501. | "Intermolecular forces and non-bonded interactions: Superoperator nonlinear TDDFT response approach,"
**U. Harbola and S. Mukamel**
*Phys. Rev. A 70, 052506 (2004)* | pdf |

502. | "Coherence and correlations in multitime quantum measurements of stochastic quantum trajectories"
**V. Chernyak, F. Sanda, and S. Mukamel**
*Phys. Rev. E 73, 036119 (2006)* | pdf |

503. | "Coherent low-frequency motions of hydrogen bonded acetic acid dimers in the liquid phase"
**K. Heyne, N. Huse, J. Dreyer, E.Nibbering, T. Elsaesser, and S. Mukamel**
*J. Chem. Phys. 121, 902 (2004)* | pdf |

504. | "Chemical imaging of single 4,7,12,15-tetrakis[2,2]paracyclophane by spatially resolved vibrational spectroscopy"
**N. Liu, C. Silien, W. Ho, J. B. Maddox, S. Mukamel, B. Liu, and G.C. Bazan**
*J. Chem. Phys. 127, 244711 (2007)* | pdf |

505. | "Peptide secondary structure determination by three-pulse coherent vibrational spectroscopies; A simulation study"
**D. Abramavicius, W. Zhuang, and S. Mukamel**
*J. Phys. Chem. B 108, 18034 (2004)* | pdf |

506. | "Generalized TDDFT response functions for spontaneous density fluctuations and nonlinear response: Resolving the causality paradox in real time"
**S. Mukamel**
*Phys. Rev. A 71, 024503 (2005)* | pdf |

507. | "Reversible switching among three adsorbate configurations in a single [2,2]paracyclophane based molecules"
**C. Silien, N. Liu, W. Ho, J. B. Maddox, S. Mukamel, B. Liu, and G. C. Bazan**
*Nano Lett. 8, 208 (2008)* | pdf |

508. | "Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map"
**T. Hayashi, T. Jansen, W. Zhuang, and S. Mukamel**
*J. Phys. Chem. A 109 64 (2005)* | pdf |

509. | "Superoperator many-body theory of molecular currents: Non-equilibrium Green functions in real time"
**U. Harbola and S. Mukamel**
*Theory and Applications of Computational Chemistry: The First 40 Years, 373-396 C. E. Dykstra, G. Frenking, K. S. Kim and G. E. Scuseria, Elsevier, Amsterdam (2005)* | pdf |

510. | "Cooperative effects in photon statistics of molecular dimers with spectral diffusion"
**F. Sanda and S.Mukamel**
*J. Chem. Phys. 124, 124103 (2006)* | pdf |

511. | "Exciton annihilation on dendrimeric trees"
**S. Raychaudhuri, Y. Shapir, and S. Mukamel**
*J. Lumin. 111, 343 (2005)* | pdf |

512. | "Dephasing-induced vibronic resonances in difference frequency generation spectroscopy"
**R. Venkatramani and S. Mukamel**
*J. Phys. Chem. B 109, 8132 (2005)* | pdf |

513. | "Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysis"
**W. Zhuang, D. Abramavicius, and S. Mukamel**
*PNAS 102, 7443 (2005)* | pdf |

514. | "Coherent third-order spectroscopic probes of molecular chirality"
**D. Abramavicius and S. Mukamel**
*J. Chem. Phys. 122 134305 (2005)* | pdf |

515. | "Intermolecular forces and generalized TDDFT response functions in Liouville space"
**S. Mukamel, A. Cohen, and U. Harbola.**
*Edited M. Marques, F. Nogueira, A. Rubio and E. K. U. Gross, Springer-Verlag, (2005)* | pdf |

516. | "Stochastic Liouville equations for hydrogen-bonding fluctuations and their signatures in two dimensional vibrational spectroscopy of water"
**T.l.C. Jansen, T. Hayashi, W. Zhuang, and S. Mukamel**
*J. Chem. Phys. 123, 114504 (2005)* | pdf |

517. | "Multipoint correlation function for continuous time random walk models of anomalous diffusion"
**F. Sanda and S. Mukamel**
*Phys. Rev. E 72, 031108 (2005)* | pdf |

518. | "Non-equilibrium superoperator Greens function approach to inelastic resonances in STM currents"
**U. Harbola, J.B. Maddox, and S. Mukamel**
*Phys. Rev. B 73, 205404 (2006)* | pdf |

519. | "Time-domain chirally-sensitive three-pulse coherent probes of vibrational excitons in proteins"
**D. Abramavicius and S. Mukamel**
*Chem. Phys. 318 50 (2005)* | pdf |

