Coarse-grained polyethylene: Including cross terms in bonded interactions and introducing anisotropy into the model for the orthorhombic crystal

Our previous paper (E.A. Zubova, I.A. Strelnikov, N.K. Balabaev, A.V. Savin, M.A. Mazo, and L.I. Manevich, Polym. Sci., Ser. A 59 (1) (2017)) addressed the simplest coarse-grained model of polyethylene and alkanes. The CH₂ group in this united-atom model is replaced with a bead. In the framework of the model, nonbonded interactions are described by the Lennard-Jones potential (6–12), whereas the potential for bonded interactions accounts for the bonds between beads and for coarse grained angles and dihedral angles but not for the cross terms between them. We found the area of geometrical parameters of the model where all the three known crystalline phases of polyethylene are stable at low temperatures. We parametrized the force field of the model using the dynamic properties of the system, namely, the inelastic neutron scattering spectrum of the orthorhombic phase of polyethylene. However, the simplest model underestimates the value of the elastic modulus along the chains of the crystal by a factor of two. The derived setting angle of the molecules also differs appreciably from the experimental data. Moreover, the acoustic dispersion curves for the modes with the wave vector directed along the chain axis deviate from the experimental data at low frequencies. In the present study, we included the cross terms into the bonded interactions. This made it possible to reproduce the experimental elastic modulus along the chains of the crystal and to decrease the frequency range for the optical skeletal dispersion curve to proper values. As for the beads, we separated force centers for the bonded and nonbonded interactions, which enabled us to reproduce the optical skeletal curve and to bring the anisotropy of interchain interactions in line with the experiment. However, the model fails to reproduce the balance of interactions between the neighboring chains in the crystal. For this, a different form of the potential energy of van der Waals interactions seems to be needed.     

1,8-二巯基芘分子电学特性的理论研究

Based on the first principle,electrical properties of a molecular junction consisting of pyrene-1,8-dithiol molecule and gold surface have been investigated. The cluster of three gold atoms is used to simulate the gold surface. Density functional theory is employed to obtain the electronic structures of the molecule and the extended molecule. Then the frontier orbital theory and the perturbation theory are used to determine the interaction energy between the molecule and the gold surface quantitatively. The elastic Green function method is applied to study the current-voltage properties of the molecular junction. Numerical results show that the sulfur atoms can be chemically absorbed on the gold surface and the bonding between the molecule and gold is mainly covalent-typed. The fermienergy of the extended molecular system lies between the HOMO and the LUMO and closer to the HOMO of the system. When the external applied bias is lower than 1 V,there is a current gap for the molecular junction. With the increasing of the bias,the conductance of the junction exhibits plateaus. These electrical properties are closely related with the electronic structures of the molecular junction. The extended molecular orbits have great contribution to the charge transport. Localized molecular orbits give little contribution to the current while charge transport is taken place by tunneling.     

Adhesion of Pseudomonas putida NCIB 9816-4 to a naphthalene-contaminated soil

The effect of a soil contaminant on the initial adhesion to the soil of a contaminant-degrading soil microorganism in the exponential phase was investigated using naphthalene as the soil contaminant and Pseudomonas putida strain NCIB 9816-4 as the naphthalene-degrading bacteria. P. putida strain DK-1, which is not capable of degrading naphthalene, was used as a control. P. putida NCIB 9816-4 in the exponential phase showed the more adhesion to the soil than that in the stationary phase. In contrast, P. putida DK-1 showed the increased adhesion to the soil when it was in the stationary phase. P. putida NCIB 9816-4 in the exponential phase showed the preferred adhesion to the naphthalene-contaminated soil, whereas the adhesion of P. putida DK-1 was not affected by naphthalene. From the data of surface hydrophobicities of the cells and the soil, the microbial adhesion, especially the initial adhesion to the naphthalene-contaminated soil, takes place through the hydrophobic interaction. We suspect that the surface hydrophobicity of P. putida NCIB 9816-4 in the exponential phase might be increased during the uptake of naphthalene, which caused the preferred adhesion to the naphthalene-contaminated soil.     

