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Unke OT, Chmiela S, Gastegger M, Schütt KT, Sauceda HE, Müller KR. SpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects. Nat Commun 2021; 12:7273. [PMID: 34907176 PMCID: PMC8671403 DOI: 10.1038/s41467-021-27504-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/16/2021] [Indexed: 01/12/2023] Open
Abstract
Machine-learned force fields combine the accuracy of ab initio methods with the efficiency of conventional force fields. However, current machine-learned force fields typically ignore electronic degrees of freedom, such as the total charge or spin state, and assume chemical locality, which is problematic when molecules have inconsistent electronic states, or when nonlocal effects play a significant role. This work introduces SpookyNet, a deep neural network for constructing machine-learned force fields with explicit treatment of electronic degrees of freedom and nonlocality, modeled via self-attention in a transformer architecture. Chemically meaningful inductive biases and analytical corrections built into the network architecture allow it to properly model physical limits. SpookyNet improves upon the current state-of-the-art (or achieves similar performance) on popular quantum chemistry data sets. Notably, it is able to generalize across chemical and conformational space and can leverage the learned chemical insights, e.g. by predicting unknown spin states, thus helping to close a further important remaining gap for today's machine learning models in quantum chemistry.
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Affiliation(s)
- Oliver T Unke
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany.
- DFG Cluster of Excellence "Unifying Systems in Catalysis" (UniSysCat), Technische Universität Berlin, 10623, Berlin, Germany.
| | - Stefan Chmiela
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany
| | - Michael Gastegger
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany
- DFG Cluster of Excellence "Unifying Systems in Catalysis" (UniSysCat), Technische Universität Berlin, 10623, Berlin, Germany
| | - Kristof T Schütt
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany
| | - Huziel E Sauceda
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany
- BASLEARN, BASF-TU joint Lab, Technische Universität Berlin, 10587, Berlin, Germany
| | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany.
- Department of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Korea.
- Max Planck Institute for Informatics, Stuhlsatzenhausweg, 66123, Saarbrücken, Germany.
- BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Google Research, Brain team, Berlin, Germany.
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Karlsson D, van Leeuwen R, Pavlyukh Y, Perfetto E, Stefanucci G. Fast Green's Function Method for Ultrafast Electron-Boson Dynamics. PHYSICAL REVIEW LETTERS 2021; 127:036402. [PMID: 34328754 DOI: 10.1103/physrevlett.127.036402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
The interaction of electrons with quantized phonons and photons underlies the ultrafast dynamics of systems ranging from molecules to solids, and it gives rise to a plethora of physical phenomena experimentally accessible using time-resolved techniques. Green's function methods offer an invaluable interpretation tool since scattering mechanisms of growing complexity can be selectively incorporated in the theory. Currently, however, real-time Green's function simulations are either prohibitively expensive due to the cubic scaling with the propagation time or do neglect the feedback of electrons on the bosons, thus violating energy conservation. We put forward a computationally efficient Green's function scheme which overcomes both limitations. The numerical effort scales linearly with the propagation time while the simultaneous dressing of electrons and bosons guarantees the fulfillment of all fundamental conservation laws. We present a real-time study of the phonon-driven relaxation dynamics in an optically excited narrow band-gap insulator, highlighting the nonthermal behavior of the phononic degrees of freedom. Our formulation paves the way to first-principles simulations of electron-boson systems with unprecedented long propagation times.
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Affiliation(s)
- Daniel Karlsson
- Department of Physics, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Robert van Leeuwen
- Department of Physics, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Yaroslav Pavlyukh
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle, Germany
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Enrico Perfetto
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Gianluca Stefanucci
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Tuovinen R, van Leeuwen R, Perfetto E, Stefanucci G. Electronic transport in molecular junctions: The generalized Kadanoff-Baym ansatz with initial contact and correlations. J Chem Phys 2021; 154:094104. [PMID: 33685185 DOI: 10.1063/5.0040685] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The generalized Kadanoff-Baym ansatz (GKBA) offers a computationally inexpensive approach to simulate out-of-equilibrium quantum systems within the framework of nonequilibrium Green's functions. For finite systems, the limitation of neglecting initial correlations in the conventional GKBA approach has recently been overcome [Karlsson et al., Phys. Rev. B 98, 115148 (2018)]. However, in the context of quantum transport, the contacted nature of the initial state, i.e., a junction connected to bulk leads, requires a further extension of the GKBA approach. In this work, we lay down a GKBA scheme that includes initial correlations in a partition-free setting. In practice, this means that the equilibration of the initially correlated and contacted molecular junction can be separated from the real-time evolution. The information about the contacted initial state is included in the out-of-equilibrium calculation via explicit evaluation of the memory integral for the embedding self-energy, which can be performed without affecting the computational scaling with the simulation time and system size. We demonstrate the developed method in carbon-based molecular junctions, where we study the role of electron correlations in transient current signatures.
