On the cavitation energy of water

Free-energy-perturbation theory from molecular dynamics calculations has been used to obtain the DeltaG of adjoining cavities' formation in water. The DeltaGs for systems with three, five and seven cavities are compared with that of a single cavity of the same volume, and found to be in good agreement. The conditions under which the analytical formulation of the energy of cavity formation proposed by Pierotti holds are discussed. The data for a single cavity have been tabulated and can lend themselves to a simple numerical implementation in standard quantum chemical packages, which can be used when high accuracy for DeltaG(cav) is required.     

Interface interactions in modulated phases,and upsilon points

Certain features in Frenkel-Kontorova and other models of phases with a one-dimensional modulation can be analyzed by assuming parallel interfaces separating sets of lattice planes belonging to two different phases, and treating the free energy to create interfaces, as well as the interaction of two, three, or more interfaces, as phenomenological parameters. A strategy employed by Fisher and Szpilka for interacting defects can be extended to the case of interfaces, allowing a systematic study of the phase diagram by ignoring all interface interactions, and then successively taking into account pair, triple, and higher-order terms. The possible phase diagrams which can occur near the point where =0 include: various sorts of endpoints analogous to critical endpoints, an accumulation point of first-order transitions and triple points, and a self-similar structure which we call an upsilon point, which turns out to be an accumulation point of an infinite number of segments of first-order transition lines, each of which terminates in two upsilon points.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Microstructural and physicochemical study of the buried Fe/AlGaAs(100) interface by transmission electron microscopy and x‐ray emission spectroscopy

Among the magnetic metal/semiconductor contacts, the Fe/GaAs system has been widely studied owing to its potential applications in electronic devices. In contrast, there are not many studies concerning the Fe/Al_xGa_1?xAs contact, and in particular there are no reports concerning the changes induced in the interfacial zone by the presence of Al. In this work, thin polycrystalline iron films were deposited by ion beam sputtering at room temperature on a 300 nm thick Al_0.25Ga_0.75As layer grown by molecular beam epitaxy onto GaAs(001). X‐ray diffraction analysis showed that the iron films are polycrystalline, and indications of a (002) texture of the film were observed. The fine scale analysis of the interface was achieved by high‐resolution transmission electron microscopy (HRTEM) observations, the results of which are compared with the physicochemical information obtained from electron‐induced x‐ray emission spectroscopy, by analysing the Al 3p valence states at the Fe/Al_xGa_1?xAs interface. The HRTEM experiments on cross‐section samples indicate that the interfacial zone between iron and AlGaAs is limited to <1.5 nm in thickness. X‐ray emission spectroscopy showed the presence of Al atoms in an FeAl‐like environment at the interface, and the existence of wrong bonds and point defects. The estimated width of the perturbed interface (2.0 ± 0.5 nm) is in agreement with the HRTEM results. Copyright © 2003 John Wiley & Sons, Ltd.     

Study on δ‐form complex in syndiotactic polystyrene–organic molecules systems. IV. Formation of complexes with a mixture of solvents and structural changes during the sorption of solvents by syndiotactic polystyrene mesophase membranes

The syndiotactic polystyrene (sPS) δ form was crystallized from mixtures with different compositions of p‐chlorotoluene–chlorobenzene (p‐CT–CB) and p‐chlorotoluene–1,1,2‐trichloroethane (p‐CT–TCE). The presence of the δ form and TTGG helical conformation was confirmed by Fourier transform infrared and wide‐angle X‐ray diffraction (WAXD) analyses. In sPS/p‐CT–CB and sPS/p‐CT–TCE δ‐form membranes, the relative absorbance (RA) of the p‐chlorotoluene (p‐CT) solvent peak was very high even at very low concentrations of p‐CT in comparison with the RA of higher concentrations of chlorobenzene (CB) or 1,1,2‐trichloroethane (TCE) in the mixtures. However, the RAs of both CB and TCE solvent peaks decreased with decreasing concentrations of CB and TCE in the mixtures. A negligible decrease in the RA of the TTGG helical content was observed with a decreasing concentration of CB or TCE. The WAXD results showed that the 2θ peak positions of the [010] and [ 10] planes of the sPS/p‐CT–CB and sPS/p‐CT–TCE δ‐form membranes appeared in the same position and were almost equal to those of the sPS–p‐CT δ‐form membrane. The mesophases of the sPS–p‐CT [p‐CT (A‐M)] and sPS–TCE [TCE (A‐M)] membranes were used for the sorption studies with different concentrations of various solvents. The sorption amount of aromatic solvents by both p‐CT (A‐M) and TCE (A‐M) mesophase membranes was higher than that of aliphatic solvents, regardless of the size, shape, and nature of the molecular cavity. The 2θ peak of the [010] plane of the sPS membranes slowly approached the original δ‐form value when the sPS mesophase membranes were immersed in various solvents of different concentrations for 48 h. The shifting of the 2θ peak of the [010] plane to the original δ form depended on the nature and concentration of the immersion solvents. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2380–2387, 2005     

Adsorption at liquid interfaces: The generalized Frumkin isotherm and interfacial structure