520. | "Electrostatic DFT map for the complete vibrational amide band of NMA"
**T. Hayashi, W. Zhuang, and S. Mukamel**
*J. Phys. Chem. A 109, 9747 (2005)* | pdf |

521. | "Nonlinear vibrational response of the amide I, II, III and A bands of NMA: Simulation study based on an electrostatic DFT map"
**T. Hayashi, W. Zhuang, and S. Mukamel**
*TRVS XII Conference Proceeding (2005)* | pdf |

522. | "Stacking effect of polyflourene on the chemical shift and electron transport"
**W.S. Kim, J. Kim, J.K. Park, S. Mukamel, S.K. Rhee, Y.K. Choi, and J.Y. Lee**
*J. Phys. Chem. B 109 2686 (2005)* | pdf |

523. | "Coherent-control of pump-probe signals of helical structures by adaptive pulse polarizations"
**D. Voronine, D. Abramavicius, and S. Mukamel**
*J. Chem. Phys. 123, 034104 (2006)* | pdf |

524. | "Chirality-induced signals in coherent multidimensional spectroscopy of excitons"
**D. Abramavicius and S. Mukamel**
*J. Chem. Phys. 124, 034113 (2006)* | pdf |

525. | "Simulation Protocols for Coherent Femtosecond Vibrational Spectra of Peptides"
**W. Zhuang, D. Abramavicius, T. Hayashi, and S. Mukamel**
*J. Phys. Chem. B 110, 3362 (2006)* | pdf |

526. | "Anomalous continuous-time-random-walk spectral diffusion in coherent third order optical response"
**F. Sanda, and S. Mukamel**
*Phys. Rev. E 73, 011103 (2006)* | pdf |

527. | "Many-body theory of current-induced fluorescence in molecular junctions"
**U. Harbola, J. B. Maddox, and S. Mukamel**
*Phys. Rev. B 73, 1 (2006)* | pdf |

528. | "Simulation of single molecule inelastic electron tunneling signals in paraphenylene-vinylene oligomers and distyrylbenzene[2.2]paracyclophanes"
**J.B. Maddox, U. Harbola, N. Liu, C. Silien, W. Ho, G.C. Bazan, and S.Mukamel**
*J. Phys. Chem. A 110, 6329 (2006)* | pdf |

529. | "Multiple core-hole coherence in X-ray four-wave-mixing spectroscopies"
**S. Mukamel**
*Phys. Rev. B 72, 235110 (2005)* | pdf |

530. | "Coherent femtosecond optical analogues of multidimensional NMR"
**S. Mukamel, and W. Zhuang**
*PNAS 102, 13717 (2005)* | pdf |

531. | "Simulation of XANES and X-ray fluorescence spectra of optically excited molecules"
**R.K. Pandey and S. Mukamel**
*J. Chem. Phys. 124, 094106 (2006)* | pdf |

532. | "Fluctuation theorems for quantum master equations"
**M. Esposito and S. Mukamel**
*Phys. Rev. E 73, 046129 (2006)* | pdf |

533. | " Non-equilibrium superoperator GW-equations"
**U. Harbola and S. Mukamel**
*J. Chem. Phys. 124, 044106 (2006)* | pdf |

534. | "Optical coherence and theoretical study of the excitation dynamics of a cyclophane-linked oligophenylenevinlene dimer"
**A. Moran, J. Kim, R. Nome, N. Scherer, J. Maddox, S. Mukamel, J. Hong, and G. Bazan**
*J. Chem. Phys 124, 194904 (2006)* | pdf |

535. | "Stochastic simulation of chemical exchange in 2D IR spectroscopy"
**F. Sanda and S. Mukamel**
*J. Chem. Phys. 125, 014507 (2006)* | pdf |

536. | "Probing molecular chirality via excitonic nonlinear response"
**D. Abramavicius, W. Zhuang, and S. Mukamel**
*J. Phys. B 36, 5051 (2006)* | pdf |

537. | "Two dimensional vibrational optical probes for peptide fast folding investigation"
**W. Zhuang, D. Abramavicius, and S. Mukamel**
*PNAS 103, 18934 (2006)* | pdf |

538. | "Simulation of XANES and X-ray fluorescence of organometallic compounds in the ground and optically excited states"
**R. Pandey and S. Mukamel**
*J. Phys. Chem. 124, 094106 (2006)* | pdf |

539. | "Correlated hydrogen bonding fluctuations and vibrational cross peaks in NMA: Simulation based on a complete electrostatic DFT map"
**T. Hayashi and S. Mukamel**
*J. Chem. Phys 125, 194510 (2006)* | pdf |

