Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces

We report the first atomistic simulation of two stacked nucleosome core particles (NCPs), with an aim to understand, in molecular detail, how they interact, the effect of salt concentration, and how different histone tails contribute to their interaction, with a special emphasis on the H4 tail, known to have the largest stabilizing effect on the NCP-NCP interaction. We do not observe specific K16-mediated interaction between the H4 tail and the H2A-H2B acidic patch, in contrast with the findings from crystallographic studies, but find that the stacking was stable even in the absence of this interaction. We perform simulations with the H4 tail (partially/completely) removed and find that the region between LYS-16 and LYS-20 of the H4 tail holds special importance in mediating the inter-NCP interaction. Performing similar tail-clipped simulations with the H3 tail removed, we compare the roles of the H3 and H4 tails in maintaining the stacking. We discuss the relevance of our simulation results to the bilayer and other liquid-crystalline phases exhibited by NCPs in vitro and, through an analysis of the histone-histone interface, identify the interactions that could possibly stabilize the inter-NCP interaction in these columnar mesophases. Through the mechanical disruption of the stacked nucleosome system using steered molecular dynamics, we quantify the strength of inter-NCP stacking in the presence and absence of salt. We disrupt the stacking at some specific sites of internucleosomal tail-DNA contact and perform a comparative quantification of the binding strengths of various tails in stabilizing the stacking. We also examine how hydrophobic interactions may contribute to the overall stability of the stacking and find a marked difference in the role of hydrophobic forces as compared with electrostatic forces in determining the stability of the stacked nucleosome system.

Effect of W addition on the electrical switching of VO2 thin films

Vanadium Oxide has been a frontrunner in the field of oxide electronics because of its metal-insulator transition (MIT). The interplay of different structures of VO2 has played a crucial role in deciding the magnitude of the first order MIT. Substitution doping has been found to introduce different polymorphs of VO2. Hence the role of substitution doping in stabilizing the competing phases of VO2 in the thin film form remains underexplored. Consequently there have been reports both discounting and approving such a stabilization of competing phases in VO2. It is reported in the literature that the bandwidth of the hysteresis and transition temperature of VO2 can be tuned by substitutional doping of VO2 with W. In this work, we have adopted a novel technique called, Ultrasonic Nebulized Spray Pyrolysis of Aqueous Combustion Mixture (UNSPACM) to deposit VO2 and W- doped VO2 as thin films. XRD and Raman spectroscopy were used to investigate the role of tungsten on the structure of VO2 thin films. Morphology of the thin films was found to be consisting of globular and porous nanoparticles of size similar to 20nm. Transition temperature decreased with the addition of W. We found that for 2.0 at % W doping in VO2, the transition temperature has reduced from 68 degrees C to 25 degrees C. It is noted that W-doping in the process of reducing the transition temperature, alters the local structure and also increases room temperature carrier concentration. (c) 2016 Author(s).

Effect of non-uniform magnetic field on crystal growth by floating-zone method in microgravity

The magnetic damping effect of the non-uniform magnetic field on the floating-zone crystal growth process in microgravity is studied by numerical simulation. The results show that the non-uniform magnetic field with designed configuration can effectively reduce the flow near the free surface and then in the melt zone. At the same time, the designed magnetic field can improve the impurity concentration non-uniformity along the solidification interface. The primary principles of the magnetic field configuration design are also discussed.

Effect of structural relaxation on deformation behaviour of Zr-based metallic glass

Structural relaxation through isothermal annealing at tempertature below glass transition is conducted on Zr46.75Ti8.25Cu7.5Ni10Be27.5 (Vitreloy-4) bulk metallic glass. Defect concentration is correlated with the annealing time t according to differential scanning calorimetry thermalgrams. The effects of structural relaxation on mechanical properties and deformation behaviour are investigated by using instrumented nanoindentation. It is found that as-cast alloy exhibits pronounced serration flow during the loading process of nanoindentation, and the size and number of serrations decrease with the annealing time. The change of the deformation behaviour with structural relaxation is explained using a free volume model.

The Effect of Periodic Segmentation Cracks on the Interfacial Debonding: Study on Interfacial Stresses

Hard coatings on relatively soft substrate always face the danger of debonding along the interface. Interfacial stresses are considered to be the initial driving force for the interfacial debonding of the relatively strong bonded coatings. Interfacial stresses due to the mismatch of strain between the coating and substrate are simulated with FEM firstly. The distribution of the interfacial stresses is achieved, which confirms an excessive stresses concentration near the interface end. Subsequently, the redistribution of interfacial stresses is calculated for a coating with periodic segmentation cracks. Results indicate that the distribution of interfacial stresses is altered greatly with the periodic segmentation cracks. To reveal the effect of the spacing of the periodic segmentation cracks on the distribution of interfacial stresses, different crack density is modeled within the coating. It is found that that the peak values of the interfacial stresses decrease with the increase of crack density, i.e. with reduction of spacing of segmentation cracks.

