Shaul Mukamel

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map
    Tomoyuki Hayashi
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 125:194510. 2006
  2. pmc Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding
    Hao Ren
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Phys Chem Chem Phys 15:19457-64. 2013
  3. pmc Multidimensional attosecond resonant X-ray spectroscopy of molecules: lessons from the optical regime
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Annu Rev Phys Chem 64:101-27. 2013
  4. pmc A coherent nonlinear optical signal induced by electron correlations
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Chem Phys 127:221105. 2007
  5. doi request reprint Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signals
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 134:161101. 2011
  6. pmc Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study
    Christopher Nj Marai
    Graduate Program in Biochemistry and Structural Biology, State University of New York at Stony Brook, New York, 11794 3400, USA
    PMC Biophys 3:8. 2010
  7. pmc Coherent multidimensional optical probes for electron correlations and exciton dynamics: from NMR to X-rays
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California, USA
    Acc Chem Res 42:553-62. 2009
  8. ncbi request reprint Many-body approaches for simulating coherent nonlinear spectroscopies of electronic and vibrational excitons
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Chem Rev 104:2073-98. 2004
  9. ncbi request reprint Interplay of slow bath fluctuations and energy transfer in 2D spectroscopy of the FMO light-harvesting complex: benchmarking of simulation protocols
    Benoit Palmieri
    University of California at Irvine, 1102 Natural Sciences 2, Irvine, California 92697 2025, USA
    Phys Chem Chem Phys 12:108-14. 2010
  10. pmc Simulation protocols for coherent femtosecond vibrational spectra of peptides
    Wei Zhuang
    Department of Chemistry, University of California at Irvine, California 92697 2025, USA
    J Phys Chem B 110:3362-74. 2006

Collaborators

Detail Information

Publications80

  1. ncbi request reprint Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map
    Tomoyuki Hayashi
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 125:194510. 2006
    ..The amide I frequency is negatively correlated with the hydrogen bond on carbonyl C[double bond]O, whereas the amide A and III are negatively and positively correlated, respectively, with the hydrogen bond on amide N-H...
  2. pmc Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding
    Hao Ren
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Phys Chem Chem Phys 15:19457-64. 2013
    ..Characteristic two dimensional (2D) SRR features of various folding states are identified. Structural fluctuations erode the cross peaks and the correlation between diagonal peaks is a good indicator of the α-helix formation. ..
  3. pmc Multidimensional attosecond resonant X-ray spectroscopy of molecules: lessons from the optical regime
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Annu Rev Phys Chem 64:101-27. 2013
    ....
  4. pmc A coherent nonlinear optical signal induced by electron correlations
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Chem Phys 127:221105. 2007
    ..The peak pattern in two-dimensional plots, obtained by displaying the signal versus two frequencies conjugated to two pulse delays, provides a direct visualization and specific signatures of the many-electron wave functions...
  5. doi request reprint Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signals
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 134:161101. 2011
    ..We show that even though the external spectral and temporal parameters of the pulses may be independently controlled, the effective temporal and spectral resolution of the experiment may not exceed the fundamental bandwidth limitation...
  6. pmc Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study
    Christopher Nj Marai
    Graduate Program in Biochemistry and Structural Biology, State University of New York at Stony Brook, New York, 11794 3400, USA
    PMC Biophys 3:8. 2010
    ..In addition to exploring the folding mechanism the work presented here can be applied in combination with experiment to refine and validate current molecular dynamics force fields.PACS Codes: 87.15.Cc, 87.15.hm, 87.15.hp...
  7. pmc Coherent multidimensional optical probes for electron correlations and exciton dynamics: from NMR to X-rays
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California, USA
    Acc Chem Res 42:553-62. 2009
    ..Common principles underlie these techniques in coherent spectroscopy for spins, valence electrons, and core electronic excitations, spanning frequencies from radiowaves to hard X-rays...
  8. ncbi request reprint Many-body approaches for simulating coherent nonlinear spectroscopies of electronic and vibrational excitons
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Chem Rev 104:2073-98. 2004
  9. ncbi request reprint Interplay of slow bath fluctuations and energy transfer in 2D spectroscopy of the FMO light-harvesting complex: benchmarking of simulation protocols
    Benoit Palmieri
    University of California at Irvine, 1102 Natural Sciences 2, Irvine, California 92697 2025, USA
    Phys Chem Chem Phys 12:108-14. 2010
    ..The spectral signatures at these different levels of theory are compared and simulation cost is estimated. Approaches which do require statistical averaging over disorder are orders of magnitude slower...