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Affiliation(s)
- Riku Tuovinen
- QTF Centre of Excellence, Turku Centre for Quantum Physics, Department of Physics and Astronomy, University of Turku, 20014 Turku, Finland
| | - Robert van Leeuwen
- Department of Physics, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Enrico Perfetto
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Gianluca Stefanucci
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Krumland J, Valencia AM, Pittalis S, Rozzi CA, Cocchi C. Understanding real-time time-dependent density-functional theory simulations of ultrafast laser-induced dynamics in organic molecules. J Chem Phys 2020; 153:054106. [PMID: 32770886 DOI: 10.1063/5.0008194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Real-time time-dependent density functional theory, in conjunction with the Ehrenfest molecular dynamics scheme, is becoming a popular methodology to investigate ultrafast phenomena on the nanoscale. Thanks to recent developments, it is also possible to explicitly include in the simulations a time-dependent laser pulse, thereby accessing the transient excitation regime. However, the complexity entailed in these calculations calls for in-depth analysis of the accessible and yet approximate (either "dressed" or "bare") quantities in order to evaluate their ability to provide us with a realistic picture of the simulated processes. In this work, we analyze the ultrafast dynamics of three small molecules (ethylene, benzene, and thiophene) excited by a resonant laser pulse in the framework of the adiabatic local-density approximation. The electronic response to the laser perturbation in terms of induced dipole moment and excited-state population is compared to the results given by an exactly solvable two-level model. In this way, we can interpret the charge-carrier dynamics in terms of simple estimators, such as the number of excited electrons. From the computed transient absorption spectra, we unravel the appearance of nonlinear effects such as excited-state absorption and vibronic coupling. In this way, we observe that the laser excitation affects the vibrational spectrum by enhancing the anharmonicities therein, while the coherent vibrational motion contributes to stabilizing the electronic excitation already within a few tens of femtoseconds.
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Affiliation(s)
- Jannis Krumland
- Humboldt-Universität zu Berlin, Physics Department and IRIS Adlershof, 12489 Berlin, Germany
| | - Ana M Valencia
- Humboldt-Universität zu Berlin, Physics Department and IRIS Adlershof, 12489 Berlin, Germany
| | | | | | - Caterina Cocchi
- Humboldt-Universität zu Berlin, Physics Department and IRIS Adlershof, 12489 Berlin, Germany
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Cohen G, Galperin M. Green’s function methods for single molecule junctions. J Chem Phys 2020; 152:090901. [DOI: 10.1063/1.5145210] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Guy Cohen
- The Raymond and Beverley Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Galperin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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Perfetto E, Trabattoni A, Calegari F, Nisoli M, Marini A, Stefanucci G. Ultrafast Quantum Interference in the Charge Migration of Tryptophan. J Phys Chem Lett 2020; 11:891-899. [PMID: 31944766 DOI: 10.1021/acs.jpclett.9b03517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Extreme-ultraviolet-induced charge migration in biorelevant molecules is a fundamental step in the complex path leading to photodamage. In this work we propose a simple interpretation of the charge migration recently observed in an attosecond pump-probe experiment on the amino acid tryptophan. We find that the decay of the prominent low-frequency spectral structure with increasing pump-probe delay is due to a quantum beating between two geometrically distinct, almost degenerate charge oscillations. Quantum beating is ubiquitous in these systems, and at least on the few-to-tens of femtosecond time scales, it may dominate over decoherence the line intensities of time-resolved spectra. We also address the experimentally observed phase shift in the charge oscillations of two different amino acids, tryptophan and phenylalanine. Our results indicate that a beyond mean-field treatment of the electron dynamics is necessary to reproduce the correct behavior.
