Physics of strongly coupled quark-gluon plasma

This review covers our current understanding of strongly coupled Quark-Gluon Plasma (sQGP), especially theoretical progress in: (i) explaining the RHIC data by hydrodynamics; (ii) describing lattice data using electric-magnetic duality; (iii) understanding of gauge-string duality known as AdS/CFT and its application for “conformal” plasma. In view of the interdisciplinary nature of the subject, we include a brief introduction into several topics “for pedestrians”. Some fundamental questions addressed are: Why is sQGP such a good liquid? What is the nature of (de)confinement and what do we know about “magnetic” objects creating it? Do they play any important role in sQGP physics? Can we understand the AdS/CFT predictions, from the gauge theory side? Can they be tested experimentally? Can AdS/CFT duality help us understand rapid equilibration/entropy production? Can we work out a complete dynamical “gravity dual” to heavy ion collisions?     

Impact of surface science on the understanding of kinetics of heterogeneous catalytic reactions

The kinetics of chemical reactions in gas and liquid phases are usually described by employing the conventional mass-action law equations. The laws governing the kinetics of heterogeneous catalytic reactions are as a rule much more complex due to adsorbate–adsorbate lateral interactions, surface heterogeneity, spontaneous and adsorbate-induced changes in a surface, and/or limited mobility of reactants. The importance of these factors was recognized by the heterogeneous catalysis community far before the surface-science era. Only with the development of surface science, however, has it become possible to study in detail the non-ideality of rate processes on solid surfaces. In the present paper, we survey the main conceptual results currently available in this field and illustrate the impact of surface science on its development. Specifically, we outline the approaches used to describe elementary reaction steps and the whole reaction kinetics near and far from equilibrium, including such topics as kinetic phase transitions, pattern formation, kinetic oscillations and chaos, and pressure- and structure-gap problems. All these phenomena and problems are demonstrated to provide promising opportunities for further experimental and theoretical studies.     

Solid-state nuclear magnetic resonance investigations of the nature, property, and activity of acid sites on solid catalysts

Further progress in the field of heterogeneous catalysis depends on our knowledge of the nature and behavior of surface sites on solid catalysts and of the mechanisms of chemical reactions catalyzed by these materials. In the past decades, solid-state NMR spectroscopy has been developed to an important tool for routine characterization of solid catalysts. The present work gives a review on experimental approaches and applications of solid-state NMR spectroscopy for investigating Brønsted and Lewis sites on solid acids. Studies focusing on the generation of surface sites via post-synthesis modification routes of microporous and mesoporous materials support the development of new and the improvement of existing catalyst systems. High-temperature and flow techniques of in situ solid-state NMR spectroscopy allow a deeper insight into the mechanisms of heterogeneously catalyzed reactions and open the way for studying the activity of acidic surface sites. They help to clarify the activation of reactants on Brønsted and Lewis acid sites and improve our understanding of mechanisms affecting the selectivity of acid-catalyzed reactions.     

Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.     

Science with radioactive beams: The alchemist's dream

Nuclear science is being transformed by a new capacity to create beams of radioactive nuclei. Until now all of our knowledge of nuclear physics and the applications which flow from it has been derived from studies of radioactive decay and nuclear reactions induced by beams of the 283 stable or long-lived nuclear species we can find on Earth. Here we describe first how beams of radioactive nuclei can be created. The present status of nuclear physics is then reviewed before potential applications to nuclear physics, nuclear astrophysics, materials science, bio-medical, and environmental studies are described.     

Biomedical surface science: Foundations to frontiers

Surfaces play a vial role in biology and medicine with most biological reactions occurring at surfaces and interfaces. The foundations, evolution, and impact of biomedical surface science are discussed. In the 19th century, the first observations were made that surfaces control biological reactions. The advancements in surface science instrumentation that have occurred in the past quarter of a century have significantly increased our ability to characterize the surface composition and molecular structure of biomaterials. Similar advancements have occurred in material science and molecular biology. The combination of these advances have allowed the development of the biological model for surface science, where the ultimate goal is to gain a detailed understanding of how the surface properties of a material control the biological reactivity of a cell interacting with that surface. Numerous examples show that the surface properties of a material are directly related to in vitro biological performance such as protein adsorption and cell growth. The challenge is to fully develop the biological model for surface science in the highly complex and interactive in vivo biological environment. Examples of state-of-the-art biomedical surface science studies on surface chemical state imaging, molecular recognition surfaces, adsorbed protein films, and hydrated surfaces are presented. Future directions and opportunities for surface scientists working in biomedical research include exploiting biological knowledge, biomimetics, precision immobilization, self-assembly, nanofabrication, smart surfaces, and control of non-specific reactions.     

