Bond orientational order, molecular motion, and free energy of high-density DNA mesophases.

By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change between two distinct regions on the liquid-crystalline phase diagram: (i) a higher density hexagonally packed region with long-range bond orientational order in the plane perpendicular to the average molecular direction and (ii) a lower density cholesteric region with fluid-like positional order. X-ray scattering on highly ordered DNA arrays at high density and with the helical axis oriented parallel to the incoming beam showed a sixfold azimuthal modulation of the first-order diffraction peak that reflects the macroscopic bond-orientational order. Transition to the less-dense cholesteric phase through osmotically controlled swelling shows the loss of this bond orientational order, which had been expected from the change in optical birefringence patterns and which is consistent with a rapid onset of molecular positional disorder. This change in order was previously inferred from intermolecular force measurements and is now confirmed by 31P NMR. Controlled reversible swelling and compaction under osmotic stress, spanning a range of densities between approximately 120 mg/ml to approximately 600 mg/ml, allow measurement of the free-energy changes throughout each phase and at the phase transition, essential information for theories of liquid-crystalline states.

Equilibria involving cyanogen iodide and the free energy of cyanogen ...

Thesis t.-p. attached to the cover of the reprint from the Journal of the American chemical society, vol. XL, no. 3, March 1918, by Gilbert N. Lewis and Donald B. Keyes.

Determination of the equilibrium between chlorine, water, hydrochloric acis and chloric acid : the free energy of the chlorate ion /

Thesis (Ph15 .D.)--University of California, Berkeley, 1917.

Protein deposition at polymer surfaces:the bulk and surface structure-property effects of hydrogels

The primary objective of this research has been to investigate the interfacial phenomenon of protein adsorption in relation to the bulk and surface structure-property effect s of hydrogel polymers. In order to achieve this it was first necessary to characterise the bulk and surface properties of the hydrogels, with regard to the structural chemistry of their component monomers. The bulk properties of the hydrogels were established using equilibrium water content measurements, together with water-binding studies by differential scanning calorimetry (D.S.C.). Hamilton and captive air bubble-contact angle techniques were employed to characterise the hydrogel-water interface and from which by a mathematical derivation, the interfacial free energy (ðsw) and the surface free energy components (ð psv, ðdsv, ðsv) were obtained. From the adsorption studies using the radio labelled iodinated (125I) proteins of human serum albumin (H.S.A.) and human fibrinogen (H.Fb.), it was Found that multi-layered adsorption was occurring and that the rate and type of this adsorption was dependent on the physico-chemical behaviour of the adsorbing protein (and its bulk concentration in solution), together with the surface energetics of the adsorbent polymer. A potential method for the invitro evaluation of a material's 'biocompatibility' was also investigated, based on an empirically observed relationship between the adsorption of albumin and fibrinogen and the 'biocompatibility' of polymeric materials. Furthermore, some consideration was also given to the biocompatibility problem of proteinaceous deposit formation on hydrophilic soft' contact lenses and in addition a number of potential continual wear contact lens formulations now undergoing clinical trials,were characterised by the above techniques.

Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Anisotropic surface chemistry of aspirin crystals

The wettability of the (001), (100), and (011) crystallographic facets of macroscopic aspirin crystals has been experimentally investigated using a sessile drop contact angle (θ) method. θ for a nonpolar liquid was very similar for all three facets, though significant θ differences were observed for three polar probe liquids. The observed hydrophobicity of the (001) and (100) facets is ascribed to a reduced hydrogen bonding potential at these surfaces, whilst the observed hydrophilicity of facet (011) may be attributed to presence of surface carboxylic functionalities as confirmed by X-ray photoelectron spectroscopy (XPS). The dispersive component of the surface free energy (γ) was similar for all three facets (35 ± 2 mJ/m). The total surface energy, γs varied between 46 and 60 mJ/m due to significant variations in the polar/acid-base components of γ for all facets. Surface polarity as determined by γ measurements and XPS data were in good agreement, linking the variations in wettability to the concentration of oxygen containing surface functional groups. In conclusion, the wettability and the surface energy of a crystalline organic solid, such as aspirin, was found to be anisotropic and facet dependant, and in this case, related to the presence of surface carboxylic functionalities. © 2007 Wiley-Liss, Inc. and the American Pharmacists Association.

Free energy functional expansion as the generalized approach to the equation of state of dense fluids

A version of the thermodynamic perturbation theory based on a scaling transformation of the partition function has been applied to the statistical derivation of the equation of state in a highpressure region. Two modifications of the equations of state have been obtained on the basis of the free energy functional perturbation series. The comparative analysis of the experimental PV T- data on the isothermal compression for the supercritical fluids of inert gases has been carried out. © 2012.

Path Optimization in Free Energy Calculations

Free energy calculations are a computational method for determining thermodynamic quantities, such as free energies of binding, via simulation.

Currently, due to computational and algorithmic limitations, free energy calculations are limited in scope.

In this work, we propose two methods for improving the efficiency of free energy calculations.

First, we expand the state space of alchemical intermediates, and show that this expansion enables us to calculate free energies along lower variance paths.

We use Q-learning, a reinforcement learning technique, to discover and optimize paths at low computational cost.

Second, we reduce the cost of sampling along a given path by using sequential Monte Carlo samplers.

We develop a new free energy estimator, pCrooks (pairwise Crooks), a variant on the Crooks fluctuation theorem (CFT), which enables decomposition of the variance of the free energy estimate for discrete paths, while retaining beneficial characteristics of CFT.