540. | "Coherent control of cross peaks in chirality-induced two-dimensional optical signals of excitons"
**D. Voronine, D. Abramavicius, and S. Mukamel**
*J. Chem. Phys. 125, 224504 (2006)* | pdf |

541. | "Exciton dynamics in a disordered conjugated polymer: Three-pulse photon-echo and transient grating experiments"
**J. Sperling, K. Matuszna, P. Baum, A. Nemeth, F. Sanda, E. Riedle, H.F. Kauffmann, S. Mukamel, and F. Milota**
*Chem. Phys. 349, 244 (2008)* | pdf |

542. | "Probing anomalous relaxation by coherent multidimensional optical spectroscopy"
**F. Sanda and S. Mukamel**
*Phys. Rev. Lett. 98, 080603 (2007)* | pdf |

543. | "Quantum master equation for electron transport through quantum dots and single molecules"
**U. Harbola, M. Esposito, and S. Mukamel**
*Phys. Rev. B 74, 234309 (2006)* | pdf |

544. | "Manipulating multidimensional electronic spectra of excitons by polarization pulse-shaping"
**D. Voronine, D. Abramavicious, and S. Mukamel**
*J.Chem. Phys. 126, 044508 (2007)* | pdf |

545. | "Two-color electric field resolved transient grating spectroscopy of an oligophenylenevinylene dimer"
**A. Moran, J. Maddox, J. Hong, J. Kim, R. Nome, G. Bazan, S. Mukamel, and N. Scherer**
*In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Corcum and D.M. Jonas (editors) Springer Verlag (2006)* | pdf |

546. | "Three-Pulse photon echo in a dense potassium vapor"
**V. Lorenz, S. Cundiff, W. Zhuang, and S. Mukamel**
*In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006)* | pdf |

547. | "Signatures of chemical exchange in 2D vibrational spectroscopy; Simulation based on the stochastic Liouville equations"
**F. Sanda, W. Zhuang, T.l.C. Jansen, T. Hayashi, and S. Mukamel**
*In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006)* | pdf |

548. | "Manipulating Multidimensional Nonlinear Spectra of Excitons by Coherent Control with Polarization Pulse Shaping", D. Voronine, D. Abramavicius and S. Mukamel. In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Corkum and D.M. Jonas( editors) Springer Verlag (2006). | pdf |

549. | "Coherent Infrared Pulse Sequences for Probing Molecular Chirality", W. Zhuang, D. Abramavicius and S. Mukamel. In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006). | pdf |

550. | "Lineshapes and Correlations in Two Dimensional Vibrational Signals of NMA", T. Hayashi, W. Zhuang and S. Mukamel. In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006). | pdf |

551. | "Simulation of Two-Dimensional Infrared Spectroscopy of Amyloid Fibrils", W. Zhuang, D. Abramavicious, D. Voronine and S. Mukamel, PNAS 104, 14233-14236 (2007) | pdf |

552. | "Fluctuation theorem for counting statistics in electron transport through quantum junctions"
**M. Esposito, U. Harbola, and S. Mukamel**
*Phys. Rev. B 75, 155316 (2007)* | pdf |

553. | "Multipoint Correlation Functions for Photon Statistics in Single Molecule Spectroscopy; Stochastic Dynamics in Liouville Space," F. Sanda and S. Mukamel, in "Theory, Modelling and Evaluation of Single Molecule Measurments," Editors E. Barkai, F. Brown, M. Orrit and H. Yang. World Sci. Pages 93-137 (2008). | pdf |

554. | "Stochastic Liouville equations for coherent multidimensional spectroscopy of excitons"
**F. Sanda and S. Mukamel**
*J. Phys. Chem. B 112, 14212 (2008)* | pdf |

555. | "Simulation of X-ray absorption near edge of organ metallic compounds in the ground and optically excited states"
**R. Pandey and S. Mukamel**
*J. Phys. Chem. A 111, 805 (2007)* | pdf |

556. | "Conductance bistability in a single porphyrin molecule in a STM junction: A many-body simulation study"
**J. B. Maddox, U. Harbola, K. Mayoral, and S. Mukamel**
*J. Phys. Chem. C 111, 9516 (2007)* | pdf |

557. | "Two-dimensional optical spectroscopy of excitons in semiconductor quantum wells: Liouville-space pathways analysis"
**L. Yang, I. Schweigert, S. Cundiff, and S. Mukamel**
*Phys. Rev. B 75, 125302 (2007)* | pdf |

