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Quantum Mechanics / Molecular Mechanics (QM/MM)
Hybrid Methodology (Warshel, 1976)
Two-layer ONIOM-Electronic Embedding (EE)
(Morokuma), G03.
-
-
-

-

MM
MM
QM OEC
MM OEC
MM OEC



-
QM OEC

-
-




-
-
QM DFT B3LYP/lacvp MM Amber Force Field
UB3LYP ONIOM-EE optimizations
DFT QM/MM J.A. Gascon and V.S. Batista,
Biophys. J. 87, 2931-2941 (2004) J.A. Gascon,
E.M. Sproviero and V.S. Batista, J. Chem. Theor.
Comput. 2, 11-20 (2005) DFT QM/MM Self-Consistent
Protein Polarization J.A. Gascon, S.S.F. Leung,
E.R. Batista and V.S. Batista, J. Chem. Theor.
Comput. 2, 175-186 (2006)
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DFT-QM/MM Model of the S1 State Sproviero, E.M
et. al. J. Chem. Theor. Comput., (2006)
41119-1134 Curr. Op. Struct. Biol., (2007)
17173-180 Phil. Trans. Royal Soc. London B
3631149-1156 (2008) Coord. Chem. Rev.
252395-415 (2008) J. Am. Chem. Soc.
1303428-3442 (2008) J. Am. Chem. Soc.
1306427-6430 (2008).
E189
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QM/MM vs. XRD Models EXAFS spectra
QM/MM
Experimental EXAFS data Holger Dau M. Haumann,
C. Muller, P. Liebisch, L. Iuzzolino, J. Dittmer,
M. Grabolle, T. Neisius,W. Meyer-Klaucke, and H.
Dau. Biochemistry, 418941908, 2005.
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QM/MM vs. X-ray Models Overall Electronic Density
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XRD vs. Polarized-EXAFS Models
Sproviero et al. J. Am. Chem. Soc. 130
67286730 (2008)
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EXAFS-based Structural Refinement (ESR) Method
DFT-QM/MM and R-QM/MM Models
Sproviero et al. J. Am. Chem. Soc. 130
67286730 (2008)
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XRD vs. R-QM/MM models
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Coord. Chem. Rev. 252395-415 (2008) J. Am.
Chem. Soc. 1303428-3442 (2008)

• Mn oxidization
• Cluster distortions
• Ligand rearrangements
• Water binding and exchange

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OO Bond Formation
Reduction
Nucleophilic Attack
ARG357 catches a proton from Ws when the O-O
distance is c.a. 2.1 Å.
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Dioxygen Formation Proton Translocation
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QM/MM S-state Intermediates Calculated vs.
Experimental EXAFS Spectra
Exp. (Holger Dau) Calc. (QM/MM)
Coord. Chem. Rev. 252395-415 (2008) J. Am.
Chem. Soc. 1303428-3442 (2008)
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Water Channels
Coord. Chem. Rev. 252395-415 (2008) J. Am.
Chem. Soc. 1303428-3442 (2008)
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Benchmark Calculations E.M. Sproviero, J.A.
Gascon, J.P. McEvoy,  G.W. Brudvig and V.S.
Batista J. Inorg. Biochem. (2006) 100, 786-800.
MnIIIMnIV (m-O)2 (H2O)2 (terpy)23
MnIIIMnIV (m-O)2 (phen)43
Mn3O4 (bpy)4 (H2O)24
Mn4O4 (Ph2PO2)6
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Water oxidation by catalytic Mn-complexes
Crabtree, Brudvig and co-workers Science 283,
1524-1527 (1999) Science 312, 1941-1943 (2006)
J. Chem. Edu. (2005) p. 791-794.

• MnIV(m-O)2MnIII (H2O)2 (terpy)23
• (terpy 2,2'6,2''-terpyridine)

Time, Hours
The active state in OO bond formation is the
highly oxidized MnV-oxo state, after oxidization
by the oxygen-atom transfer reagent oxone (HSO5-)
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hn
hn
Stroma
Stroma
Fe2
QA
QB
hn
ChlZ
Pheo
Thylakoid Membrane
Thylakoid Membrane
P680
CP43
D1
TyrD
TyrZ
D2
Cyt b559
Cl-
Mn4Ca
OEC
CP47
23 kDa
Lumen
Lumen
33 kDa
17 kDa
Artificial Photosynthesis
Natural Photosynthesis
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Photocatalytic Cell
Crabtree, Brudvig, Schmuttenmaer, Batista