  10. pmc Simulation protocols for coherent femtosecond vibrational spectra of peptides
    Wei Zhuang
    Department of Chemistry, University of California at Irvine, California 92697 2025, USA
    J Phys Chem B 110:3362-74. 2006
    ..Real-space truncation of the scattering matrix of the nonlinear exciton equations significantly reduces the computational cost, making it particularly attractive for slow fluctuations in large globular proteins...
  11. pmc Simulation study of chiral two-dimensional ultraviolet spectroscopy of the protein backbone
    Darius Abramavicius
    Department of Chemistry, University of California, Irvine, California, USA
    J Am Chem Soc 132:7769-75. 2010
    ..Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism...
  12. pmc Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide
    Jianping Wang
    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 9104 6323, USA
    J Phys Chem B 112:5930-7. 2008
    ..Our results show that 2D IR of peptide with single (13)C isotopic labeling can be used to probe the electrostatic environment of the peptide local structure...
  13. pmc Coherent two dimensional infrared spectroscopy of a cyclic decapeptide antamanide. A simulation study of the amide-I and A bands
    Cyril Falvo
    Department of Chemistry, University of California Irvine, Irvine, CA, USA
    J Phys Chem B 112:12479-90. 2008
    ..Multidimensional spectroscopy reveals intramolecular couplings and gives information on its dynamics. A two-color amide-I and amide-A crosspeak is predicted and analyzed in terms of local structure...
  14. pmc Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptide
    Neelanjana Sengupta
    Department of Chemistry, University of California at Irvine, Irvine, California 92697 2025, USA
    J Phys Chem B 113:12037-49. 2009
    ....
  15. ncbi request reprint Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map
    Tomoyuki Hayashi
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Phys Chem A 109:64-82. 2005
    ..This allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations...
  16. pmc Probing electron correlations in molecules by two-dimensional coherent optical spectroscopy
    Zhenyu Li
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Am Chem Soc 130:3509-15. 2008
    ....
  17. pmc Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses
    Jason D Biggs
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 136:174117. 2012
    ..2 eV FWHM) pulses tuned to the oxygen and nitrogen K-edges. Crosspeaks in 2D signals reveal electronic Franck-Condon overlaps between valence orbitals and relaxed orbitals in the presence of the core-hole...
  18. pmc Unravelling coherent dynamics and energy dissipation in photosynthetic complexes by 2D spectroscopy
    Darius Abramavicius
    Natural Sciences, University of California, Irvine, California 92697 2025, USA
    Biophys J 94:3613-9. 2008
    ..The proposed pulse sequences may also be applied to reveal information on the robustness of quantum states in the presence of fluctuating environments in other nanoscopic complexes and devices...
  19. pmc Two-dimensional vibrational optical probes for peptide fast folding investigation
    Wei Zhuang
    Department of Chemistry, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 103:18934-8. 2006
    ..g. circular dichroism) and identify structures indistinguishable by NMR...
  20. pmc Double-quantum resonances and exciton-scattering in coherent 2D spectroscopy of photosynthetic complexes
    Darius Abramavicius
    Department of Chemistry, 1102 Natural Sciences 2, University of California, Irvine, CA 92697 2025, USA
    Proc Natl Acad Sci U S A 105:8525-30. 2008
    ..An alternative physical interpretation of these signals in terms of quasiparticle scattering is developed...
  21. doi request reprint Quantum oscillatory exciton migration in photosynthetic reaction centers
    Darius Abramavicius
    Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, California 92697 2025, USA
    J Chem Phys 133:064510. 2010
    ..These signatures of quantum transport may be observed by two dimensional coherent optical spectroscopy...
  22. pmc Chirality-based signatures of local protein environments in two-dimensional optical spectroscopy of two species photosynthetic complexes of green sulfur bacteria: simulation study
    Dmitri V Voronine
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    Biophys J 95:4896-907. 2008
    ..Pulse polarization configurations are designed that can separate the coherent and incoherent exciton dynamics contributions to the two-dimensional spectra...