558. | "Two-dimensional infrared surface spectroscopy for CO on Cu(100): Detection of intermolecular coupling of adsorbates"
**Y. Nagata, Y. Tanimura, and S. Mukamel**
*J. Chem. Phys. 126, 204703 (2007)* | pdf |

559. | "Sum-over-states as quasiparticle pictures of coherent correlation spectroscopy; femtosecond analogues of multidimensional NMR"
**S. Mukamel, R. Oszwaldowski, and D. Abramavicious**
*Phys. Rev. B 75, 245305 (2007)* | pdf |

560. | "Electrostatic interactions in phospholipid membranes revealed by coherent 2D IR spectroscopy"
**V. Volkov, R. Chelli, W. Zhuang, F. Nuti, Y. Takaoka, A. Papini, S. Mukamel, and R. Righini**
*PNAS, 104, 15323 (2007)* | pdf |

561. | "Probing interactions between core-electron transitions by ultrafast two-dimensional x-ray coherent correlation spectroscopy"
**I. Schweigert and S. Mukamel**
*J. Chem. Phys. 128, 184307 (2008)* | pdf |

563. | "Coherent ultrafast core-hole correlation spectroscopy: X-ray analogues of multidimensional NMR"
**I.V. Schweigert and S. Mukamel**
*Phys. Rev. Lett. 99, 163001 (2007)* | pdf |

564. | "Superoperator Non-Equilibrium Green's Function Theory for Density Correlation and Response Functions", U. Harbola and S. Mukamel, (submitted to Phys. Rev. Lett., 2006) | no pdf |

565. | "Comment on "Failure of the Jarzynski identity for a simple quantum system"
**S. Mukamel**
*cond-mat/0701003vl (2006)* | pdf |

566. | "Partially-time-ordered Schwinger-Keldysh loop expansion of coherent nonlinear optical susceptibilities"
**S. Mukamel**
*Phys. Rev. A 77, 023801 (2008)* | pdf |

567. | "Vibrational-exciton couplings for the amide I, II, III and A modes of peptides"
**T. Hayashi and S. Mukamel**
*J. Phys. Chem. 11, 11032 (2007)* | pdf |

568. | "Statistics and fluctuation theorem for boson and fermion transport through mesoscopic junctions"
**U. Harbola, M. Esposito, and S. Mukamel**
*Phys. Rev. B 76, 085408 (2007)* | pdf |

569. | "Computational studies on electron and proton transfer in phenol-imidazole-base triads"
**S. Yan, S. Kang, T. Hayashi, S. Mukamel, and J.Y. Lee**
J. Comp. Chem. 31, 393 (2009) | pdf |

570. | "Entropy fluctuation theorems in driven open systems: Application to electron counting statistics"
**M. Esposito, U. Harbola, and S. Mukamel**
*Phys. Rev. E 76, 031132 (2007)* | pdf |

571. | "Anomalous lineshapes and aging effects in two-dimensional correlation spectroscopy"
**F. Sanda and S. Mukamel**
*J. Chem. Phys. 127, 154107 (2007)* | pdf |

572. | "Two-dimensional electronic correlation spectroscopy of the npi* and pipi* protein backbone transitions: A simulation study"
**Z.Li, D. Abramavicius, W. Zhuang, and S. Mukamel**
*Chem. Phys. 341, 29 (2007)* | pdf |

573. | "Two-dimensional correlation spectroscopy of two-exciton resonances"
**L. Yang and S. Mukamel**
*Phys. Rev. Lett. 100, 057402 (2008)* | pdf |

574. | "Transport and correlated fluctuations in the nonlinear optical response of excitons"
**D. Abramavicius, L. Valkunas, and S. Mukamel**
*Europhys. Lett. 80, 17005 (2007)* | pdf |

575. | "Probing valence electronic wavepacket dynamics by all x-ray stimulated Raman spectroscopy; A simulation study"
**I.V. Schweigert and S. Mukamel**
*Phys. Rev. A. 76, 0125041 (2007)* | pdf |

576. | "Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve-residue peptide"
**J. Wang, W. Zhuang, S. Mukamel, and R. Hochstrasser**
*J. Phys. Chem B, 112, 5930 (2008)* | pdf |

577. | "Ultrafast optical spectroscopy of spectral flucuations in a dense atomic vapor"
**V.O. Lorenz, S. Mukamel, W. Zhuang, and S.T. Cundiff**
*Phys. Rev. Lett. 100, 013603 (2008)* | pdf |

578. | "Unraveling coherent dynamics and energy dissipation in photosynthetic complexes by 2D spectroscopy"
**D. Abramavicius, D. Voronine, and S. Mukamel**
*Biophys. J. 94, 3613 (2008)* | pdf |

