Biodiesel is defined as fatty acid mono-alkylesters and is produced from triacylglycerols. In the current article we provide an overview of the structure, diversity and regulation of the metabolic pathways leading to intracellular fatty acid and triacylglycerol accumulation in three types of organisms (bacteria, algae and fungi) of potential biotechnological interest and discuss possible intervention points to increase the cellular lipid content. The key steps that regulate carbon allocation and distribution in lipids include the formation of malonyl-CoA, the synthesis of fatty acids and their attachment onto the glycerol backbone, and the formation of triacylglycerols. The lipid biosynthetic genes and pathways are largely known for select model organisms. Comparative genomics allows the examination of these pathways in organisms of biotechnological interest and reveals the evolution of divergent and yet uncharacterized regulatory mechanisms. Utilization of microbial systems for triacylglycerol and fatty acid production is in its infancy; however, genomic information and technologies combined with synthetic biology concepts provide the opportunity to further exploit microbes for the competitive production of biodiesel.

Recent developments in the field of anisotropic flow in nuclear collision are reviewed. The results from the top AGS energy to the top RHIC energy are discussed with emphasis on techniques, interpretation, and uncertainties in the measurements.

The initial objective of the Berkeley Structural Genomics Center was to obtain a near complete three-dimensional (3D) structural information of all soluble proteins of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter has fewer than 700 genes. A semiautomated structural genomics pipeline was set up from target selection, cloning, expression, purification, and ultimately structural determination. At the time of this writing, structural information of more than 93percent of all soluble proteins of M. genitalium is avail able. This chapter summarizes the approaches taken by the authors' center.

In the UK the study of laser produced plasmas and their applications began in the universities and evolved to a current system where the research is mainly carried out at the Rutherford Appleton Laboratory Central Laser Facility ( CLF) which is provided to support the universities. My own research work has been closely tied to this evolution and in this review I describe the history with particular reference to my participation in it.

Over the past decade there has been a natural drive to extend the investigation of dynamic surfaces in fluid environments to higher resolution characterization tools. Various aspects of solution crystal growth have been directly visualized for the first time. These include island nucleation and growth using transmission electron microscopy and scanning tunneling microscopy; elemental step motion using scanning probe microscopy; and the time evolution of interfacial atomic structure using various diffraction techniques. In this lecture we will discuss the use of one such in situ method, scanning probe microscopy, as a means of measuring surface dynamics during crystal growth and dissolution. We will cover both practical aspects of imaging such as environmental control, fluid flow, and electrochemical manipulation, as well as the types of physical measurements that can be made. Measurements such as step motion, critical lengths, nucleation density, and step fluctuations, will be put in context of the information they provide about mechanistic processes at surfaces using examples from metal and mineral crystal growth.

Boron nitride (BN) is a synthetic binary compound located between III and V group elements in the Periodic Table. However, its properties, in terms of polymorphism and mechanical characteristics, are rather close to those of carbon compared with other III-V compounds, such as gallium nitride. BN crystallizes into a layered or a tetrahedrally linked structure, like those of graphite and diamond, respectively, depending on the conditions of its preparation, especially the pressure applied. Such correspondence between BN and carbon readily can be understood from their isoelectronic structures [1, 2]. On the other hand, in contrast to graphite, layered BN is transparent and is an insulator. This material has attracted great interest because, similar to carbon, it exists in various polymorphic forms exhibiting very different properties; however, these forms do not correspond strictly to those of carbon. Crystallographically, BN is classified into four polymorphic forms: Hexagonal BN (h-BN) (Figure 1(b)); rhombohedral BN (r-BN); cubic BN (c-BN); and wurtzite BN (w-BN). BN does not occur in nature. In 1842, Balmain [3] obtained BN as a reaction product between molten boric oxide and potassium cyanide under atmospheric pressure. Thereafter, many methods for its synthesis were reported. h-BN and r-BN are formed under ambient …

Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique for studying bi-molecular interactions at the atomic scale. Our NMR lab is involved in the identification of small molecules, or ligands that bind to target protein receptors, such as tetanus (TeNT) and botulinum (BoNT) neurotoxins, anthrax proteins and HLA-DR10 receptors on non-Hodgkin's lymphoma cancer cells. Once low affinity binders are identified, they can be linked together to produce multidentate synthetic high affinity ligands (SHALs) that have very high specificity for their target protein receptors. An important nanotechnology application for SHALs is their use in the development of robust chemical sensors or biochips for the detection of pathogen proteins in environmental samples or body fluids. Here, we describe a recently developed NMR competition assay based on transferred nuclear Overhauser effect spectroscopy (trNOESY) that enables the identification of sets of ligands that bind to the same site, or a different site, on the surface of TeNT fragment C (TetC) than a known ''marker'' ligand, doxorubicin. Using this assay, we can identify the optimal pairs of ligands to be linked together for creating detection reagents, as well as estimate the relative binding constants for ligands competing for the same site.

