Article
Chemistry, Physical
Devin A. Matthews
Summary: The LS-THC-MP3 method shows favorable small errors in test systems with up to 40 first-row atoms, with potential for higher efficiency via a more streamlined method of generating grids through pruning. A practical crossover is achieved around 240 correlated electrons. Despite identified drawbacks, LS-THC demonstrates significant potential for practical application to MP3 and other wavefunction methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Computer Science, Software Engineering
Srinivas Eswar, Koby Hayashi, Grey Ballard, Ramakrishnan Kannan, Michael A. Matheson, Haesun Park
Summary: This study addresses the problem of low-rank approximation of massive dense nonnegative tensor data by proposing a distributed-memory parallel computing solution that loads input data across multiple nodes and uses efficient and scalable parallel algorithms. The software package presented allows for extension in terms of data, algorithm, and architecture, while carefully avoiding unnecessary communication and computation. Efficiency and scalability results are reported for both synthetic and real-world data sets.
ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE
(2021)
Article
Environmental Sciences
Onuwa Okwuashi, Christopher E. Ndehedehe, Dupe Nihinlola Olayinka
Summary: This research explores the novel application of Tensor Partial Least Squares (TPLS) for hyperspectral image classification. The results show that TPLS performed better than unfolded PLS, but fell short of traditional classifiers.
GEOCARTO INTERNATIONAL
(2022)
Article
Spectroscopy
Stephen Merriman, Dinesh Chandra, Marc Borowczak, Ali Dhinojwala, David Benko
Summary: Using ATR-FTIR spectroscopy for direct quantitative analysis is highly desirable for many sample systems due to advantages such as rapid spectra collection and being completely non-destructive. However, for complex sample matrices, the feasibility of direct quantitative analysis using ATR-FTIR is uncertain. In this study, a method was developed to simultaneously quantify the concentration of three different antidegradents directly on rubber samples using ATR-FTIR spectra.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Automation & Control Systems
Huiwen Yu, Dillen Augustijn, Rasmus Bro
Summary: This paper proposes novel extrapolation-based PARAFAC2 algorithms which achieve faster convergence speeds and outperform existing methods. A comprehensive investigation and comparison of various extrapolation algorithms is conducted using simulated and real data.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Engineering, Multidisciplinary
Matthias Wurm
Summary: Solving overdetermined linear systems with individual uncertainties is important in various disciplines. This paper presents a robust and fast method for computing the solution and covariance matrix of such systems.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2022)
Article
Computer Science, Information Systems
Xiaokang Wang, Huiwen Wang, Zhichao Wang, Shan Lu, Ying Fan
Summary: This paper proposes a new method to identify the causal structure of asset risk spillover network and characterize the joint return distribution of the global financial system using directed acyclic graph skeleton estimation. Through a two-stage approach, the effectiveness of the proposed method is demonstrated through simulation studies.
INFORMATION SCIENCES
(2021)
Article
Chemistry, Analytical
Jie Huang, Xiaojing Chen, Zhonghao Xie, Shujat Ali, Xi Chen, Leiming Yuan, Chengxi Jiang, Guangzao Huang, Wen Shi
Summary: This study explores the application of laser-induced breakdown spectroscopy (LIBS) combined with partial least squares (PLS) model for predicting copper concentrations in T. granosa. The study uses the robust partial least squares (RSIMPLS) method to process high-dimensional LIBS data and successfully improves the prediction accuracy of copper concentrations.
ANALYTICAL METHODS
(2023)
Article
Engineering, Aerospace
Xiang Guo, Yu Zhang, Hao Zhou, Yuefeng Zhao, Qile Zhao
Summary: The study shows that using M-estimation can improve the precision and consistency of orbit determination in satellite POD, with significant improvements observed in the dynamic orbit.
ADVANCES IN SPACE RESEARCH
(2022)
Article
Mathematics, Applied
Linjian Ma, Edgar Solomonik
Summary: This paper introduces a novel family of algorithms that use perturbative corrections to optimize the quadratic optimization subproblems in CP and Tucker decomposition. The proposed pairwise perturbation algorithms are easy to control and achieve convergenceto minima that are as good as ALS.
NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS
(2022)
Article
Mathematics, Applied
Navjot Singh, Linjian Ma, Hongru Yang, Edgar Solomonik
Summary: The paper introduces a parallel implementation of the Gauss-Newton method for CP decomposition, which iteratively solves linear least squares problems to improve accuracy. It explores the convergence of the Gauss-Newton method compared to alternating least squares for finding exact and approximate CP decompositions.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2021)
Article
Engineering, Electrical & Electronic
Ayed M. Alrashdi
Summary: This paper presents an asymptotic high-dimensional analysis of the regularised zero-forcing receiver in a massive MIMO communication system for the recovery of BPSK modulated signals. The authors assume spatially correlated and imperfectly known channel matrix, and use the LMMSE method to estimate the channel matrix. The derived asymptotic expressions of MSE and BER provide solutions to practical optimization problems.
