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VeloxChem: GPU-Accelerated Fock Matrix Construction Enabling Complex Polarization Propagator Simulations of Circular Dichroism Spectra of G-Quadruplexes
KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.ORCID-id: 0000-0001-6508-8355
KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.ORCID-id: 0000-0002-9720-5429
KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Teoretisk kemi och biologi. KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.ORCID-id: 0000-0002-1191-4954
2025 (engelsk)Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 129, nr 2, s. 633-642Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

An automatic code generated C++/HIP/CUDA implementation of the (auxiliary) Fock, or Kohn-Sham, matrix construction for execution in GPU-accelerated hardware environments is presented. The module is developed as part of the quantum chemistry software package VeloxChem, employing localized Gaussian atomic orbitals. The performance and scaling characteristics are analyzed in view of the specific requirements for self-consistent field optimization and response theory calculations. As an example, the electronic circular dichroism spectrum of a G-quadruplex is calculated at the level of time-dependent density functional theory in conjunction with the range-separated CAM-B3LYP exchange-correlation functional. Computational issues due to the high-density of states following the adoption of large-scale model systems are here bypassed with use of the complex polarization propagator approach. The origin of the negative Cotton effect in the long-wavelength onset of the experimental spectrum is elucidated in large-scale modeling and shown to be associated with the TTA nucleobase linkers in the G-quadruplex.

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American Chemical Society (ACS) , 2025. Vol. 129, nr 2, s. 633-642
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URN: urn:nbn:se:kth:diva-359305DOI: 10.1021/acs.jpca.4c07510ISI: 001387038800001PubMedID: 39739694Scopus ID: 2-s2.0-85215269952OAI: oai:DiVA.org:kth-359305DiVA, id: diva2:1932632
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QC 20250130

Tilgjengelig fra: 2025-01-29 Laget: 2025-01-29 Sist oppdatert: 2025-01-30bibliografisk kontrollert

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Li, XinLinares, MathieuNorman, Patrick

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