Combining these two advancements, we show that for some test models, optimal expanded-space paths have a nearly 80% reduction in variance relative to the standard path.

Additionally, our free energy estimator converges at a more consistent rate and on average 1.8 times faster when we enable path searching, even when the cost of path discovery and refinement is considered.

Understanding Co-translational Protein Targeting and Lithium Dendrite Formation through Free Energy Simulations and Coarse-Grained Models

We describe the application of alchemical free energy methods and coarse-grained models to study two key problems: (i) co-translational protein targeting and insertion to direct membrane proteins to the endoplasmic reticulum for proper localization and folding, (ii) lithium dendrite formation during recharging of lithium metal batteries. We show that conformational changes in the signal recognition particle, a central component of the protein targeting machinery, confer additional specificity during the the recognition of signal sequences. We then develop a three-dimensional coarse-grained model to study the long-timescale dynamics of membrane protein integration at the translocon and a framework for the calculation of binding free energies between the ribosome and translocon. Finally, we develop a coarse-grained model to capture the dynamics of lithium deposition and dissolution at the electrode interface with time-dependent voltages to show that pulse plating and reverse pulse plating methods can mitigate dendrite growth.

Improved moisture and hydrocarbons barrier of epoxy resin-based coating

To improve the surface characteristics of epoxy resin coatings, a treatment by fluorine-containing plasma was used to develop a coating with low surface free energy and improved chemical resistance. Through the coating analysis it was possible to verify information about the CF(n) bond formation and the fluorination depth. The best plasma process parameters presented the best fluorination depth, 90 nm, and fluorine concentration was nearly 30%. The improvement in contact angle of water was 50% and of raw petroleum was 130%. Salt spray test proves that the coating fluorination decreases the chance of substrate corrosion.

Effect of sodium, amine and stannous fluoride at the same concentration and different pH on in vitro erosion

Objective: This study aimed to compare the effects 0.5% and 1% sodium, amine and stannous fluoride at different pH on enamel erosion in vitro. Methods: Bovine enamel samples were submitted to a cyclic de- and remineralisation for 3 days. Each day, the samples were exposed for 120 min to pooled human saliva and subsequently treated with one of the fluoride solutions for 3 min: amine fluoride (AmF, 0.5% and 1% F(-)), sodium fluoride (NaF, 0.5% and 1% F(-)), each at pH 3.9 and 7.0, and stannous fluoride (SnF(2), 0.5% and 1% F-), at pH: 3.9. Additionally, two groups were treated with fluoride-free placebo solutions (pH: 3.9 and 7.0) and one group served as control (no fluoridation). Ten specimens each group were inserted in a so-called artificial mouth and eroded six times daily with hydrochloric acid (pH 2.6) for 90 s each intermitted by exposure to artificial saliva (1 h). After 3 days, enamel loss was analyzed profilometrically and evaluated statistically by ANOVA. Results: Only the acidic 0.5% and 1% SnF(2) and 1% AmF solutions were able to reduce erosive enamel loss significantly, while all other solutions and placebos did not differ significantly from the control. Between the acidic SnF(2) and the 1% AmF solutions no significant differences could be detected. Conclusion: At the same concentrations, acidic SnF(2) and AmF may be more effective than NaF to protect enamel against erosion. (C) 2009 Elsevier Ltd. All rights reserved.

Selection of operational parameters for the production of instant soy protein isolate by pulsed fluid bed agglomeration

The objective of this study was to select the optimal operational conditions for the production of instant soy protein isolate (SPI) by pulsed fluid bed agglomeration. The spray-dried SPI was characterized as being a cohesive powder, presenting cracks and channeling formation during its fluidization (Geldart type A). The process was carried out in a pulsed fluid bed, and aqueous maltodextrin solution was used as liquid binder. Air pulsation, at a frequency of 600 rpm, was used to fluidize the cohesive SPI particles and to allow agglomeration to occur. Seventeen tests were performed according to a central composite design. Independent variables were (i) feed flow rate (0.5-3.5 g/min), (ii) atomizing air pressure (0.5-1.5 bar) and (iii) binder concentration (10-50%). Mean particle diameter, process yield and product moisture were analyzed as responses. Surface response analysis led to the selection of optimal operational parameters, following which larger granules with low moisture content and high process yield were produced. Product transformations were also evaluated by the analysis of size distribution, flowability, cohesiveness and wettability. When compared to raw material, agglomerated particles were more porous and had a more irregular shape, presenting a wetting time decrease, free-flow improvement and cohesiveness reduction. (C) 2010 Elsevier B.V. All rights reserved.

Properties of hydrogenated amorphous carbon films deposited by PECVD and modified by SF6 plasma

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structure of redispersible SnO2 nanoparticles

Suspensions of undoped SnO2 nanoparticles and containing Eu3+ ions were prepared by a sol-gel procedure. Using the classical synthesis method ( precipitation), the particles tend to grow by a coarsening process in order to minimize the surface free energy. This effect can strongly be reduced by the addition of an amide and surfactant during the synthesis, which decreases the surface free energy of the colloidal particles. These additives promote the formation of powders composed of very small primary particles formed by a crystallite of 10 Angstrom, and exhibit good redispersion properties. The local and long order structures of the redispersible powder were studied by X-rays absorption spectroscopy at Sn L-I edge and X-rays diffraction, respectively. The structure of the colloidal aggregates in suspension was investigated by small angle X-rays scattering (SAXS). SAXS results indicate the sol are composed by a polidisperse system of hard spheres resulting of agglomeration of the primary particles and their size increasing by agglomeration for progressively higher Eu3+ content.