The prospect of modeling across disparate length and time scales to achieve a predictive multiscale description of real materials properties has attracted widespread research interest in the last decade. To be sure, the challenges in such multiscale modeling are many, and in demanding cases, such as mechanical properties or dynamic phase transitions, multiple bridges extending from the atomic level all the way to the continuum level must be built. Although often overlooked in this process, one of the most fundamental and important problems in multiscale modeling is that of bridging the gap between first-principles quantum mechanics, from which true predictive power for real materials emanates, and the large-scale atomistic simulation of thousands or millions of atoms, which is usually essential to describe the complex atomic processes that link to higher length and time scales. For example, to model single-crystal plasticity at micron length scales via dislocation-dynamics simulations that evolve the detailed dislocation microstructure requires accurate large-scale atomistic information on the mobility and interaction of individual dislocations. Similarly, modeling the kinetics of structural phase transitions requires linking accurate large-scale atomistic information on nucleation processes with higher length and time scale growth processes.

The Earth's climate is determined by a number of complex connected physical, chemical and biological processes occurring in the atmosphere, land and ocean. The radiative properties of the atmosphere, a major controlling factor of the Earth's climate, are strongly affected by the biophysical state of the Earth's surface and by the atmospheric abundance of a variety of trace constituents. These constituents include long-lived greenhouse gases (LLGHGs) such as carbon dioxide (CO{sub 2}), methane (CH{sub 4}) and nitrous oxide (N{sub 2}O), as well as other radiatively active constituents such as ozone and different types of aerosol particles. The composition of the atmosphere is determined by processes such as natural and anthropogenic emissions of gases and aerosols, transport at a variety of scales, chemical and microphysical transformations, wet scavenging and surface uptake by the land and terrestrial ecosystems, and by the ocean and its ecosystems. These processes and, more generally the rates of biogeochemical cycling, are affected by climate change, and involve interactions between and within the different components of the Earth system. These interactions are generally nonlinear and may produce negative or positive feedbacks to the climate system. An important aspect of climate research is to identify potential feedbacks and assess …

Most groups of chondritic meteorites experienced diverse styles of secondary alteration to various degrees that resulted in formation of hydrous and anhydrous minerals (e.g., phyllosilicates, magnetite, carbonates, ferrous olivine, hedenbergite, wollastonite, grossular, andradite, nepheline, sodalite, Fe,Ni-carbides, pentlandite, pyrrhotite, Ni-rich metal). Mineralogical, petrographic, and isotopic observations suggest that the alteration occurred in the presence of aqueous solutions under variable conditions (temperature, water/rock ratio, redox conditions, and fluid compositions) in an asteroidal setting, and, in many cases, was multistage. Although some alteration predated agglomeration of the final chondrite asteroidal bodies (i.e. was pre-accretionary), it seems highly unlikely that the alteration occurred in the solar nebula, nor in planetesimals of earlier generations. Short-lived isotope chronologies ({sup 26}Al-{sup 26}Mg, {sup 53}Mn-{sup 53}Cr, {sup 129}I-{sup 129}Xe) of the secondary minerals indicate that the alteration started within 1-2 Ma after formation of the Ca,Al-rich inclusions and lasted up to 15 Ma. These observations suggest that chondrite parent bodies must have accreted within the first 1-2 Ma after collapse of the protosolar molecular cloud and provide strong evidence for an early onset of aqueous activity on these bodies.

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Beginning in the early 1970s, a number of research and development efforts were undertaken at U.S. National Laboratories with a goal of developing high power lasers whose characteristics were suitable for investigating the feasibility of laser-driven fusion. A number of different laser systems were developed and tested at ever larger scale in pursuit of the optimum driver for laser fusion experiments. Each of these systems had associated with it a unique pulsed power option. A considerable amount of original and innovative engineering was carried out in support of these options. Ultimately, the Solid-state Laser approach was selected as the optimum driver for the application. Following this, the Laser Program at the Lawrence Livermore National Laboratory and the University of Rochester undertook aggressive efforts directed at developing the technology. In particular, at Lawrence Livermore National Laboratory, a series of laser systems beginning with the Cyclops laser and culminating in the present with the National Ignition Facility were developed and tested. As a result, a large amount of design information for solid-state laser pulsed power systems has been documented. Some of it is in the form of published papers, but most of it is buried in internal memoranda, engineering reports and LLNL …

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We will provide a review of some of the physics which can be addressed by studying fluctuations and correlations in heavy ion collisions. We will discuss Lattice QCD results on fluctuations and correlations and will put them into context with observables which have been measured in heavy-ion collisions. Special attention will be given to the QCD critical point and the first order co-existence region, and we will discuss how the measurement of fluctuations and correlations can help in an experimental search for non-trivial structures in the QCD phase diagram.

