Confinement and viscoelastic effects on chain closure dynamics

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, t(c) similar to Nd-2, and that in case (b), t(c) similar to N-2/(2 (2H)), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t(c) similar to N-3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729041]

High-temperature kinetics of the reaction between CN and hydrocarbons using a novel high-enthalpy flow tube

More than 70 molecules of varied nature have been identified in the envelopes of carbon-rich stars through their spectral fingerprints in the microwave or far infrared regions. Many of them are carbon chain molecules and radicals, and a significant number are unique to the circumstellar medium. The determination of relevant laboratory kinetics data is critical to keep up with the development of the high spectral and spatial resolution observations and of the refinement of chemical models. Neutralneutral reactions of the CN radical with unsaturated hydrocarbons could be a dominant route in the formation of cyanopolyynes, even at low temperatures and deserve a detailed laboratory investigation. The approach we have developed aims to bridge the temperature gap between resistively heated flow tubes and shock tubes. The present kinetic measurements are obtained using a new reactor combining a high-enthalpy source with a flow tube and a pulsed laser photolysislaser-induced fluorescence system to probe the undergoing chemical reactions. The high-enthalpy flow tube has been used to measure the rate constant of the reaction of the CN radical with propane (C3H8), propene (C3H6), allene (C3H4), 1,3-butadiene (1,3-C4H6), and 1-butyne (C4H6) over a temperature range extending from 300 to 1200 K. All studied reactions of CN with unsaturated hydrocarbons are rapid, with rate coefficients greater than 10-10 cm3 center dot molecule-1 center dot s-1 and exhibit slight negative temperature dependence above room temperature. (c) 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 753766, 2012

Gas sensing response analysis of p-type porous chromium oxide thin films

The ethanol sensing properties of porous Cr2O3 thin films deposited by the ultrasonic nebulized spray pyrolysis of an aqueous combustion mixture is reported. The impact of the precursor selection and various deposition parameters on the film crystallinity, surface morphology and stoichiometry are studied using thermo-gravimetric analysis, X-ray diffraction, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy and atomic force microscopy techniques. The film morphology exhibits a highly porous nature, as a result of the exothermic combustion reaction during film deposition. The gas sensing properties of these films are investigated in the temperature range of 200-375 degrees C for ethanol. The films show two different regions of response for ethanol above and below 300 degrees C. A good relationship between the response and the ethanol concentration is observed, and is modeled using an empirical relation. The possible mechanism and the surface chemical reactions of ethanol over the chromium oxide surface are discussed.

Vertical electric field induced bacterial growth inactivation on amorphous carbon electrodes

The objective of the present work is to understand the vertical electric field stimulation of the bacterial cells, when grown on amorphous carbon substrates in vitro. In particular, the antibacterial activity against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli are studied using MTTassay, live/dead assay and inner membrane permeabilization assays. In our experiments, the carbon substrate acts as one electrode and the counter electrode is positioned outside the culture medium, thus suppressing the current, electrokinetic motions and chemical reactions. Guided by similar experiments conducted in our group on neuroblastoma cells, the present experimental results further establish the interdependence of field strength and exposure duration towards bacterial growth inactivation in vitro. Importantly, significant reduction in bacterial viability was recorded at the 2.5 V/cm electric field stimulation conditions, which does not reduce the neural cell viability to any significant extent on an identical substrate. Following electrical stimulation, the bacterial growth is significantly inhibited for S. aureus bacterial strain in an exposure time dependent manner. In summary, our experiments establish the effectiveness of the vertical electric field towards bacterial growth inactivation on amorphous carbon substrates, which is a cell type dependent phenomenon (Gram-positive vs. Gram-negative). (C) 2014 Elsevier Ltd. All rights reserved.

Ionic Bonding between Artificial Atoms

Conventional solids are prepared from building blocks that are conceptually no larger than a hundred atoms. While van der Waals and dipole-dipole interactions also influence the formation of these materials, stronger interactions, referred to as chemical bonds, play a more decisive role in determining the structures of most solids. Chemical bonds that hold such materials together are said to be ionic, covalent, metallic, dative, or otherwise a combination of these. Solids that utilize semiconductor nanocrystal quantum dots as building units have been demonstrated to exist; however, the interparticle forces in such materials are decidedly not chemical. Here we demonstrate the formation of charge transfer states in a binary quantum dot mixture. Charge is observed to reside in quantum confined states of one of the participating quantum dots. These interactions lead to materials that may be regarded as the nanoscale analog of an ionic solid. The process by which these materials form has interesting parallels to chemical reactions in conventional chemistry.

