Fourier transform convolution integrals applied to generalized Born molecular volume.

Generalized Born methods are currently among the solvation models most commonly used for biological applications. We reformulate the generalized Born molecular volume method initially described by (Lee et al, 2003, J Phys Chem, 116, 10606; Lee et al, 2003, J Comp Chem, 24, 1348) using fast Fourier transform convolution integrals. Changes in the initial method are discussed and analyzed. Finally, the method is extensively checked with snapshots from common molecular modeling applications: binding free energy computations and docking. Biologically relevant test systems are chosen, including 855-36091 atoms. It is clearly demonstrated that, precision-wise, the proposed method performs as good as the original, and could better benefit from hardware accelerated boards.

Flight energetics in relation to sexual differences in the mating behaviour of a mayfly, Siphlonurus aestivalis

Mayflies (Ephemeroptera) are known to have short adult life-spans. Adults are unable to feed, and they utilize reserves stored during their aquatic larval stage. Energy reserves (fat, glycogen, and free sugars) of mature larvae, subimagoes and imagoes of both sexes of Siphlonurus aestivalis Eaton were compared. All the stages of both sexes had low glycogen and free sugar contents, and the only significant change occurred during the transformation of the mature larva to subimago when almost all the reserves of free sugars were used up. Glycogen and free sugars may serve as energy sources permitting individuals to swim and fly out of the water during emergence. Fat made up most of the energy reserves of mature larvae and was the main source of energy used during the final development of both sexes. Young adult males had high fat reserves which they used as a source of energy for their swarming flights. In contrast, females did not seem to use a significant amount of fat for flight. This difference is probably related to the different mating strategies of the sexes in this species. Males perform long flights waiting for females, whereas females perform only brief flights to mate and reproduce.

Activation of human meiosis-specific recombinase Dmc1 by Ca2+.

Rad51 and its meiotic homolog Dmc1 are key proteins of homologous recombination in eukaryotes. These proteins form nucleoprotein complexes on single-stranded DNA that promote a search for homology and that perform DNA strand exchange, the two essential steps of genetic recombination. Previously, we demonstrated that Ca2+ greatly stimulates the DNA strand exchange activity of human (h) Rad51 protein (Bugreev, D. V., and Mazin, A. V. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 9988-9993). Here, we show that the DNA strand exchange activity of hDmc1 protein is also stimulated by Ca2+. However, the mechanism of stimulation of hDmc1 protein appears to be different from that of hRad51 protein. In the case of hRad51 protein, Ca2+ acts primarily by inhibiting its ATPase activity, thereby preventing self-conversion into an inactive ADP-bound complex. In contrast, we demonstrate that hDmc1 protein does not self-convert into a stable ADP-bound complex. The results indicate that activation of hDmc1 is mediated through conformational changes induced by free Ca2+ ion binding to a protein site that is distinct from the Mg2+.ATP-binding center. These conformational changes are manifested by formation of more stable filamentous hDmc1.single-stranded DNA complexes. Our results demonstrate a universal role of Ca2+ in stimulation of mammalian DNA strand exchange proteins and reveal diversity in the mechanisms of this stimulation.

The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase.

Hsp70-Hsp40-NEF and possibly Hsp100 are the only known molecular chaperones that can use the energy of ATP to convert stably pre-aggregated polypeptides into natively refolded proteins. However, the kinetic parameters and ATP costs have remained elusive because refolding reactions have only been successful with a molar excess of chaperones over their polypeptide substrates. Here we describe a stable, misfolded luciferase species that can be efficiently renatured by substoichiometric amounts of bacterial Hsp70-Hsp40-NEF. The reactivation rates increased with substrate concentration and followed saturation kinetics, thus allowing the determination of apparent V(max)' and K(m)' values for a chaperone-mediated renaturation reaction for the first time. Under the in vitro conditions used, one Hsp70 molecule consumed five ATPs to effectively unfold a single misfolded protein into an intermediate that, upon chaperone dissociation, spontaneously refolded to the native state, a process with an ATP cost a thousand times lower than expected for protein degradation and resynthesis.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

Effects of medium on nuclear properties in multifragmentation

In multifragmentation of hot nuclear matter, properties of fragments embedded in a soup of nucleonic gas and other fragments should be modified as compared with isolated nuclei. Such modifications are studied within a simple model where only nucleons and one kind of heavy nuclei are considered. The interaction between different species is described with a momentum-dependent two-body potential whose parameters are fitted to reproduce properties of cold isolated nuclei. The internal energy of heavy fragments is parametrized according to a liquid-drop model with density- and temperature-dependent parameters. Calculations are carried out for several subnuclear densities and moderate temperatures, for isospin-symmetric and asymmetric systems. We find that the fragments get stretched due to interactions with the medium and their binding energies decrease with increasing temperature and density of nuclear matter.

