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DFT Calculations on the Effect of Solvation on the Tautomeric Reactions for wobble Gua-Thy and Canonical Gua-Cyt Base-Pairs

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Journal of Modern Physics 2013年第3期4卷 422-431页

作者： Kazuya Nomura Ryota Hoshino Eisuke Shimizu Yasuhiro Hoshiba Victor I. Danilov Noriyuki Kurita Department of Computer Science and Engineering Toyohashi University of Technology Toyohashi Japan Department of Molecular and Quantum Biophysics Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine

To elucidate the reaction mechanism from wobble Guanine-Thymine (wG-T) to tautomeric G-T base-pairs, we investigate its transition state (TS) by density functional theory (DFT) calculations, in vacuum and in water approximated by continuum solvation model. From the comparison of these results, we attempt to elucidate the effect of solvation on the tautomeric reaction for wG-T. In addition, the same DFT calculations are performed for the canonical G-C base-pair, in order to reveal the difference in the activation energy for the reactions involving wG-T and G-C. The obtained TS structures between wG-T and G*-T/G-T* (asterisk is an enol-form of base) are almost the same in vacuum and in water. However, the activation energy is 16.6 and 19.1 kcal/mol in vacuum and in water, respectively, indicating that the effect of solvation enlarges the energy barrier for the reactions from wG-T to G-T*/G*-T. The activation energy for the tautomeric reaction from G-C to G*-C* is also evaluated to be 15.8 and 12.9 kcal/mol in vacuum and in water, respectively. Therefore, it is expected that the tautomeric reaction from wG-T to G*-T/G-T* can occur in vacuum with a similar probability as that from G-C to G*-C*. We furthermore investigate the TS structure for wG-BrU to reveal the effect of the BrU introduction into wG-T. The activation energy is 14.5 and 16.7 kcal/mol in vacuum and in water, respectively. Accordingly, the BrU introduction is found to increase the probability of the tautomeric reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G bases is accelerated by the introduction of wG-BrU base-pair.

关键词： DFT wobble Base Pair Base Pair Tautomerization Transition State Activation Energy Solvation

论瞬时轴线垂直度、平均回转轴线垂直度与wobble的关系

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中国惯性技术学报 2002年第1期10卷 55-59页

作者：任顺清陈世杰李玉华哈尔滨工业大学哈尔滨150001

用姿态变换的方法推导了平均轴线垂直度、瞬时轴线垂直度和倾角回转误差(wobble)三者之间的关系,从而得出了瞬时轴线垂直度和平均回转轴线垂直度的数据处理方法。

关键词：垂直度姿态变换瞬时轴线平均回转轴线倾角回转误差惯导测试设备 wobble

Linearization of the Liouville Equation, Multiple Splits of the Chandler Frequency, Markowitz wobbles, and Error Analysis

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International Journal of Geosciences 2012年第5期3卷 930-951页

作者： Cheh Pan Pan Filter Technology Saratoga USA

The rotation of the physical Earth is far more complex than the rotation of a biaxial or slightly triaxial rigid body can represent. The linearization of the Liouville equation via the Munk and MacDonal perturbation scheme has oversimplified polar excitation physics. A more conventional linearization of the Liouville equation as the generalized equation of motion for free rotation of the physical Earth reveals: 1) The reference frame is most essential, which needs to be unique and physically located in the Earth;2) Physical angular momentum perturbation arises from motion and mass redistribution to appear as relative angular momentum in a rotating Earth, which excites polar motion and length of day variations;3) At polar excitation, the direction of the rotation axis in space does not change besides nutation and precession around the invariant angular momentum axis, while the principal axes shift responding only to mass redistribution;4) Two inertia changes appear simultaneously at polar excitation;one is due to mass redistribution, and the other arises from the axial near-symmetry of the perturbed Earth;5) The Earth at polar excitation becomes slightly triaxial and axially near-symmetrical even it was originally biaxial;6) At polar excitation, the rotation of a non-rigid Earth becomes unstable;7) The instantaneous figure axis or mean excitation axis around which the rotation axis physically wobbles is not a principal axis;8) In addition to amplitude excitation, the Chandler wobble possesses also multiple frequency-splits and is slow damping;9) Secular polar drift is after the products of inertia and always associated with the Chandler wobble;both belong to polar motion;10) The Earth will reach its stable rotation only after its rotation axis, major principal axis, and instantaneous figure axis or mean excitation axis are all completely aligned with each other to arrive at the minimum energy configuration of the system;11) The observation of the multiple splits of t

关键词： Liouville Equation Polar Motion Chandler wobble Markowitz wobble Error Analysis

The transfer RNA genes in Oryza sativa ***

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Science China(Life Sciences) 2002年第5期45卷 504-511页

作者：王希胤史晓黎郝柏林 College of Life Science Peking University Beijing China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing China Department of Mathematics and Physics Hebei Institute of Science and Technology Tangshan China The T-life Research Center Fudan University Shanghai China

The availability of the draft genome sequence of Oryza sativa L. ssp. indica has made it possible to study the rice tRNA genes. A total of 596 tRNA genes, including 3 selenocysteine tRNA genes and one suppressor tRNA gene are identified in 127551 rice contigs. There are 45 species of tRNA genes and the revised wobble hypothesis proposed by Guthrie and Abelson is perfectly obeyed. The relationship between codon usage and the number of corresponding tRNA genes is discussed. Redundancy may exist in the present list of tRNA genes and novel ones may be found in the future. A set of 33 tRNA genes is discovered in the complete chloroplast genome of Oryza sativa L. ssp. indica. These tRNA genes are identical to those in ssp. japonica identified by us independently from the origional annotation.