• J. Chem. Theor. Comput. 4, 1119-1134 (2006) QM/MM
  Model of the OEC of Photosystem II, Eduardo M.
  Sproviero, Jose A. Gascon, James P. McEvoy,  Gary
  W. Brudvig and Victor S. Batista.
• Photochem. Photobiol. 4, 940-949 (2005) The
  Mechanism of Photosynthetic Water Splitting,
  James P. McEvoy, Jose A. Gascon, Victor S.
  Batista and Gary W. Brudvig.
• J. Inorg. Biochem. 100, 786-800 (2006)
  Characterization of Synthetic Oxomanganese
  Complexes and the Inorganic-Core of the
  O2-Evolving Complex in Photosystem II Evaluation
  of the DFT/B3LYP Level of Theory, Eduardo M.
  Sproviero, Jose A. Gascon, James P. McEvoy,  Gary
  W. Brudvig and Victor S. Batista.

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Dye-Sensitized Solar Cells
Thoss, Wang, Persson Ramakrishna, Willig, May,
Prezhdo

• Interfacial Electron Transfer Dynamics
• Relevant timescales and mechanisms
• Dependence of electronic dynamics on the crystal
  symmetry
• Thermal Fluctuations
• Hole Relaxation Dynamics
• Coherent-control
• Decoherence timescale
• Effect of nuclear dynamics on electronic quantum
  coherences

L.G.C. Rego, L. F. Santos and V. S. Batista, Ann.
Rev. Phys. Chem. in press (2008) L.G.C. Rego,
S.G. Abuabara and V. S. Batista, J. Mod. Optics
542817-2627 (2007) S.G. Abuabara, L.G.C. Rego
and V. S. Batista, J. Mod. Optics 53, 2519-2532
(2006) S.G. Abuabara, L.G.C. Rego and V.S.
Batista, J. Am. Chem. Soc. 122, 18234
(2005) L.G.C. Rego, S.G. Abuabara and V.S.
Batista, Quant. Inform. Comput. 5, 318
(2005) L.G.C. Rego, S.G. Abuabara and V.S.
Batista, J. Chem. Phys. 122, 154709 (2005)
L.G.C. Rego and V.S. Batista, J. Am. Chem. Soc.
125, 7989 (2003)
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Functionalized Anatase/MnIV(m-O)2MnIII (H2O)2
(terpy)23
Catechol HOMO
terpy HOMO
Complex HOMO
1.48 eV
466 nm
508 nm
380 nm
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Functionalized Anatase Density of States
(D.O.S.)
adsorbate/ catechol
anatase
terpy
adsorbate
catechol
(H2O)MnIII (O)2MnIV (OH2)
CB
150 fs
508 nm

terpy LUMO

1.48 eV
HOMO
Catechol HOMO
terpy HOMO

lt 415 nm Fujishima Honda Nature (1972)
23837-38
TiO2 HOMO
VB
39
Injection Dynamicsduring the first 83 fs
40
Survival Probability after Photoexcitation at 508
nm terpy/cat state 133
41
Anatase visible sensitization with Oxo-Mn
ligandsTheory vs. Experiments
S.G. Abuabara, C. Cayde, J. Baxter, C.A.
Schmuttenmaer, R.H. Crabtree, G.W. Brudvig and
V.S. Batista, J. Phys. Chem. C 11111982-11990
(2007)
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S.G. Abuabara, C. Cayde, J. Baxter, C.A.
Schmuttenmaer, R.H. Crabtree, G.W. Brudvig and
V.S. Batista, J. Phys. Chem. C 11111982-11990
(2007)
6 K
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S.G. Abuabara, C. Cayde, J. Baxter, C.A.
Schmuttenmaer, R.H. Crabtree, G.W. Brudvig and
V.S. Batista, J. Phys. Chem. C 11111982-11990
(2007)
Ultrafast electron injection from with Oxo-Mn
CatalystsTheory vs. Experiments
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Robust Linkers based on Derivatized Acac Anchors
W. McNamara, R. Snoeberger, C. Cayde, G. Li,
Schmuttenmaer, R.H. Crabtree, G.W. Brudvig and
V.S. Batista, J. Am. Chem. Soc. submitted (2008)
(a) Mn complex 1 MnII(H2O)3(3)2 (terpy)
2,26,2-terpyridine) (b) surface-complex
1/TiO2-NP. Color scheme C (gray), H (white), Mn
(purple), N (blue), O (red), Ti (green).
45
Acknowledgments

