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

Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center

The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling TDA and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (HL) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe[2+] and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe[2+] ion, its replacement by Zn[2+], or its removal are found to affect the T[DA] value by factors within 2.2. The calculated T[DA] values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments

Utility of a single adjusting compartment: a novel methodology for whole body physiologically-based pharmacokinetic modelling

<p>Abstract</p> <p>Background</p> <p>There are various methods for predicting human pharmacokinetics. Among these, a whole body physiologically-based pharmacokinetic (WBPBPK) model is useful because it gives a mechanistic description. However, WBPBPK models cannot predict human pharmacokinetics with enough precision. This study was conducted to elucidate the primary reason for poor predictions by WBPBPK models, and to enable better predictions to be made without reliance on complex concepts.</p> <p>Methods</p> <p>The primary reasons for poor predictions of human pharmacokinetics were investigated using a generic WBPBPK model that incorporated a single adjusting compartment (SAC), a virtual organ compartment with physiological parameters that can be adjusted arbitrarily. The blood flow rate, organ volume, and the steady state tissue-plasma partition coefficient of a SAC were calculated to fit simulated to observed pharmacokinetics in the rat. The adjusted SAC parameters were fixed and scaled up to the human using a newly developed equation. Using the scaled-up SAC parameters, human pharmacokinetics were simulated and each pharmacokinetic parameter was calculated. These simulated parameters were compared to the observed data. Simulations were performed to confirm the relationship between the precision of prediction and the number of tissue compartments, including a SAC.</p> <p>Results</p> <p>Increasing the number of tissue compartments led to an improvement of the average-fold error (AFE) of total body clearances (CL_tot) and half-lives (T_1/2) calculated from the simulated human blood concentrations of 14 drugs. The presence of a SAC also improved the AFE values of a ten-organ model from 6.74 to 1.56 in CL_tot, and from 4.74 to 1.48 in T_1/2. Moreover, the within-2-fold errors were improved in all models; incorporating a SAC gave results from 0 to 79% in CL_tot, and from 14 to 93% in T_1/2of the ten-organ model.</p> <p>Conclusion</p> <p>By using a SAC in this study, we were able to show that poor prediction resulted mainly from such physiological factors as organ blood flow rate and organ volume, which were not satisfactorily accounted for in previous WBPBPK models. The SAC also improved precision in the prediction of human pharmacokinetics. This finding showed that the methodology of our study may be useful for functionally reinforcing a WBPBPK model.</p

Upper Limit on Gravitational Wave Backgrounds at 0.2 Hz with Torsion-bar Antenna

We present the first upper limit on gravitational wave (GW) backgrounds at an unexplored frequency of 0.2 Hz using a torsion-bar antenna (TOBA). A TOBA was proposed to search for low-frequency GWs. We have developed a small-scaled TOBA and successfully found {\Omega}gw(f) < 4.3 \times 1017 at 0.2 Hz as demonstration of the TOBA's capabilities, where {\Omega}gw (f) is the GW energy density per logarithmic frequency interval in units of the closure density. Our result is the first nonintegrated limit to bridge the gap between the LIGO band (around 100 Hz) and the Cassini band (10-6 - 10-4 Hz).Comment: 4 pages, 5 figure

BIOMECHANICAL STUDY ON DIFFERENT DIRECTIONS FOR RUNNING JUMPS FOCUSED ON THE TAKEOFF PREPARATION

This study aimed to elucidate the difference in CG parameters from three steps, prejump to takeoff step of the jump motion (running jump), and obtain primary data on takeoff preparation action. Five male jumpers associated with the university track and field department were trained to perform their best at (1) approach run with no takeoff (RUN), (2) jumping as far as possible (long jump [LJ]), and (3) jumping as high as possible (high jump [HJ]), which were recorded using a three-dimensional capture system. As a result, significant differences were observed in not only the takeoff but also the takeoff preparation phase regarding CG parameters, suggesting the need to focus on the takeoff preparation phase as a factor that determines jump direction. Moreover, HJ and LJ suppressed an increase in vertical velocity one step prior, and by takeoff at a lower CG, the athletes allowed for an easier increase in takeoff angle and jump height. However, to resist a decrease in horizontal velocity, LJ transitioned to takeoff in a manner closer to RUN and without changing takeoff preparation as much as that in HJ. Thus, adjusting vertical velocity and height one step before takeoff can influence takeoff angle

On Detection of Black Hole Quasi-Normal Ringdowns: Detection Efficiency and Waveform Parameter Determination in Matched Filtering

Gravitational radiation from a slightly distorted black hole with ringdown waveform is well understood in general relativity. It provides a probe for direct observation of black holes and determination of their physical parameters, masses and angular momenta (Kerr parameters). For ringdown searches using data of gravitational wave detectors, matched filtering technique is useful. In this paper, we describe studies on problems in matched filtering analysis in realistic gravitational wave searches using observational data. Above all, we focus on template constructions, matches or signal-to-noise ratios (SNRs), detection probabilities for Galactic events, and accuracies in evaluation of waveform parameters or black hole hairs. We have performed matched filtering analysis for artificial ringdown signals which are generated with Monte-Carlo technique and injected into the TAMA300 observational data. It is shown that with TAMA300 sensitivity, the detection probability for Galactic ringdown events is about 50% for black holes of masses greater than $20 M_{\odot}$ with SNR $> 10$. The accuracies in waveform parameter estimations are found to be consistent with the template spacings, and resolutions for black hole masses and the Kerr parameters are evaluated as a few % and $\sim 40$, respectively. They can be improved up to $< 0.9$ and $< 24$ for events of ${\rm SNR} \ge 10$ by using fine-meshed template bank in the hierarchical search strategy.Comment: 10 pages, 10 figure