Public understanding of science and the perception of nanotechnology: the roles of interest in science,methodological knowledge,epistemological beliefs,and beliefs about science

In this article, we report data from an online questionnaire study with 587 respondents, representative for the adult U.S. population in terms of age, gender, and level of education. The aim of this study was to assess how interest in science and knowledge as well as beliefs about science are associated with risk and benefit perceptions of nanotechnology. The findings suggest that the U.S. public is still rather unfamiliar with nanotechnology. Those who have some knowledge mainly have gotten it from TV and the Internet. The content of current media reports is perceived as fairly positive. Knowledge of scientific methods is unrelated to benefit and risk perceptions, at least when other predictors are controlled. In contrast, positive beliefs about science (e.g., its impact on economy or health) and more sophisticated epistemological beliefs about the nature of scientific knowledge are moderately linked to more positive perceptions of nanotechnology. The only exception is the perception of scientific uncertainty: This is associated with less positive evaluations. Finally, higher engagement with science is associated with higher risk perceptions. These findings show that laypersons who are engaged with science and who are aware of the inherent uncertainty of scientific evidence might perceive nanotechnology in a somewhat more differentiated way, contrary to how it is portrayed in the media today.     

Role of surface science in catalysis

Around the time of World War I, Langmuir advanced a simple theory of chemisorption and showed how it could be used to formulate rate laws for reactions occurring on surfaces. From that time on, surface science has played an important role in heterogeneous catalysis. Between the two world wars, simple studies of extents of adsorption by catalyst surfaces led to the concept of activated adsorption and to a universally used method for determining the high surface areas associated with the pore structures of catalytic materials. After World War II, the application of various spectroscopic and structural probes made it possible to investigate catalyst surfaces at a more microscopic level. Studies with idealized surfaces such as the faces of single crystals in ultra-high vacuum apparatus also made their appearance. By the end of the twentieth century, direct information was being obtained on the rates of elementary reactions of well-defined surface species. The results of such work are beginning to put “finishing touches” on the great insight of early pioneers in surface science and heterogeneous catalysis. Much has been accomplished, but exciting opportunities still remain.     

Diffusion-influenced reactions

We summarize three of our recent results on diffusion-influenced reactions in solutions. All deal with the concentration dependence of the reaction rate when the reactants must first diffuse together before reaction can occur. When one species (the sink species) is not dilute, the rate cannot be obtained by solution of a pair diffusion equation; the correlations among the sinks for the diffusing species must be accounted for. First, we consider fluorescence quenching when the quenchers are not dilute. For charged quenchers and fluorophores we discuss how the solution dielectric constant and ionic strength can strongly influence the deviations from the linear Stern-Volmer behavior (the dilute sink result) which arise due to the sink correlations. Second, we consider heterogeneous catalysis where a reactive species is adsorbed onto a surface and must surface diffuse to reactive sites (the sinks). We find that surface diffusion can be an important factor contributing to the rate of reaction; especially when surface diffusion is rapid relative to the adsorption/desorption rate. Third, we discuss diffusion influenced reactions with sinks which are long ellipsoids. Dilute long ellipsoids provide a large rate enhancement relative to a spherical sink; we show that this rate enhancement survives when nondilute ellipsoids are considered.     

Surface science done at third generation synchrotron radiation facilities

In this paper we present a few examples of surface science done at third generation synchrotron facilities. As explained in the introduction, third generation sources are characterised by a gain in brightness of three or four orders of magnitude. This allows performing experiments which were difficult or impossible before. The first part of the paper is dealing with experiments on magnetic materials and shows how dichroism and surface diffraction can bring new information. In the second part, we discuss two examples related to catalysis: the elementally resolved imaging of chemical waves and the structure of chemisorbs layers on a nickel surface at atmospheric pressure.

How do atoms assemble in monatomic liquids? Do they form clusters? This question has been without answer for many years and it is only recently that an X-ray experiment has solved the problem. The fourth part of the paper describes recent results on the electronic properties of high T_c superconductors and heavy fermions, studied by high resolution photoemission. Finally, we present a prospect of a few experiments that could be done in the near future.     