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Affiliation(s)
- E Perfetto
- Dipartimento di Fisica , Università di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
- CNR-ISM , Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
| | - A Trabattoni
- Center for Free-Electron Laser Science (CFEL) , DESY , 22607 Hamburg , Germany
| | - F Calegari
- Center for Free-Electron Laser Science (CFEL) , DESY , 22607 Hamburg , Germany
- Institute for Photonics and Nanotechnologies , IFN-CNR , 20133 Milano , Italy
- Institut fur Experimentalphysik , Universität Hamburg , D-22761 Hamburg , Germany
| | - M Nisoli
- Institute for Photonics and Nanotechnologies , IFN-CNR , 20133 Milano , Italy
- Dipartimento di Fisica , Politecnico di Milano , 20133 Milano , Italy
| | - A Marini
- CNR-ISM , Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
| | - G Stefanucci
- Dipartimento di Fisica , Università di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
- INFN , Sezione di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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Perfetto E, Sangalli D, Palummo M, Marini A, Stefanucci G. First-Principles Nonequilibrium Green’s Function Approach to Ultrafast Charge Migration in Glycine. J Chem Theory Comput 2019; 15:4526-4534. [DOI: 10.1021/acs.jctc.9b00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- E. Perfetto
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit), Area della Ricerca di Roma 1, Via Salaria Km 29.3, I-00016 Monterotondo Scalo, Italy
| | - D. Sangalli
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit), Area della Ricerca di Roma 1, Via Salaria Km 29.3, I-00016 Monterotondo Scalo, Italy
| | - M. Palummo
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - A. Marini
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit), Area della Ricerca di Roma 1, Via Salaria Km 29.3, I-00016 Monterotondo Scalo, Italy
| | - G. Stefanucci
- Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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Perfetto E, Stefanucci G. CHEERS: a tool for correlated hole-electron evolution from real-time simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:465901. [PMID: 30359327 DOI: 10.1088/1361-648x/aae675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We put forward a practical nonequilibrium Green's function (NEGF) scheme to perform real-time evolutions of many-body interacting systems driven out of equilibrium by external fields. CHEERS is a computational tool to solve the NEGF equation of motion in the so called generalized Kadanoff-Baym ansatz and it can be used for model systems as well as first-principles Hamiltonians. Dynamical correlation (or memory) effects are added to the Hartree-Fock dynamics through a many-body self-energy. Applications to time-dependent quantum transport, time-resolved photoabsorption and other ultrafast phenomena are discussed.
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Affiliation(s)
- E Perfetto
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit), Area della ricerca di Roma 1, Monterotondo Scalo, Italy. Dipartimento di Fisica, Università di Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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Bassman L, Krishnamoorthy A, Kumazoe H, Misawa M, Shimojo F, Kalia RK, Nakano A, Vashishta P. Electronic Origin of Optically-Induced Sub-Picosecond Lattice Dynamics in MoSe 2 Monolayer. NANO LETTERS 2018; 18:4653-4658. [PMID: 29990437 DOI: 10.1021/acs.nanolett.8b00474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomically thin layers of transition metal dichalcogenide (TMDC) semiconductors exhibit outstanding electronic and optical properties, with numerous applications such as valleytronics. While unusually rapid and efficient transfer of photoexcitation energy to atomic vibrations was found in recent experiments, its electronic origin remains unknown. Here, we study the lattice dynamics induced by electronic excitation in a model TMDC monolayer, MoSe2, using nonadiabatic quantum molecular dynamics simulations. Simulation results show sub-picosecond disordering of the lattice upon photoexcitation, as measured by the Debye-Waller factor, as well as increasing disorder for higher densities of photogenerated electron-hole pairs. Detailed analysis shows that the rapid, photoinduced lattice dynamics are due to phonon-mode softening, which in turn arises from electronic Fermi surface nesting. Such mechanistic understanding can help guide optical control of material properties for functionalizing TMDC layers, enabling emerging applications such as phase change memories and neuromorphic computing.
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Affiliation(s)
| | | | - Hiroyuki Kumazoe
- Department of Physics , Kumamoto University , Kumamoto 860-8555 , Japan
| | - Masaaki Misawa
- Department of Physics , Kumamoto University , Kumamoto 860-8555 , Japan
| | - Fuyuki Shimojo
- Department of Physics , Kumamoto University , Kumamoto 860-8555 , Japan
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Perfetto E, Sangalli D, Marini A, Stefanucci G. Ultrafast Charge Migration in XUV Photoexcited Phenylalanine: A First-Principles Study Based on Real-Time Nonequilibrium Green's Functions. J Phys Chem Lett 2018; 9:1353-1358. [PMID: 29494772 DOI: 10.1021/acs.jpclett.8b00025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The early-stage density oscillations of the electronic charge in molecules irradiated by an attosecond XUV pulse takes place on femto- or subfemtosecond time scales. This ultrafast charge migration process is a central topic in attoscience because it dictates the relaxation pathways of the molecular structure. A predictive quantum theory of ultrafast charge migration should incorporate the atomistic details of the molecule, electronic correlations, and the multitude of ionization channels activated by the broad-bandwidth XUV pulse. We propose a first-principles nonequilibrium Green's function method fulfilling all three requirements and apply it to a recent experiment on the photoexcited phenylalanine amino acid. Our results show that dynamical correlations are necessary for a quantitative overall agreement with the experimental data. In particular, we are able to capture the transient oscillations at frequencies 0.15 and 0.30 PHz in the hole density of the amine group as well as their suppression and the concomitant development of a new oscillation at frequency 0.25 PHz after ∼14 fs.
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Affiliation(s)
- E Perfetto
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
- Dipartimento di Fisica , Università di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - D Sangalli
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
| | - A Marini
- CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) , Area della Ricerca di Roma 1, Via Salaria Km 29.3 , I-00016 Monterotondo Scalo , Italy
| | - G Stefanucci
- Dipartimento di Fisica , Università di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
- INFN, Sezione di Roma Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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