Functional modes of proteins are among the most robust

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result should prove helpful in the context of several applications proposed recently, like for solving difficult molecular replacement problems or for fitting atomic structures into low-resolution electron density maps. It may also pave the way for the development of methods allowing us to predict such motions accurately.     

Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase

High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.     

Conformational dynamics of photoexcited conjugated molecules

Time-dependent photoexcitation and optical spectroscopy of pi-conjugated molecules is described using a new method for the simulation of excited state molecular dynamics in extended molecular systems with sizes up to hundreds of atoms. Applications are made to poly(p-phenylene vinylene) oligomers. Our analysis shows self-trapping of excitations on about six repeat units in the course of photoexcitation relaxation, identifies specific slow (torsion) and fast (bond-stretch) nuclear motions strongly coupled to the electronic degrees of freedom, and predicts spectroscopic signatures of molecular conformations.     

Analysis of magnetic resonance line shape under slow molecular motions

A new approach is considered to the analysis of the magnetic resonance line shape under slow molecular motions. The essence of the approach consists in calculating the coefficientsa _n in the Taylor expansion G(t). A straightforward procedure has been developed for calculating the coefficientsa _n for molecular motions described by random Markov processes.Translated from Izvestiya Vysshikh Uchebnyh Zavedenii, Fizika, No. 7, pp. 48–52, July, 1982.     

Dynamical molecular disorder and diffuse scattering in an alkane/urea incommensurate inclusion compound

The diffraction pattern of n-alkane/urea inclusion compounds is known to contain a broad diffuse scattering related to the molecular form factor of the alkane species, indicating individual rotational and/or translational disorder of these molecules. Inelastic coherent neutron scattering reveals for the first time the entirely dynamical character of the alkane molecular disorder around room temperature. This observation fully agrees with a recent model of the coherent scattering cross section of totally uncorrelated motions. In the ordered phase this diffuse scattering remains, but elastic, and very low energy molecular vibrational modes are evidenced. These observations are discussed in relation with previous incoherent neutron scattering results. Received 9 February 2001 and Received in final form 1st August 2001     

Highly noninstantaneous solitons in liquid-core photonic crystal fibers

The nonlinear propagation of pulses in liquid-filled photonic crystal fibers is considered. Because of the slow reorientational nonlinearity of some molecular liquids, the nonlinear modes propagating inside such structures can be approximated, for pulse durations much shorter than the molecular relaxation time, by temporally highly nonlocal solitons, analytical solutions of a linear Schr?dinger equation. The physical relevance of these novel solitons is discussed.     

Vibrational energy transfer in a protein molecule

Mode coupling in a protein molecule was studied by a molecular dynamics simulation of the intramolecular vibrational energy transfer in myoglobin at near zero temperature. It was found that the vibrational energy is transferred from a given normal mode to a very few number of selective normal modes. These modes are selected by the relation between their frequencies, like Fermi resonance, governed by the third order mode coupling term. It was also confirmed that the coupling coefficients had high correlation with how much the coupled modes geometrically overlapped with each other.     

Solution dynamics of the natural bioactive molecule capsaicin: a relaxation study

Nuclear magnetic resonance spectroscopy is a straightforward technique for studying molecular dynamics that range in timescale from picosecond (motions faster than molecular reorientation) to those that occur in real-time. This approach is important to highlight the behavior of bioactive molecules in solution, and to acquire information about action mechanisms and potential pharmacological effects. Proton and carbon-13 spin–lattice relaxation experiments were performed to calculate the reorientational correlation time for protonated carbons. Capsaicin showed complex dynamical properties and the results revealed two regions with different dynamical properties: the aliphatic region with fast reorientation motions and the aromatic region with slow motions.     

Thermodynamic evolution of antiphase boundaries in GaP/Si epilayers evidenced by advanced X-ray scattering

We have investigated quantitatively anti-phase domains (APD) structural properties in 20 nm GaP/Si epilayers grown by molecular beam epitaxy, using fast, robust and non-destructive analysis methods. These analyses, including atomic force microscopy and X-ray diffraction, are applied to samples grown by various molecular beam epitaxy growth modes. Roughness, lateral crystallite size of the epilayer, ratio of antiphase domains and their relationship are discussed. It is shown that both these analysis methods are useful to clarify the physical mechanisms occurring during the heterogeneous growth. Low temperature migration enhanced epitaxy is found to guarantee smoother surface than conventional molecular beam epitaxy. Effect of annealing temperature on antiphase boundaries (APBs) thermodynamics is discussed. The modification of the thermodynamic equilibrium through a thermal activation of APBs motion is expected to play an important role in the dynamic evolution of surfaces during thermal annealing and growth.     

Study of slow molecular motions in α-Crystallin by proton magnetic spin-lattice relaxation in the doubly rotating frame

Proton magnetic spin-lattice relaxation in the effective field H₂ acting in the doubly rotating frame (DRF) was first applied to the study of slow internal protein dynamics in the submillisecond range of correlation times in the solid state. In this method the local dipolar magnetic field is reduced by the magic-angle rotating-frame method so that the resonance frequency of the relaxation experiment may be set below the value of the local field. As a result, unachievable by the standard nuclear magnetic resonance (NMR) relaxation techniques, slow molecular motions become experimentally accessible. The second effective field H₂ is produced by the shallow sine-wave phase modulation of the H₁ pulse. The registration of the DRF spin-lattice relaxation signal takes place directly during the continuous H₁ pulse by means of an additional low-frequency radio-frequency coil oriented along the H₀ field and operating at the rotating-frame NMR frequency of 100 kHz. The measurements of the spin-lattice relaxation time in the DRF within a wide temperature range have been performed in dry and hydrated α-crystallin powders. This is the major protein in the eye lens, which prevents the uncontrolled aggregation of proteins and keeps the lens transparent. The results demonstrate that the protein hydration does not change the amplitude of slow side-chain motions but significantly shortens its correlation time: from about 50 to about 0.5 μs in dry and hydrated samples, respectively. The hydration also decreases the activation energy and restricts the distribution of the correlation times.     

