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Authors = Paul Ayers

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26 pages, 3758 KiB  
Review
Information Theory Meets Quantum Chemistry: A Review and Perspective
by Yilin Zhao, Dongbo Zhao, Chunying Rong, Shubin Liu and Paul W. Ayers
Entropy 2025, 27(6), 644; https://doi.org/10.3390/e27060644 - 16 Jun 2025
Viewed by 1165
Abstract
In this survey, we begin with a concise introduction to information theory within Shannon’s framework, focusing on the key concept of Shannon entropy and its related quantities: relative entropy, joint entropy, conditional entropy, and mutual information. We then demonstrate how to apply these [...] Read more.
In this survey, we begin with a concise introduction to information theory within Shannon’s framework, focusing on the key concept of Shannon entropy and its related quantities: relative entropy, joint entropy, conditional entropy, and mutual information. We then demonstrate how to apply these information-theoretic tools in quantum chemistry, adopting either classical or quantum formalisms based on the choice of information carrier involved. Full article
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13 pages, 4042 KiB  
Article
Chiral Jahn–Teller Distortion in Quasi-Planar Boron Clusters
by Dongbo Zhao, Yilin Zhao, Tianlv Xu, Xin He, Shankai Hu, Paul W. Ayers and Shubin Liu
Molecules 2024, 29(7), 1624; https://doi.org/10.3390/molecules29071624 - 4 Apr 2024
Cited by 1 | Viewed by 1534
Abstract
In this work, we have observed that some chiral boron clusters (B16, B20, B24, and B28) can simultaneously have helical molecular orbitals and helical spin densities; these seem to be [...] Read more.
In this work, we have observed that some chiral boron clusters (B16, B20, B24, and B28) can simultaneously have helical molecular orbitals and helical spin densities; these seem to be the first compounds discovered to have this intriguing property. We show that chiral Jahn–Teller distortion of quasi-planar boron clusters drives the formation of the helical molecular spin densities in these clusters and show that elongation/enhancement in helical molecular orbitals can be achieved by simply adding more building blocks via a linker. Aromaticity of these boron clusters is discussed. Chiral boron clusters may find potential applications in spintronics, such as molecular magnets. Full article
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15 pages, 1430 KiB  
Article
Co-Clinical Imaging Metadata Information (CIMI) for Cancer Research to Promote Open Science, Standardization, and Reproducibility in Preclinical Imaging
by Stephen M. Moore, James D. Quirk, Andrew W. Lassiter, Richard Laforest, Gregory D. Ayers, Cristian T. Badea, Andriy Y. Fedorov, Paul E. Kinahan, Matthew Holbrook, Peder E. Z. Larson, Renuka Sriram, Thomas L. Chenevert, Dariya Malyarenko, John Kurhanewicz, A. McGarry Houghton, Brian D. Ross, Stephen Pickup, James C. Gee, Rong Zhou, Seth T. Gammon, Henry Charles Manning, Raheleh Roudi, Heike E. Daldrup-Link, Michael T. Lewis, Daniel L. Rubin, Thomas E. Yankeelov and Kooresh I. Shoghiadd Show full author list remove Hide full author list
Tomography 2023, 9(3), 995-1009; https://doi.org/10.3390/tomography9030081 - 11 May 2023
Cited by 3 | Viewed by 4057
Abstract
Preclinical imaging is a critical component in translational research with significant complexities in workflow and site differences in deployment. Importantly, the National Cancer Institute’s (NCI) precision medicine initiative emphasizes the use of translational co-clinical oncology models to address the biological and molecular bases [...] Read more.
