Vibrational heat-bath configuration interaction (VHCI)-a selected configuration interaction technique for vibrational structure theory-has recently been developed in two independent works [J. H. Fetherolf and T. C. Berkelbach, J. Chem. Phys. 154, 074104 (2021); A. U. Bhatty and K. R. Brorsen, Mol. Phys. 119, e1936250 (2021)], where it was shown to provide accuracy on par with the most accurate vibrational structure methods with a low computational cost. Here, we eliminate the memory bottleneck of the second-order perturbation theory correction using the same (semi)stochastic approach developed previously for electronic structure theory. This allows us to treat, in an unbiased manner, much larger perturbative spaces, which are necessary for high accuracy in large systems. Stochastic errors are easily controlled to be less than 1 cm-1. We also report two other developments: (i) we propose a new heat-bath criterion and an associated exact implicit sorting algorithm for potential energy surfaces expressible as a sum of products of one-dimensional potentials; (ii) we formulate VHCI to use a vibrational self-consistent field (VSCF) reference, as opposed to the harmonic oscillator reference configuration used in previous reports. Our tests are done with quartic and sextic force fields, for which we find that with VSCF, the minor improvements to accuracy are outweighed by the higher computational cost associated the matrix element evaluations. We expect VSCF-based VHCI to be important for more general potential representations, for which the harmonic oscillator basis function integrals are no longer analytic.
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http://dx.doi.org/10.1063/5.0172702 | DOI Listing |
RSC Chem Biol
January 2025
Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine Kamigyo-ku 465 Kajii-cho Kyoto 602-8566 Japan
A multiomic study of the structural characteristics of type A and B influenza viruses by means of highly spectrally resolved Raman spectroscopy is presented. Three virus strains, A H1N1, A H3N2, and B98, were selected because of their known structural variety and because they have co-circulated with variable relative prevalence within the human population since the re-emergence of the H1N1 subtype in 1977. Raman signatures of protein side chains tyrosine, tryptophan, and histidine revealed unequivocal and consistent differences for pH characteristics at the virion surface, while different conformations of two C-S bond configurations in and methionine rotamers provided distinct low-wavenumber fingerprints for different virus lineages/subtypes.
View Article and Find Full Text PDFSci Rep
January 2025
Electrical and Computer Engineering Department, University of Memphis, Memphis, TN, 38152, USA.
Oral squamous cell carcinoma (OSCC) is the most common form of oral cancer, with increasing global incidence and have poor prognosis. Tumour-infiltrating lymphocytes (TILs) are recognized as a key prognostic indicator and play a vital role in OSCC grading. However, current methods for TILs quantification are based on subjective visual assessments, leading to inter-observer variability and inconsistent diagnostic reproducibility.
View Article and Find Full Text PDFJ Mol Graph Model
January 2025
Department of Mathematics & Actuarial Science, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, Tamil Nadu, 600048, India. Electronic address:
Topological indices are numerical invariants that provide key insights into the structural properties of molecular graphs and are crucial in predicting physio-chemical and biological activities. This paper applies established computational methodologies for analyzing benzenoid networks and their application to polycyclic aromatic hydrocarbons (PAHs) through degree-based topological indices computed via M-polynomial and NM-polynomial approaches. By examining tessellations, including linear chain, hexagonal, rhomboidal, and triangular configurations alongside their line graphs, this work highlights the influence of molecular topology on biological activity.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Qingdao Institute for Theoretical and Computational Sciences and Center for Optics Research and Engineering, Shandong University, Qingdao 266237, China.
As an approximation to SDSCI [static-dynamic-static (SDS) configuration interaction (CI), a minimal MRCI; , , 1481], SDSPT2 [ , , 2696] is a CI-like multireference (MR) second-order perturbation theory (PT2) that treats single and multiple roots in the same manner. This feature permits the use of configuration selection over a large complete active space (CAS) to end up with a much reduced reference space ̃, which is connected only with a small portion (̃) of the full first-order interacting space connected to . The most expensive portion of the reduced interacting ̃ space (which involves three active orbitals) can further be truncated by partially bypassing its generation followed by an integral-based cutoff.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China.
The exploration of materials with nanoscale noncollinear configurations has been continuously attracting attention due to the prospective applications in high-performance magnetic devices. Compared to ferromagnetic materials, noncollinear structures in frustrated magnets hold greater research value due to their smaller sizes and unique properties. However, an effective description of the nanoscale noncollinear domain structures in frustrated magnets is lacking.
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