About

Shaul Mukamel is a Distinguished Professor at the University of California, Irvine, within the Department of Chemistry. His research interests encompass Theoretical and Computational Physical Chemistry and Chemical Physics, with a focus on Polymer, Materials, Nanoscience. His work involves the study of complex chemical systems through advanced theoretical and computational methods, contributing to the understanding of physical and chemical phenomena at the molecular level.

Research topics

• Physics
• Optics
• Chemistry
• Physical chemistry
• Quantum mechanics
• Chemical physics
• Atomic physics
• Molecular physics
• Photochemistry
• Materials science
• Computational chemistry
• Thermodynamics
• Chromatography

Selected publications

• Photon entanglement-enhanced multidimensional spectroscopy of exciton correlations in photosynthetic aggregates

  DESY Publication Database (PUBDB) (Deutsches Elektronen-Synchrotron) · 2026-01-01

  articleOpen accessSenior author

  We propose a photonic entanglement-enhanced multidimensional spectroscopic technique that is sensitive to exciton-exciton correlations at the ultrafast timescale. The signal demonstrates utility for monitoring the coherent signatures of exciton-exciton correlation dynamics in the presence of phonon-induced dissipation. Simulations of the signal for a photosynthetic aggregate is shown to reveal the superior ability of the entanglement-enhanced photonic sources to probe ultrafast dynamics while scaling linearly with the field intensity.The non-classical correlations are shown to aid in the exploration of hidden resonances originating from exciton correlations. Probing these resonances with high time-frequency resolution offers a distinctive advantage for nonlinear spectroscopy of molecular aggregates.

  PublisherDOI

• Time-Resolved X-ray Photoelectron Spectroscopy: A Direct Probe of Bond Order Rearrangements During Ultrafast Excited-State Intramolecular Proton Transfer

  ChemRxiv · 2026-03-18

  articleOpen access

  Excited-state intramolecular proton transfer (ESIPT) provides a minimal yet rich framework for studying bond order rearrangements during chemical reactions. We 1 combine linear-response time-dependent density functional theory, ab initio molecular dynamics, and neural network potentials including nuclear quantum effects to compute time-resolved X-ray photoelectron spectra (tr-XPS) during ESIPT in 10hydroxybenzo[h]quinoline (HBQ) and its deuterated analog (DBQ). By tuning the photoionization probe energy, site-specific sensitivity is achieved through selective ionization of core electrons from either the donor O atom or the acceptor N atom. The tr-XPS signal exhibits a strong dependence on the ESIPT reaction coordinate through changes in photoelectron yield and binding energy. Differences in ESIPT timescales and isotope-dependent oscillatory spectral features between HBQ and DBQ enable direct connections to local bond order rearrangements near the probed X-ray chromophores. These results demonstrate that tr-XPS provides a powerful probe of ESIPT dynamics and highlight its potential for future experimental realization.

  PublisherOA PDFDOI

• Photon entanglement-enhanced multidimensional spectroscopy of exciton correlations in photosynthetic aggregates

  DESY Publication Database (PUBDB) (Deutsches Elektronen-Synchrotron) · 2026-01-01

  articleOpen accessSenior author

  Nonlinear spectroscopic techniques using entangled photon pairs can provide an opportunity to exploit non-classical correlations encoded in two-photon wavefunctions to manipulate two-exciton wavefunctions. We propose an entangled photon pair-enhanced multidimensional spectroscopic technique that is sensitive to exciton-exciton interactions and correlations at the femtosecond timescale. Simulations for a dissipative system, namely, the photosynthetic aggregate reveal the superior ability of entangled photon pairs, compared to both transform-limited and frequency-chirped laser pulses, to manipulate excited-state absorption pathways.The corresponding spectral features in the two-dimensional spectrogram are interpreted in terms of one- and two-exciton resonances. The signal scales linearly with the incoming intensity of the photon sources. We show that classifying these resonances using entangled photon source in the perturbative limit allow for probing exciton correlations at the natural energy scale. These insights can be used to explore multi-exciton dynamics in molecular systems using multiphoton entanglement.