  23. pmc Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges
    Wei Zhuang
    Department of Chemistry, University of California at Irvine, CA 92697 2025, USA
    Angew Chem Int Ed Engl 48:3750-81. 2009
    ..Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen-bonding fluctuations, protein folding, and chemical-exchange processes are discussed...
  24. pmc Lindblad equations for strongly coupled populations and coherences in photosynthetic complexes
    Benoit Palmieri
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 130:204512. 2009
    ..Simulations for a model dimer reproduce all observed strong coupling effects...
  25. pmc Simulation of two-dimensional ultraviolet spectroscopy of amyloid fibrils
    Jun Jiang
    Chemistry Department, University of California Irvine, Irvine, California, USA
    J Phys Chem B 114:12150-6. 2010
    ....
  26. pmc Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysis
    Wei Zhuang
    Department of Chemistry, University of California, Irvine, CA 92697 2025, USA
    Proc Natl Acad Sci U S A 102:7443-8. 2005
    ..Comparison of signals generated in different directions shows that the double-quantum-coherence signal has a higher sensitivity to the couplings compared with the single-quantum-coherence (photon echo) technique...
  27. doi request reprint Energy-transfer and charge-separation pathways in the reaction center of photosystem II revealed by coherent two-dimensional optical spectroscopy
    Darius Abramavicius
    Department of Chemistry, University of California, Irvine, Irvine, California 92697 2025, USA
    J Chem Phys 133:184501. 2010
    ..The simulated third order two-dimensional signals, generated in the directions -k(1)+k(2)+k(3), k(1)-k(2)+k(3), and k(1)+k(2)-k(3), clearly reveal the exciton migration and the charge-separation processes...
  28. pmc Coherent infrared multidimensional spectra of the OH stretching band in liquid water simulated by direct nonlinear exciton propagation
    Cyril Falvo
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Chem Phys 130:184501. 2009
    ..The photon echo is particularly sensitive to the frequency fluctuations and molecular reorientation, whereas the double-quantum coherence provides a unique probe for intermolecular couplings and two-exciton coherence...
  29. ncbi request reprint Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy
    Frantisek Sanda
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 125:014507. 2006
    ..Simulations reproduce the main features recently observed in the OD stretch of phenol in benzene...
  30. ncbi request reprint Coherent control of cross-peaks in chirality-induced two-dimensional optical signals of excitons
    Dmitri V Voronine
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 125:224504. 2006
    ..Superpositions of various tensor components which generate the optimized signals are constructed using a genetic learning algorithm. Exciton couplings and bath correlations may be extracted from these highly resolved signals...
  31. pmc Multidimensional measures of impulsively driven stochastic systems based on the Kullback-Leibler distance
    Saar Rahav
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 81:031116. 2010
    ..For overdamped stochastic dynamics two-dimensional KLRF shows a qualitatively different variation with the time delays between pulses, depending on whether the system is initially in a steady state or in thermal equilibrium...
  32. ncbi request reprint Vibrational-exciton couplings for the amide I, II, III, and A modes of peptides
    Tomoyuki Hayashi
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Phys Chem B 111:11032-46. 2007
    ..The simulated infrared amide I and II absorptions and CD spectra of 24 residue alpha-helical motifs (SPE3) are in good agreement with experiment...
  33. pmc Broadband infrared and Raman probes of excited-state vibrational molecular dynamics: simulation protocols based on loop diagrams
    Konstantin E Dorfman
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    Phys Chem Chem Phys 15:12348-59. 2013
    ..The Fourier uncertainty ΔωΔt > 1 is never violated. ..
  34. pmc Disentangling multidimensional femtosecond spectra of excitons by pulse shaping with coherent control
    Darius Abramavicius
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Chem Phys 120:8373-8. 2004
    ..Numerical simulations demonstrate how poorly resolved weak features may be amplified and observed by using optimized optical pulses, specifically shaped to achieve a desired spectroscopic target...
  35. pmc Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy
    Zaizhi Lai
    Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
    J Phys Chem B 117:4661-9. 2013
    ..We show that the high resolution structural sensitivity of 2DIR can differentiate the ensemble evolution of protein and thus provides a microscopic picture of the folding process...
  36. pmc Suppression of population transport and control of exciton distributions by entangled photons
    Frank Schlawin
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    Nat Commun 4:1782. 2013
    ..Classical light is fundamentally limited by the frequency-time uncertainty, whereas entangled photons have independent temporal and spectral characteristics not subjected to this uncertainty...