Determination of compression behaviour of coating layer

The strength properties of paper coating layer are very important in converting and printing operations. Too great or low strength of the coating can affect several problems in printing. One of the problems caused by the strength of coating is the cracking at the fold. After printing the paper is folded to final form and the pages are stapled together. In folding the paper coating can crack causing aesthetic damage over printed image or in the worst case the centre sheet can fall off in stapling. When folding the paper other side undergoes tensile stresses and the other side compressive stresses. If the difference between these stresses is too high, the coating can crack on the folding. To better predict and prevent cracking at the fold it is good to know the strength properties of coating layer. It has measured earlier the tensile strength of coating layer but not the compressive strength. In this study it was tried to find some way to measure the compressive strength of the coating layer and investigate how different coatings behave in compression. It was used the short span crush test, which is used to measure the in-plane compressive strength of paperboards, to measure the compressive strength of the coating layer. In this method the free span of the specimen is very small which prevent buckling. It was measured the compressive strength of free coating films as well as coated paper. It was also measured the tensile strength and the Bendtsen air permeance of the coating film. The results showed that the shape of pigment has a great effect to the strength of coating. Platy pigment gave much better strength than round or needle-like pigment. On the other hand calcined kaolin, which is also platy but the particles are aggregated, decreased the strength substantially. The difference in the strength can be explained with packing of the particles which is affecting to the porosity and thus to the strength. The platy kaolin packs up much better than others and creates less porous structure. The results also showed that the binder properties have a great effect to the compressive strength of coating layer. The amount of latex and the glass transition temperature, Tg, affect to the strength. As the amount of latex is increasing, the strength of coating is increasing also. Larger amount of latex is binding the pigment particles better together and decreasing the porosity. Compressive strength was increasing when the Tg was increasing because the hard latex gives a stiffer and less elastic film than soft latex.

Review of the synthesis of layered double hydroxides: a thermodynamic approach

The synthesis of layered double hydroxides (LDHs) by hydrothermal-LDH reconstruction and coprecipitation methods is reviewed using a thermodynamic approach. A mixture model was used for the estimation of the thermodynamics of formation of LDHs. The synthesis and solubility of LDHs are discussed in terms of standard molar Gibbs free energy change of reaction. Data for numerous divalent and trivalent metals as well as for some monovalent and tetravalent metals that may be part of the LDH structure have been compiled. Good agreement is found between theoretical and experimental data. Diagrams and tables for the prediction of possible new LDH materials are provided.

An Interface Damage Model for the Simulation of Delamination Under Variable-Mode Ratio in Composite Materials

A thermodynamically consistent damage model for the simulation of progressive delamination under variable mode ratio is presented. The model is formulated in the context of the Damage Mechanics. The constitutive equation that results from the definition of the free energy as a function of a damage variable is used to model the initiation and propagation of delamination. A new delamination initiation criterion is developed to assure that the formulation can account for changes in the loading mode in a thermodynamically consistent way. The formulation proposed accounts for crack closure effets avoiding interfacial penetration of two adjacent layers aftercomplete decohesion. The model is implemented in a finite element formulation. The numerical predictions given by the model are compared with experimental results

Synthesis of quinoxaline 1,4-di-N-oxide derivatives on solid support using room temperature and microwave-assisted solvent-free procedures

We describe the synthesis of 12 new ethyl and methyl quinoxaline-7-carboxylate 1,4-di-N-oxide derivatives on solid supports with room temperature and microwave-assisted solvent-free procedures. Results show that solid supports have good catalytic activity in the formation of quinoxaline 1,4-di-N-oxide derivatives. We found that florisil and montmorillonite KSF and K10 could be used as new, easily available, inexpensive alternatives of catalysts. Additionally, room temperature and microwave-irradiation solvent-free synthesis was more efficient than a conventional procedure (Beirut reaction), reducing reaction time and increasing yield.

INVESTIGAÇÃO DA SUPRESSÃO DE FLUORESCÊNCIA DE SORO ALBUMINA BOVINA E HUMANA POR COMPLEXO DE RUTÊNIO

The binding of [RuCl2(L)] (L = N,N-bis(7-methyl-2-pyridylmethylene)-1,3-diiminopropane) to bovine and human serum albumin was investigated by the fluorescence quenching technique. The comparison of the quenching effect of serum albumin fluorescence by ruthenium complex allowed the estimation of subdomain IB in BSA and subdomain IIA in HSA as the binding sites for this complex. The results of fluorescence titration revealed that ruthenium complex quenches the intrinsic fluorescence of BSA through a dynamic quenching mechanism, while HSA has a static quenching mechanism. The thermodynamic parameters indicated that hydrophobic forces played a major role in the binding of ruthenium complex to proteins. The process of binding was a spontaneous process in which Gibbs free energy change was negative.

A model for specific interactions of manganese-phthalocyanine in protic media

Extinction coefficients (e) changes of manganese phthalocyanine (Mn-Pc) were studied in different organic solvents and related to solvent polarity scales; (Kosower's values (Z), Dimroth's values (E T), donor numbers (DN) and linear solvation energy relationships (LSER) or linear free energy relationships (LFER));, theoretical molecular orbital calculations and ligand/solvent coordination processes in order to predict molecular interaction with the medium and identification of predominant intermolecular forces.