Preclinical imaging is a critical component in translational research with significant complexities in workflow and site differences in deployment. Importantly, the National Cancer Institute’s (NCI) precision medicine initiative emphasizes the use of translational co-clinical oncology models to address the biological and molecular bases of cancer prevention and treatment. The use of oncology models, such as patient-derived tumor xenografts (PDX) and genetically engineered mouse models (GEMMs), has ushered in an era of co-clinical trials by which preclinical studies can inform clinical trials and protocols, thus bridging the translational divide in cancer research. Similarly, preclinical imaging fills a translational gap as an enabling technology for translational imaging research. Unlike clinical imaging, where equipment manufacturers strive to meet standards in practice at clinical sites, standards are neither fully developed nor implemented in preclinical imaging. This fundamentally limits the collection and reporting of metadata to qualify preclinical imaging studies, thereby hindering open science and impacting the reproducibility of co-clinical imaging research. To begin to address these issues, the NCI co-clinical imaging research program (CIRP) conducted a survey to identify metadata requirements for reproducible quantitative co-clinical imaging. The enclosed consensus-based report summarizes co-clinical imaging metadata information (CIMI) to support quantitative co-clinical imaging research with broad implications for capturing co-clinical data, enabling interoperability and data sharing, as well as potentially leading to updates to the preclinical Digital Imaging and Communications in Medicine (DICOM) standard. Full article
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14 pages, 1096 KiB  
Article
Excited-State Polarizabilities: A Combined Density Functional Theory and Information-Theoretic Approach Study
by Dongbo Zhao, Xin He, Paul W. Ayers and Shubin Liu
Molecules 2023, 28(6), 2576; https://doi.org/10.3390/molecules28062576 - 12 Mar 2023
Cited by 12 | Viewed by 2701
Abstract
Accurate and efficient determination of excited-state polarizabilities (α) is an open problem both experimentally and computationally. Following our previous work, (Phys. Chem. Chem. Phys. 2023, 25, 2131−2141), in which we employed simple ground-state (S0) density-related functions from the information-theoretic [...] Read more.
Accurate and efficient determination of excited-state polarizabilities (α) is an open problem both experimentally and computationally. Following our previous work, (Phys. Chem. Chem. Phys. 2023, 25, 2131−2141), in which we employed simple ground-state (S0) density-related functions from the information-theoretic approach (ITA) to accurately and efficiently evaluate the macromolecular polarizabilities, in this work we aimed to predict the lowest excited-state (S1) polarizabilities. The philosophy is to use density-based functions to depict excited-state polarizabilities. As a proof-of-principle application, employing 2-(2′-hydroxyphenyl)benzimidazole (HBI), its substituents, and some other commonly used ESIPT (excited-state intramolecular proton transfer) fluorophores as model systems, we verified that either with S0 or S1 densities as an input, ITA quantities can be strongly correlated with the excited-state polarizabilities. When transition densities are considered, both S0 and S1 polarizabilities are in good relationships with some ITA quantities. The transferability of the linear regression model is further verified for a series of molecules with little or no similarity to those molecules in the training set. Furthermore, the excitation energies can be predicted based on multivariant linear regression equations of ITA quantities. This study also found that the nature of both the ground-state and excited-state polarizabilities of these species are due to the spatial delocalization of the electron density. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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15 pages, 2891 KiB  
Article
Assessing Heat Management Practices in High Tunnels to Improve the Production of Romaine Lettuce
by Muzi Zheng, Brian Leib, David Butler, Wesley Wright, Paul Ayers, Douglas Hayes and Amir Haghverdi
Agriculture 2019, 9(9), 203; https://doi.org/10.3390/agriculture9090203 - 14 Sep 2019
Cited by 1 | Viewed by 4049
Abstract
A three-year experiment evaluated the beneficial effects of independent and combined practices on thermal conditions inside high tunnels (HTs), and further investigated the temperature impacts on lettuce production. Specific practices included mulching (polyethylene and biodegradable plastic films, and vegetative), row covers, cover crops, [...] Read more.