  37. pmc Zeeman shift of two-dimensional optical signals of Mg-porphyrin dimers with circularly polarized beams
    Justo J Rodriguez
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Chem Phys 137:205102. 2012
    ..For different molecular geometries, only the intensity of the 2D spectrum peaks changes while the form of the Zeeman shifts in the 2D frequency space is modified...
  38. pmc Core and valence excitations in resonant X-ray spectroscopy using restricted excitation window time-dependent density functional theory
    Yu Zhang
    Department of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697, USA
    J Chem Phys 137:194306. 2012
    ..Simulated RIXS and 1D SXRS signals give some insights into the correlation of different excitations in the molecule...
  39. pmc Exciton delocalization and transport in photosystem I of cyanobacteria Synechococcus elongates: simulation study of coherent two-dimensional optical signals
    Darius Abramavicius
    Chemistry Department, University of California Irvine, California 92697 2025, USA
    J Phys Chem B 113:6097-108. 2009
    ..The active space of the complex covering the RC, the linker, and the delocalized antenna states is common to PSI complexes in bacteria and plants...
  40. ncbi request reprint Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine
    Thomas la Cour Jansen
    Department of Chemistry, University of California, Irvine, CA 92697 2025, USA
    J Chem Phys 121:10577-98. 2004
    ..We find that fluctuations of the Ramachandran angles which hardly affect the linear absorption can be effectively probed by two-dimensional spectra. The signal generated at k(1)+k(2)-k(3) is particularly sensitive to such fluctuations...
  41. ncbi request reprint Simulation of X-ray absorption near edge spectra of organometallic compounds in the ground and optically excited states
    R K Pandey
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Phys Chem A 111:805-16. 2007
    ..Phys. Chem. A 2006, 110, 38). The calculated absorption spectra of optically excited states can be used to simulate ultrafast optical pump/X-ray probe experiments...
  42. pmc Simulation of two-dimensional infrared spectroscopy of amyloid fibrils
    Wei Zhuang
    Department of Chemistry, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 104:14233-6. 2007
    ..These signals may provide new constraints for refining of the currently available NMR structure. Two-dimensional correlation spectroscopy also can differentiate the turn structure of Ab42 and other Ab derivatives...
  43. doi request reprint Probing multiple core-hole interactions in the nitrogen K-edge of DNA base pairs by multidimensional attosecond X-ray spectroscopy. A simulation study
    Daniel M Healion
    Department of Chemistry, University of California Irvine, 456 Rowland Hall, Irvine, California 92697, USA
    J Phys Chem A 112:11449-61. 2008
    ..Sum over states calculations of the signals reveal changes in cross-peak intensities between hydrogen-bonded and stacked base pairs. Nucleobase analogues are proposed for investigating base-stacking and hydrogen-bonding interactions...
  44. ncbi request reprint Coherent third-order spectroscopic probes of molecular chirality
    Darius Abramavicius
    Chemistry Department, University of California, Irvine, CA 92697 2025, USA
    J Chem Phys 122:134305. 2005
    ..Applications are made to alpha and 3(10) helical infinite peptides...
  45. pmc Deep UV resonance Raman spectroscopy of β-sheet amyloid fibrils: a QM/MM simulation
    Hao Ren
    Department of Chemistry, University of California, Irvine, Irvine, California 92697, USA
    J Phys Chem B 115:13955-62. 2011
    ..We propose that the AmIII band redshift upon deuteration is caused by the loss of coupling between C(α)-H bending and N-D bending modes, rather than by peptide bond hydration...
  46. pmc Spectral diffusion at the water/lipid interface revealed by two-dimensional fourth-order optical spectroscopy: a classical simulation study
    Yuki Nagata
    Department of Chemistry, University of California, Irvine, California 92697, United States
    J Am Chem Soc 133:3276-9. 2011
    ..The top-layer water has slower spectral diffusion...
  47. pmc Vibrational sum-frequency generation spectroscopy at the water/lipid interface: molecular dynamics simulation study
    Yuki Nagata
    University of California, Irvine, California 92617, USA
    J Am Chem Soc 132:6434-42. 2010
    ..This decoupling explains the slow relaxation dynamics of water measured in the time-resolved SFG experiment. Despite the similarity of the SFG spectra, the peak origins of water/lipid and water/vapor interfaces are different...