The thermodynamics of adsorption of amphiphilic surface-active compounds at the interface between two immiscible liquids is considered. At the interface, these molecules are supposed to replace a few of the adsorbed molecules of both solvents. Classical isotherms of adsorption (Frumkin, Frumkin-Damaskin, Langmuir, Henry) were based on the model of non-penetrable interface, where an adsorbate can substitute only molecules of one solvent. At the interface between two immiscible electrolytes, nonpolar oil/water interfaces, and liquid membranes amphiphilic molecules can substitute molecules of both solvent and classic isotherms cannot be used. The generalization of Frumkin isotherm for permeable and non-permeable interfaces, known as the Markin-Volkov isotherm, gives the possibility to analyze adsorption in a general case. The adsorption isotherms of pentafluorobenzoic acid at the octane/water interface at different pHs were measured by the drop-weight method. The thermodynamic parameters of pentafluorobenzoic acid (PFBA) adsorption at octane/water interface were determined. From the measurements of PFBA adsorption, the structure of the octane/water interface was determined. Substitution of one adsorbed octane molecule requires approximately three adsorbed PFBA molecules. This result shows that the orientation of solvent molecules at the interface is different from the bulk. Adsorbed octane molecules have a lateral orientation with respect to the interface. Gibbs free energy of adsorption equilibrium and thermodynamic parameters of PFBA adsorption show that the adsorption of PFBA at the octane/water interface is accompanied by a reduction in the attraction between adsorbed PFBA molecules as the pH decreases to the acidic region. Published in Russian in Elektrokhimiya, 2006, Vol. 42, No. 10, pp. 1194–1200. The text was submitted by the authors in English.     

PREPARATION OF PERFLUOROOCTANOYL-MODIFIED POLY(VINYL-ALCOHOL)S AND THEIR ADSORPTION AT AN AIR-WATER INTERFACE

Perfluorooctanoyl modified poly(vinyl alcohol)s (FPVA) were prepared by means of substituting a small amountof hydroxyl groups on the backbone of poly(vinyl alcohol), for which the initial degree of polymerization is equal to 1750.The substitution extent, defined by the number of substituting units in a chain, for the four FPVA samples was in the range of0.5-5 perfluorooctanoyl groups per chain. The FPVA samples with the highest substitution extent still had good solubility inwater. It was shown by experimental measurement at 30.0±0.1℃ that the surface tension of the aqueous solution of thehighest substituted FPVA decreased to 16.6 mN/In at a higher concentration, e.g about 0.1 g/mL. Obviously,macromolecules of FPVA exhibit a very strong tendency to adsorb at the air-water interface, because the hydrophobicperfluorooctanoyl groups in FPVA have a very high surface activity as they are in small molecular fluorinated surfactants.The chain conformation of such a model polymer adsorbed on the air-water interface was also discussed.     

Influence of the variable wall thickness of the sample tubes and a quartz Dewar on the EPR signal intensity in a single TE102 and double TE104 rectangular cavity

The response of a single TE₁₀₂ and double TE₁₀₄ rectangular cavity to the insertion of samples contained in tubes with variable wall thickness and a quartz Dewar into the cavity has been analyzed. A direct, indirect, and concurrent (positive or negative) “lens effect” inside the double TE₁₀₄ rectangular cavity is discussed. The experimental dependence of the EPR signal intensity on the wall thickness of the sample tube, δ, for the line-like samples with identical length of the sample material column, L=30 mm, recorded in the microwave cavity showed a directly proportional increase of the relative “lens effect” with the increase of the wall thickness of the tube in the interval, δ∈<0.1 mm, >0.5 mm. The insertion of the variable-temperature double-wall quartz Dewar (home-built, resonant frequency shift, ca. −300 MHz) into the single TE₁₀₂ rectangular cavity showed the same relative “lens effect”, with ca. 1.5-time increase of the EPR signal intensity, for a point-like sample and the line-like samples with material columns of diameter of 1 and 1.3 mm, and wall thickness of the sample tubes, δ∈<0.1 mm, >0.5 mm. The increased effect of the Dewar arises because the active volume of the quartz Dewar tube walls is always much more larger than the active volume of the sample tube wall. In the case of the double TE₁₀₄ rectangular cavity, the insertion of the quartz Dewar: (i) into the same cavity, in which the sample is present, caused a direct “lens effect”, with ca. 1.8-fold increase of the EPR signal intensity; however, (ii) into the complementary cavity, in which the sample is absent, caused an indirect “lens effect”, with ca. 0.6-fold decrease of the EPR signal intensity. With the Dewar and sample in one cavity and a large empty sample tube in the complementary cavity, a concurrent (positive or negative) “lens effect” can be observed. Thus, the possible increase/decrease of the EPR signal intensity depends on the volume ratio of the quartz Dewar tube walls and large sample tube wall inserted into the double TE₁₀₄ rectangular cavity. Each of the above phenomena may be a significant source error in quantitative EPR spectrometry unless the samples to be compared in the quantitative EPR analysis are contained in sample tubes having the same wall thickness and each EPR spectra should be recorded inside an identical quartz Dewar.     

腔长失调对光腔衰荡法测量精度的影响

 只考虑腔长失调因素下建立了反射率模拟测量的理论模型。根据高斯光束传输规律分析了腔长失调对衰荡腔模式耦合的影响，推导了腔长失调与谐振腔输出脉冲信号、衰荡信号与反射率之间的关系，模拟了腔长失调在±10mm范围内的光脉冲衰荡现象。结果表明：对于光敏面直径为0.2mm的高速探测器，为了保证10^-6的测量精度，腔长的失调量应控制在±1mm之间。在光路调节中采用具有对数变换功能的示波器和动态范围较大的探测器，可以提高测量精度。     

回旋速调管放大器输出腔的特性研究

 利用变截面波导的耦合模理论，根据输出腔中电场幅值分布函数所满足的微分方程组，编写了具有自动优化功能的计算程序，分析研究了不同渐变角度、考虑腔体损耗前后和输出腔与外电路失配时，谐振频率、腔体品质因数和高频场幅值沿轴分布的变化情况，为进一步研究高频场与电子注的互作用和输出腔奠定了基础。