Article
Astronomy & Astrophysics
V. C. Tavares, C. J. A. P. Martins
Summary: The study concludes that the potential in these models needs to be extremely flat, and the dark energy equation of state deviates within 95.4% confidence levels for the rolling tachyon and Chaplygin components.
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
Biochemistry & Molecular Biology
Dan Parkin, Mitsunori Takano
Summary: The generalized Born (GB) model is a powerful method for accelerating MD simulations of charged biological molecules in water, and the adjustment of parameters is essential for accurate calculation of the Coulomb energy. This study clarifies that increasing the intrinsic radius rho in the GB model enhances the Coulomb bond stability through the interaction energy term. The use of larger values for the intrinsic radii of hydrogen and oxygen atoms, together with a relatively small value for the spatial integration cutoff, can better reproduce the Coulombic attraction between protein molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Interdisciplinary Applications
Helmut Harbrecht, Michael Multerer
Summary: This article discusses fast direct solvers for nonlocal operators by combining wavelet representation with nested dissection ordering scheme to reduce fill-in during matrix factorization and achieve the exact inverse of the compressed system matrix with only a moderate increase in nonzero entries. Numerical experiments are conducted for various nonlocal operator applications to illustrate the efficacy of the approach.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Computer Science, Interdisciplinary Applications
Miguel Angel Soler, Ozge Ozkilinc, Yamanappa Hunashal, Paolo Giannozzi, Gennaro Esposito, Federico Fogolari
Summary: Biomolecular electrostatics plays a crucial role in biological function and recognition. The Poisson-Boltzmann equation and the Generalized Born model are commonly used methods to study biomolecular electrostatics. This work presents a tutorial on the program Bluues, which can efficiently calculate various properties related to electrostatic effects and pH dependence.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Engineering, Multidisciplinary
Ravi G. Patel, Nathaniel A. Trask, Mitchell A. Wood, Eric C. Cyr
Summary: The paper presents a framework for discovering continuum models from high-fidelity molecular simulation data using neural networks to parameterize governing physics. The approach is effective for various physics, including local and nonlocal diffusion processes and single and multiphase flows, with the learned operator able to generalize to system characteristics not included in the training sets.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2021)
Article
Mechanics
Paul Bouteiller, Jeremy Bleyer, Karam Sab
Summary: This paper presents a method for obtaining consistent generalized inertias through the use of a complementary energy principle in elastodynamics, which is then applied to extend a stress-based layerwise plate model in a dynamic setting. The effectiveness of this approach is validated through modal analysis of various anisotropic composite laminates.
INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES
(2022)
Article
Multidisciplinary Sciences
Seth M. Hirsh, Sara M. Ichinaga, Steven L. Brunton, J. Nathan Kutz, Bingni W. Brunton
Summary: In this paper, a theoretical connection between HAVOK and the Frenet-Serret frame from differential geometry is established, and an improved algorithm is developed to identify more stable and accurate models. The study demonstrates that the sub- and super-diagonal entries of the linear model correspond to the intrinsic curvatures in the Frenet-Serret frame, and modifying the algorithm to promote this antisymmetric structure improves modeling accuracy even with noisy, low-data limits.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Chemistry, Physical
Kye Won Wang, Jumin Lee, Han Zhang, Donghyuk Suh, Wonpil Im
Summary: Implicit solvent models are widely used in various molecular dynamics programs, with CHARMM-GUI's Implicit Solvent Modeler supporting different GB implicit solvent simulations for protein, DNA, RNA, glycan, and ligand systems. Generated systems and input files by ISM produce similar results and show better performance for ligand screening compared to docking. This indicates that ISM is a useful and reliable tool for various implicit solvent simulation applications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Mechanics
Gianluca Rizzi, Geralf Hutter, Angela Madeo, Patrizio Neff
Summary: The stability and modeling limits of investigated continuum are examined by considering a family of infinitesimal isotropic generalized continuum models and solving the simple shear problem analytically. The shear stiffness mu* serves as a qualitative measure characterizing different generalized continuum moduli, which is generally dependent on length-scale. Interesting limit cases are highlighted to interpret material parameters in the investigated continua.
ARCHIVE OF APPLIED MECHANICS
(2021)
Article
Mathematics
Feng Hong, Lu Tian, Viswanath Devanarayan
Summary: High-dimensional data applications require the use of statistical and machine-learning algorithms to identify optimal biomarker signatures based on patient characteristics for predicting clinical outcomes in biomedical research. Regularization, particularly L-1-based regularization, is commonly used to improve prediction performance and feature selection. However, choosing the penalty parameter for regularization can be unstable and may lead to inflated predictive performance estimates. This paper proposes a Monte Carlo approach for robust regularization parameter selection and an additional cross-validation wrapper for objectively evaluating the final model's predictive performance.