The effect of an insoluble surfactant on the skin friction of a bubble

In this paper, we develop a novel moving mesh method suitable for solving axisymmetric free-boundary problems, including the Marangoni effect induced by surfactant or temperature variation. This method employs a body-fitted grid system where the gas-liquid interface is one line of the grid system. We model the surfactant equation of state with a non-linear Langmuir law, and, for simplicity, we limit ourselves to the situation of an insoluble surfactant. We solve complicated dynamic boundary conditions accurately on the gas-liquid interface in the framework of finite-volume methods. Our method is used to study the effect of a surfactant on the skin friction of a bubble in a uniaxial flow. For the limiting case where the surface diffusivity is zero, the effect of a tangential stress generated by the surface tension gradient, allows us to explain a new phenomenon in high concentration regimes: larger surface tension, but also larger deformation. Furthermore, this condition leads to the formation of boundary layers and flow separation at high Reynolds numbers. The influence of these complex flow patterns is examined. © 2005 Elsevier SAS. All rights reserved.

The effect of straining mode on void growth

Large strain finite element method is employed to investigate the effect of straining mode on void growth. Axisymmetric cell model embedded with spherical void is controlled by constant triaxiality: loading,while plane-stress model containing a circular void is loaded by constant ratio of straining. Elastic-plastic material is used for the matrix in both cases. It is concluded that, besides the known effect of triaxiality, the straining mode which intensifies the plastic concentration around the void is also a void growth stimulator. Experimental results are cited to justify the computation results.

Studies of the Effect of a Coal Concentrator on NO Formation in Swirling Coal Combustion

To develop low-pollution burners, the effect of a coal concentrator on NO formation in swirling coal combustion is studied using both numerical simulation and experiments. The isothermal gas-particle two-phase velocities and particle concentration in a cold model of swirl burners with and without coal concentrators were measured using the phase Doppler particle anemometer (PDPA). A full two-fluid model of reacting gas-particle flows and coal combustion with an algebraic unified second-order moment (AUSM) turbulence-chemistry model for the turbulent reaction rate of NO formation are used to simulate swirling coal combustion and NO formation with different coal concentrators. The results give the turbulent kinetic energy, particle concentration, temperature and NO concentration in cases of with and without coal concentrators. The predicted results for cold two-phase flows are in good agreement with the PDPA measurement results, showing that the coal concentrator increases the turbulence and particle concentration in the recirculation zone. The combustion modeling results indicate that although the coal concentrator increases the turbulence and combustion temperature, but still can remarkably reduce the NO formation due to creating high coal concentration in the recirculation zone.

On the mechanism of void growth and the effect of straining mode in ductile materials

Finite element analysis is employed to investigate void growth embedded in elastic-plastic matrix material. Axisymmetric and plane stress conditions are considered. The simulation of void growth in a unit cell model is carried out over a wide range of triaxial tensile stressing or large plastic straining for various strain hardening materials to study the mechanism of void growth in ductile materials. Triaxial tension and large plastic strain encircling around the void are found to be of most importance for driving void growth. The straining mode of incremental loading which favors the necessary strain concentration around void for its growth can be characterized by the vanishing condition of a parameter called "the third invariant of generalized strain rate". Under this condition, it accentuates the internal strain concentration and the strain energy stored/dissipated within the material layer surrounding the void. Experimental results are cited to justify the effect of this loading parameter. (C) 2000 Elsevier Science Ltd. All rights reserved.

Toxic effect of Raphia vinifera on fish leech (Piscicola geometra)

This study examines acute toxicity of Raphia vinifera on fish leech, Piscicola geometra. The leeches with a mean total length of (TL) 4.2+1.0cm were exposed to various concentrations of both crude powdered and ethanolic extracts of the botanical. Median lethal concentration (LC50) was determined with static-renewal tests using logarithmic and arithmetic graphic methods. The LC50 (for 96 hours of crude powdered (aqueous) extracts of the botanical on Piscicola geometra was 1.10 ppm arithmetically and 1.14ppm logarithmically. The 95% confidence limits was 0.10ppm arithmetically and 0.12ppm logarithmically. The LC50 of ethanolic extract of the poison at 96-h was 0.5ppm arithmetically and 0.48ppm logarithmically. The 95% confidence limits were less than 0.10ppm. The use of extracts of R. vinifera in the control of leeches in fish ponds is discussed

Effect of cerium oxide on the precipitation of silver nanoparticles in femtosecond laser irradiated silicate glass

We investigated the effect of cerium oxide on the precipitation of Ag nanoparticles in silicate glass via a femtosecond laser irradiation and successive annealing. Absorption spectra show that Ce3+ ions may absorb part of the laser energy via multiphoton absorption and release free electrons, resulting in an increase of the concentration of Ag atoms and a decrease of the concentration of hole-trapped color centers, which influence precipitation of the Ag nanoparticles. In addition, we found that the formed Ag-0 may reduce Ce4+ ions to Ce3+ ions during the annealing process, which inhibits the growth of the Ag nanoparticles.