Mechanism from isotope effects

Abstract Isotope effects represent perhaps one of the most versatile tools available to investigators interested in the determination of reaction mechanism, particularly in the case of the mechanistic enzymologist. Interpretation of isotope effect data is somewhat more difficult for enzyme reactions, since the chemical or isotope-dependent step(s) is(are) normally not solely rate-limiting as they are for non-enzyme-catalyzed reactions. One can, however, take advantage of rate-limitation by multiple steps in an enzyme-catalyzed reaction to obtain information on a number of aspects of mechanism. In this paper, simple theory for the application of isotope effects to reaction mechanism is developed, and applied to organic reactions and those catalyzed by enzymes. Techniques used to measure isotope effects depend somewhat on the isotope used, that is radioisotope vs. stable isotope, or hydrogen isotope vs. heavier atoms. Techniques to be discussed include competitive and noncompetitive (or internal discrimination) measurements. In enzymecatalyzed reactions, information can be obtained on the order of addition of reactants and release of products, and this will be illustrated using the 6-phosphogluconate and alcohol dehydrogenase reactions. The use of multiple isotope effects can be used to distinguish between stepwise and concerted reactions, and this will be illustrated with the formate and glucose 6-phosphate dehydrogenase and malic enzyme reactions.     

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聚变堆第一壁表面和PFC材料内的氚滞留量、堆系统总的氚投料量多高？在启动和运行的开始阶段的氚坑深度,氚坑时间的大小是多少？在TBM氚增殖包层内固体氚增殖剂中的氚能否高效率地被载氚气体带出来并且以高效率地提取回收？能否找到某些新机制解决这些问题是决定实现ITER的预期目标和最终实现聚变能的实际运用成败的关键问题。本文第(Ⅰ)部分回答前面两个问题,在下期第(Ⅱ)部分将进行创新的探索性研究并且提出某些减少氚滞留量和改善氚提取回收效率的新方案,例如：基于氘饱和的海绵效应;第一壁表面建立氘和铍的伴同沉积层;基于在低频外电场作用下载氚气分子和硅酸锂颗粒电极化旋转催化同位素交换速率增强提高载氚气提取氚效率“SPB方法”等等。     

Role of surface and interface science in chemical vapor deposition diamond technology

Diamond is well known as the hardest material in nature. It also has other unique bulk physical and mechanical properties, such as very high thermal conductivity and broad optical transparency, which enable a number of new applications now that large areas of diamond can be fabricated by the new diamond plasma chemical vapor deposition (CVD) technologies. However, some of the most interesting properties of diamond, including the ability to be grown over large areas by CVD processes, result not from its bulk properties but from its special and unique surface chemistry. The surface chemistry derived properties are as remarkable as the bulk properties, and in the end may enable the development of new applications, technologies, and industries which are at least as important as those based on the bulk properties. Some of these surface properties are extreme chemical inertness, low surface energy, low friction coefficients, negative electron affinity, biological inertness, and high over-voltage electrode behavior. The surface science and some of the interesting ongoing research in these areas are explored and illustrated, and unresolved questions are highlighted.     

The evolution of catalytic function

It is very likely that the main driving force of enzyme evolution is the requirement to improve catalytic and regulatory efficiency which results from the intrinsic performance as well as from the spatial and functional organization of enzymes in living cells.Kinetic co-operativity may occur in simple monomeric proteins if they display “slow” conformational transitions, at the cost of catalytic efficiency. Oligomeric enzymes on the other hand can be both efficient and co-operative. We speculate that the main reason for the emergence of co-operative oligomeric enzymes is the need for catalysts that are both cooperative and efficient. As it is not useful for an enzyme to respond to a change of substrate concentration in a complex kinetic way, the emergence of symmetry has its probable origin in a requirement for “functional simplicity”.In a living cell, enzyme are associated with other macromolecules and membranes. The fine tuning of their activity may also be reached through mutations of the microenvironment. Our hypothesis is that these mutations are related to the vectorial transport of molecules, to achieve the hysteresis loops of enzyme reactions generated by the coupling of reaction and diffusion, through the co-operativity brought about by electric interactions between a charged substrate and a membrane, and last but not least, through oscillations. As the physical origins of these effects are very simple and do not require complex molecular devices, it is very likely that the functional advantage generated by the spatial and functional organization of enzyme molecules within the cell have appeared in prebiotic catalysis or very early during the primeval stages of biological evolution.We shall began this paper by presenting the nature of the probable earliest catalysts in the RNA world.     