Rapid reduction of GO by hydrogen spill-over mechanism by in situ generated nanoparticles at room temperature and their catalytic performance towards 4-nitrophenol reduction and ethanol oxidation

Here, we report the clean and facile synthesis of Pt and Pd nanoparticles decorated on reduced graphene oxide (rGO) by the simultaneous reduction of graphene oxide (GO) and the metal ions in Mg/acid medium. As-generated Pt and Pd nanoparticles serve as a heterogeneous catalyst for the further reduction of the rGO by the hydrogen spill-over process. The C/O ratio is much higher as compared to the rGO obtained by the reduction of GO by only Mg/acid. Overall, the process is rapid, facile and green that does not require any toxic chemical agent or any rigorous chemical reactions. We perform the catalytic reduction of 4-nitophenol (4-NP) to 4-aminophenol (4-AP) at room temperature by Pd@rGO and Pt@rGO. The reduction is complete within 35 s for Pd@rGO and 60 s for Pt@rGO when 50 mu g of hybrid catalyst is used for 0.5 ml of 1 mM of 4-NP. In case of ethanol oxidation, the current density for Pd@rGO is comparable to commercial Pt/C but is doubled for Pt@rGO. Overall, both structures show highly stable catalytic activity compared to commercial Pt/C. (C) 2014 Elsevier B.V. All rights reserved.

Implication of a sigma-Methane Complex en Route to Elimination of Methane from a Ruthenium Complex: An Experimental and Theoretical Investigation

The five-coordinated 16-electron complex Ru(Me)(dppe)(2)]OTf] (3) undergoes methane elimination at room temperature to afford the ortho-metalated species (dppe){(C6H5)(C6H4)PCH2CH2P(C6H5)(2)}Ru]OTf] (7). Methane elimination, monitored using NMR spectroscopy, revealed no intermediate throughout the reaction. The NOE between Ru-Me protons and ortho phenyl protons and an agostic interaction trans to the methyl group were found in complex 3 by NMR spectroscopy, which form the basis for three plausible pathways for methane elimination and ortho metalation: pathway I (through spatial interaction), pathway II (through oxidative addition and reductive elimination), and pathway III (through agostic interaction). Methane elimination from complex 3 via pathway I was discounted, since it involves interactions through space and not through bonds. Moreover, the calculated energy barrier for the pathway I transition state was quite high (71.3 kcal/mol), which also indicates that this pathway is very unlikely. Furthermore, no spectroscopic evidence for oxidatively added seven-coordinated Ru(IV) species was found and the computed energy barrier of the transition state for pathway II was moderately high (41.1 kcal/mol), which suggests that this cannot be the right pathway for methane elimination and ortho-metalation of complex 3. On the other hand, indirect evidence in the form of chemical reactions point to the most plausible pathway for methane elimination, pathway III, via the intermediacy of a sigma-CH4 complex that could not be found spectroscopically. DFT calculations at several levels on this pathway showed an initial low-barrier rearrangement through TS1 to a square-pyramidal intermediate wherein methyl and agostic C-H are cis to each other. Migration of hydrogen from agostic C-H and elimination of methane proceed through the transition state TS2, which retains a weak metal-H bonding through most parts of the reaction coordinate. Upon comparison of all three pathways, pathway III was found to be the most likely for methane elimination and ortho-metalation of complex 3.

Effect of strain rate response and pin diameter on mechanically mixed layer formation and wear mechanisms in a Ti6Al4V-SS316L pair

Three mechanisms operate during wear of materials. These mechanisms include the Strain Rate Response (SRR - effect of strain rate on plastic deformation), Tribo-Chemical Reactions (TCR) and formation of Mechanically Mixed Layers (MML). The present work investigates the effect of these three in context of the formation of MML. For this wear experiments are done on a pin-on-disc machine using Ti64 as the pin and SS316L as the disc. It is seen that apart from the speed and load, which control the SRR and TCR, the diameter of the pin controls the formation of MML, especially at higher speeds.

Dynamic Characteristics of Spherically Converging Detonation Waves

The spherically converging detonation wave was numerically investigated by solving the one-dimensional multi-component Euler equations in spherical coordinates with a dispersion-controlled dissipative scheme. Finite rate and detailed chemical reaction models were used and numerical solutions were obtained for both a spherical by converging detonation in a stoichiometric hydrogen-oxygen mixture and a spherically focusing shock in air. The results showed that the post-shock pressure approximately arises to the same amplitude in vicinity of the focal point for the two cases, but the post-shock temperature level mainly depends on chemical reactions and molecular dissociations of a gas mixture. While the chemical reaction heat plays an important role in the early stage of detonation wave propagation, gas dissociations dramatically affect the post-shock flow states near the focal point. The maximum pressure and temperature, non-dimensionalized by their initial value, are approximately scaled to the propagation radius over the initial detonation diameter. The post-shock pressure is proportional to the initial pressure of the detonable mixture, and the post-shock temperature is also increased with the initial pressure, but in a much lower rate than that of the post-shock pressure.

Numerical Investigation On Detonation Cell Evolution In A Channel With Area-Changing Cross Section

The two-dimensional cellular detonation propagating in a channel with area-changing cross section was numerically simulated with the dispersion-controlled dissipative scheme and a detailed chemical reaction model. Effects of the flow expansion and compression on the cellular detonation cell were investigated to illustrate the mechanism of the transverse wave development and the cellular detonation cell evolution. By examining gas composition variations behind the leading shock, the chemical reaction rate, the reaction zone length, and thermodynamic parameters, two kinds of the abnormal detonation waves were identified. To explore their development mechanism, chemical reactions, reflected shocks and rarefaction waves were discussed, which interact with each other and affect the cellular detonation in different ways.