Theoretical conformational analysis of the methylamide of N-acetyl-L-alanyl-L-prolyl-L-alanine. II

Summary 1. Spatial forms of Ac-L-Ala-L-Pro-L-Ala-NHMe with trans peptide bonds are the most preferred. Elongation of the peptide chain promotes the stabilization of the trans configuration of the tertiary amide group.2. In the structure of the compound investigated, the dominating role is played by the interaction of the neighboring residues.3. Of the six types of conformations of X-Pro-Y observed in proteins, the first four belong to the preferred forms of the Ac-L-Ala-L-Pro-L-Ala-NHMe molecule.M. M. Shemyakin Institute of Bioorganic Chemistry, Academy of Science of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 626–630, September–October, 1975.     

Numerical analysis of relaxation times of multiple quantum coherences in the system with a large number of spins

We study the decay of multiple quantum (MQ) NMR coherences in systems with the large number of equivalent spins. As being created on the preparation period of the MQ NMR experiment, they decay due to the dipole-dipole interactions (DDI) on the evolution period of this experiment. It is shown that the relaxation time decreases with the increase in MQ coherence order (according to the known results) and in the number of spins. We also consider the modified preparation period of the MQ NMR experiment [G. A. Alvarez and D. Suter, Phys. Rev. Lett. 104, 230403 (2010)] concatenating the short evolution periods under the secular DDI Hamiltonian (the perturbation) with the evolution period under the nonsecular averaged two-spin/two-quantum Hamiltonian. The influence of the perturbation on the decoherence rate is investigated for the systems consisting of 200-600 equivalent spins.     

脉冲激光溅射下固液界面生长的碳纳米管及其机理初探

以脉冲激光束直接溅射浸在水中的单质碳样品，发现在固液界而也能产生碳纳米管．实验还发现碳纳米管的形成与样品的结构有密切的关联：石墨的层状结构越完整，碳纳米管的形成越容易，而且石墨层而相对于激光束的取向也会显著地影响碳纳米管的生成．通过对实验结果的分析，探讨了激光液相溅射产生碳纳米管的机理，认为激光溅射产生的碳蒸气被水束缚在固液的界而内，而完整的晶而使碳蒸气在界而内的分布具有准二维的性质，为碳纳米管的生长提供了较为理想的环境．     

Surface tension of the Widom-Rowlinson model

We consider the computation of the surface tension of the fluid-fluid interface for the Widom-Rowlinson [J. Chem. Phys. 52, 1670 (1970)] binary mixture from direct simulation of the inhomogeneous system. We make use of the standard mechanical route, in which the surface tension follows from the computation of the normal and tangential components of the pressure tensor of the system. In addition to the usual approach, which involves simulations of the inhomogeneous system in the canonical ensemble, we also consider the computation of the surface tension in an ensemble where the pressure perpendicular (normal) to the planar interface is kept fixed. Both approaches are seen to provide consistent values of the interfacial tension. The issue of the system-size dependence of the surface tension is addressed. In addition, simulations of the fluid-fluid coexistence properties of the mixture are performed in the semigrand canonical ensemble. Our results are compared with existing data of the Widom-Rowlinson mixture and are also examined in the light of the vapor-liquid equilibrium of the thermodynamically equivalent one-component penetrable sphere model.     

高分子链在球内表面上的吸附/排空转变

应用自洽场理论(SCFT)研究了受限于球内的高分子溶液的结构,重点关注高分子链在受限壁附近的行为.根据自洽场理论数值计算结果,讨论了球半径、高分子与球限制壁的相互作用、高分子平均浓度等因素对球内高分子浓度分布的影响.从高分子浓度分布和吸附/排空层厚度可以发现,在一定的条件下,受限的高分子在受限壁上会发生吸附/排空转变.吸附/排空转变与受限球大小、高分子链长和平均浓度,以及高分子链与受限壁之间相互作用都有关系.理论预测发生吸附/排空转变时的高分子与球限制壁的临界相互作用参数与链长的倒数成线性关系,且斜率与球半径有关.限制球越小,要发生吸附/排空转变,需要高分子与球之间有更大的临界吸引能.     

