CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Kenji Sumida, David L. Rogow, Jarad A. Mason, Thomas M. McDonald, Eric D. Bloch, Zoey R. Herm, Tae-Hyun Bae, Jeffrey R. Long

Carbon Dioxide Capture in Metal–Organic Frameworks

For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.

Interaction Models for Water in Relation to Protein Hydration

This critical review will be of interest to the experts in porous solids (including catalysis), but also solid state chemists and physicists. It presents the state-of-the-art on hybrid porous solids, their advantages, their new routes of synthesis, the structural concepts useful for their ‘design’, aiming at reaching very large pores. Their dynamic properties and the possibility of predicting their structure are described. The large tunability of the pore size leads to unprecedented properties and applications. They concern adsorption of species, storage and delivery and the physical properties of the dense phases. (323 references)

Hybrid porous solids: past, present, future

Impatti, adattamento e vulnerabilita Le cause e le responsabilita dei cambiamenti climatici sono state trattate sul numero di ottobre della rivista Cda. Approfondiamo l’argomento presentando il documento: “Cambiamenti climatici 2007: impatti, adattamento e vulnerabilita” votato ad aprile 2007 dal secondo gruppo di lavoro del Comitato Intergovernativo sui Cambiamenti Climatici (Intergovernmental Panel on Climate Change). Si tratta del secondo di tre documenti che compongono il quarto rapporto sui cambiamenti climatici.

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Climate Change 2007: Impacts, Adaptation and Vulnerability.

1. Cement Manufacture 2. Composition of Cement Phases 3. The Hydration of Portland Cement 4. Calcium Aluminate Cements 5. Properties of Concrete with Mineral and Chemical Admixtures 6. Special Cements 7. Developments with Oilwell Cements 8. Gypsum in Cements 9. Alkali-Silica Reaction in Concrete 10. Delayed Ettringite Formation 11. Chloride-Corrosion in Cementitious Systems 12. Blastfurnace Cements 13. Properties and Applications of Natural Pozzolanas 14. Pulverised Fuel Ash as a Cement Extender 15. Metakaolin as a Pollolanic Addition to Concrete 16. Condensed Silica Fume as a Cement Extender 17. Cement-Based Composite Micro-Structures 18. X-Ray Powder Diffraction Analysis of Cements 19. Electron Microscopy of Cements 20. Electrical Monitoring Methods in Cement Science 21. Nuclear Magnetic Resonance Spectroscopy and Magnetic Resonance Imaging Studies of Cements and Cement-Based Materials 22. The Use of Synchroton Sources in the Study of Cement Materials

Structure and Performance of Cements

The very large breathing effect of a metal-organic framework during CO 2 adsorption is discussed. An experiment was conducted for the case of CO2 adsorption at room temperature for porous chromium (III) terephthalate MIL-53. The structural topology of MIL-53 consists of a 4 4 net with tilted chains of CrIIIO4(OH) 2 octahedra sharing trans hydroxyl groups solid. These chains are linked through the carboxylate groups of the terephthalate ions forming a 3D framework. An in situ solid-state NMR study of the hydration of MIL-53HT showed that the shrinkage that occurred upon insertion of water molecules resulted from the onset of two types of strong hydrogen bonds. The first type involves the hydrogen atoms of water molecules and the oxygen atoms of the bridging carboxylate groups. The second type, which seems to be more energetically favorable, links OH groups to inserted water molecules.

An Explanation for the Very Large Breathing Effect of a Metal–Organic Framework during CO2 Adsorption

Financial ratios are used for all kinds of purposes. These include the assessment of the ability of a firm to pay its debts, the evaluation of business and managerial success and even the statutory regulation ofa firm's performance. Not surprisingly they become norms and actually affect performance.' The traditional textbooks of financial analysis also emphasise the need for a firm to use industry-wide averages as targets (Fouike, 1968), and there is evidence that firms do adjust their financial ratios to such targets.^ Whittington (1980) identified two principal uses of financial ratios. The traditional, normative use ofthe measurement ofa firm's ratio compared with a standard, and the positive use in estimating empirical relationships, usually for predictive purposes. The former dates back to the late nineteenth century and the increase in US bank credit given as a result of the Civil War when current and non-current items were segregated and the ratio of current assets to current liabilities was developed (Horrigan, 1968; and Dev, 1974), From then the use of ratios both for credit purposes and managerial analysis, focusing on profitability measures soon began. Around 1919 the du Pont Company began to use its famous ratio 'triangle' system to evaluate its operating results, underpinning the modern interfirm comparison scheme introduced in the UK by the British Institute of Management and the British Productivity Council in 1959,

The Analysis and Use of Financial Ratios: A Review Article

Computer simulation calculations on liquid water, aqueous solutions and biological interfaces have been made almost universally assuming pair-additive interactions. Experimental and theoretical evidence implies this is a serious oversimplification. The development and testing of a different approach is reviewed in which many-body forces are specifically taken into account through molecular polarisation. Solution and interfacial properties of aqueous systems are particularly sensitive to such forces.

Cooperative effects in simulated water

Recent evidence of a general, global decline of stratospheric ozone has heightened concern about possible ecological consequences of increases in solar ultraviolet-B (UV-B, 280-320 nm) radiation resulting from ozone depletion. The influence of UV-B radiation (280-320 nanometers) on the morphology of 12 common dicot and monocot crop or weed species was examined to determine whether any common responses could be found that might, in turn, be useful in predicting possible changes in competitive balance under solar UV-B enhancement. Under glasshouse conditions, UV-B exposure (simulating a 20% reduction in stratospheric ozone at Logan, Utah) was found to reduce leaf blade and internode lengths and increase leaf and axillary shoot production in several species. Overall, the directions of these trends were similar in the majority of species that exhibited a significant response. These morphological changes occurred without any significant reduction in total shoot dry matter production. There was no clear distinction in the response of crops and weeds, though monocots were found to be generally more responsive than dicots. Previous work in dense canopies has shown that the photomorphogenetic effects of UV-B alter leaf placement and thereby influence competition for light. Our results suggest that, under these conditions, changes in competitive balancemore » resulting from increased UV-B might be expected more frequently when monocots are involved in mixtures, rather than mixtures of only dicots.« less

Paul Barnes

Papers

Structure and Performance of Cements

An Explanation for the Very Large Breathing Effect of a Metal–Organic Framework during CO2 Adsorption

The Analysis and Use of Financial Ratios: A Review Article

Cooperative effects in simulated water

Morphological responses of crop and weed species of different growth forms to ultraviolet-B radiation