Residue-specific NH exchange rates studied by NMR diffusion experiments

We present a novel approach to the investigation of rapid (>2s(-1)) NH exchange rates in proteins, based on residue-specific diffusion measurements. (1)H, (15)N-DOSY-HSQC spectra are recorded in order to observe resolved amide proton signals for most residues of the protein. Human ubiquitin was used to demonstrate the proposed method. Exchange rates are derived directly from the decay data of the diffusion experiment by applying a model deduced from the assumption of a two-site exchange with water and the "pure" diffusion coefficients of water and protein. The "pure" diffusion coefficient of the protein is determined in an experiment with selective excitation of the amide protons in order to suppress the influence of magnetization transfer from water to amide protons on the decay data. For rapidly exchanging residues a comparison of our results with the exchange rates obtained in a MEXICO experiment showed good agreement. Molecular dynamics (MD) and quantum mechanical calculations were performed to find molecular parameters correlating with the exchangeability of the NH protons. The RMS fluctuations of the amide protons, obtained from the MD simulations, together with the NH coupling constants provide a bilinear model which shows a good correlation with the experimental NH exchange rates.     

Analysis of inelastic x-ray scattering spectra of low-temperature water

We analyze a set of high-resolution inelastic x-ray scattering (IXS) spectra from H2O measured at T=259, 273, and 294 K using two different phenomenological models. Model I, called the "dynamic cage model," combines the short time in-cage dynamics described by a generalized Enskog kinetic theory with a long-time cage relaxation dynamics described by an alpha relaxation. This model is appropriate for supercooled water where the cage effect is dominant and the existence of an alpha relaxation is evident from molecular-dynamics (MD) simulation data of extended simple point charge (SPC/E) model water. Model II is essentially a generalized hydrodynamic theory called the "three effective eigenmode theory" by de Schepper et al. 11. This model is appropriate for normal liquid water where the cage effect is less prominent and there is no evidence of the alpha relaxation from the MD data. We use the model I to analyze IXS data at T=259 K (supercooled water). We successfully extract the Debye-Waller factor, the cage relaxation time from the long-time dynamics, and the dispersion relation of high-frequency sound from the short time dynamics. We then use the model II to analyze IXS data at all three temperatures, from which we are able to extract the relaxation rate of the central mode and the damping of the sound mode as well as the dispersion relation for the high-frequency sound. It turns out that the dispersion relations extracted from the two models at their respective temperatures agree with each other giving the high-frequency sound speed of 2900+/-300 m/s. This is to be compared with a slightly higher value reported previously, 3200+/-320 m/s, by analyzing similar IXS data with a phenomenological-damped harmonic oscillator model 22. This latter model has traditionally been used exclusively for the analysis of inelastic scattering spectra of water. The k-dependent sound damping and central mode relaxation rate extracted from our model analyses are compared with the known values in the hydrodynamic limit.     

Water modeled signal removal and data quantification in localized MR spectroscopy using a time-scale postacquistion method

We have previously shown the continuous wavelet transform (CWT), a signal-processing tool, which is based upon an iterative algorithm using a lorentzian signal model, to be useful as a postacquisition water suppression technique. To further exploit this tool we show its usefulness in accurately quantifying the signal metabolites after water removal. However, due to the static field inhomogeneities, eddy currents, and "radiation damping," the water signal and the metabolites may no longer have a lorentzian lineshape. Therefore, another signal model must be used. As the CWT is a flexible method, we have developed a new algorithm using a gaussian model and found that it fits the signal components, especially the water resonance, better than the lorentzian model in most cases. A new framework, which uses the two models, is proposed. The framework iteratively extracts each resonance, starting by the water peak, from the raw signal and adjusts its envelope to both the lorentzian and the gaussian models. The model giving the best fit is selected. As a consequence, the small signals originating from metabolites when selecting, removing, and quantifying the dominant water resonance from the raw time domain signal are preserved and an accurate estimation of their concentrations is obtained. This is demonstrated by analyzing (1H) magnetic resonance spectroscopy unsuppressed water data collected from a phantom with known concentrations at two different field strengths and data collected from normal volunteers using two different localization methods.     