Calibration methods for microdialysis sampling in vivo: muscle and adipose tissue

Calibration methods for microdialysis sampling were studied in the muscle and adipose tissue of rats. Both the delivery method and the no-net-flux method were used to determine the extraction efficiency (EE) of acetaminophen and caffeine in both tissues. There was no concentration dependence of the EE either in vitro or in vivo for either acetaminophen or caffeine. The EEs determined by the delivery and no-net-flux methods were not different. However, the EEs of both caffeine and acetaminophen determined in vitro were significantly higher than those determined in the muscle and adipose. This indicates that mass transfer in the tissue is the rate-determining factor for the EE in vivo. The relative difference between the EE in vitro and the EE in the muscle was smaller than the difference between the EE in vitro and the EE in the adipose. In addition, the EE in the muscle decreased more than the EE in the adipose after the animal was euthanized. This indicated that exchange between the extracellular fluid and plasma is the rate-determining step in mass transport relative to microdialysis sampling. This has a more significant effect on the EE in the muscle than the EE in the adipose. Both the delivery and no-net-flux methods can be used to calibrate microdialysis probes in the muscle and adipose.     

The three-wire model and Lichtenecker’s equation for calculations of the conductivity of ion-exchange columns

The approaches to the evaluation of the conductivity of ion-exchange columns are analyzed. Specifically, the three-wire model and Lichtenecker’s power equation are examined. The problem of how the coefficient of ion-exchange column filling and the parameter characterizing the state of conducting phases with respect to the current flow are related to the parameters involved in the equations of the three-wire model is treated theoretically. The common points and the coincident portions of the functions obtained in each of the approaches and some discrepancies between the functions are found. The discrepancies are determined by the special features of the models under consideration. Original Russian Text ? N.P. Gnusin, N.P. Berezina, N.A. Kononenko, O.A. Demina, L.A. Annikova, 2009, published in Zhurnal Fizicheskoi Khimii, 2009, Vol. 83, No. 1, pp. 122–126.     

Investigation of the reliability of piezoelectric chemical sensors

The aim of the research was to study the functional change of sensitivity, selectivity and overall stability of piezoelectric chemical sensors. A test device was built and experiments have been carried out to estimate the degradation of the piezoelectric sensor performance. Sensing materials were inspected by a scanning electron microscope (SEM) to investigate the surface structures. Strong correlation was found between the reliability and the quality of the sensing material surface. The surface formation depended upon the physical and chemical properties of the sensing materials. Both the electrostatic and structural features influenced the interactions between the sensor surface and the analytes. Interactions during the adsorption and desorption of volatile compounds could not only be estimated by the van der Waals interactions. The contact area of interactions, where the secondary chemical forces play a significant role, was determined by the surface structure and the molecular structure of the sensing material. Polarity and different surface formation were found to be the most important factors to improve the discrimination capability of piezoelectric chemical sensors. The same investigations were repeated after 3 months. The most remarkable comparison was the appearance of the SEM images. A relationship was also recognized between the elapsed time and the degradation of the selectivity of the detectors. The method developed can be used to estimate the applicability of a piezoelectric chemical sensor.     

Contact angle hysteresis of microbead suspensions

Microbead suspensions are often used in microfluidic devices for transporting biomolecules. An experimental investigation on the wettability of microbead suspension is presented in this study. The variation in the surface tension and the equilibrium contact angle with the change in the volume fraction of the microbead is presented here. The surface tension of the microbead suspension is measured with the pendant drop technique, whereas the dynamic contact angle measurements, i.e., advancing and receding contact angles, are measured with the sessile drop technique. An equilibrium contact angle of a suspension with particular volume fraction is determined by computing an average over the measured advancing and receding contact angles. It is observed that the surface tension and the equilibrium contact angle determined from advancing and receding contact angles vary with the magnitude of the microbeads volume fraction in the suspension. A decrease in the surface tension with an increase in the volume fraction of the microbead suspension is observed. The advancement and the recession in contact line for dynamic contact angle measurements are achieved with the motorized dosing mechanism. For microbead suspensions, the advancement of the contact line is faster as compared to the recession of the contact line for the same flow rate. The presence of microbeads assists in the advancement and the recession of the contact line of the suspension. A decrease in the equilibrium contact angles with an increase in the microbead suspension volume fraction is observed. Inclusion of microbeads in the suspension increases the wetting capability for the considered combination of the microbead suspension and substrate. Finally, empirical correlations for the surface tension and the contact angle of the suspension as a function of microbead volume fraction are proposed. Such correlations can readily be used to develop mechanistic models for the capillary transport of microbead suspensions related to LOC applications.     