Article
Mathematics, Interdisciplinary Applications
Manar A. Alqudah, Rehana Ashraf, Saima Rashid, Jagdev Singh, Zakia Hammouch, Thabet Abdeljawad
Summary: The research introduces a fuzzy hybrid approach merged with a homotopy perturbation transform method to solve fuzzy fractional Cauchy reaction-diffusion equations with fuzzy initial conditions. The simulation results demonstrate that the fuzzy SHPTM is a viable strategy for precisely and accurately analyzing the behavior of the proposed model.
FRACTAL AND FRACTIONAL
(2021)
Article
Mathematics, Applied
Rehana Ashraf, Saima Rashid, Fahd Jarad, Ali Althobaiti
Summary: This article introduces the application of the Shehu homotopy perturbation transform method (SHPTM) via fuzziness, which combines the homotopy perturbation method and the Shehu transform. The proposed methodology allows us to reliably find fuzzy fractional equal width, modified equal width, and variants of modified equal width models with fuzzy initial conditions. Additionally, the method demonstrates superiority in investigating fractional nonlinear systems and considers fuzzy set theory for different nonlinearities.
Article
Computer Science, Information Systems
Yongjun Liu, Guisheng Liao, Jingwei Xu, Zhiwei Yang, Yingzeng Yin
Summary: In this article, the utilization of preamble information to enhance the performance of passive MIMO radar is studied. Two derived GLRTs are proposed and compared, showing improved performance compared to GLRTs without using preamble information. The comparison with GLRTs for active MIMO radar also demonstrates varying performance of the derived GLRTs.
IEEE SYSTEMS JOURNAL
(2021)
Article
Environmental Sciences
Andrew W. Whelan, Jeffery B. Cannon, Seth W. Bigelow, Brandon T. Rutledge, Andrew J. Sanchez Meador
Summary: Modeling forest attributes using lidar data is a useful tool for forest management, but the correlation between lidar and ground-based measurements presents challenges. Voxel-based metrics show promise in characterizing forest structure and distinguishing between diverse forest types. These metrics can improve the characterization of leaf area distribution and horizontal forest structure, leading to general models of forest attributes applicable in complex landscapes.
REMOTE SENSING OF ENVIRONMENT
(2023)
Article
Chemistry, Multidisciplinary
Ayesha Ashraf, John M. Herbert, Shabbir Muhammad, Bilal Ahmad Farooqi, Umar Farooq, Muhammad Salman, Khurshid Ayub
Summary: The interaction mechanism between graphene/nPT composite materials and gaseous analytes CO, NH3, SO2, and NO2 is explored using density functional theory calculations. The change in the highest occupied molecular orbital/lowest unoccupied molecular orbital gap of the composite indicates the change in conductivity upon complexation with the analyte. The computational framework established in this study can be used to evaluate and design gas sensor materials.
Article
Chemistry, Physical
Ying Zhu, John M. Herbert
Summary: In this study, high harmonic spectra for H-2 and H-2(+) were simulated using an atom-centered Gaussian representation of the density and a complex absorbing potential. The results showed that this approach can achieve better resolution compared to grid-based algorithms.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Bushra Alam, Hanjie Jiang, Paul M. Zimmerman, John M. Herbert
Summary: The restricted active space spin-flip (RAS-SF) formalism is a cost-effective method for describing strong correlation in single-reference configuration interaction. In this study, we introduced both equilibrium and nonequilibrium solvation corrections for computing vertical transition energies using RAS-SF wave functions. Benchmark calculations were performed for various photo-induced charge transfer models, and the results demonstrate the importance of the RAS-SF + PCM methodology in studying charge-separated states in solution and photovoltaic materials.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Montgomery Gray, John M. Herbert
Summary: This study systematically investigates the convergence of XSAPT interaction energies and energy components with respect to the choice of Gaussian basis sets. Errors can be reduced using correlation-consistent basis sets and new versions with limited augmentation. The use of Pople-style basis sets may afford good results if a large number of polarization functions are included.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Kevin Carter-Fenk, John M. Herbert
Summary: In this study, we propose improvements to the dispersion damping potentials in the effective fragment potential (EFP) and evaluate their performance using a new database of ionic liquid constituents. We recommend a new parameter-free dispersion damping function as a replacement for the current one used in EFP.