Coupled hydrodynamic-acoustic modeling of sound generated by impacting cylindrical water jets

A coupled hydrodynamic-acoustic model describing acoustic propagation in a fluid containing multiple bubbles is proposed and applied to simulate noise generated by impacting water jets. The total pressure is decomposed into a "hydrodynamic" part and an "acoustic" part and computed using different schemes. The hydrodynamic pressure field is calculated independently using a generalized hydrodynamic model, and the pressure variations serve as sources in the wave equation for the acoustic pressure. A numerical algorithm developed to calculate wave propagation in an irregular region is used to account for the existence of the cavities. Noise generated by the impact of two cylindrical water jets is predicted. The computed near-field pressure is compared with the experimental data.     

基于碰撞能量模型的非线性碰摩评估研究

提出了一种用于评估非线性碰摩的碰撞能量模型(IEM),根据模型特性可得出IEM指标η用于评估碰摩故障的严重程度或发生概率. 通过对在不同阻尼比ζ状态下IEM指标η随转速比Ω的响应变化趋势研究,给出了η随ζ和Ω的响应联合分布. 结合IEM模型特性提出了"敏感区域"的概念. 此区域概念的提出,不仅对于转子设备的操作运行具有较大的参考价值,对于转子系统的设计更有重要的指导意义. 关键词： 碰撞能量模型 碰摩 转子系统 故障诊断     

Theoretical and numerical approach to "magic angle" of stone skipping

We investigate the condition for the bounce of circular disks which obliquely impacts on the fluid surface. An experiment [C. Clanet, F. Hersen, and L. Bocquet, Nature (London) 427, 29 (2004)] revealed that there exists a "magic angle" of 20 degrees between a disk's face and water surface in which the condition of the lowest impact speed necessary for a bounce is minimized. We perform a three-dimensional simulation of the disk-water impact by means of the smoothed particle hydrodynamics. Furthermore, we analyze the impact with a model of the ordinary differential equation (ODE). Our simulation is in good agreement with the experiment. The analysis with the ODE model gives us a theoretical insight into the "magic angle" of stone skipping.     

High-temperature dynamic behavior in bulk liquid water: A molecular dynamics simulation study using the OPC and TIP4P-Ew potentials

Classical molecular dynamics simulations were performed to study the high-temperature (above 300 K) dynamic behavior of bulk water, specifically the behavior of the diffusion coefficient, hydrogen bond, and nearest-neighbor lifetimes. Two water potentials were compared: the recently proposed “globally optimal” point charge (OPC) model and the well-known TIP4P-Ew model. By considering the Arrhenius plots of the computed inverse diffusion coefficient and rotational relaxation constants, a crossover from Vogel–Fulcher–Tammann behavior to a linear trend with increasing temperature was detected at T* ≈ 309 and T* ≈ 285 K for the OPC and TIP4P-Ew models, respectively. Experimentally, the crossover point was previously observed at T* ± 315–5 K. We also verified that for the coefficient of thermal expansion α _P (T, P), the isobaric α _P (T) curves cross at about the same T* as in the experiment. The lifetimes of water hydrogen bonds and of the nearest neighbors were evaluated and were found to cross near T*, where the lifetimes are about 1 ps. For T < T*, hydrogen bonds persist longer than nearest neighbors, suggesting that the hydrogen bonding network dominates the water structure at T < T*, whereas for T > T*, water behaves more like a simple liquid. The fact that T* falls within the biologically relevant temperature range is a strong motivation for further analysis of the phenomenon and its possible consequences for biomolecular systems.     