IET SIGNAL PROCESSING
(2022)
Article
Optics
Zhenyu Li, Hui Zhang, Binh Thi Thanh Nguyen, Shaobo Luo, Patricia Yang Liu, Jun Zou, Yuzhi Shi, Hong Cai, Zhenchuan Yang, Yufeng Jin, Yilong Hao, Yi Zhang, Ai-Qun Liu
Summary: The smart sensor achieves label-free multicomponent chemical analysis with a high prediction accuracy and simple detection strategy using a label-free ring resonator and neural network model, promising great potential for applications in various fields.
PHOTONICS RESEARCH
(2021)
Article
Mathematics, Applied
Yajie Yu, Hanyu Li
Summary: In this paper, two strategies are proposed to tackle the high cost issue in tensor ring decomposition and three ALS-based algorithms are designed. By simplifying the calculation of coefficient matrices and stabilizing the ALS subproblems, the algorithms improve computational efficiency and numerical stability.
NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Xiaokang Wang, Shan Lu, Rui Zhou, Huiwen Wang
Summary: This paper proposes a two-stage DAG skeleton estimation approach for highly correlated data. The first stage involves a novel neighborhood selection method based on sparse partial least squares regression, while the second stage estimates the DAG skeleton by evaluating conditional independence hypotheses. Simulation studies and tests on publicly available datasets demonstrate the effectiveness of the proposed method.
PATTERN RECOGNITION
(2023)
Article
Chemistry, Physical
Christoph Bannwarth, Todd J. Martinez
Summary: The article presents an approach to unify ab initio and semiempirical electronic structure code paths. By separating the wavefunction ansatz and the matrix representations of operators, the Hamiltonian can refer to either an ab initio or semiempirical treatment. The authors built a semiempirical integral library and interfaced it to the GPU-accelerated electronic structure code TeraChem. This approach enables the combination of semiempirical Hamiltonians with the full functionality of the ab initio electronic structure code.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Caroline T. Sargent, Derek P. Metcalf, Zachary L. Glick, Carlos H. Borca, C. David Sherrill
Summary: Using the many-body expansion method, we predicted crystal lattice energies (CLEs) with flexibility in theoretical methods. We computed two-body contributions of 23 molecular crystals using different quantum chemical levels and compared them with coupled-cluster in the complete basis set (CBS) limit. Accurate calculations were achieved for interaction energies of distant dimers using certain methods, reducing the computational expense of coupled-cluster by up to 98%.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Vinicius Wilian D. Cruzeiro, Yuanheng Wang, Elisa Pieri, Edward G. Hohenstein, Todd J. Martinez
Summary: This article introduces how to set up the GPU-accelerated electronic structure program TeraChem as an electronic structure server, which can be easily accessed by third-party client programs. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages. By incorporating the TCPB client into Amber for QM/MM simulations, significant time savings and speedup have been achieved compared to prior implementations. The practical application of TCPB is demonstrated through the computation of the free energy profile of a model chromophore.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Chemistry, Physical
Umberto Raucci, Hayley Weir, Sukolsak Sakshuwong, Stefan Seritan, Colton B. Hicks, Fabio Vannucci, Francesco Rea, Todd J. Martinez
Summary: This article outlines methods to eliminate the barriers preventing the wider chemistry community from performing quantum chemistry calculations. These methods include GPU-accelerated quantum chemistry in the cloud, AI-driven natural molecule input methods, and extended reality visualization. The article also highlights the exciting applications of these methods in computing and visualizing spectra, 3D structures, molecular orbitals, and other chemical properties.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Rameshwar L. Kumawat, C. David Sherrill
Summary: High-order quantum chemistry methods were used to study the intermolecular interaction energies and their components for hydrogen-bonded DNA nucleobase pairs and non-natural Hachimoji nucleobase pairs. The most attractive component of the interaction energies was found to be the electrostatic interactions, followed closely by the sum of induction/polarization and London dispersion. Non-natural Hachimoji base pairs exhibited stronger interactions than the corresponding natural base pairs, while the natural base pairs were more stabilized in their Hoogsteen geometries. Hoogsteen geometries were less favorable for non-natural Hachimoji base pairs compared to Watson-Crick geometries.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Editorial Material
Chemistry, Physical
Michele Ceriotti, Lasse Jensen, David E. Manolopoulos, Todd Martinez, David R. Reichman, Francesco Sciortino, C. David Sherrill, Qiang Shi, Carlos Vega, Lai-Sheng Wang, Emily A. Weiss, Xiaoyang Zhu, Jenny Stein, Tianquan Lian
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Carlos H. Borca, Zachary L. Glick, Derek P. Metcalf, Lori A. Burns, C. David Sherrill
Summary: The use of many-body expansion (MBE) method, combining CCSD(T)/CBS for closest dimers and trimers and MP2 for more distant ones, shows promising results in efficiently calculating lattice energies in organic crystals. The effectiveness of MP2(+ATM) as a replacement for CCSD(T)/CBS is demonstrated. The CCSD(T)/CBS best estimate of the lattice energy at 0 K is -54.01 kJ mol(-1).
