Derivation of extremely slow dynamics of protein motion based on entropy invariance

It is a mysterious fact that protein systems often show an extremely slow dynamics of their molecular motions with time scales much longer than nanosecond order, although their characteristic frequencies obtained by the normal mode analysis fall in much shorter temporal regions. This Letter provides a heuristic account for why and how such extremely slow modes of protein motions naturally emerge from fast molecular modes on the basis of an idea of entropy invariance in the principal component analysis.     

飞行器大攻角复杂流动的POD和DMD对比分析

基于非结构/混合网格、耗散自适应2阶混合格式以及脱体涡模拟（detached eddy simulation,DES）方法开展了现代战斗机模型复杂分离流动的数值模拟,并与有限的平均气动力试验数据进行了对比,结果表明计算具有合理性,在此基础上进一步应用本征正交分解（proper orthogonal decomposition,POD）和动力学模态分解（dynamic mode decomposition,DMD）方法对数值模拟流场的非定常特性进行了对比分析.研究表明飞行器背风区流场由一对边条涡的螺旋运动主导,旋涡破裂前在横向空间截面上流场是中性稳定的,同时主涡核的运动是多频耦合的.POD和DMD的对比分析则表明:两者模态配对的方式不同,但主要模态之间具有一定相关性;POD模态中包含多种频率的运动,而且能量较集中于主模态,流场重构效率更高;DMD则将流场的主要特征运动提取为一些单频模态的组合,同时能够给出模态的稳定性.      

Vibrationally resolved photoabsorption spectroscopy of red fluorescent protein chromophore anions

Photoabsorption studies of red fluorescent protein chromophore anions have been performed at the ELISA electrostatic heavy-ion storage ring. The broad absorption band due to electronic excitation of the chromophores is tuned to a longer wavelength (redshifted) by extending the electronic conjugation of the molecule. A clear vibrational progression is resolved with E(vib) approximately 380 and 520 cm(-1) for two different forms of the chromophore. The vibrational modes correspond to collective motions of the entire molecular structure. It is argued that the excited electronic state has an equilibrium configuration far from that of the electronic ground state, i.e., poor Franck Condon overlap.     

The effect of spin on the non-linear resonant motions of a dynamical system

The motions of a two degree of freedom mechanical oscillator in a state of internal resonance due to the non-linear coupling between its modes are analyzed by the method of multiple scales. The system is connected by a motor to a vertical shaft driven at a constant spin rate relative to inertial space. It is shown that the non-linear resonance phenomenon can effectively be controlled by properly changing the spin rate of the motor. In addition, the transition curves that separate the non-linear resonant and the non-resonant motions of the system are also determined analytically by a straightforward perturbation method. The analytical expression for the transition curves is used in connection with the multiple scale analysis to yield a refined approximation for the main characteristics of the non-linear resonant motion.     

Infrared spectra of the superionic conductors Na,K, Rb,Ag and Ti β-aluminates

A detailed analysis of the infrared reflectivity spectra of the superionic conductors X β-aluminates (X = Na, K, Ag, Rb and Tl) is presented. A Kramers-Kronig analysis and the oscillator fits to the data have yielded the frequencies of the transverse optic and associated longitudinal optic modes. A model which ignores the coupling between the spinel blocks accounts for the number of observed infrared modes as well as the Raman modes. It is shown that even for the modes characteristic of the motions of the disordered X-ions, the wave vector selection rule is still valid. The results are discussed with the available theoretical calculations.     

Experimental study of coupled vibration in a finite periodic dual-layered structure with transverse connection

The analytical equations of the transfer matrix method are further derived for the multi-coupled vibration of flexural and longitudinal waves in a periodic dual-layered beam structure with connection branches, with full consideration given to the flexural and longitudinal motions that are tri-coupled at each connection. Measurements of mobilities at the junctions on the uni-layered beam and the cross-layered beam are made. The numerical results agree well with the experimental results at all frequencies from 10 to 2000 Hz, which verifies the theoretical methodology for the multi-coupled vibration in a finite dual-layered beam. The cross-layer energy transmission is calculated, which reveals that the transmitted longitudinal energy is enhanced not only at the longitudinal resonant modes but also at the flexural resonant modes of the connection branches due to the structural wave coupling. The flexural energy is excited by wave coupling and becomes stronger at the longitudinal resonant modes and the flexural resonant modes of the connection branches. The cross-layer vibration motions from coupled waves in the branches can be effectively controlled by the attached cantilevers with mass at the resonance modes. This method can be used to control the structure-borne sound transmission in multi-layer beam structures.     

