Research Topics
| Shaul MukamelSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory mapTomoyuki 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...- Communication: Comment on the effective temporal and spectral resolution of impulsive stimulated Raman signalsShaul 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... - Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation studyChristopher 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... - Coherent multidimensional optical probes for electron correlations and exciton dynamics: from NMR to X-raysShaul 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... - Interplay of slow bath fluctuations and energy transfer in 2D spectroscopy of the FMO light-harvesting complex: benchmarking of simulation protocolsBenoit 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... - A coherent nonlinear optical signal induced by electron correlationsShaul 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... - Many-body approaches for simulating coherent nonlinear spectroscopies of electronic and vibrational excitonsShaul Mukamel
Department of Chemistry, University of California, Irvine, California 92697, USA
Chem Rev 104:2073-98. 2004 - Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptideJianping 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... - Simulation study of chiral two-dimensional ultraviolet spectroscopy of the protein backboneDarius 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... - Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic mapTomoyuki 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... - Coherent two dimensional infrared spectroscopy of a cyclic decapeptide antamanide. A simulation study of the amide-I and A bandsCyril 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... - Simulation protocols for coherent femtosecond vibrational spectra of peptidesWei 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... - Probing electron correlations in molecules by two-dimensional coherent optical spectroscopyZhenyu Li
Department of Chemistry, University of California, Irvine, California 92697, USA
J Am Chem Soc 130:3509-15. 2008.... - Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptideNeelanjana Sengupta
Department of Chemistry, University of California at Irvine, Irvine, California 92697 2025, USA
J Phys Chem B 113:12037-49. 2009.... - Two-dimensional vibrational optical probes for peptide fast folding investigationWei 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... - Double-quantum resonances and exciton-scattering in coherent 2D spectroscopy of photosynthetic complexesDarius 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... - Unravelling coherent dynamics and energy dissipation in photosynthetic complexes by 2D spectroscopyDarius 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... - Chirality-based signatures of local protein environments in two-dimensional optical spectroscopy of two species photosynthetic complexes of green sulfur bacteria: simulation studyDmitri 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... - Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challengesWei 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... - Lindblad equations for strongly coupled populations and coherences in photosynthetic complexesBenoit 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... - Simulation of two-dimensional ultraviolet spectroscopy of amyloid fibrilsJun Jiang
Chemistry Department, University of California Irvine, Irvine, California, USA
J Phys Chem B 114:12150-6. 2010.... - Quantum oscillatory exciton migration in photosynthetic reaction centersDarius 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... - Stochastic simulation of chemical exchange in two dimensional infrared spectroscopyFrantisek 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... - Vibrational-exciton couplings for the amide I, II, III, and A modes of peptidesTomoyuki 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... - Coherent infrared multidimensional spectra of the OH stretching band in liquid water simulated by direct nonlinear exciton propagationCyril 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... - Coherent control of cross-peaks in chirality-induced two-dimensional optical signals of excitonsDmitri 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... - Multidimensional measures of impulsively driven stochastic systems based on the Kullback-Leibler distanceSaar 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... - Energy-transfer and charge-separation pathways in the reaction center of photosystem II revealed by coherent two-dimensional optical spectroscopyDarius 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... - Simulation of X-ray absorption near edge spectra of organometallic compounds in the ground and optically excited statesR 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... - Exciton delocalization and transport in photosystem I of cyanobacteria Synechococcus elongates: simulation study of coherent two-dimensional optical signalsDarius 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... - Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanineThomas 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... - Probing multiple core-hole interactions in the nitrogen K-edge of DNA base pairs by multidimensional attosecond X-ray spectroscopy. A simulation studyDaniel 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... - Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysisWei 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... - Simulation of two-dimensional infrared spectroscopy of amyloid fibrilsWei 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... - Disentangling multidimensional femtosecond spectra of excitons by pulse shaping with coherent controlDarius 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... - Spectral diffusion at the water/lipid interface revealed by two-dimensional fourth-order optical spectroscopy: a classical simulation studyYuki 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... - Probing amyloid fibril growth by two-dimensional near-ultraviolet spectroscopyJun 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... - 2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpieceSayan 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... - Vibrational sum-frequency generation spectroscopy at the water/lipid interface: molecular dynamics simulation studyYuki 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... - Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles studyJun 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... - Deep UV resonance Raman spectroscopy of ?-sheet amyloid fibrils: a QM/MM simulationHao 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(?)-H bending and N-D bending modes, rather than by peptide bond hydration... - Multipoint correlation functions for continuous-time random walk models of anomalous diffusionFrantisek Sanda
Department of Chemistry, University of California, Irvine, California 92697, USA
Phys Rev E Stat Nonlin Soft Matter Phys 72:031108. 2005.... - Manipulating stimulated coherent anti-Stokes Raman spectroscopy signals by broad-band and narrow-band pulsesSaar 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... - Coherent third-order spectroscopic probes of molecular chiralityDarius 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... - Coherent control protocol for separating energy-transfer pathways in photosynthetic complexes by chiral multidimensional signalsDmitri 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... - First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptideZhenyu 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... - Electrostatic DFT map for the complete vibrational amide band of NMATomoyuki Hayashi
Department of Chemistry, University of California, Irvine, California 92697-2025, USA
J Phys Chem A 109:9747-59. 2005.... - Coherent femtosecond multidimensional probes of molecular vibrationsShaul Mukamel
Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
Proc Natl Acad Sci U S A 102:13717-8. 2005 - Phase-space algorithm for simulating quantum nonlinear response functions of bosons using stochastic classical trajectoriesBenoit 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... - Simulation strategies and signatures of chaos in classical nonlinear responseChristoph 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... - Stimulated coherent anti-Stokes Raman spectroscopy (CARS) resonances originate from double-slit interference of two-photon Stokes pathwaysSaar 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... - Fluctuation theorems for quantum master equationsMassimiliano 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... - Stochastic Liouville equations for hydrogen-bonding fluctuations and their signatures in two-dimensional vibrational spectroscopy of waterThomas 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... - Coherent low-frequency motions of hydrogen bonded acetic acid dimers in the liquid phaseKarsten 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... - Role of water in electron-initiated processes and radical chemistry: issues and scientific advancesBruce C Garrett
Chemical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
Chem Rev 105:355-90. 2005 - Dephasing-induced vibronic resonances in difference frequency generation spectroscopyRavindra 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... - Stacking effect of polyfluorene on the chemical shift and electron transportWoo 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... - Probing anomalous relaxation by coherent multidimensional optical spectroscopyFrantisek 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... - Resonant enhancement and dissipation in nonequilibrium van der Waals forcesAdam E Cohen
Department of Physics, 382 Via Pueblo Mall, Stanford University, Stanford, California 94305-4060, USA
Phys Rev Lett 91:233202. 2003.... - Anomalous lineshapes and aging effects in two-dimensional correlation spectroscopyFrantisek 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... - Chirality-induced signals in coherent multidimensional spectroscopy of excitonsDarius 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...
Research Grants
- FEMTOSECOND CORRELATION SPECTROSCOPIC PROBESShaul Mukamel; Fiscal Year: 2004..Applications will be made to energy transfer processes in photodynamic therapy. ..
- Multidimensional Femtosecond Correlation Spectroscopic Probe BiomoleculesShaul Mukamel; Fiscal Year: 2007..Specific signatures of hydrogen bonding between amino acid residues, and with water in multidimentional infrared signals, will be predicted. ..
- Multidimensional Femtosecond Correlation Spectroscopic Probes of BiomoleculesShaul 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. ..