  PublisherDOI

• AI protocol for retrieving protein dynamic structures from two-dimensional infrared spectra

  Proceedings of the National Academy of Sciences · 2025-02-14 · 5 citations

  articleOpen accessCorresponding

  Understanding the dynamic evolution of protein structures is crucial for uncovering their biological functions. Yet, real-time prediction of these dynamic structures remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a powerful tool for analyzing protein dynamics. However, translating its complex, low-dimensional signals into detailed three-dimensional structures is a daunting task. In this study, we introduce a machine learning-based approach that accurately predicts dynamic three-dimensional protein structures from 2DIR descriptors. Our method establishes a robust "spectrum-structure" relationship, enabling the recovery of three-dimensional structures across a wide variety of proteins. It demonstrates broad applicability in predicting dynamic structures along different protein folding trajectories, spanning timescales from microseconds to milliseconds. This approach also shows promise in identifying the structures of previously uncharacterized proteins based solely on their spectral descriptors. The integration of AI with 2DIR spectroscopy offers insights and represents a significant advancement in the real-time analysis of dynamic protein structures.

  PublisherOA PDFDOI

• Graphdiyne/Borophene heterostructures: Tailoring stable anode materials for high-efficiency lithium-ion batteries

  Journal of Power Sources · 2025-02-24 · 5 citations

  articleCorresponding
  PublisherDOI

• Multi-Dimensional Spectroscopy with Intense Entangled Beams: Entanglement-Enabled Phase Matching in a Collinear Beam Geometry

  The Journal of Physical Chemistry Letters · 2025-11-13 · 1 citations

  articleOpen accessSenior authorCorresponding

  The experimental realization of quantum molecular spectroscopy with entangled photons remains challenging owing to the low signal-to-noise ratio resulting from the use of low-flux entangled photons. High-flux entangled photons via intense entangled beams can be used to improve the signal-to-noise ratio, but the presence of unentangled photons contaminates the quantum signal stemming from entangled photons. Here, we demonstrate how intense entangled beams can be used in multi-dimensional spectroscopy while retaining the advantage of photon entanglement. Our approach is broadly applicable to odd-ordered nonlinear spectroscopies, and it generates purely quantum spectroscopic signals. The proposed approach allows the recording of desired phase-matched signals even in a collinear beam geometry, which lifts the requirement of complicated beam geometry setups for phase matching in multi-dimensional spectroscopies.

  PublisherDOI

• Conical Intersections Studied by the Configuration-Interaction-Corrected Tamm–Dancoff Method

  Journal of Chemical Theory and Computation · 2025-03-18 · 11 citations

  articleOpen access

  Conical intersections directly mediate the internal energy conversion in photoinduced processes in a wide range of chemical and biological systems. Because of the Brillouin theorem, many conventional electronic structure methods, including configuration interaction with single excitations from a Hartree–Fock reference and time-dependent density functional theory in either the linear response approximation (TDDFT) or Tamm–Dancoff approximation (DFT-TDA), have the wrong dimensionality for conical intersections between the ground state (S0) and the first excited state (S1) of the same multiplicity. This leads to unphysical state crossings. Here, we implement and assess the configuration-interaction-corrected Tamm–Dancoff approximation (CIC-TDA) that restores the correct dimensionality of conical intersections by including the coupling between the reference state and the intersecting excited state. We apply the CIC-TDA method to the S1/S0 conical intersections in ammonia (NH3), ethylene (C2H4), bithiophene (C8H6S2), azobenzene (C12H10N2), and 11-cis retinal protonated Schiff base (PSB11) in vacuo. We show that this black-box approach can produce potential energy surfaces (PESs) of comparable accuracy to multireference wave function methods. The method validated here can allow cost-efficient explorations of photoinduced electronically nonadiabatic dynamics, especially for large molecules and complex systems.