• NSF Career Award CHE 0345984
• NSF Nanoscale Exploratory Research (NER) Award
  ECS 0404191
• NSF ECCS 0725118
• ACS Petroleum Research Funds 37789-G6
• Research Corporation, Innovation Award RI0702
• NIH 2R01-GM043278-14
• DOE DE-FG02-07ER15909
• US-Israel BSF
• Sloan Fellowship
• Dreyfus Teacher-Scholar Award
• Hellman Family Fellowship
• Yale Junior Faculty Fellowship in the Natural
  Sciences 2005-2006
• DOE Allocation of Supercomputer Time at NERSC
• Thank you !

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Hole-Relaxation Dynamics in the Semiconductor
Band Gap

• Sabas G. Abuabara, Luis G.C. Rego and Victor S.
  Batista, J. Mod. Optics 53, 2519-2532 (2006)
• Sabas G. Abuabara, Luis G.C. Rego and Victor S.
  Batista, J. Chem. Phys. 122, 154709 (2005)
• Luis G.C. Rego, Sabas G. Abuabara and Victor S.
  Batista, Quant. Inform. Comput. 5, 318 (2005)

t0 ps
t15 ps
Super-exchange hole transfer
47
Inhibiting Hole Super-Exchange by multiple
unitary-quick pulses
We investigate the feasibility of manipulating
the underlying hole relaxation dynamics by merely
affecting the relative phases of the state
components (e.g., by using femtosecond laser
pulses)
Sabas G. Abuabara, Luis G.C. Rego and Victor S.
Batista, J. Mod. Optics 53, 2519-2532 (2006)
Sabas G. Abuabara, Luis G.C. Rego and Victor S.
Batista, Quant. Inform. Comput. 5, 318 (2005)
L
C
LUMO
CB
superexchange
hole
HOMO
w12
phase-shift pulses
HOMO-1
VB
TiO2 semiconductor
Adsorbate molecules (C, L,)
48
Inhibiting Hole Super-Exchange by multiple
phase-shift pulses, contd
Sabas G. Abuabara, Luis G.C. Rego and Victor S.
Batista, Quant. Inform. Comput. 5, 318
(2005) Sabas G. Abuabara, Luis G.C. Rego and
Victor S. Batista, J. Mod. Optics 53, 2519-2532
(2006) Luis G.C. Rego, Lea F. Santos and Victor
S. Batista, Ann. Rev. Phys. Chem. in press (2008)
Apply pulsed radiation tuned to frequency w21
Particular case ultrashort 2-p pulses with t
200 fs
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Investigation of Coherent-Control contd
Sabas G. Abuabara, Luis G.C. Rego and Victor S.
Batista, Quant. Inform. Comput. 5, 318 (2005)
2-p pulses (200 fs spacing)
14 fs
60 fs
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Example Double-Well Coupled to an Auxiliary State
two state perturbative model intuition borne out
in exact QD simulation
tunneling splitting
localized states
We freeze the motion of a tunneling particle
without collapsing the quantum state without
changing the total energy of the system, or the
energy tunneling barrier.
Numerically implement pulses as
modeling ultrashort (fs) pulse train
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Coherent-Control of Tunneling Dynamics with
Stochastic Unitary-Pulses
Initial Population Decay
Potential
Energy
P(t)
Double-Well

? 400 a.u.
Coordinate a.u.
Time a.u.
Energy
P(t)
Barrier
Coordinate a.u.
Time a.u.
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Acknowledgments

• NSF Career Award CHE 0345984
• NSF Nanoscale Exploratory Research (NER) Award
  ECS 0404191
• NSF ECCS 0725118
• ACS Petroleum Research Funds 37789-G6
• Research Corporation, Innovation Award RI0702
• NIH 2R01-GM043278-14
• DOE DE-FG02-07ER15909
• US-Israel BSF
• Sloan Fellowship
• Dreyfus Teacher-Scholar Award
• Hellman Family Fellowship
• Yale Junior Faculty Fellowship in the Natural
  Sciences 2005-2006
• DOE Allocation of Supercomputer Time at NERSC
• Thank you !