Improving spectroscopic line parameters by means of atmospheric spectra: Theory and example for water vapor and solar absorption spectra

Current atmospheric remote sensing experiments measuring high resolution spectra apply instruments of similar quality as the laboratory experiments that are especially equipped to derive spectroscopic parameters. We propose a method that uses high quality atmospheric spectra to improve the spectroscopic parameterization. It is an optimal estimation method that applies the uncertainty ranges given in current spectroscopic databases as a priori covariance and the residuals between the simulated and measured atmospheric spectra as new measurements. We test the method by updating the current HITRAN parameters of 49 mid-infrared water vapor lines (situated in 15 spectral windows between 795 and ) by the information present in high quality ground-based Fourier transform infra-red (FTIR) spectra. We show that the application of a speed dependent Voigt line shape model is important. The updated water vapor parameterization, compared to the original one, leads to lower residuals, larger measurement information content, and better agreement between remotely sensed and coincident in situ water vapor profiles. Using the new line parameterization, a state-of-the-art ground-based FTIR system is able to monitor upper tropospheric water vapor amounts and middle/upper tropospheric HDO/H₂O ratios.     

Analysis of a fully packed loop model arising in a magnetic Coulomb phase

The Coulomb phase of spin ice, and indeed the I(c) phase of water ice, naturally realize a fully packed two-color loop model in 3D. We present a detailed analysis of the statistics of these loops: we find loops spanning the system multiple times hosting a finite fraction of all sites while the average loop length remains finite. We contrast the behavior with an analogous 2D model. We connect this body of results to properties of polymers, percolation and insights from Schramm-Loewner evolution processes. We also study another extended degree of freedom, called worms, which appear as "Dirac strings" in spin ice. We discuss implications of these results for the efficiency of numerical cluster algorithms, and address implications for the ordering properties of a broader class of magnetic systems, e.g., with Heisenberg spins, such as CsNiCrF(6) or ZnCr(2)O(4).     

Retention capacity of random surfaces

We introduce a "water retention" model for liquids captured on a random surface with open boundaries and investigate the model for both continuous and discrete surface heights 0,1,…,n-1 on a square lattice with a square boundary. The model is found to have several intriguing features, including a nonmonotonic dependence of the retention on the number of levels: for many n, the retention is counterintuitively greater than that of an (n+1)-level system. The behavior is explained using percolation theory, by mapping it to a 2-level system with variable probability. Results in one dimension are also found.     

Sequences in neural networks with temporal association

We solve the dynamics of the strongly diluted version of a model recently proposed by Herz et al. to store sequences of patterns with spatio-temporal retrieval properties. We analyze the spurious sequence solutions and we find the region in the (,T) plane where the only relevant attractors are the learnt cycles.     

A reaction–diffusion model for market fluctuations – A relation between price change and traded volumes

Two decades ago Bak et al. (1997) [3] proposed a reaction–diffusion model to describe market fluctuations. In the model buyers and sellers diffuse from opposite ends of a 1D interval that represents a price range. Trades occur when buyers and sellers meet. We show analytically and numerically that the model well reproduces the square-root relation between traded volumes and price changes that is observed in real-life markets. The result is remarkable as this relation has commonly been explained in terms of more elaborate trader strategies. We furthermore explain why the square-root relation is robust under model modifications and we show how real-life bond market data exhibit the square-root relation.     

Multiscale model of gradient evolution in turbulent flows

A multiscale model for the evolution of the velocity gradient tensor in turbulence is proposed. The model couples "restricted Euler" (RE) dynamics describing gradient self-stretching with a cascade model allowing energy exchange between scales. We show that inclusion of the cascade process is sufficient to regularize the finite-time singularity of the RE dynamics. Also, the model retains geometrical features of real turbulence such as preferential alignments of vorticity and joint statistics of gradient tensor invariants. Furthermore, gradient fluctuations are non-Gaussian, skewed in the longitudinal case, and derivative flatness coefficients are in good agreement with experimental data.     

The temperature dependence of the resistive response of superconducting Pb films upon picosecond optical excitation

We report a study of the temperature dependence of the transient resistivity of superconducting Pb thin films excited by short duration (70 ps) laser pulses of varying irradiances. The results are analyzed in terms of a model proposed by Elesin which features the existence of a nonstationary, inhomogeneous, intermediate state.     