  PublisherOA PDFDOI

• Stimulated x-ray Raman scattering for selective preparation of dark states bypassing optical selection rules

  Physical review. A/Physical review, A · 2025-05-30

  articleOpen access

  We present an x-ray based stimulated Raman approach to control the preparation of populations and coherent superpositions of (valence) electronic states in generic molecular systems, including optically dark states. Leveraging on the unique properties of core-level excitations as intermediates of the Raman process, we demonstrate that optically forbidden singlet-singlet and singlet-triplet transitions are made accessible. We explore the role of both intrinsic molecular properties (transition dipole moments and involved molecular orbitals) and external field parameters to explain the efficiency and selectivity of the process towards specific classes of electronic states, and to control it towards the amplification of desired populations or superpositions. While the reported mechanism naturally applies to virtually all organic and bio-organic molecules and can straightforwardly be extended to a broader class of molecules, atoms and materials, detailed results for two molecular systems are here reported as a testbed of the proposed approach, for which experimental feasibility is eventually discussed

  PublisherOA PDFDOI

• Nonlinear optical spectroscopy of open quantum systems

  The Journal of Chemical Physics · 2025-02-19 · 2 citations

  articleOpen access

  The development of experimental techniques at the nanoscale has enabled the performance of spectroscopic measurements on single-molecule current-carrying junctions. These experiments serve as a natural intersection for the research fields of optical spectroscopy and molecular electronics. We present a pedagogical comparison between the perturbation theory expansion of standard nonlinear optical spectroscopy and the (non-self-consistent) perturbative diagrammatic formulation of the nonequilibrium Green's functions method (which is widely used in molecular electronics), highlighting their similarities and differences. By comparing the two approaches, we argue that the optical spectroscopy of open quantum systems must be analyzed within the more general Green's function framework.

  PublisherOA PDFDOI

• Tracing Long-Lived Atomic Coherences Generated via Molecular Conical Intersections

  Physical Review Letters · 2025-10-16 · 1 citations

  articleOpen access

  Accessing coherences is key to fully understand and control ultrafast dynamics of complex quantum systems like molecules. Most photochemical processes are mediated by conical intersections, which generate coherences between electronic states in molecules. We show with accurate calculations performed on gas-phase methyl iodide that electronic coherences of spin-orbit-split states persist in atomic iodine after dissociation. Our simulation predicts a maximum magnitude of vibronic coherence in the molecular regime of 0.75% of the initially photoexcited state population. Upon dissociation, one-third of this coherence magnitude is transferred to a long-lived atomic coherence where vibrational decoherence can no longer occur. To trace these dynamics, we propose a tabletop experimental approach-heterodyned attosecond four-wave-mixing spectroscopy. This technique can temporally resolve small electronic coherence magnitudes and reconstruct the full complex coherence function via phase cycling. Hence, heterodyned attosecond four-wave-mixing spectroscopy leads the way to a complete understanding and optimal control of spin-orbit-coupled electronic states in photochemistry.

  PublisherDOI

Recent grants

• Molecular Radiative and Relaxation Processes

  NSF · $534k · 2020–2023

• Molecular Relaxation and Radiative Processes

  NSF · $498k · 2005–2008

• NIH Grant R01GM059230

  NIH · $3.2M · 2014

• OP-Molecular Radiative and Relaxation Processes

  NSF · $560k · 2017–2021

• Molecular Radiative and Relaxation Processes

  NSF · $707k · 2023–2027

Frequent coauthors

• Vladimir Chernyak

  174 shared

• Jérémy R. Rouxel

  Argonne National Laboratory

  119 shared

• Darius Abramavičius

  96 shared

• Marco Garavelli

  92 shared

• Sergei Tretiak

  Los Alamos National Laboratory

  80 shared

• Upendra Harbola

  Indian Institute of Science Bangalore

  77 shared

• Yu Zhang

  Ames National Laboratory

  73 shared

• Konstantin E. Dorfman

  Hainan University

  73 shared

Education

• Ph.D., summa cum laude, Chemistry

  Tel Aviv University

  1976

• M. Sc., summa cum laude, Chemistry

  Tel Aviv University

  1971

• B. Sc.. cum laude, Chemistry

  Tel Aviv University

  1969