Article
Chemistry, Physical
John M. Martyn, Yuan Liu, Zachary E. Chin, Isaac L. Chuang
Summary: Simulating the unitary dynamics of a quantum system is a fundamental problem in quantum mechanics, and quantum computers have an advantage in simulating electronic dynamics. This paper presents a fully-coherent simulation algorithm based on quantum signal processing, which can efficiently simulate time-dependent quantum systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Guillaume Le Breton, Oriane Bonhomme, Emmanuel Benichou, Claire Loison
Summary: In this study, electronic gamma(2 omega, omega, omega,0) and beta(2 omega, omega, omega) for water molecules in liquid water are computed using QM/MM calculations. The average value of gamma(2 omega, omega, omega,0) is smaller in the liquid phase compared to the gas phase, with a relatively small standard deviation among molecules. The study demonstrates that the average bulk second hyperpolarizability gamma(2 omega, omega, omega,0) can be used to describe the electrostatic effects of the distant neighborhood on the first hyperpolarizability beta(2 omega, omega, omega).
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Peter Reinholdt, Willem Van den Heuvel, Jacob Kongsted
Summary: The polarizable density embedding (PDE) model is an advanced fragment-based QM/QM embedding model that improves the description of electrostatics and includes non-electrostatic repulsion. We developed analytic geometric gradients for the PDE model to optimize the geometry of QM regions within large molecular environments. We also propose a hybrid PDE-LJ model that produces good quality solute-solvent structures for density functional theory (DFT) calculations.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Computer Science, Interdisciplinary Applications
Ken Mattsson, Ylva Ljungberg Rydin
Summary: In this article, implicit finite difference approximations for the first and second derivatives are derived. The boundary closures are based on the banded-norm summation-by-parts framework and the boundary conditions are enforced using a weak penalty method. Up to 8th order global convergence is achieved. The finite difference approximations lead to implicit ODE systems, and spectral resolution characteristics are obtained by tuning the internal difference stencils. The accuracy and stability properties are demonstrated for linear hyperbolic problems in 1D and the 2D compressible Euler equations.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Review
Chemistry, Physical
Michele Nottoli, Lorenzo Cupellini, Filippo Lipparini, Giovanni Granucci, Benedetta Mennucci
Summary: Multiscale models combining quantum mechanical and classical descriptions are popular for simulating properties and processes of complex systems. However, the application of these models to light-driven processes is relatively new and some methodological and numerical problems remain to be solved, especially for the polarizable formulation.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 72
(2021)
Article
Multidisciplinary Sciences
Bin Yan, Nikolai A. Sinitsyn
Summary: This paper investigates the computational capabilities of quantum annealing, finding evidence of better convergence and energy relaxation rates compared to classical annealing. It also shows the existence of an analytical solution for a specific problem, beyond the adiabatic limit for quantum annealing, providing insights into the accuracy of nonadiabatic computations. The study suggests that energy relaxation can differ in classical and quantum spin glasses when assisted by external time-dependent fields, and in certain cases, quantum annealing can achieve a considerable quantum speedup in computations.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Multidisciplinary
Yazen M. Alawaideh, Bashar M. Al-khamiseh
Summary: In this study, we extended the Hamilton formulation to continuous systems with second-order fractional derivatives and applied it to Podolsky's generalized electrodynamics. By comparing the results with Dirac's approach, we validated Podolsky's theory. Using the combined Riemann-Liouville fractional derivative operator and fractional variational theory, we derived the fractional Euler equations and fractional Hamilton equations, finding compatibility between the Hamiltonian equations of motion and Euler-Lagrange equations.
Article
Physics, Multidisciplinary
Jeong Ryeol Choi
Summary: The researcher has developed a quantum formalism based on a linear invariant theorem to provide an exact quantum-classical correspondence for damped oscillatory systems perturbed by arbitrary forces, removing the global quantum constant from their quantum results. The study specifically illustrates the precise correspondence of quantum energy with classical energy.