Nitrate removal from groundwater using Amberlite IRN-78: Modelling the system

A laboratory study was conducted to investigate the ability of Amberlite IRN-78 ion-exchange resin for the removal of nitrate from different waters. Aim of the present study is to propose a simple model that simulates the equilibrium data for this ion-exchange system.Tests were performed using two synthetic waters and two groundwaters. In the case of synthetic water, experimental data are reported for the ion-exchange equilibria determination in the absence or presence of chloride. For both groundwater types, “Salvatierra city” and “Miajadas city”, an ion-exchange Langmuir-type model is proposed, taking into account the presence of other competitive anions in solution, specifically chloride, sulphate and bicarbonate. Although the model is very simple, it is consistent with the experimental results. Finally, a general Langmuir-type expression is proposed for all water types, synthetic or natural. This equation considers the presence of other anions in solution by means of the parameter C_0T.     

Ionic composition of a humid air plasma under ionizing radiation

A kinetic model is proposed for ion–molecular processes involving charged particles of a humid air plasma produced by a fast electron beam. The model includes more than 600 processes involving electrons and 41 positive and 14 negative ions, including hydrated ions H₃O⁺ (H₂O) _n and O ₂ ^? (H₂O) _n with n = 1, 2, …, 12. The energy costs of production of electron–ion pairs and electronic and vibrational (for water molecules, also rotational) excitation of molecules are calculated in nitrogen, oxygen, water vapor, air, and humid air. A method is proposed for calculating the energy costs in mixtures by the calculation data in pure gases. The evolution of the plasma composition is studied by the numerical solution of a system of 56 time-dependent balance equations for the number of charged particles of plasma by the fourth-order Runge–Kutta method. The steady-state composition of plasma is determined by solving nonlinear steady-state balance equations for the ionization rates of humid air from 10 to 10¹⁶ cm^–3/s and the fraction of water molecules from 10^–3% to 1.5%. It is established that, for water vapor content (the ratio of the number density of water molecules to the total number density of air molecules) of 0.015–1.5% in air at atmospheric pressure and room temperature, the main ion species are two types of positive ions H₃O⁺ (H₂O) _n with the number of water molecules n = 5, 6 and three species of negative ions O ₂ ^? (H₂O) _n with n = 5, 8, 9.     

基于水样类型识别的光谱COD测量方法

基于紫外吸收光谱的COD测量方法,尽管具有快速、实时、免试剂、无污染等优势。但该方法对于组分多变的水样适应性不强,构建的单一计算模型不能适用于所有待测水样类型,导致其在复杂环境下测量准确度较低,从而限制了其应用领域。本研究提出一种基于水样类型识别的测量方法。其过程包括:动态识别水样类型→自动选择相应的"吸光度(Auv)-COD"算法模型→计算COD。该方法有效提高了紫外光谱法COD测量的准确度和适用性。该研究在传统的光谱识别技术的基础上,针对COD实际测量的特点加以改进。选取水样吸光度曲线的形貌特征作为水样类型的表征参数,利用LM-BP神经网络作为识别算法。并引入了"历史数据队列"、"历史识别因子"的概念,在此基础上形成了级联的神经网络结构。该算法实现了COD测量应用中的高准确度的光谱识别,进而提高了复杂环境下COD测量的精度。大量实验测试和结果表明,与传统的光谱识别技术相比,该方法在COD测量应用中具有更好的鲁棒性和准确性。水样类型识别准确率达98%以上。同时算法结构简单,计算量小,适用于资源受限的小型化COD测量仪。当仪器在复杂多变的水环境中进行测量时,采用该算法测量得到的COD精度有显著的提高。该方法的提出为光谱COD测量法在水体组分多变场合的应用及提高其测量精度提供了技术保证,可望解决传统紫外光谱COD测量法难以适应变化和复杂水环境应用的问题。