Molecular Quantum Dynamics: A Quantum Computing Perspective

Ollitrault, Pauline J.; Miessen, Alexander; Tavernelli, Ivano

doi:10.1021/acs.accounts.1c00514

Cited by 50 publications

(39 citation statements)

References 70 publications

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“…Perspectives of the development of novel information-rich spectroscopic techniques and challenges facing ultrafast multidimensional spectroscopy have been discussed in recent reviews. ,, The wider use of the EOM methods, aided perhaps by future developments of machine learning techniques , and (possibly) by quantum computing methods and algorithms, − may move the frontiers of femtosecond spectroscopy of functional materials toward higher-order signals and higher pulse intensities for better characterization of reactive intermediates and photochemical pathways.…”

Section: Summary and Perspectives Of Spectroscopic Equation-of-motion...mentioning

confidence: 99%

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals

2022

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Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system–field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.

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Section: Summary and Perspectives Of Spectroscopic Equation-of-motion...mentioning

confidence: 99%

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals

2022

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“…Quantum Processing Units (QPUs) use the effects of quantum mechanics for methods of information transfer among bit-like devices (i.e., quantum bits, or “qubits”). Due to the qubits’ ability to hold multiple states, QPUs could ideally solve molecular kinetics calculations as they could represent every electron within a protein ( 42 ), given that QPUs can be treated as extra-large electrons due to their macroscopic quantum effects. Quantum processors provide superposition and entanglement features on their qubits and have the potential to take exponential scale problems and turn them into polynomial or even log scale problems.…”

Section: Introductionmentioning

confidence: 99%

“…However, the largest QPUs that exist as per the writing of this paper are the Xanadu Borealis device with 216 qubits ( 43 ), the IBM Eagle with 127 qubits and the Google Bristlecone with 72 qubits ( 44 ). As one qubit simulates one extra-large electron ( 42 ), it would take many hundreds of qubits to model even the simplest proteins ( 45 ).…”

Section: Introductionmentioning

confidence: 99%

SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK

et al. 2022

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The pulmonary surfactant protein A (SP-A) is a constitutively expressed immune-protective collagenous lectin (collectin) in the lung. It binds to the cell membrane of immune cells and opsonizes infectious agents such as bacteria, fungi, and viruses through glycoprotein binding. SARS-CoV-2 enters airway epithelial cells by ligating the Angiotensin Converting Enzyme 2 (ACE2) receptor on the cell surface using its Spike glycoprotein (S protein). We hypothesized that SP-A binds to the SARS-CoV-2 S protein and this binding interferes with ACE2 ligation. To study this hypothesis, we used a hybrid quantum and classical in silico modeling technique that utilized protein graph pruning. This graph pruning technique determines the best binding sites between amino acid chains by utilizing the Quantum Approximate Optimization Algorithm (QAOA)-based MaxCut (QAOA-MaxCut) program on a Near Intermediate Scale Quantum (NISQ) device. In this, the angles between every neighboring three atoms were Fourier-transformed into microwave frequencies and sent to a quantum chip that identified the chemically irrelevant atoms to eliminate based on their chemical topology. We confirmed that the remaining residues contained all the potential binding sites in the molecules by the Universal Protein Resource (UniProt) database. QAOA-MaxCut was compared with GROMACS with T-REMD using AMBER, OPLS, and CHARMM force fields to determine the differences in preparing a protein structure docking, as well as with Goemans-Williamson, the best classical algorithm for MaxCut. The relative binding affinity of potential interactions between the pruned protein chain residues of SP-A and SARS-CoV-2 S proteins was assessed by the ZDOCK program. Our data indicate that SP-A could ligate the S protein with a similar affinity to the ACE2-Spike binding. Interestingly, however, the results suggest that the most tightly-bound SP-A binding site is localized to the S2 chain, in the fusion region of the SARS-CoV-2 S protein, that is responsible for cell entry Based on these findings we speculate that SP-A may not directly compete with ACE2 for the binding site on the S protein, but interferes with viral entry to the cell by hindering necessary conformational changes or the fusion process.

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“…A computation of molecular properties within the Born-Oppenheimer approximation requires solving the electronic structure problem, fitting the results of potential energy calculations to produce global PES and solving the nuclear dynamics problem with the PES thus obtained. Several algorithms have been recently developed for solving electronic structure [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] and nuclear dynamics [17][18][19][20][21][22] problems on noisy intermediate-scale quantum (NISQ) computers. However, quantum algorithms for producing global PES of polyatomic molecules have not yet been demonstrated.…”

Section: Introductionmentioning

confidence: 99%

Quantum Gaussian process model of potential energy surface for a polyatomic molecule

Dai¹,

Krems²

2022

Preprint

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With gates of a quantum computer designed to encode multi-dimensional vectors, projections of quantum computer states onto specific qubit states can produce kernels of reproducing kernel Hilbert spaces. We show that quantum kernels obtained with a fixed ansatz implementable on current quantum computers can be used for accurate regression models of global potential energy surfaces (PES) for polyatomic molecules. To obtain accurate regression models, we apply Bayesian optimization to maximize marginal likelihood by varying the parameters of the quantum gates. This yields Gaussian process models with quantum kernels. We illustrate the effect of qubit entanglement in the quantum kernels and explore the generalization performance of quantum Gaussian processes by extrapolating global six-dimensional PES in the energy domain.

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Molecular Quantum Dynamics: A Quantum Computing Perspective

Abstract: This work presents a novel quantum algorithm to simulate nonadiabatic quantum dynamics on a spatial grid with product formulas.

Cited by 50 publications

References 70 publications

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals

SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK

Quantum Gaussian process model of potential energy surface for a polyatomic molecule

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