Complex conductivity of water-saturated packs of glass beads

The low-frequency conductivity response of water-saturated packs of glass beads reflects a combination of two processes. One process corresponds to the polarization of the mineral/water interface coating the surface of the grains. The other process corresponds to the Maxwell-Wagner polarization associated with accumulation of the electrical charges in the pore space of the composite medium. A model of low-frequency conductivity dispersion is proposed. This model is connected to a triple-layer model of electrochemical processes occurring at the surface of silica. This model accounts for the partition of the counterions between the Stern and the diffuse layers. The polarization of the mineral/water interface is modeled by the electrochemical polarization model of Schurr for a spherical grain. We take into account also the DC surface conductivity contribution of protons of the sorbed water and the contribution of the diffuse layer. At the scale of a macroscopic representative elementary volume of the porous material, the electrochemical polarization of a single grain is convoluted with the grain size distribution of the porous material. Finally, the Maxwell-Wagner polarization is modeled using the complex conductivity of a granular porous medium obtained from the differential effective medium theory. The predictions of this model agree well with experimental data of spectral induced polarization. Two peaks are observed at low frequencies in the spectrum of the phase. The first peak corresponds to the distribution of the size of the beads and the second peak is due to the roughness of the grains.     

Äquidensitometrie: Eine Methode zur Beurteilung der Struktur von Plasmen—Qualitative Beurteilung des Lanthan-Gleichstrombogens durch Äquidensitometrie von monochromatischen Bogenphotographien

A new method has been developed for the experimental characterization of d.c. arc plasmas. The method consists of the combination of the spectral photography of d.c. arc plasmas with a slitless, stigmatic plane-grating spectrograph and the characterization of the photographs with the aid of photographic equidensitometry. The principles of the method are described. The method is used for the investigation of a lanthanum d.c. arc plasma. The qualitative results of the measurements of the axial distributions of the light emission and lanthanum and calcium particle concentrations in the arc are discussed. The limitations and shortcomings of the method are pointed out.     

Calculations of the distribution of trace impurities in cylindrical pores

The equilibrium distribution of a trace impurity and the self-diffusion coefficients of molecules of the base component and the trace impurity in narrow cylindrical pores were calculated using the lattice-gas model. Two types of lattice structures with six and eight closest neighbors were considered. The sizes of the base component and impurity molecules were taken to be identical. Lateral interactions were taken into account in the quasi-chemical approximation. The equilibrium distributions of the trace impurity across a pore section in the gas and liquid phases of the base component and at the interface for the case of capillary condensation were considered. The probability of existence of isolated dimeric clusters was estimated and the self-diffusion coefficients of the base component and trace impurity for a single-phase distribution of the base component were calculated. The effects of the energy of interaction of impurities with the pore walls and the concentration of the base component on the diffusion mobility of the impurities were analyzed. The concentration dependences of the partition coefficient for the trace impurity between the pore center and the pore wall and the concentration dependences of the self-diffusion coefficients for the trace impurity molecules become nonmonotonic with an increase in the base component concentration. These effects are due to the displacement of the impurity from the near-surface area to the bulk of a pore following an increase in the pore coverage by the base component and to higher mobility of the impurity in the free bulk of the pore. Further filling of the pore bulk reduces the mobility of all molecules. The energetics of intermolecular interactions also plays a certain role. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 605–615, April, 2000.     

Radiation effects on the immiscible polymer blend of nylon1010 and high-impact polystyrene (HIPS) I: Gel/dose curves,mathematical expectation theorem and thermal behaviour

This paper studies the radiation properties of the immiscible blend of nylon1010 and HIPS. The gel fraction increased with increasing radiation dose. The network was found mostly in nylon1010, the networks were also found in both nylon1010 and HIPS when the dose reaches 0.85 MGy or more. We used the Charleby–Pinner equation and the modified Zhang–Sun-Qian equation to simulate the relationship with the dose and the sol fraction. The latter equation fits well with these polymer blends and the relationship used by it showed better linearity than the one by the Charleby–Pinner equation. We also studied the conditions of formation of the network by the mathematical expectation theorem for the binary system. Thermal properties of polymer blend were observed by DSC curves. The crystallization temperature decreases with increasing dose because the cross-linking reaction inhibited the crystallization procession and destroyed the crystals. The melting temperature also reduced with increasing radiation dose. The dual melting peak gradually shifted to single peak and the high melting peak disappeared at high radiation dose. However, the radiation-induced crystallization was observed by the heat of fusion increasing at low radiation dose. On the other hand, the crystal will be damaged by radiation. A similar conclusion may be drawn by the DSC traces when the polymer blends were crystallized. When the radiation dose increases, the heat of fusion reduces dramatically and so does the heat of crystallization.     