Contribution of quantum molecular flexibility to the second virial coefficient of water vapor

The contribution of essentially quantum internal molecular motions to the second virial coefficient B2 of water vapor is analyzed in the framework of the path integral approach. A general purpose ab initio polarizable force field QMPFF2 or a nonpolarizable three-site water model are used with oscillator and Morse valence potentials. It is demonstrated that the contribution may be significant but depends strongly on the form of the intramolecular potential. In the case of the more realistic stretching Morse potential, inclusion of quantum molecular flexibility into the simulation reduces the virial coefficient by 20%-40%. Also, the internal modes make a contribution to the difference in the virial coefficient for light and heavy water, which is opposite to that of the intermolecular motions, so that the net effect can even change the sign at higher temperatures.     

Analysis of magnetization instability patterns in spin-transfer nano-oscillators

The stability of large precessional magnetization motions induced by spin-polarized currents in spin-transfer nano-oscillators is discussed. Quantitative analytical predictions are obtained for the critical values of spin-polarized injected current and external magnetic field at which the oscillator magnetization precession becomes unstable. It is shown that the mechanism leading to instability is parametric resonance of well-defined pairs of magnetostatically coupled perturbation modes. The amplitude of these modes grows to large non-thermal values when the oscillator frequency matches the mean of the natural frequencies of the two coupled modes. Analytical predictions are obtained for the space-time structure and symmetry of the magnetization patterns that are formed at the instability. Analytical results are compared with numerical simulations of spin-transfer-driven magnetization dynamics.     

Dispersion and excitation of waves in a model of artery: effect of surrounding tissues

The dispersion relations, involving attenuation parameters, are given for the lowest modes of propagation in a model of artery consisting of a cylindrical, elastic, thin-walled tube filled with a Newtonian viscous liquid and placed in a medium showing elastic stiffness and internal damping. The amplitudes of the modes generated by the most plausible physiological motions are calculated as functions of the surrounding parameters. Some modes neglected in the existing analyses are shown to be excited with rather high amplitudes that may have important physiological consequences.     

Collective nature of the boson peak and universal transboson dynamics of glasses

Using probe molecules with resonant nuclei and nuclear inelastic scattering, we are able to measure the density of states exclusively for collective motions with a correlation length of more than approximately 20 A. Such spectra exhibit an excess of low-energy modes (boson peak). This peak behaves in the same way as that observed by conventional methods. This shows that a significant part of the modes constituting the boson peak is of collective character. At energies above the boson peak, the reduced density of states of the collective motions universally exhibits an exponential decrease.     

Excitation of linearly stable waves in a multispecies plasma

Excitation of electrostatic modes as a result of the injection of an argon beam into a multispecies plasma is investigated. It is shown that the injection of a warm artificial beam into a thermal plasma may excite waves of significant amplitude with a range of phase velocities which are linearly stable. These waves appear as a result of the correlation between motions of an individual particle in a Vlasov fluid. When the free energy is derived from a warm beam and the linear instability diminishes due to the large temperature of the beam, the competing mechanism of thermal fluctuations is responsible for the main excitation of waves. This mechanism is valid for the various modes in a multispecies plasma with a higher enhancement at the lower hybrid than at the ion-ion hybrid modes     

Transient vibration phenomena in deep mine hoisting cables. Part 2: Numerical simulation of the dynamic response

A simulation model is presented which investigates the dynamic response of a deep mine hoisting cable system during a winding cycle. The response, namely the lateral motions of the catenary cable and the longitudinal motion of the vertical rope with conveyance is observed on the fast time scale, and the slow time scale is introduced to monitor the variation of slowly varying parameters of the system. The cable equivalent proportional damping parameters, and periodic excitation functions resulting from the cross-over cable motion on the winder drum are identified. Subsequently, the model is solved numerically using parameters of a double-drum multi-rope system. Since the system eigenvalues are widely spread and the problem is of stiff nature, the numerical simulation is conducted using a stiff solver. The results of the simulation demonstrate various transient non-linear resonance phenomena arising in the system during the wind. The nominal ascending cycle simulation results reveal adverse dynamic behaviour of the catenary largely due to the autoparametric interactions between the in- and out-of-plane modes. Principal parametric resonances of the lateral modes also occur, and conditions for autoparametric interactions between the lateral and longitudinal modes arise. Additionally, a transition through a number of primary longitudinal resonances takes place during the wind. The adverse dynamic motions in the system promote large oscillations in the cable tension which must be considered significant with respect to fatigue of the cable. It is noted that a small change in the winding velocity may cause large changes in the dynamic response due to the resonance region shifts. Consequently, the resonance modal interactions can be avoided, to a large extent, if the winding velocity is increased to an appropriate level.     