Article
Chemistry, Physical
Bhaskar Rana, Gregory J. O. Beran, John M. Herbert
Summary: This study considers molecules with pi-electron conjugation and finds that delocalisation error in density functional theory affects their conformational energies. By using density-corrected methods, the errors can be significantly reduced, enabling accurate calculations of molecular crystals.
Article
Chemistry, Physical
Montgomery Gray, John M. Herbert
Summary: This study investigates the interaction energies and components in porous frameworks and finds that the van der Waals interaction is the main driving force for parallel-displaced pi-stacking, while electrostatics plays a minor role. The presence of a guest molecule limits the available slip-stacking configurations in COF-1.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Kevin Carter-Fenk, Britta A. Johnson, John M. Herbert, Gregory K. Schenter, Christopher J. Mundy
Summary: A new simulation method is used to directly study the generation of hydrated electrons from the charge-transfer-to-solvent state. The simulations reveal a two-step process involving ionization and solute reorganization leading to the equilibrated ground state of the solvated electron. This methodology has implications for photochemical electron transfer processes in solution, with potential application in photocatalysis and energy transfer.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Subrata Jana, John M. M. Herbert
Summary: The methods for computing core-level ionization energies are evaluated and compared. The full core hole approach and Slater's transition concept are considered, with the latter showing mean errors of 0.3-0.4 eV compared to experiment. A shifted Slater transition method requiring only initial-state Kohn-Sham eigenvalues is found to be a simple and practical way to compute core-level binding energies. It is particularly useful for simulating transient x-ray experiments.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Subrata Jana, John M. M. Herbert
Summary: This article examines methods for calculating X-ray absorption spectra using a constrained core hole, which may contain a fractional electron. These methods are based on Slater's transition concept and generalize it by using Kohn-Sham orbital energies to determine core-to-valence excitation energies. The tested methods achieve robust convergence by avoiding promoting electrons beyond the lowest unoccupied molecular orbital. The best-case accuracy of these methods is found to be 0.3-0.4 eV with respect to experiment for K-edge transition energies. Higher-lying near-edge transitions have larger absolute errors, but these can be reduced below 1 eV by introducing an empirical shift based on a charge-neutral transition-potential method combined with specific functionals like SCAN, SCAN0, or B3LYP. This procedure allows for obtaining an entire excitation spectrum from a single fractional-electron calculation, without the need for state-by-state calculations based on ground-state density functional theory. The shifted transition-potential approach proposed in this study is particularly useful for simulating transient spectroscopies and in complex systems where excited-state Kohn-Sham calculations are challenging.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Paige E. Bowling, Dustin R. Broderick, John M. Herbert
Summary: Electronic structure calculations on enzymes with hundreds of atoms can be costly, but fragment-based approximations provide a cost-effective solution. The many-body expansion method allows calculations on enzyme models with 500-600 atoms and compares well with benchmarks. Different boundary conditions can affect the convergence of the calculations, highlighting the need for appropriate assessments of errors in fragment-based approximations. Protocols involving three-body or two-body calculations combined with a full-system correction offer accurate results at a lower computational cost, making high-level quantum chemistry applicable to large systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Correction
Chemistry, Physical
Kevin Carter-Fenk, Britta A. Johnson, John M. Herbert, Gregory K. Schenter, Christopher J. Mundy
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Dustin R. Broderick, John M. Herbert
Summary: The many-body expansion is a method used to calculate electronic structure in large systems. This study presents an algorithm to overcome the combinatorial bottleneck in many-body expansion and implements it in a software application called Fragment. The results show that this method allows for unprecedentedly large-scale calculations with high accuracy.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Paige E. Bowling, Dustin R. Broderick, John M. Herbert
Summary: Electronic structure calculations on enzymes are improved by fragment-based approximations and many-body expansion. When using amino acid fragments with ionic side chains, low-dielectric boundary conditions are necessary to restore rapid convergence. Traditional gas-phase calculations do not provide accurate benchmarks for assessing errors in fragment-based approximations. Three-body and two-body protocols with a full-system correction achieve high-level quantum chemistry calculations on large systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Montgomery Gray, John M. Herbert
Summary: In this study, the slip-stacking in porous frameworks, such as COF-1, is investigated by computing interaction energies and their components. It is found that the van der Waals interaction potential drives the system into a slip-stacked geometry, while electrostatics only plays a minor role. Even in the absence of solvent molecules, a modest lateral offset is preferred in COF-1.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