关键词： tRNA gene, wobble hypothesis, codon usage, pseudo-tRNA gene, Oryza sativa, chloroplast.

Clearance angle and evolution of depth of cut in actuated disc cutting

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Journal of Rock Mechanics and Geotechnical Engineering 2019年第3期11卷 644-658页

作者： Sevda Dehkhoda Bryce Hill CSIRO Minerals Resources Queensland Centre for Advanced Technologies

This paper investigates the effect of cutter clearance angle on variation of depth of cut and cutting process with an actuated disc cutting(ADC).ADC is a cyclic cutting method with two main characteristics:(i)a disk-shape cutter is used to attack the rock in an undercutting mechanism;and(ii)the cutter is dynamically actuated as it is moved across the ***,the cutting process of such system is periodic,each recurrence known as actuation *** first ADC model,developed in 2016,represented an idealization of the technology with a flat disc cutter,where no clearance angle was *** evolution of the contact between the disc and the rock was,therefore,computed only on horizontal x-y plane,ignoring the effect of normal component of the force acting on *** article reports on a study that incorporates the cutter inclination angle in derivation of cutter/rock interface *** extends the proposed kinematic and geometry based model to take into account the variable depth of cut in estimating the forces associated with cutting in one actuation *** were conducted using wobble to test the predictions of the improved model at various operating *** model predictions are matched with the experimental results and effects of various factors are analysed.

关键词： Actuated disc cutting Undercutting Force model wobble Hard rock cutting

International tidal gravity reference values at Wuhan station

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Science China Earth Sciences 2000年第1期43卷 77-83页

作者：许厚泽孙和平徐建桥陶国祥 Laboratory of Dynamic Geodesy Institute of Geodesy and Geophysics Chinese Academy of Sciences Wuhan 430077 China

The international tidal gravity reference values at Wuhan station are determined accurately based on the comprehensive analysis of the tidal gravity observations obtained from 8 instruments. By comparing these with those in the tidal models given by Dehant (1997) while considering simultaneously (i) the global satellite altimeters tidal data, and (ii) the Schwiderski global tidal data and the local ones along the coast of China, it is found that the average discrepancy of the amplitude factors and of the phase differences for four main waves are given as 5.2% and 3.6% and as 0.16?and 0.08?respectively. They are improved evidently compared to those determined in early stage, indicating the important procedures in improving the Wuhan international tidal gravity reference values when including the long-series observations obtained with a superconducting gravimeter, and when considering the influence of the ocean loading and of the nearly daily free wobble of the Earth’s core.

关键词： international tidal gravity reference values observations with superconducting gravimeter influence of the ocean tides and of the nearly daily free wobble of the Earth’s core.

Predictive performance of'Diprifusor'TCI system in patients during upper abdominal surgery under propofol/fentanyl anesthesia

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2005年第1期6卷 43-48页

作者：李玉红徐建红杨建军田婕徐建国 Department of Anesthesiology.First Affiliated Hospital School of Medicine Zhejiang UniversityHangzhou310003China Department of Anesthesiology Nanjing Jinling HospitalNanjing210002China Department of Anesthesiology Nanjing Jinlin HospitalNanjing210002China

Objective:To evaluate the predictive performance of‘Diprifusor’TCI(target-controlled infusion)system for its betterapplication in clinical ***:The predictive performance of a‘Diprifusor’TCI system was investigated in 27Chinese patients(16 males and 11 females)during upper abdominal surgery under total intravenous anesthesia(TIVA)withpropofol/*** arterial propofol concentrations were compared with the values predicted by the TCI infusion *** was determined by the median performance error(MDPE),the median absolute performance error(MDAPE),thedivergence(the percentage change of the absolute PE with time),and the wobble(the median absolute deviation of each PE fromthe MDPE).Results:The median(range)values of 14.9%(-21.6%～42.9%)for MDPE,23.3%(6.9%～62.5%)for MDAPE,-1.9%h^(-1)(-32.7%～23.0% h^(-1))for divergence,and 18.9%(4.2%～59.6%)for wobble were obtained from 227 samples from all *** the studied population,the PE did not increase with time but with increasing target propofol concentration,particularly fol-lowing ***:The control of depth of anaesthesia was good in all patients undergoing upper abdominal surgicaloperation and the predictive performance of the‘Diprifusor’target controlled mthsion system was considered acceptable forclinical *** the relatively bigger wobble showed that the pharmacokinetic model is not so suitable and requires im-provement.

关键词： Target-controlled infusion(TCI) ‘Diprifusor’TC1 system Predictive performance assessment wobble Infusion