Internal dynamics and hydration of solid proteins by1H NMR relaxation and FTIR spectroscopy

Temperature dependences of¹H nonselective nuclear magnetic resonanceT ₁ andT ₂ relaxation times measured at 27 MHz have been studied on solid human serum albumin (HSA) samples at various hydrations. The data were interpreted in terms of three kinds of internal motions in a protein and microdynamic parameters of the motions were obtained by a “model-free” approach. Two fast motions with correlation times lying in the range of tens to hundreds picoseconds were shown to be essentially insensitive to hydration. Unlike lysozyme and bovine albumin, HSA reveals relaxation transition due to slow motion in the room temperature range thus allowing one to obtain microdynamic parameters more precisely. Hydration leads to a shortening of the correlation time from hundreds to tens nanoseconds and to a less restricted movement. The comparison of the hydration dependence of relaxation parameters with infrared spectra of HSA side chain groups clearly shows that methyl protons are evidently involved in a slow motion, following the saturation of the protein globule surface by water. The same dependence correlating with solvent accessible surface areas was shown to exist for some other proteins. In addition to the main set of protons performing a solidlike movement, a small amount of much more mobile protons is also present with its proportion rising steeply with hydration and temperature. The origin of these protons is discussed.     

Protein dynamics on different timescales

Protein dynamics is studied on metmyoglobin by Mössbauer investigations with synchrotron radiation, conventional Mössbauer spectroscopy and incoherent neutron scattering. In the center of interest is the time sensitivity of mean square displacements, 〈x²〉 of special atoms in the protein molecule. Phonon assisted Mössbauer effect labels internal vibrations at the heme iron on a time scale from 6.5 fs to 0.65 ps. The incoherent neutron scattering yields quasi diffusive motions of side chain hydrogens on a time scale faster 100 ps. The quasi diffusive broad lines in the Mössbauer spectrum indicate slow motions of larger segments of the molecule between about 100 ns and 100 ps.     

Anharmonic effects of periodic molecular systems in the vibron model approximation

The vibron model approximation to take into account anharmonic effects in periodic systems is discussed. This is achieved by considering a simple one-dimensional molecular crystal with four degrees of freedom. In this case the lattice dynamical treatment is separated into two sets of modes, the modes associated to the molecular degrees of freedom and those corresponding to the motions of the centre of mass of the molecules. The non-interacting molecular modes are studied in detail, and analytical expressions for the energies and wave functions for the two-phonon manifold are obtained. A local-normal mode transition as a function of the interaction parameters is identified, similar to that in isolated molecular systems.     

Interaction of electronic structure and nuclear dynamics on the S1 reaction surface for the ring opening of cyclohexadiene

For the ultrafast photoinduced ring opening of cyclohexadiene the S₁ state plays a central role, providing the possibility to rapidly decay to the ground state. In this paper we follow the path of a wavepacket propagating in the reactive coordinate space of the S₁ surface. We present a detailed analysis of the corresponding electronic and nuclear motions. With the help of a projection method and a normal-mode analysis, the vibrational modes driving the reaction might be detected experimentally. Received: 10 November 1999 / Published online: 13 July 2000     

Low-frequency vibrational motions in proteins: Physical mechanisms and effect on functioning

A possibility for the low-frequency (terahertz) vibrational motions of large parts of protein molecules is considered and the characteristic frequencies are estimated. The problem of damping of these motions is discussed and the effect of solvent molecules on the model low-frequency molecular oscillators is experimentally studied using Raman spectroscopy. The data obtained show that the effect of solvent is not reduced to a decrease in the Q factor and causes variations in frequencies and relative amplitudes of the low-frequency oscillations.     

PVPh/PEO共混物动力学演化过程的NMR研究

聚合物共混物中链段的慢取向运动与其玻璃化转变行为和宏观力学性质密切关联,而基于化学位移各向异性重聚的~(13)C CODEX(centerband-only detection of exchange)固体核磁共振(SSNMR)技术能够有效表征共混物中链段的慢取向运动.该文利用~(13)C CODEX NMR技术详细研究了相容性聚合物共混物聚乙烯基苯酚/聚氧乙烯(PVPh/PEO)中的刚性组分PVPh在较宽温度范围内的慢取向运动特性与玻璃化转变过程的关联.研究表明,在玻璃化转变起始温度以下,PVPh主链的分子运动被冻结,而侧基存在b-松弛的慢取向运动;在玻璃化转变起始温度附近,PVPh主链具有明显的慢取向运动,而且主链和侧基是一种协同的分子运动.该文利用NMR技术揭示了共混物中的玻璃化转变起止温度分别对应于高分子主链慢取向运动CODEX信号的开始和极大值处的温度.     

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.     

Influence of sublayer atoms on Si(100) surface reconstructions

Influence of sublayer atoms on Si(100) surface reconstruction has been examined with density functional theory and molecular dynamic simulation. We found that the displacements of sublayer atoms under the buckled dimer affect the motions of their neighboring atoms and thus play an important role in determining the surface reconstructions. The present results reveal the relationship between the surface dimer reconstruction and the motion of the sublayer atoms and provide an account for experimental observations of Si(100) surface reconstructions at very low temperatures.     

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.