Evaporitic environments are found in a variety of depositional environments as early as the Archean. The depositional settings, microbial community and mineralogical composition vary significantly as no two settings are identical. The common thread linking all of the settings is that evaporation exceeds precipitation resulting in elevated concentrations of cations and anions that are higher than in oceanic systems. The Dead Sea and Storrs Lake are examples of two diverse modern evaporitic settings as the former is below sea level and the latter is a coastal lake on an island in the Caribbean. Each system varies in water chemistry as the Dead Sea dissolved ions originate from surface weathered materials, springs, and aquifers while Storrs Lake dissolved ion concentration is primarily derived from sea water. Consequently some of the ions, i.e., Sr, Ba are found at significantly lower concentrations in Storrs Lake than in the Dead Sea. The origin of the dissolved ions are ultimately responsible for the pH of each system, alkaline versus mildly acidic. Each system exhibits unique biogeochemical properties as the extreme environments select certain microorganisms. Storrs Lake possesses significant biofilms and stromatolitic deposits and the alkalinity varies depending on rainfall and storm activity. The microbial community …

Nature uses enzymes to activate otherwise unreactive compounds in remarkable ways. For example, DNases are capable of hydrolyzing phosphate diester bonds in DNA within seconds,[1-3]--a reaction with an estimated half-life of 200 million years without an enzyme.[4] The fundamental features of enzyme catalysis have been much discussed over the last sixty years in an effort to explain the dramatic rate increases and high selectivities of enzymes. As early as 1946, Linus Pauling suggested that enzymes must preferentially recognize and stabilize the transition state over the ground state of a substrate.[5] Despite the intense study of enzymatic selectivity and ability to catalyze chemical reactions, the entire nature of enzyme-based catalysis is still poorly understood. For example, Houk and co-workers recently reported a survey of binding affinities in a wide variety of enzyme-ligand, enzyme-transition-state, and synthetic host-guest complexes and found that the average binding affinities were insufficient to generate many of the rate accelerations observed in biological systems.[6] Therefore, transition-state stabilization cannot be the sole contributor to the high reactivity and selectivity of enzymes, but rather, other forces must contribute to the activation of substrate molecules. Inspired by the efficiency and selectivity of Nature, synthetic chemists have admired the ability of enzymes …

Of the many candidates employed for understanding the erosion of critical Extreme Ultraviolet Lithography (EUVL) components, potential energy damage remains relatively uninvestigated. Unlike the familiar kinetic energy sputtering, which is a consequence of the momentum transferred by an ion to atoms in the target, potential energy sputtering occurs when an ion rapidly collects charge from the target as it neutralizes. Since the neutralization energy of a singly charged ion is typically on the order of 10 eV, potential energy effects are generally neglected for low charge state ions, and hence the bulk of the sputtering literature. As an ion's charge state is increased, the potential energy (PE) increases rapidly, e.g. PE(Xe{sup 1+})= 11 eV, PE(Xe{sup 10+}) = 810 eV, PE(Xe{sup 20+}) = 4.6 keV, etc. By comparison, the binding energy of a single atom on a surface is typically about 5 eV, so even relatively inefficient energy transfer mechanisms can lead to large quantities of material being removed, e.g. 25% efficiency for Xe{sup 10+} corresponds to {approx} 40 atoms/ion. By comparison, singly charged xenon ions with {approx} 20 keV of kinetic energy sputter only about 5 atoms/ion at normal incidence, and less than 1 atom/ion at typical EUV source energies. …

Arguments pertaining to the mind-brain connection and to the physical effectiveness of our conscious choices have been presented in two recent books, one by John Searle, the other by Jaegwon Kim. These arguments are examined, and it is argued that the difficulties encountered arise from a defective understanding and application of a pertinent part of contemporary science, namely quantum mechanics.