Particle deposition and layer formation at the crossflow microfiltration

A microscopic model of the layer formation and the cake growth at the crossflow microfiltration will be introduced. The model considers the hydrodynamic, adhesive and friction forces acting on a single particle during the filtration process. It can be shown that mainly the balance between the lift force and the drag force of the filtrate flow determines the layer formation at the membrane. Particle attachment to the layer is mostly an irreversible process. This is due to the large influence of the adhesive forces. The irreversibility of particle attachment was proved by experiments with monodisperse particles. The introduced model allows the prediction of the instationary crossflow filtration processes. The filtration rate and structure of the formed layer can be calculated. In the case of a filtration at constant transmembrane pressure the model calculation shows a good correspondence to the experimental results.     

A push/pull surface-mode liquid-crystal shutter: Technology and applications

The construction, operating principles and electro-optics of a surface-mode liquid-crystal shutter are reviewed. The shutter is composed of two glass plates, the inner surfaces of which are coated with a transparent electrically conductive layer. The substrates are treated to induce parallel director alignment. Polarizers are placed on the front and back of the cell oriented at right angles to each other and at 45° to the director. In the surface mode of operation a sustaining voltage is applied to the cell. This causes the director in the centre of the cell always to be oriented parallel to the electric field. The amplitude of the applied voltage determines the thickness of the surface layer-the layer in which the director orientation varies from parallel to the surface to parallel to the electric field. Light travelling through the cell will encounter retardation only in the surface layers. Hence the voltage controls the retardation of the cell, and by that means the polarization state of the light travelling through the cell. By adjusting the voltage so that the retardation is changed from 0λ to ½λ the shutter can switch from open to closed. It is possible to construct a faster-switching shutter. This so-called push/pull shutter is composed of three elements in optical series. The first two are surface-mode cells oriented such that their directors are perpendicular. The third element is a quarter-wave plate with its axes parallel to the directors. The three elements are placed between orthogonal polarizers, with the directors oriented at 45° to the polarizers axes. The closed state of the shutter is obtained by placing one shutter in the high-voltage 0λ state and the other in the low-voltage ¼λ state. The open state of the shutter is obtained by switching the voltage levels applied to the two cells. The operating principles and the electro-optics of this device are discussed in detail.     

The effect of spacer length on the polymerization of diacetylenes in sams on gold surfaces

The influence of the molecular architecture of diacetylene disulfides on the structure and polymerizability of self assembled monolayers on gold was investigated. The position of the diacetylene group was varied systematically by adjusting the length of the tail and the spacer. For the structures studied, the longer the tail, the higher the akyl chain crystallinity as sensed by IR spectroscopy, and the higher the polymerization efficiency as probed by resonance Raman spectroscopy. The influence of the spacer on the polymerizability is more complicated. It is conjectured that the spacer reduces the lattice strain due to the misfit of the arrangement of the anchor groups and the arrangement of the diacetylene units and the polydiacetylene backbone, respectively. Simple modeling reveals that the number of the methylene units (odd or even) and the overall length both influence the arrangement. The highest polymerization efficiency is found for the longest, odd numbered spacer.     

Dissecting the photocycle of the bacteriorhodopsin E204Q mutant from kinetic multichannel difference spectra. Extension of the method of singular value decomposition with self-modeling to five components.

Kinetic multichannel difference spectroscopy in the visible spectral range of the Glu204 --> Gln(E204Q) site-directed mutant of bacteriorhodopsin revealed five spectrally distinct metastable intermediates, as for the wild type. Due to the perturbation of the extracellular proton release cluster, the late O intermediate accumulates in much higher amounts in this mutant, and the photocycle is not complicated by the pH-dependent branching observed in the wild type protein. This mutant is therefore more amenable than the wild type to the determination of the intermediate spectra with the method of singular value decomposition with self-modeling, developed recently for three components (Zimányi et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 4408-4413, 4414-4419). The method provides the most reliable spectra so far, defining the time evolution of the intermediates essential to the determination of the reaction scheme that describes the photocycle. The analysis confirms published results on this mutant by and large, but revises the locations of the L intermediates in the photocycle. In addition, it allows identification of the pH-dependent transitions of the photocycle, and offers an alternative mechanism for the pH dependence of the yield and kinetics of the late O intermediate.