A three-year experiment evaluated the beneficial effects of independent and combined practices on thermal conditions inside high tunnels (HTs), and further investigated the temperature impacts on lettuce production. Specific practices included mulching (polyethylene and biodegradable plastic films, and vegetative), row covers, cover crops, and irrigation with collected rainwater or city water. The study conducted in eastern Tennessee was a randomized complete block split-split plot design (RCBD) with three HTs used as replicates to determine fall lettuce weight (g/plant) and lettuce survival (#/plot), and the changes in soil and air temperature. The black and clear plastic mulches worked best for increasing plant weight, but when compared to the bare ground, the higher soil temperature from the plastics may have caused a significant reduction in lettuce plants per plot. Moreover, the biodegradable mulch did not generate as much soil warming as black polyethylene, yet total lettuce marketable yield was statistically similar to that for the latter mulch treatment; while the white spunbond reduced plant weight when compared with black plastic. Also, row covers provided an increased nighttime air temperature that increased soil temperature, hence significantly increased lettuce production. Cover crops reduced lettuce yield, but increased soil temperatures. Additionally, irrigation using city water warmed the soil and provided more nutrients for increased lettuce production over rainwater irrigation. Full article
(This article belongs to the Special Issue Agricultural Irrigation)
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13 pages, 469 KiB  
Article
A Case Study in the Application of the Systematic Approach to Training in the Logging Industry
by Elise Lagerstrom, Sheryl Magzamen, William Brazile, Lorann Stallones, Paul Ayers and John Rosecrance
Safety 2019, 5(3), 43; https://doi.org/10.3390/safety5030043 - 8 Jul 2019
Cited by 1 | Viewed by 7152
Abstract
The purpose of this research was to develop and assess a targeted emergency first-aid and safety training program for professional loggers in Montana. There were two key objectives for the program: (1) participant demonstration of recall and retention of key concepts and (2) [...] Read more.
The purpose of this research was to develop and assess a targeted emergency first-aid and safety training program for professional loggers in Montana. There were two key objectives for the program: (1) participant demonstration of recall and retention of key concepts and (2) improved participant reception in comparison to the previous year’s training program. The Systematic Approach to Training provided the overall model for the development and conduct of the training program. Qualitative and quantitative analyses were used to assess the effectiveness of the training program. The training program was administered to 873 loggers. Pre-, post-, and follow-up examinations were used to assess recall and retention of key learning objectives, while surveys were used to assess learner reception of the updated training program. Post-training survey data indicated increases in training applicability, understanding of learning objectives, and overall course enjoyment of the updated program in comparison to the previous year’s training program. Participants scored significantly higher on the post-training exams, which demonstrated recall of key training objectives. The results obtained by the training evaluation will guide future research and the continued development of the training program to align with ongoing analysis activities and participant suggestions. Full article
(This article belongs to the Special Issue Agricultural Safety and Health)
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12 pages, 486 KiB  
Article
A Diagonally Updated Limited-Memory Quasi-Newton Method for the Weighted Density Approximation
by Matthew Chan, Rogelio Cuevas-Saavedra, Debajit Chakraborty and Paul W. Ayers
Computation 2017, 5(4), 42; https://doi.org/10.3390/computation5040042 - 26 Sep 2017
Cited by 2 | Viewed by 4604
Abstract
We propose a limited-memory quasi-Newton method using the bad Broyden update and apply it to the nonlinear equations that must be solved to determine the effective Fermi momentum in the weighted density approximation for the exchange energy density functional. This algorithm has advantages [...] Read more.
We propose a limited-memory quasi-Newton method using the bad Broyden update and apply it to the nonlinear equations that must be solved to determine the effective Fermi momentum in the weighted density approximation for the exchange energy density functional. This algorithm has advantages for nonlinear systems of equations with diagonally dominant Jacobians, because it is easy to generalize the method to allow for periodic updates of the diagonal of the Jacobian. Systematic tests of the method for atoms show that one can determine the effective Fermi momentum at thousands of points in less than fifteen iterations. Full article
(This article belongs to the Special Issue In Memory of Walter Kohn—Advances in Density Functional Theory)
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