  48. pmc 2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece
    Sayan Bagchi
    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6323, USA
    J Phys Chem B 113:11260-73. 2009
    ..Both experiment and simulations show that the cross peaks between the carboxylate and the amide-I bands are significantly diminished above the melting temperature...
  49. pmc Probing amyloid fibril growth by two-dimensional near-ultraviolet spectroscopy
    Jun Jiang
    Chemistry Department, University of California, Irvine, Irvine, California 92697, USA
    J Phys Chem B 115:6321-8. 2011
    ..Intensities of specific peaks provide a direct measure of the number of peptides in a fibril. These signals could be used to monitor the fibril growth kinetics, one peptide at a time...
  50. pmc Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study
    Jun Jiang
    Chemistry Department, University of California Irvine, USA
    Phys Chem Chem Phys 13:2394-400. 2011
    ..Our simulations suggest that 2DNUV spectra could provide a useful local probe for the structure and kinetics of fibrils...
  51. pmc Multidimensional x-ray spectroscopy of valence and core excitations in cysteine
    Jason D Biggs
    Department of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697, USA
    J Chem Phys 138:144303. 2013
    ..The coupling between valence- and core-excited states can be visualized in three-dimensional plots, revealing the origin of the polarizability that controls the simpler pump-probe SXRS signals. ..
  52. pmc Time-, frequency-, and wavevector-resolved x-ray diffraction from single molecules
    Kochise Bennett
    University of California, Irvine, California 92697 2025, USA
    J Chem Phys 140:204311. 2014
    ..Our theory and simulations can guide future experimental studies on the structures of nano-particles and proteins. ..
  53. pmc Double-core excitations in formamide can be probed by X-ray double-quantum-coherence spectroscopy
    Yu Zhang
    Department of Chemistry, University of California, 450 Rowland Hall, Irvine, California 92697, USA
    J Chem Phys 138:144301. 2013
    ....
  54. pmc Time-resolved broadband Raman spectroscopies: a unified six-wave-mixing representation
    Konstantin E Dorfman
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 139:124113. 2013
    ..Simulations for the stochastic two-state-jump model illustrate the origin of the absorptive and dispersive features observed experimentally. ..
  55. pmc Time resolved photoelectron spectroscopy of thioflavin T photoisomerization: a simulation study
    Hao Ren
    Department of Chemistry, University of California, Irvine, California 92617, USA
    J Phys Chem A 117:6096-104. 2013
    ..The evolution of the twisting process can be directly probed by photoelectron emission with energies ε ≥ 1.0 eV before the molecule reaches the φ1-twisted configuration (~300 fs)...
  56. pmc Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix
    Jason D Biggs
    Department of Chemistry, University of California, Irvine, CA 92697 2025, USA
    Philos Trans A Math Phys Eng Sci 370:3709-27. 2012
    ..We give guidelines for the assignment of relevant pathways and provide rules for the interpretation of existing nonlinear experiments in carotenoids...
  57. ncbi request reprint Multipoint correlation functions for continuous-time random walk models of anomalous diffusion
    Frantisek Sanda
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 72:031108. 2005
    ....
  58. pmc Manipulating stimulated coherent anti-Stokes Raman spectroscopy signals by broad-band and narrow-band pulses
    Saar Rahav
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Chem Phys 131:194510. 2009
    ..Qualitatively different contributions from the two processes are predicted for the signal generated by an overlapping narrow (picosecond) and broad-band (femtosecond) pulse...
  59. pmc Coherent-control of linear signals: frequency-domain analysis
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 139:164113. 2013
    ..The frequency-domain wave-mixing analysis presented here unifies several arguments made earlier with respect to the conditions whereby coherent control schemes may be used. ..
  60. ncbi request reprint Fluctuation theorems for quantum master equations
    Massimiliano Esposito
    Department of Chemistry, University of California, Irvine, California 92697, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 73:046129. 2006
    ..A quantum integral fluctuation theorem, a steady-state fluctuation theorem, and the Jarzynski relation are derived in a similar way as for classical stochastic dynamics...
  61. pmc Probing ring currents in Mg-porphyrins by pump-probe spectroscopy
    Justo J Rodriguez
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Phys Chem A 116:11095-100. 2012
    ..In analogy to magnetic circular dichroism, it probes the symmetry of degenerate excited states...