FRONTIERS IN PHYSICS
(2021)
Article
Acoustics
Xin Su, Eburilitu Bai
Summary: The free vibration of orthotropic rectangular thin plates with four free edges on two-parameter elastic foundations is studied using the symplectic superposition method. The original vibration problem is converted into two sub-vibration problems by analyzing the boundary conditions, and the fundamental solutions of these sub-vibration problems are obtained using the separation variable method. The symplectic superposition solution of the original vibration problem is then obtained by superimposing the fundamental solutions of the sub-problems.
JOURNAL OF VIBRATION AND CONTROL
(2022)
Article
Energy & Fuels
Suhan Zhang, Wei Gu, Xiao-ping Zhang, Hai Lu, Shuai Lu, Ruizhi Yu, Haifeng Qiu
Summary: This paper proposes a fully analytical method to describe thermal dynamics, avoiding inaccuracies and complexities associated with traditional numerical methods. By establishing an equivalent model and deriving temperature expressions, the influence of thermal dynamics in the heat and electricity integrated energy system is accurately reflected.
Article
Computer Science, Information Systems
Masahito Hayashi
Summary: We propose an analytical algorithm for calculating the channel capacity of a classical channel without any iteration, which is the first of its kind compared to existing algorithms that require iterations depending on the desired precision. The algorithm has specific conditions for the channel. We apply this algorithm to examples and observe its performance. Furthermore, we extend it to the channel capacity of a classical-quantum (cq-) channel. Unlike existing studies that require iterations, our extended analytical algorithm does not require iteration and provides an exact optimum value.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2023)
Article
Multidisciplinary Sciences
Dmitri Asonov, Maksim Krylov, Vladimir Omelyusik, Anastasiya Ryabikina, Evgeny Litvinov, Maksim Mitrofanov, Maksim Mikhailov, Albert Efimov
Summary: Classical polygraph screenings are commonly used by important industries such as banking, law enforcement agencies, and federal governments. The concern of scientific communities is the susceptibility to errors in these screenings, which can be attributed to both the method and human errors by polygraph examiners. We demonstrate the application of machine learning to detect examiner errors and successfully create a second-opinion tool to identify human errors in the examiners' conclusions, thereby reducing subjectivity in polygraph screenings. We present novel features that improve the accuracy of the model and experimental results on variations in lying behavior across different topics. Our findings are a significant step towards reevaluating traditional polygraph practices.
SCIENTIFIC REPORTS
(2023)
Article
Spectroscopy
Omer Tamer, Merve Simsek, Davut Avci, Yusuf Atalay
Summary: This study evaluated the hyperpolarizability parameters of seventeen flavonol derivatives and characterized their spectroscopic properties and quantum chemical parameters. The results suggest that flavonol derivatives with rational substitution may have potential applications in nonlinear optics.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Physics, Multidisciplinary
Saidakhmat N. Lakaev, Alexander K. Motovilov, Saidakbar Kh Abdukhakimov
Summary: In this paper, we study the Schrodinger operators H-lambda mu(K) associated with a system of two identical fermions on the two-dimensional lattice Z(2), which have first and second nearest-neighboring-site interactions lambda and mu, respectively. We establish a partition of the (lambda, mu) plane, where in each connected component, the Schrodinger operator H-lambda mu(0) has a fixed number of eigenvalues below the bottom of the essential spectrum and above its top. Furthermore, we provide a sharp lower bound for the number of isolated eigenvalues of H-lambda mu(K) in each connected component.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Astronomy & Astrophysics
Andrew Mummery
Summary: This paper discusses the "theory of propagating fluctuations" in the aperiodic variability observed in accreting black hole X-ray binary systems. It derives the Fourier transforms of the Green's function solutions of the thin disc equations and finds solutions for both Newtonian discs and general relativistic solutions with a vanishing ISCO stress. The study highlights the spin dependence of observable variability properties of black hole discs and suggests that observations of aperiodic variability may provide a new way to directly constrain black hole spins.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2023)
Correction
Chemistry, Physical
Piero Lafiosca, Tommaso Giovannini, Michele Benzi, Chiara Cappelli
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Juergen Gauss, Simon Blaschke, Sophia Burger, Tommaso Nottoli, Filippo Lipparini, Stella Stopkowicz
Summary: A rigorous analysis of the use of Cholesky decomposition (CD) for two-electron integrals in quantum-chemical calculations with finite or perturbative magnetic fields is carried out. The article investigates the consideration of permutational symmetry in such calculations and proposes a modified CD procedure for the finite-field case. It also derives CD expressions for derivative two-electron integrals in the case of a perturbative magnetic field. The suggested methods are validated through numerical examples involving several hundred basis functions.
