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Usage of a Hamiltonian perturbation theory for a nonconservative system is counterintuitive and, in general, a technical impossibility by definition. However, the time-independent dual Hamiltonian formalism for the nonconservative systems has opened the door for using various conservative perturbation theories for investigating the dynamics of such systems. Here we demonstrate that the Lie transform Hamiltonian perturbation theory can be adapted to find the perturbative solutions and the frequency corrections for the dissipative oscillatory systems. As a further application, we use the perturbation theory to analytically calculate the Hannay angle for the van der Pol oscillator's limit cycle trajectory when its parameters-the strength of the nonlinearity and the frequency of the linear part-evolve cyclically and adiabatically. For this van der Pol oscillator, we also numerically calculate the corresponding geometric phase and establish its equivalence with the Hannay angle.
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http://dx.doi.org/10.1103/PhysRevE.97.062209 | DOI Listing |
J Chem Phys
September 2025
Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, SK-84215 Bratislava, Slovakia.
An explicitly correlated extension of a pair-function based perturbation theory is presented. The reference is obtained as the antisymmetrized product of strongly orthogonal geminals, termed Strictly Localized Geminals (SLG), which can capture static correlation at mean-field cost. Geminals entering SLG are spin unrestricted, in general, and are expanded in the one-electron basis of the natural orbitals of the unrestricted Hartree-Fock wavefunction.
View Article and Find Full Text PDFJ Phys Chem A
September 2025
Univ. Rennes, CNRS, IPR (Institut de Physique de Rennes), UMR 6251, Rennes F-35000, France.
We present the first dataset of collisional (de)-excitation rate coefficients of HCN induced by CO, one of the main perturbing gases in cometary atmospheres. The dataset spans the temperature range of 5-50 K. It includes both state-to-state rate coefficients involving the lowest ten and nine rotational levels of HCN and CO, respectively, and the so-called "thermalized" rate coefficients over the rotational population of CO at each kinetic temperature.
View Article and Find Full Text PDFJ Chem Phys
September 2025
Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium.
We model Auger spectra using second-order Møller-Plesset perturbation (MP2) theory combined with complex-scaled basis functions. For this purpose, we decompose the complex MP2 energy of the core-hole state into contributions from specific decay channels and propose a corresponding equation-of-motion (EOM) method for computing the doubly ionized final states of Auger decay. These methods lead to significant savings in computational cost compared to our recently developed approaches based on coupled-cluster theory [F.
View Article and Find Full Text PDFBrief Bioinform
August 2025
College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, P. R. China.
Drug-induced hepatotoxicity (DIH), characterized by diverse phenotypes and complex mechanisms, remains a critical challenge in drug discovery. To systematically decode this diversity and complexity, we propose a multi-dimensional computational framework integrating molecular structure analysis with disease pathogenesis exploration, focusing on drug-induced intrahepatic cholestasis (DIIC) as a representative DIH subtype. First, a graph-based modularity maximization algorithm identified DIIC risk genes, forming a DIIC module and eight disease pathogenesis clusters.
View Article and Find Full Text PDFACS Omega
September 2025
Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510 Ciudad de Mexico, Mexico.
In this study, we introduce a set of novel computational strategies based on second-order Mo̷ller-Plesset perturbation theory (MP2), enhanced through acceleration techniques, such as the resolution of the identity (RI). These approaches are further refined via spin-component scaling (SCS), following Grimme's methodology, and are specifically calibrated for the quantitatively accurate prediction of weak interaction energiesinteractions that play a critical role in biological systems. Among the developed methods, three variants exhibit outstanding performance, surpassing the accuracy of several state-of-the-art, nondynamical electronic structure techniques.
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