  62. pmc Dissecting two-dimensional ultraviolet spectra of amyloid fibrils into beta-strand and turn contributions
    Justo J Rodriguez
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Phys Chem B 116:8830-5. 2012
    ..This signal may be used to determine the proportion of turns and β-strands...
  63. ncbi request reprint Electrostatic DFT map for the complete vibrational amide band of NMA
    Tomoyuki Hayashi
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Phys Chem A 109:9747-59. 2005
    ....
  64. pmc First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptide
    Zhenyu Li
    Department of Chemistry, University of California, Irvine, California 92697, USA
    J Phys Chem A 111:11579-83. 2007
    ..Additional cross-peaks between the side chain and the backbone are observed when using a chirality-induced pulse polarization configuration...
  65. pmc Coherent control protocol for separating energy-transfer pathways in photosynthetic complexes by chiral multidimensional signals
    Dmitri V Voronine
    Department of Chemistry, University of California, Irvine, California, USA
    J Phys Chem A 115:4624-9. 2011
    ..The optimal signals obtained by manipulating the ratios of various 2D spectral peaks reveal detailed information about the excitation dynamics...
  66. pmc Phase-space algorithm for simulating quantum nonlinear response functions of bosons using stochastic classical trajectories
    Benoit Palmieri
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 82:046706. 2010
    ..The stability matrices can be propagated simultaneously with the Langevin equations for the parameters. The formalism is generalized for a many-body boson system coupled to a harmonic bath...
  67. pmc Coherent femtosecond multidimensional probes of molecular vibrations
    Shaul Mukamel
    Department of Chemistry, University of California, Irvine, CA 92697 2025, USA
    Proc Natl Acad Sci U S A 102:13717-8. 2005
  68. doi request reprint Two-photon spectroscopy of excitons with entangled photons
    Frank Schlawin
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 139:244110. 2013
    ..Quantum light effects are most pronounced at weak intensities when entangled photon pairs are well separated, and are gradually diminished at higher intensities when different photon pairs overlap. ..
  69. ncbi request reprint Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans-N-methylacetamide at the nitrogen and oxygen K-edges
    Daniel Healion
    Department of Chemistry, University of California, Irvine, California 92697 2025, USA
    J Chem Phys 134:124101. 2011
    ....
  70. pmc Stimulated coherent anti-Stokes Raman spectroscopy (CARS) resonances originate from double-slit interference of two-photon Stokes pathways
    Saar Rahav
    Department of Chemistry, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 107:4825-9. 2010
    ..Specific vibrational resonances may then be readily detected using pulse shapers through derivatives with respect to pulse parameters...
  71. ncbi request reprint Simulation strategies and signatures of chaos in classical nonlinear response
    Christoph Dellago
    Department of Chemistry, University of Rochester, New York 14627, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 67:035205. 2003
    ..These offer the possibility to characterize chaos beyond the commonly used Lyapunov exponents and suggest new experimentally accessible measures of chaos...
  72. ncbi request reprint Stochastic Liouville equations for hydrogen-bonding fluctuations and their signatures in two-dimensional vibrational spectroscopy of water
    Thomas la Cour Jansen
    Institute for Theoretical Physics and Materials Science Centre, University of Groningen, The Netherlands
    J Chem Phys 123:114504. 2005
    ..The asymmetry of the photon-echo spectra (larger linewidth on the blue side than on the red side) predicted by the FSJ is in better agreement with recent experiments...
  73. ncbi request reprint Coherent low-frequency motions of hydrogen bonded acetic acid dimers in the liquid phase
    Karsten Heyne
    Max Born Institut fur Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D 12489 Berlin, Germany
    J Chem Phys 121:902-13. 2004
    ..Oscillations due to the excitonic coupling between the two O-H or O-D stretching oscillators are absent as is independently confirmed by experiments on mixed dimers with uncoupled O-H and O-D stretching oscillators...
  74. ncbi request reprint Chirality-induced signals in coherent multidimensional spectroscopy of excitons
    Darius Abramavicius
    Theoretical Physics Department, Faculty of Physics of Vilnius University, Sauletekio Avenue 9, Building 3, 10222 Vilnius, Lithuania
    J Chem Phys 124:034113. 2006
    ..Numerical simulations demonstrate the sensitivity of third-order signals to the secondary structural motiffs of peptides...