Article
Chemistry, Physical
Michele Nottoli, Patrizia Mazzeo, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: Hybrid TDDFT/MM approaches are popular for describing electronic transitions of molecules in solution or complex matrices. However, when combined with a polarisable force field, problems may arise. This paper presents a possible solution by introducing a Delta SCF formulation, which is expected to be particularly suitable for accurately describing charge-transfer states.
Article
Chemistry, Physical
Patrizia Mazzeo, Shaima Hashem, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: In this study, we propose a new method that combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method to investigate the excited-state dynamics of molecules embedded in complex matrices. We apply this method to the photoactivation of the blue-light-using flavin (BLUF) domain of the AppA protein and demonstrate the presence of a proton-coupled electron transfer (PCET) process, which has been suggested in other BLUF proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Medicinal
Sara Gomez, Piero Lafiosca, Franco Egidi, Tommaso Giovannini, Chiara Cappelli
Summary: UV-Resonance Raman (RR) spectroscopy is a valuable tool for studying drug-receptor binding. Computational approaches tuned for supramolecular complexity greatly enhance the extraction of molecular-level information from experimental RR spectra. This paper proposes a protocol for simulating RR spectra of complex systems using a quantum mechanics/molecular mechanics (QM/MM) approach. The protocol is successfully applied to investigate the RR spectra of the chemotherapy drug doxorubicin (DOX) intercalated into DNA, with computed results showing good agreement with experimental data, validating the computational protocol's reliability.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Piero Lafiosca, Luca Nicoli, Luca Bonatti, Tommaso Giovannini, Stefano Corni, Chiara Cappelli
Summary: We propose quantum mechanics/frequency dependent fluctuating charge (QM/ω FQ) and fluctuating dipoles (QM/ω FQFμ) multiscale approaches for modeling surface-enhanced Raman scattering spectra of molecular systems adsorbed on plasmonic nanostructures. These methods utilize classical physics to describe the plasmonic properties of noble metal nanostructures and graphene-based materials, with the inclusion of an ad-hoc correction for quantum tunneling. Selected test cases demonstrate the robustness and reliability of both QM/ω FQ and QM/ω FQFμ approaches, as their computed results agree with available experiments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Tommaso Giovannini, Gioia Marrazzini, Marco Scavino, Henrik Koch, Chiara Cappelli
Summary: This paper presents a new multiscale approach for studying the electronic structure of open shell molecular systems in an external environment. The method involves coupling multilevel Hartree-Fock and Density Functional Theory with Molecular Mechanics force fields. The system is divided into active and inactive parts, describing relevant interactions at the quantum level, while the surrounding Molecular Mechanics part allows for a consistent treatment of long-range electrostatic and polarization effects. The approach is also extended to the calculation of hyperfine coupling constants and applied to selected nitroxyl radicals in an aqueous solution.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Chemistry, Multidisciplinary
Michele Nottoli, Mattia Bondanza, Patrizia Mazzeo, Lorenzo Cupellini, Carles Curutchet, Daniele Loco, Louis Lagardere, Jean-Philip Piquemal, Benedetta Mennucci, Filippo Lipparini
Summary: This article describes the development, implementation, and application of a polarizable QM/MM strategy based on the AMOEBA polarizable force field for calculating molecular properties and performing dynamics of molecular systems embedded in complex matrices. The authors demonstrate that this technology is well-understood and mature, and it can be efficiently implemented using advanced numerical methods and linear scaling techniques. The polarizable QM/AMOEBA approach has a wide range of applications, including predicting spectroscopies and performing multiscale ab initio molecular dynamics simulations.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Applied
Sulejman Skoko, Cosimo Micheletti, Emanuele Grifoni, Franco Egidi, Tommaso Giovannini, Andrea Pucci, Chiara Cappelli
Summary: We propose a synergistic computational/experimental investigation of fluorescence spectra in aqueous solution. We develop a reliable and cost-effective computational protocol that accurately describes the solute-solvent interactions and takes into account both specific hydrogen bonding interactions and the dynamical aspects of solvation in ground and excited states. The computational protocol is successfully tested against experimentally measured spectra of water soluble fluorescent dyes, demonstrating its reliability and paving the way for cost-effective investigation of solvated systems' ES properties.