Tracking hydroxyl adsorption on TiO2 (1 1 0) through secondary emission changes

In surface science, rutile TiO₂ continues to be one of the most studied surfaces and in the catalysis field numerous groups study how adsorbates interact with this surface. All groups face the difficult problem of reproducibility due to surface preparation unknowns like defect concentration and the continuous aging of the crystals. Recent studies, using STM imaging, showed that hydroxyl adsorption takes place even in very good vacuum conditions. Upon adsorption, the surface electric field is reduced and the work function decreases. We found that this change may be readily detected in the onset energy of the secondary electrons. By following the onset region of secondary electron emission it is possible to track hydroxyl adsorption in quantities well below the detection level of XPS and LEIS. With this knowledge, we show that the time elapsed after surface preparation and water partial pressure should be accounted in the study of TiO₂ surfaces.     

Modeling the complex dynamics of enzyme-pathway coevolution

Metabolic pathways must have coevolved with the corresponding enzyme gene sequences. However, the evolutionary dynamics ensuing from the interplay between metabolic networks and genomes is still poorly understood. Here, we present a computational model that generates putative evolutionary walks on the metabolic network using a parallel evolution of metabolic reactions and their catalyzing enzymes. Starting from an initial set of compounds and enzymes, we expand the metabolic network iteratively by adding new enzymes with a probability that depends on their sequence-based similarity to already present enzymes. Thus, we obtain simulated time courses of chemical evolution in which we can monitor the appearance of new metabolites, enzyme sequences, or even entire organisms. We observe that new enzymes do not appear gradually but rather in clusters which correspond to enzyme classes. A comparison with Brownian motion dynamics indicates that our system displays biased random walks similar to diffusion on the metabolic network with long-range correlations. This suggests that a quantitative molecular principle may underlie the appearance of punctuated equilibrium dynamics, whereby enzymes occur in bursts rather than by phyletic gradualism. Moreover, the simulated time courses lead to a putative time-order of enzyme and organism appearance. Among the patterns we detect in these evolutionary trends is a significant correlation between the time of appearance and their enzyme repertoire size. Hence, our approach to metabolic evolution may help understand the rise in complexity at the biochemical and genomic levels.     

超声辐照对酶促反应影响的研究进展

综述了超声辐照对于酶活性和酶催化反应的影响,以及各种超声参数对反应的影响,并展望了超声辐照在酶促反应中的应用前景。     

Organic functionalization of group IV semiconductor surfaces: principles, examples, applications, and prospects

Organic functionalization is emerging as an important area in the development of new semiconductor-based materials and devices. Direct, covalent attachment of organic layers to a semiconductor interface provides for the incorporation of many new properties, including lubrication, optical response, chemical sensing, or biocompatibility. Methods by which to incorporate organic functionality to the surfaces of semiconductors have seen immense progress in recent years, and in this article several of these approaches are reviewed. Examples are included from both dry and wet processing environments. The focus of the article is on attachment strategies that demonstrate the molecular nature of the semiconductor surface. In many cases, the surfaces mimic the reactivity of their molecular carbon or organosilane counterparts, and examples of functionalization reactions are described in which direct analogies to textbook organic and inorganic chemistry can be applied. This article addresses the expected impact of these functionalization strategies on emerging technologies in nanotechnology, sensing, and bioengineering.     

Disentangling DNA molecules

The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.     

Resonance Raman Spectroscopy of Adsorbed Species on Solid Surfaces

Abstract

Every substance has the “bulk” which occupies almost all its content and the “surface” which is very thin layer enveloping the former. When two or more substances are in contact, the boundary layer constitutes the “interface.” Although the mass of the surface o r interface is negligibly small compared with that of the bulk, the ability of the interface in chemical reactions is far more significant than that of the bulk, because a number of chemical reactions initiate from the interfaces and the reaction rates can be controlled by the use of specifics of the surfaces, especially in catalytic and electrode reactions. Therefore, it is very important to investigate fully the structure and property of the surfaces or interfaces, which must be definitely different from those of the bulk, for elucidation of chemical behavior of materials. The clarification on bulk materials are extensively developed by spectroscopic and diffraction methods. However, as regards the features of the interface, much less knowledge is available at present. It is mainly because that in ordinary experiments, the specimen, consisting of a very small part of surface species and a very large part of bulk materials, even when the adsorbents are porous, cannot represent the characteristic nature of the surface. In other words, the specific character of interface or surface can only be observed in the monoatomic layer o r within the depth of several tens of angstroms from the interface. Besides, the surface species, which play an important role in catalytic o r electrode reactions, are often so unstable that they are detected only in situ measurements.