The Defense Waste Processing Facility (DWPF) initiated processing of Sludge Batch 4 (SB4) in May 2007. SB4 was the first DWPF sludge batch to contain significant quantities of HM or high Al sludge. Initial testing with SB4 simulants showed potential negative impacts to DWPF processing; therefore, Savannah River National Laboratory (SRNL) performed extensive testing in an attempt to optimize processing. SRNL's testing has resulted in the highest DWPF production rates since start-up. During SB4 processing, DWPF also began incorporating waste streams from the interim salt processing facilities to initiate coupled operations. While DWPF has been processing SB4, the Liquid Waste Organization (LWO) and the SRNL have been preparing Sludge Batch 5 (SB5). SB5 has undergone low-temperature aluminum dissolution to reduce the mass of sludge for vitrification and will contain a small fraction of Purex sludge. A high-level review of SB4 processing and the SB5 preparation studies will be provided.

In widely distributed systems generally, and in science-oriented Grids in particular, software, CPU time, storage, etc., are treated as"services" -- they can be allocated and used with service guarantees that allows them to be integrated into systems that perform complex tasks. Network communication is currently not a service -- it is provided, in general, as a"best effort" capability with no guarantees and only statistical predictability. In order for Grids (and most types of systems with widely distributed components) to be successful in performing the sustained, complex tasks of large-scale science -- e.g., the multi-disciplinary simulation of next generation climate modeling and management and analysis of the petabytes of data that will come from the next generation of scientific instrument (which is very soon for the LHC at CERN) -- networks must provide communication capability that is service-oriented: That is it must be configurable, schedulable, predictable, and reliable. In order to accomplish this, the research and education network community is undertaking a strategy that involves changes in network architecture to support multiple classes of service; development and deployment of service-oriented communication services, and; monitoring and reporting in a form that is directly useful to the application-oriented system so that it may …

This chapter addresses past, ongoing, and short (to 2010) and medium-term (to 2030) future actions that can be taken to mitigate GHG emissions from the manufacturing and process industries. Globally, and in most countries, CO{sub 2} accounts for more than 90% of CO{sub 2}-eq GHG emissions from the industrial sector (Price et al., 2006; US EPA, 2006b). These CO{sub 2} emissions arise from three sources: (1) the use of fossil fuels for energy, either directly by industry for heat and power generation or indirectly in the generation of purchased electricity and steam; (2) non-energy uses of fossil fuels in chemical processing and metal smelting; and (3) non-fossil fuel sources, for example cement and lime manufacture. Industrial processes also emit other GHGs, e.g.: (1) Nitrous oxide (N{sub 2}O) is emitted as a byproduct of adipic acid, nitric acid and caprolactam production; (2) HFC-23 is emitted as a byproduct of HCFC-22 production, a refrigerant, and also used in fluoroplastics manufacture; (3) Perfluorocarbons (PFCs) are emitted as byproducts of aluminium smelting and in semiconductor manufacture; (4) Sulphur hexafluoride (SF{sub 6}) is emitted in the manufacture, use and, decommissioning of gas insulated electrical switchgear, during the production of flat screen panels and semiconductors, from …

But a glance at the Livingston chart, Fig. 1, of accelerator particle energy as a function of time shows that the energy has steadily, exponentially, increased. Equally significant is the fact that this increase is the envelope of diverse technologies. If one is to stay on, or even near, the Livingston curve in future years then new acceleration techniques need to be developed. What are the new acceleration methods? In these two lectures I would like to sketch some of these new ideas. I am well aware that they will probably not result in high energy accelerators within this or the next decade, but conversely, it is likely that these ideas will form the basis for the accelerators of the next century. Anyway, the ideas are stimulating and suffice to show that accelerator physicists are not just 'engineers', but genuine scientists deserving to be welcomed into the company of high energy physicists. I believe that outsiders will find this field surprisingly fertile and, certainly fun. To put it more personally, I very much enjoy working in this field and lecturing on it. There are a number of review articles which should be consulted for references to the original literature. In …

Releases of acutely toxic airborne contaminants in or near a building can lead to significant human exposures unless prompt response measures are identified and implemented. Commonly, possible responses include conflicting strategies, such as shutting the ventilation system off versus running it in a purge (100percent outside air) mode, or having occupants evacuate versus sheltering in place. The right choice depends in part on quickly identifying the source locations, the amounts released, and the likely future dispersion routes of the pollutants. This paper summarizes recent developments to provide such estimates in real time using an approach called Bayesian Monte Carlo updating. This approach rapidly interprets measurements of airborne pollutant concentrations from multiple sensors placed in the building and computes best estimates and uncertainties of the release conditions. The algorithm is fast, capable of continuously updating the estimates as measurements stream in from sensors. The approach is employed, as illustration, to conduct two specific investigations under different situations.