Frequency response of sloshing in an annular cylindrical tank subjected to pitching excitation

Frequency responses of stable planar and rotary motions in a partially filled annular cylindrical tank, subjected to a pitching excitation at a frequency in the neighborhood of the lowest resonant frequency, are investigated. The nonlinearity of the liquid surface oscillation and the nonlinear coupling between the dominant modes and other modes (e.g., an axisymmetric mode) are considered in the response analysis of the sloshing motion. The basic equations of the liquid motion are derived by using the variational principle and the nonlinear equations of motion of the liquid surface displacement are formulated. The characteristics of the liquid motion in an annular cylindrical tank are discussed. The equations governing the amplitude of the stable planar and rotary liquid motions are derived and the stability of each motion is analyzed. An experiment was carried out using a model tank. It is shown that the nonlinear characteristic of the liquid motion in an annular cylindrical tank is more complicated than that in a circular cylindrical tank. Furthermore, it is shown that the nonlinear analysis is important for estimating the sloshing responses.     

Transition term method for the analysis of the reflected and the transmitted acoustic signals from water-saturated porous plates

Ultrasound reflection (R) and transmission (T) from an immersed porous plate of QF-20 (a registered trademark of Filtros, Ferro Corporation) are investigated. Assuming open pores boundary conditions for the theoretical computations, values of the physical constants given by Johnson et al. [D. L. Johnson, D. L. Hemmick, and H. Kojima J. Appl. Phys. 76(1), 115-125 (1994)] are used at first. Comparisons of R and T with experimental results show a discrepancy. It is then assumed that visco-elastic losses exist inside the solid part. When a small imaginary constant part is considered for the bulk moduli, a better fit is obtained between theoretical and experimental values of /R/ and /T/. However, the numerous and very close peaks prevent easy measures of the resonance amplitudes and widths. The transition terms built up from the linear combinations R-T and R+T allow these peaks to be separated. Comparisons between theory and experiments are made. This work validates, in the frequency range where the agreement is good, a method for the location of the symmetrical and antisymmetrical modes of the plate. A discrimination is also possible between modes resulting from the fluid phase motions and from the solid phase motions.     

Disturbances of Rotational Motions for String Models of Hadrons and the Stability Problem

Slight disturbances of a classical rotational motion (uniform rotation of a system) are considered for a relativistic string with massive ends and for the q-q-q and Y baryon string models. It is shown that for a string with massive ends this motion is stable in the linear approximation and the slight perturbations are representable by a series each term of which describes a standing wave of certain frequency. These modes make it possible to simulate various excited states of hadrons. At the same time, for the q-q-q and Y baryon string models the instability of rotational motions has been proved: exponentially growing modes have been detected in their perturbation spectra.     

Majorana Representation and Mean Field Approach for Interacting-Boson System

The Majorana representation, which represents a quantum state by stars on the Bloch sphere, provides us an intuitive tool to study the quantum evolution in high dimensional Hilbert space. In this work, we investigate the second quantized model and the mean-field model for the interacting-boson system in the Majorana representation. It is shown that the motions of states in the two models are same in the linear case. Furthermore, the contribution of the nonlinear interaction to the star motions in the second quantized model can be expressed by a single star part which is equal to the nonlinear part of the equation for the star in mean-field model under large boson number limit and an extra part caused by the correlation between stars. These differences and relations can not only be reflected by the population differences between the two boson modes in the two models, but also lie with the differences between the continuous changes of the second quantized evolution with the nonlinear interacting strength and the critical behavior of the mean-field evolution which related to the self-trapping effect. The reason of the difference between the two models is also discussed by an effective Hamiltonian.     

Some solutions of the equations of motion of the relativistic string with massive ends

The classical theory is discussed for the relativistic string with point masses at its ends. The dynamical equations are solved for the class of motions of this system when the time evolution parameter τ is the proper time of both massive string ends. In this case the solution of the boundary equations is given by the almost periodic functions. Constraints on the normal modes resulting from the orthonormal gauge conditions differ essentially from the Virasoro ones. Incidentally one obtains an exact solution for the half-infinite string with mass at one end. It is also proved that the exact solution for the string with massive ends cannot be a periodic function.     

Economical evaluation of the vibration characteristics of rectangular structures with sloping roofs

The effect of conserving computer effort by reducing the impact of the normally high frequency motion associated with in-plane movements is investigated for rectangular structures with a range of shallow sloping roofs. In-plane motions are found experimentally to be insignificant for predominantly bending modes and, from the standpoint of economy, are better neglected prior to computation.