Study of complexes of cadmium with some L-amino acids and vitamin-C by voltammetric technique

Voltammetric technique was used to study the binary and ternary complexes of cadmium with L-amino acids and vitamin-C (L-ascorbic acid) at pH =7.30 ± 0.01, µ = 1.0M KNO3 at 25ºC and 35ºC. Cd (II) formed 1:1:1, 1:1:2 and 1:2:1 complexes with L-lysine, L-ornithine, L-threonine, L-serine, L-phenylglycine, L-phenylalanine, L-glutamic acid and L-aspartic acid used as primary ligands and L-ascorbic acid used as secondary ligand. The trend of stability constant of complexes was L-lysine < L-ornithine < L-threonine < L-serine < L-phenylglycine < L-phenylalanine < L-glutamic acid < L-aspartic acid which can be explained on the basis of size, basicity and steric hindrance of ligands. The values of stability constant (log β) varied from 2.23 to11.33 confirm that these drugs i.e. L-amino acids or in combination with L-ascorbic acid or their complexes could be used against Cd (II) toxicity. The study has been carried out at 35ºC also to determine the thermodynamic parameters such as enthalpy change (ΔH), Free energy change (ΔG) and entropy change (ΔS) respectively.

Influence of plasma modification on surface properties and offset printability of coated paper

The properties of the paper surface play a crucial role in ensuring suitable quality and runnability in various converting and finishing operations, such as printing. Plasma surface modification makes it possible to modify the surface chemistry of paper without altering the bulk material properties. This also makes it possible to investigate the role of the surface chemistry alone on printability without influencing the porous structure of the pigment-coated paper. Since the porous structure of a pigment coating controls both ink setting and optical properties, surface chemical changes created by a plasma modification have a potential to decouple these two effects and to permit a better optimization of them both. The aim of this work was to understand the effects of plasma surface modification on paper properties, and how it influences printability in the sheet-fed offset process. The objective was to broaden the fundamental understanding of the role of surface chemistry on offset printing. The effects of changing the hydrophilicity/ hydrophobicity and the surface chemical composition by plasma activation and plasma coatings on the properties of coated paper and on ink-paper interactions as well as on sheet-fed offset print quality were investigated. In addition, the durability of the plasma surface modification was studied. Nowadays, a typical sheet-fed offset press also contains units for surface finishing, for example UVvarnishing. The role of the surface chemistry on the UV-varnish absorption into highly permeable and porous pigment-coated paper was also investigated. With plasma activation it was possible to increase the surface energy and hydrophilicity of paper. Both polar and dispersion interactions were found to increase, although the change was greater in the polar interactions due to induced oxygen molecular groups. The results indicated that plasma activation takes place particularly in high molecular weight components such as the dispersion chemicals used to stabilize the pigment and latex particles. Surface composition, such as pigment and binder type, was found to influence the response to the plasma activation. The general trend was that pilot-scale treatment modified the surface chemistry without altering the physical coating structure, whereas excessive laboratory-scale treatment increased the surface roughness and reduced the surface strength, which led to micro-picking in printing. It was shown that pilot-scale plasma activation in combination with appropriate ink oils makes it possible to adjust the ink-setting rate. The ink-setting rate decreased with linseed-oil-based inks, probably due to increased acid-base interactions between the polar groups in the oil and the plasma-treated paper surface. With mineral-oil-based inks, the ink setting accelerated due to plasma activation. Hydrophobic plasma coatings were able to reduce or even prevent the absorption of dampening water into pigmentcoated paper, even when the dampening water was applied under the influence of nip pressure. A uniform hydrophobic plasma coating with sufficient chemical affinity with ink gave an improved print quality in terms of higher print density and lower print mottle. It was also shown that a fluorocarbon plasma coating reduced the free wetting of the UV-varnish into the highly permeable and porous pigment coating. However, when the UV-varnish was applied under the influence of nip pressure, which leads to forced wetting, the role of the surface chemical composition seems to be much less. A decay in surface energy and wettability occurred during the first weeks of storage after plasma activation, after which it leveled off. However, the oxygen/carbon elemental ratio did not decrease as a function of time, indicating that ageing could be caused by a re-orientation of polar groups or by a contamination of the surface. The plasma coatings appeared to be more stable when the hydrophobicity was higher, probably due to fewer interactions with oxygen and water vapor in the air.

Substitution-Newton-Raphson method applied to the modeling of a vapour compression refrigeration system using different representations of the thermodynamic properties of R-134a

This paper gives a detailed presentation of the Substitution-Newton-Raphson method, suitable for large sparse non-linear systems. It combines the Successive Substitution method and the Newton-Raphson method in such way as to take the best advantages of both, keeping the convergence features of the Newton-Raphson with the low requirements of memory and time of the Successive Substitution schemes. The large system is solved employing few effective variables, using the greatest possible part of the model equations in substitution fashion to fix the remaining variables, but maintaining the convergence characteristics of the Newton-Raphson. The methodology is exemplified through a simple algebraic system, and applied to a simple thermodynamic, mechanical and heat transfer modeling of a single-stage vapor compression refrigeration system. Three distinct approaches for reproducing the thermodynamic properties of the refrigerant R-134a are compared: the linear interpolation from tabulated data, the use of polynomial fitted curves and the use of functions derived from the Helmholtz free energy.