Study of the effect of alcohol on single human red blood cells using near-infrared laser tweezers Raman spectroscopy

The effect of alcohol solution on single human red blood Cells (RBCs) was investigated using near-infrared laser tweezers Raman spectroscopy (LTRS). In our system, a low-power diode laser at 785 nm was applied for the trapping of a living cell and the excitation of its Raman spectrum. Such a design could simultaneously reduce the photo-damage to the cell and suppress the interference from the fluorescence on the Raman signal. The denaturation process of single RBCs in 20% alcohol solution was investigated by detecting the time evolution of the Raman spectra at the single-cell level. The vitality of RBCs was characterized by the Raman band at 752 cm(-1), which corresponds to the porphyrin breathing mode. We found that the intensity of this band decreased by 34.1% over a period of 25 min after the administration of alcohol. In a further study of the dependence of denaturation on alcohol concentration, we discovered that the decrease in the intensity of the 752 cm(-1) band became more rapid and more prominent as the alcohol concentration increased. The present LTRS technique may have several potential applications in cell biology and medicine, including probing dynamic cellular processes at the single cell level and diagnosing cell disorders in real time. Copyright (c) 2005 John Wiley T Sons, Ltd.

Mössbauer effect investigations of the hyperfine interactions and relaxation phenomena in salts of thulium

Two new phenomena have been observed in Mössbauer spectra: a temperature-dependent shift of the center of gravity of the spectrum, and an asymmetric broadening of the spectrum peaks. Both phenomena were observed in thulium salts. In the temperature range 1˚K ≤ T ≤ 5˚K the observed shift has an approximate inverse temperature dependence. We explain this on the basis of a Van Vleck type of interaction between the magnetic moment of two nearly degenerate electronic levels and the magnetic moment of the nucleus. From the size of the shift we are able to deduce an “effective magnetic field” H = (6.0 ± 0.1) x 10⁶ Gauss, which is proportional to ‹r^-3›_M‹G|J|E› where ‹r^-3›_M is an effective magnetic radial integral for the 4f electrons and |G› and |E› are the lowest 4f electronic states in Tm Cl₃·6H₂O. From the temperature dependence of the shift we have derived a preliminary value of 1 cm^-1 for the splitting of these two states. The observed asymmetric line broadening is independent of temperature in the range 1˚K ≤ T ≤ 5˚K, but is dependent on the concentration of thulium ions in the crystal. We explain this broadening on the basis of spin-spin interactions between thulium ions. From size and concentration dependence of the broadening we are able to deduce a spin-spin relaxation time for Tm Cl₃·6H₂O of the order of 10^-11 sec.

Effect of bismuth oxide on the thermal stability and Judd-Ofelt parameters of Er 3(+)/Yb3(+) co-doped aluminophosphate glasses

The Er3+/Yb3+ co-doped glasses with compositions of xBi(2)O(3)-(65-x)P2O5-4Yb(2)O(3)-11Al(2)O(3)-5BaO-15Na(2)O (where x = 0, 2.5, 5, 7.5 and 10 mol%) were prepared using the normal melt quench technique. The optical absorption spectra of the glasses were recorded in the wavelength range 300-1700 nm. The effect of Bi2O3 content on the thermal stability and absorption spectra of glasses was investigated. In addition, the Judd-Ofelt parameters and oscillator strengths were calculated by employing Judd-Ofelt theory. It was observed that the positions of the fundamental absorption edge and cut-off wavelength shifted towards red as the content of Bi2O3 increased. However, there were no red shifts found both in the peak wavelength and in the center of mass wavelength of all absorption bands with Bi2O3 content increasing. The results of Judd-Ofelt theory analysis showed that Judd-Ofelt parameters Omega(t), (t = 2, 4, 6) changed sharply when Bi2O3 concentration exceeded 5 mol%. The variation trends of experimental oscillator strength were similar with those of Judd-Ofelt parameters as function of Bi2O3 concentrations. Moreover, differential scanning calorimetry experiments showed that the increases of Bi2O3 content weakened the network structure and then lowered the thermal stability of the glasses. The spontaneous emission probability A(rad), branching ratio beta and the radiative lifetime tau(rad) were also calculated and analyzed. The stimulated emission cross-section of Er3+ was calculated according to the McCumber theory. It was found that the stimulated emission cross-section of Er3+ was monotonically increases with Bi2O3 content increasing. (C) 2006 Elsevier B.V. All rights reserved.

Effect of hydroxyl groups on nonradiative decay of Er3+: I-4(13/2)-> I-4(15/2) transition in zinc tellurite glasses

A series of zinc tellurite glasses of 75TeO(2)-20ZnO-(5-x)La2O3-xEr(2)O(3) (x=0.02, 0.05, and 0.1 mol%) with the different hydroxl groups were prepared by the conventional melt-quenching method. Infrared spectra were measured in order to estimate the exact content of OH- groups in samples. The observed increase of the fluorescence lifetime with the oxygen bubbling time has been related to the reduction in the OH- content concentration as evidenced by IR transmission spectra. Various nonradiative decay rates from I-4(13/2) of Er3+ with. the change of OH content were determined from the fluorescence lifetime and radiative decay rates were calculated on the basis of Judd-Ofelt theory. (c) 2005 Elsevier B.V. All rights reserved.