  75. ncbi request reprint Resonant enhancement and dissipation in nonequilibrium van der Waals forces
    Adam E Cohen
    Department of Physics, 382 Via Pueblo Mall, Stanford University, Stanford, California 94305 4060, USA
    Phys Rev Lett 91:233202. 2003
    ....
  76. ncbi request reprint Probing anomalous relaxation by coherent multidimensional optical spectroscopy
    Frantisek Sanda
    Charles University, Faculty of Mathematics and Physics, Ke Karlovu 5, Prague, 121 16 Czech Republic
    Phys Rev Lett 98:080603. 2007
    ..Spectroscopic signatures of stationary ensembles for 1<alpha<2 and aging effects in nonstationary ensembles with 0<alpha<1 are identified...
  77. ncbi request reprint Dephasing-induced vibronic resonances in difference frequency generation spectroscopy
    Ravindra Venkatramani
    Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, USA
    J Phys Chem B 109:8132-43. 2005
    ..Numerical simulations of two-dimensional DFG signals illustrate how the ground and excited electronic state resonances may be distinguished...
  78. ncbi request reprint Stacking effect of polyfluorene on the chemical shift and electron transport
    Woo Seong Kim
    Department of Chemistry, Chonnam National University, 300 Yongbong Dong, Bugku, Gwangju, 500 757, Korea
    J Phys Chem B 109:2686-92. 2005
    ..This was evident from the frontier molecular orbitals (HOMO and LUMO). Also, it is found that the syn conformers are very favorable for electron transport through the pi-stacked fluorene moieties...
  79. ncbi request reprint Anomalous lineshapes and aging effects in two-dimensional correlation spectroscopy
    Frantisek Sanda
    Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
    J Chem Phys 127:154107. 2007
    ..Aging random walks corresponding to waiting time distributions with diverging first moment show dependence of 2D lineshapes on initial observation time, which persist for long times...
  80. ncbi request reprint Role of water in electron-initiated processes and radical chemistry: issues and scientific advances
    Bruce C Garrett
    Chemical Science Division, Pacific Northwest National Laboratory, P O Box 999, Richland, Washington 99352, USA
    Chem Rev 105:355-90. 2005

Research Grants9

  1. FEMTOSECOND CORRELATION SPECTROSCOPIC PROBES
    Shaul Mukamel; Fiscal Year: 2001
    ..Applications will be made to energy transfer processes in photodynamic therapy. ..
  2. FEMTOSECOND CORRELATION SPECTROSCOPIC PROBES
    Shaul Mukamel; Fiscal Year: 2002
    ..Applications will be made to energy transfer processes in photodynamic therapy. ..
  3. FEMTOSECOND CORRELATION SPECTROSCOPIC PROBES
    Shaul Mukamel; Fiscal Year: 2003
    ..Applications will be made to energy transfer processes in photodynamic therapy. ..
  4. FEMTOSECOND CORRELATION SPECTROSCOPIC PROBES
    Shaul Mukamel; Fiscal Year: 2004
    ..Applications will be made to energy transfer processes in photodynamic therapy. ..
  5. Multidimensional Femtosecond Correlation Spectroscopic Probe Biomolecules
    Shaul Mukamel; Fiscal Year: 2005
    ..Specific signatures of hydrogen bonding between amino acid residues, and with water in multidimentional infrared signals, will be predicted. ..
  6. Multidimensional Femtosecond Correlation Spectroscopic Probe Biomolecules
    Shaul Mukamel; Fiscal Year: 2006
    ..Specific signatures of hydrogen bonding between amino acid residues, and with water in multidimentional infrared signals, will be predicted. ..
  7. Multidimensional Femtosecond Correlation Spectroscopic Probe Biomolecules
    Shaul Mukamel; Fiscal Year: 2007
    ..Specific signatures of hydrogen bonding between amino acid residues, and with water in multidimentional infrared signals, will be predicted. ..
  8. Multidimensional Femtosecond Correlation Spectroscopic Probes of Biomolecules
    Shaul Mukamel; Fiscal Year: 2010
    ..Surface specific technique will be applied for probing the toxicity of fibrils on membranes. Simulation techniques for probing the binding, fluctuations, and motions of biomolecular complexes will be developed. ..