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yi Xie, Zachary L. L. Glick, C. David Sherrill
Summary: This study investigates the three-body dispersion contribution to crystal lattice energies in benzene, carbon dioxide, and triazine. By using various computational methods, it is observed that these contributions converge rapidly with increasing intermolecular distances. The closest-contact distance, R-min, shows a strong correlation with the three-body contribution, while R-max is used as a cutoff criterion for considering the number of trimers. The results suggest that the MP2+ATM method can be used to compute trimers with R-min > 4 angstrom to reduce computational cost.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Y. Liu, D. M. Sanchez, M. R. Ware, E. G. Champenois, J. Yang, J. P. F. Nunes, A. Attar, M. Centurion, J. P. Cryan, R. Forbes, K. Hegazy, M. C. Hoffmann, F. Ji, M. F. Lin, D. Luo, S. K. Saha, X. Shen, X. J. Wang, T. J. Martinez, T. J. A. Wolf
Summary: Combining ultrafast electron diffraction and ab initio dynamics simulations, the authors visualize the structure of a pericyclic minimum, also known as a pericyclic minimum, in real time in a photochemical reaction. Electrocylic reactions involve the simultaneous formation and cleavage of sigma and pi bonds through a cyclic structure. This research provides experimental evidence for the importance of this structure in electrocyclic reactions.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Philip M. Nelson, Zachary L. Glick, C. David Sherrill
Summary: The focal-point approximation combines multiple lower-accuracy, faster computations to estimate a high-accuracy, slow quantum chemistry computation. By combining MP2 with CCSD(T) methods, the focal-point CCSD(T) method can approach the complete basis set (CBS) limit with only triple-xi basis sets. Compared with experimental values, the predicted harmonic and fundamental frequencies using the focal-point method have smaller mean absolute errors, and the computation time required is much less, especially for larger molecules.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Wenwen Xu, David M. M. Sanchez, Umberto Raucci, Hantao Zhou, Xinning Dong, Mingqiu Hu, Christopher J. J. Bardeen, Todd J. J. Martinez, Ryan C. C. Hayward
Summary: By incorporating diarylethene microcrystals into a polyethylene terephthalate matrix, highly ordered and compliant photomechanical composites with superior performance compared to single crystals are achieved. These composites exhibit rapid response times, sustain a high level of performance over numerous cycles, and generate high work densities.
Article
Multidisciplinary Sciences
Steven A. Spronk, Zachary L. Glick, Derek P. Metcalf, C. David Sherrill, Daniel L. Cheney
Summary: Fast and accurate calculation of intermolecular interaction energies is crucial for understanding chemical and biological processes. The Splinter dataset, which contains paired molecular fragments representing common substructures in proteins and small-molecule ligands, has been created to facilitate the development and improvement of computational methods for performing these calculations. It is expected to serve as a benchmark dataset for training and testing various methods for calculating intermolecular interaction energies.
Article
Chemistry, Multidisciplinary
Rui Xu, Jan Meisner, Alexander M. Chang, Keiran C. Thompson, Todd J. Martinez
Summary: Our recent success in utilizing GPUs to speed up quantum chemistry computations has led to the creation of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to study methane pyrolysis, uncovering the elementary reactions through GPU-accelerated simulations and refining the reaction paths using transition state theory. With 53 species and 134 reactions, the kinetic model derived from the discovered reactions is validated against experimental data and literature models. We also demonstrate the effectiveness of local brute force and Monte Carlo sensitivity analysis for identifying important reactions and improving the accuracy of the kinetic model.
Article
Chemistry, Physical
Alexander M. Chang, Jan Meisner, Rui Xu, Todd J. Martinez
Summary: This study examines the effectiveness of using metadynamics, attractive potentials, and local thermostats for accelerating reaction discovery. By constructing different reaction networks, it is found that a combination of accelerating forces is best suited for reaction discovery.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)