579. | "Double-quantum resonances and exciton-scattering in coherent 2D spectroscopy of photosynthetic complexes"
**D. Abramavicius, D. Voronine, and S. Mukamel**
*PNAS, 105, 8525 (2008)* | pdf |

580. | "Superoperator nonequilibrium Green's function theory of many-body systems; Applications to charge transfer and transport in open junctions"
**U. Harbola and S. Mukamel**
*Phys. Rep. 465, 191 (2008)* | pdf |

581. | "Causal versus noncausal description of nonlinear wave mixing: Resolving the damping-sign controversy"
**S. Mukamel**
*Phys. Rev. A. 76, 021803 (2007)* | pdf |

582. | "Nonlinear vibrational response of coupled anharmonic system - towards the 2DIR spectrums of H2O"
**A. Paarmann, T. Hayashi, S. Mukamel, and R.J.D. Miller**
*TRVS Proceedings (2007)* | pdf |

583. | "First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptide"
**Z. Li, and S. Mukamel**
*J. Phys. Chem. A 111, 11579 (2007)* | pdf |

584. | "A coherent nonlinear optical signal induced by electron correlations"
**S. Mukamel, R. Oszwaldowski, and L. Yang**
*J. Chem. Phys. 127, 221105 (2007)* | pdf |

585. | "Revealing exciton-exciton couplings in semiconductors using multidimensional four-wave mixing signals"
**L. Yang and S. Mukamel**
*Phys. Rev. B. 77, 075335 (2008)* | pdf |

586. | "Nonlinear optical spectroscopy of single, few and many molecules: Nonequilibrium Green's Function QED approach"
**C.A. Marx, U. Harbola, and S. Mukamel**
*Phys. Rev. A 77, 022110 (2008)* | pdf |

587. | "Simulating multidimensional optical wave-mixing signals with finite-pulse envelopes"
**I.V. Schweigert and S. Mukamel**
*Phys. Rev. A 77, 033802 (2008)* | pdf |

588. | "Interference effects in the counting statistics of electron transfers through a double quantum dot"
**S. Welack, M. Esposito, U. Harbola, and Shaul Mukamel**
*Phys. Rev. B 77, 195315 (2008)* | pdf |

589. | "Simulation of conductance and current-induced fluorescence of conjugated chromophores"
**J. Maddox, U. Harbola, G.C. Bazan, and S. Mukamel**
*Chem. Phys. Lett. 450, 144 (2007)* | pdf |

591. | "Probing electron correlations in molecules by two-dimensional coherent optical spectroscopy"
**Z. Li, D. Abramavicius, and S. Mukamel**
*J. Am. Chem. Soc. 130, 3509 (2008)* | pdf |

592. | "Geometry and excitation fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS and GROMOS force fields: Implications for protein ultraviolet spectra simulation"
**Z. Li, H. Yu, W. Zhuang, and S. Mukamel**
*Chem. Phys. Lett. 452, 78 (2008)* | pdf |

594. | "Many-body effects in two-dimensional optical spectra of semiconductor quantum-dot pairs; TDHF and beyond"
**R. Oszwaldowski, D. Abramavicius, and S. Mukamel**
*J. Phys.: Cond. Mat. 20, 045206 (2008)* | pdf |

596. | "Coherent multidimensional optical probes for electron correlations and exciton dynamics: From NMR to X-Rays"
**S. Mukamel, D. Abramavicius, L. Yang, W. Zhuang, I.V. Schweigert, and D.V. Voronine**
*Acc. Chem. Res. 42, 553 (2009)* | pdf |

597. | "Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; Quasiparticle vs. supermolecule perspectives"
**D. Abramavicius, B. Palmieri, D. Voronine, F. Sanda, and S. Mukamel**
*Chem. Rev. 109, 2350 (2009)* | pdf |

598. | "Nonequilbrium fluctuations, fluctuation theorems, and counting statistics in quantum systems"
**M. Esposito, U. Harbola, and S. Mukamel**
*Rev. Mod. Phys. 81, 1665 (2009)* | pdf |

599. | "Chirality-based signatures of local protein environments in two-dimensional optical spectroscopy of two species photosynthetic complexes of green sulfur bacteria: Simulation study"
**D. Voronine, D. Abramavicius, and S. Mukamel**
*Biophys. J. 95, 4896 (2008)* | pdf |

600. | "Probing intermolecular couplings in liquid water with two-dimensional infrared photon echo spectroscopy"
**A. Paarmann, T. Hayashi, S. Mukamel, and R.J.D. Miller**
*J. Chem. Phys. 128, 191103 (2008)* | pdf |