Mixed quantal-semiquantal dynamics with stochastic particles for backreaction

A mixed quantal-semiquantal theory is presented in which the semiquantal squeezed-state wave packet describes the heavy degrees of freedom. We first derive mean-field equations of motion from the time-dependent variational principle. Then, in order to take into account the interparticle correlation, in particular the 'quantum backreaction' beyond the mean-field approximation, we introduce the stochastic particle description for both the quantal and semiquantal parts. A numerical application on a model of O2 scattering from a Pt surface demonstrates that the proposed scheme gives correct asymptotic behavior of the scattering probability, with improvement over the mixed quantum-classical scheme with Bohmian particles, which is comprehended by comparing the Bohmian and the stochastic trajectories.Comment: 4 pages, 2 figure

Constraints on decaying dark matter from the extragalactic gamma-ray background

If dark matter is unstable and the mass is within GeV-TeV regime, its decays produce high-energy photons that give contribution to the extragalactic gamma-ray background (EGRB). We constrain dark matter decay by analyzing the 50-month EGRB data measured with Fermi satellite, for different decay channels motivated with several supersymmetric scenarios featuring R-parity violation. We adopt the latest astrophysical models for various source classes such as active galactic nuclei and star-forming galaxies, and take associated uncertainties properly into account. The lower limits for the lifetime are very stringent for a wide range of dark matter mass, excluding the lifetime shorter than 10^28 s for mass between a few hundred GeV and ~1TeV, e.g., for b\bar{b} decay channel. Furthermore, most dark matter models that explain the anomalous positron excess are also excluded. These constraints are robust, being little dependent on astrophysical uncertainties, unlike other probes such as Galactic positrons or anti-protons.Comment: 20 pages, 6 figures, published versio

Charge-Transfer Matrix Elements by FMO-LCMO Approach: Hole Transfer in DNA with Parameter Tuned Range-Separated DFT

A scheme for computing charge-transfer matrix elements with the linear combination of fragment molecular orbitals and the 'nonempirically tuned range-separated' density functional is presented. It takes account of the self-consistent orbital relaxation induced by environmental Coulomb field and the exchange interaction in fragment pairs at low computational scaling along the system size. The accuracy was confirmed numerically on benchmark systems of imidazole and furane homo-dimer cations. Applications to hole transfers in DNA nucleobase pairs and in a $\pi$-stack adenine octomer highlight the effects of orbital relaxation.Comment: 10 pages, 8 figure

The axial methionine ligand may control the redox reorganizations in the active site of blue copper proteins.

Structural and energetic reorganizations in redox reaction of type 1 copper proteins are studied by density functional and ab initio molecular orbital calculations. Model complexes of the active site with varying number of ligands, from Cu(SCH(3))(0/+) to Cu(SCH(3))(Im)(2)(S(CH(3))(2))(0/+), where Im denotes imidazole, are investigated. Following the findings of structural instability in Cu(I)(SCH(3))(Im)(2) and its stabilization by the addition of the axial methionine (Met) ligand model, the structure and energetics are examined as functions of the Cu-S(Met) distance in the range of 2.1-3.3 Å. The reorganization energies in both redox states exhibit a minimum at the Cu-S(Met) distance of ∼2.4 Å, whereas the ionization potential increases monotonically. The changes of reorganization energies correlate well with one of the Cu-N(His) distances rather than the Cu-S(Cys) distance. The estimated Arrhenius factor for oxidation of plastocyanin by P700(+) (in photosystem I) changes by an order of magnitude when the Cu-S(Met) distance fluctuates between 2.4 and 3.0 Å, whereas the factor for reduction of plastocyanin by cytochrome f is nearly constant. Together with the data from our previous classical molecular dynamics simulation of solvated protein, we argue that the electron transfer rate is affected, and thus may be controlled, by the fluctuation of a weakly bound axial Met ligand. We also present the assessment of various exchange-correlation functionals, including those with the long-range correction, against the CCSD(T) reference and on the basis of a perturbative adiabatic connection model. For Cu(SCH(3)) and Cu(SCH(3))(Im), simple correlations have been found between the reorganization energies and the amount of Hartree-Fock exchange

Potential energy surfaces for electron dynamics from a model of localized Gaussian wave packets with valence-bond spin-coupling: high-harmonic generation spectra from H and He atoms

Potential energy surfaces of electron dynamics (ePES) are constructed from a model of localized electron wave packets (eWP) with non-orthogonal valence-bond (VB) spin coupling and applied to quantum dynamics simulations of high harmonic generation (HHG) spectra of hydrogen and helium atoms induced by intense laser pulses. The dynamics of the single electron on the ePES is calculated by numerically solving the time-dependent Schrodinger equation. The results reasonably reproduce previous studies. The dynamics of the electron wave function, dipole moment and dipole acceleration were analyzed by comparing one- and two-dimensional calculations. It was found that the main part of the wave function remains within a few Bohrs of the nuclear position, while the part of the wave function that is several orders of magnitude smaller in probability density, which escapes the laser-induced potential barrier by quantum tunneling effect, mainly contributes to the HHG.Comment: 9 pages, 12 figure

Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol olfactory receptor

Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlfaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2--4 ns. The lifetime of the H-bond was in the range of 1--20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the $\alpha$-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 $\to$ Phe182 $\to$ (Leu259 or Tyr260) $\to$ Tyr291 induced by the ligand binding with a time scale of 4--6 ns.Comment: 6 pages, 8 figure