Optimization of tried wave-function in quantum monte-carlo method

A method for optimizing tried wave functions in quantum Monte Carlo method has been found and used to calculate the energies of molecules, such as H-2, Li-2, H-3+, H-3 and H-4. Good results were obtained.

化学反应和球面聚心爆轰波的相互作用

考察球面爆轰波聚心传播过程中，波阵面附近压力和温度不断升高引起化学反应进程的改变；对比氢氧可燃气体与氮气的数值模拟结果，分析化学反应对波面温度和压力的影响，从而考察Zeldovich理论预测聚心爆轰波后参数的精确性．数值结果表明，爆轰波聚心传播初期，放热的燃烧反应对波后热力学参数起主导作用；传播后期，波阵面趋近于对称中心时，吸热的气体解离反应变得非常活跃，解离反应对后期的汇聚压力影响不大，但会在很大程度上限制汇聚温度的升高．

Control of Large-size SiC Growth Process Using Modeling tool

Large size bulk silicon carbide (SiC) crystals are commonly grown by the physical vapor transport (PVT) method. The PVT growth of SiC crystals involves sublimation and condensation, chemical reactions, stoichiometry, mass transport, induced thermal stress, as well as defect and micropipes generation and propagation. The quality and polytype of as-grown SiC crystals are related to the temperature distribution inside the growth chamber during the growth process, it is critical to predict the temperature distribution from the measured temperatures outside the crucible by pyrometers. A radio-frequency induction-heating furnace was used for the growth of large-size SiC crystals by the PVT method in the present study. Modeling and simulation have been used to develop the SiC growth process and to improve the SiC crystal quality. Parameters such as the temperature measured at the top of crucible, temperature measured at the bottom of the crucible, and inert gas pressure are used to control the SiC growth process. By measuring the temperatures at the top and bottom of the crucible, the temperatures inside the crucible were predicted with the help of modeling tool. SiC crystals of 6H polytype were obtained and characterized by the Raman scattering spectroscopy and SEM, and crystals of few millimeter size grown inside the crucible were found without micropipes. Expansion of the crystals were also performed with the help of modeling and simulation.

碳氢燃料超音速燃烧的数值研究

本文对CH_4横向喷入超音速高温空气主流的二维流场进行了数值模拟，对CH_4-O_2的六方程反应模式进行了检验，借以对混合与燃烧过程的现象与机理加以研究，并与单方程反应模型及H_2横向喷射的情况进行了对比。得到了较为理想的结果。本文采用二维雷诺平均全N-S方程进行计算，采用热完全气体模型，用Baldwin-Lomax代数涡粘性湍流模型来模拟湍流效应。假定N_2不参加反应，CH_4-O_2反应机制选取六个基本反应，以及九个组元O、O_2、CH_3、CH_4、OH、CHO、CH_2O、CO和CO_2，应用空间二阶精度Harten-Yee隐式TVD格式，采用化学源项点隐的全隐方法数值求解。本文对多种超音速空气主流及边界条件的工部进行了数值模拟，并对其流场进行了分析。针对工作中出现的问题，提出了对下一步工作的展望。

Nonlinear oscillations in discrete and continuous systems

The first thesis topic is a perturbation method for resonantly coupled nonlinear oscillators. By successive near-identity transformations of the original equations, one obtains new equations with simple structure that describe the long time evolution of the motion. This technique is related to two-timing in that secular terms are suppressed in the transformation equations. The method has some important advantages. Appropriate time scalings are generated naturally by the method, and don't need to be guessed as in two-timing. Furthermore, by continuing the procedure to higher order, one extends (formally) the time scale of valid approximation. Examples illustrate these claims. Using this method, we investigate resonance in conservative, non-conservative and time dependent problems. Each example is chosen to highlight a certain aspect of the method.

The second thesis topic concerns the coupling of nonlinear chemical oscillators. The first problem is the propagation of chemical waves of an oscillating reaction in a diffusive medium. Using two-timing, we derive a nonlinear equation that determines how spatial variations in the phase of the oscillations evolves in time. This result is the key to understanding the propagation of chemical waves. In particular, we use it to account for certain experimental observations on the Belusov-Zhabotinskii reaction.

Next, we analyse the interaction between a pair of coupled chemical oscillators. This time, we derive an equation for the phase shift, which measures how much the oscillators are out of phase. This result is the key to understanding M. Marek's and I. Stuchl's results on coupled reactor systems. In particular, our model accounts for synchronization and its bifurcation into rhythm splitting.

Finally, we analyse large systems of coupled chemical oscillators. Using a continuum approximation, we demonstrate mechanisms that cause auto-synchronization in such systems.