Article
Chemistry, Physical
Maryam Mansoori Kermani, Hanwei Li, Alistar Ottochian, Orlando Crescenzi, Benjamin G. Janesko, Giovanni Scalmani, Michael J. Frisch, Ilaria Ciofini, Carlo Adamo, Donald G. Truhlar
Summary: Theoretical characterization of reactions of complex molecules requires accurate determination of the relative energies of intermediates and transition states. In this study, the DLPNO-CCSD(T) method was employed to provide benchmark values for Diels-Alder transition states leading to strained pentacyclic adducts. Various wave function and density functional methods were compared for their prediction of absolute and relative barrier heights. The results show that only a few density functionals can satisfactorily predict absolute barrier heights, while relative barrier heights are more accurate. The findings of this study can guide the selection of density functionals for future studies on crowded, strained transition states of large molecules.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Federica Pes, Etienne Polack, Patrizia Mazzeo, Genevieve Dusson, Benjamin Stamm, Filippo Lipparini
Summary: This Letter introduces a Quasi Time-Reversible scheme based on Grassmann extrapolation (QTR G-Ext) for accurate initial guess calculation in Born-Oppenheimer Molecular Dynamics (BOMD) simulations. The method shows excellent results on four representative large molecular systems, reducing the number of self-consistent field iterations and achieving energy-conserving simulations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Tommaso Nottoli, Ivan Gianni, Antoine Levitt, Filippo Lipparini
Summary: We introduce two open-source implementations of the locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm for finding a subset of eigenvalues and eigenvectors of large, potentially sparse matrices. We then test LOBPCG for various quantum chemistry problems, spanning medium to large, dense to sparse, well-conditioned to ill-conditioned cases, where the conventional method typically employed is Davidson's diagonalization. Numerical tests demonstrate that while Davidson's method remains the preferred choice for most quantum chemistry applications, LOBPCG offers a competitive alternative, particularly in memory-constrained scenarios, and can even outperform Davidson for ill-conditioned, non-diagonally dominant problems.
THEORETICAL CHEMISTRY ACCOUNTS
(2023)
Review
Chemistry, Multidisciplinary
Tommaso Giovannini, Chiara Cappelli
Summary: Solvent effects can significantly alter molecular spectral signals. Continuum and atomistic solvation models are the most effective approaches for properly describing these effects. This feature article reviews the continuum and atomistic descriptions in the calculation of molecular spectra, comparing their similarities and differences from a formal perspective and analyzing their computational advantages and disadvantages. Various spectral signals of increasing complexity are considered, and illustrative examples are discussed to highlight the differences between the two approaches.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Sara Gomez, Piero Lafiosca, Franco Egidi, Tommaso Giovannini, Chiara Cappelli
Summary: UV-Resonance Raman (RR) spectroscopy is a valuable tool for studying drug-receptor binding at the molecular level. In this paper, a computational protocol using a quantum mechanics/molecular mechanics (QM/MM) approach is proposed to simulate RR spectra of complex systems. The protocol is applied to investigate RR spectra of the chemotherapy drug doxorubicin (DOX) intercalated into DNA, and the computed results agree well with experimental data, demonstrating the reliability of the approach.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Sveva Sodomaco, Sara Gomez, Tommaso Giovannini, Chiara Cappelli
Summary: This study investigates the adsorption process of peptides, nucleobases, and ligands on gold using computational methods. The results show that the choice of force fields strongly affects the adsorption free energies and trends. Noncovalent interactions play a crucial role in the adsorption process. This research is important for understanding adsorption processes and designing biosensors.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
