Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Structural Transformations, Composition Anomalies and a Dramatic Collapse of Linear Polymer Chains in Dilute Ethanol-Water Mixtures

Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, excess sound absorption coefficient at low concentrations, and positive deviation from Raoult's law for vapor pressure, to mention a few. These anomalies have been attributed to different, often contradictory origins, but a quantitative understanding is still lacking. We show by computer simulation and theoretical analyses that these anomalies arise from the sudden emergence of a bicontinuous phase that occurs at a relatively low ethanol concentration of x(eth) approximate to 0.06-0.10 (that amounts to a volume fraction of 0.17-0.26, which is a significant range!). The bicontinuous phase is formed by aggregation of ethanol molecules, resulting in a weak phase transition whose nature is elucidated. We find that the microheterogeneous structure of the mixture gives rise to a pronounced nonmonotonic composition dependence of local compressibility and nonmonotonic dependence in the peak value of the radial distribution function of ethyl groups. A multidimensional free energy surface of pair association is shown to provide a molecular explanation of the known negative excess partial volume of ethanol in terms of parallel orientation and hence better packing of the ethyl groups in the mixture due to hydrophobic interactions. The energy distribution of the ethanol molecules indicates additional energy decay channels that explain the excess sound attenuation coefficient in aqueous alcohol mixtures. We studied the dependence of the solvation of a linear polymer chain on the composition of the water-ethanol solvent. We find that there is a sudden collapse of the polymer at x(eth) approximate to 0.05-a phenomenon which we attribute to the formation of the microheterogeneous structures in the binary mixture at low ethanol concentrations. Together with recent single molecule pulling experiments, these results provide new insight into the behavior of polymer chain and foreign solutes, such as enzymes, in aqueous binary mixtures.

Flow visualization in turbulent free convection over horizontal smooth and grooved surfaces

The present paper discusses the flow visualization for turbulent free convection in a tank of water with the bottom surface being a smooth or a grooved surface and the top of the water surface exposed to ambient. The grooved surface is of parallel 90 degrees V-grooves with groove height of 10 mm and groove width of 20 mm. The experiment is carried out with aspect ratio (AR) of 2.9 and Rayleigh number (Ra) in the range, 1.3 x 10(7) - 4 x 10(7). Here AR is the aspect ratio (= width of fluid layer/height of fluid layer). Heat flux at the bottom surface is from electrical heating. From the pH-dye visualization, interesting flow structures are observed and these structures are analyzed with the help of plumes dynamics and temperature variations with time. (C) 2011 Elsevier Ltd. All rights reserved.

Solvent effect on the fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using S-V plots

The fluorescence quenching studies of carboxamide namely (E)-N-(3-Chlorophenyl)-2-(3,4,5-trimethoxybenzylideneamino)-4,5,6,7 tetrahydrobenzob]thiophene-3-carboxamide ENCTTTC] by aniline and carbon tetrachloride in six different solvents namely toluene, cyclohexane, n-hexane, n-heptane, n-decane and n-pentane have been carried out at room temperature with a view to understand the quenching mechanisms. The Stern-Volmer (S-V) plots have been found to be nonlinear with a positive deviation for all the solvents studied. In order to interpret these results we have invoked the ground state complex formation and sphere of action static quenching models. Using these models various quenching rate parameters have been determined. The magnitudes of these parameters suggest that sphere of action static quenching model agrees well with the experimental results. Hence the positive deviation is attributed to the static and dynamic quenching. Further, with the use of Finite Sink approximation model, it was possible to check these bimolecular reactions as diffusion-limited and to estimate independently distance parameter R' and mutual diffusion coefficient D. Finally an effort has been made to correlate the values of R' and D with the values of the encounter distance R and the mutual coefficient D determined using the Edward's empirical relation and Stokes Einstein relation. (C) 2011 Elsevier B.V. All rights reserved.

Geosphere laminations in free groups

We construct for free groups, which are codimension one analogues of geodesic laminations on surfaces. Other analogues that have been constructed by several authors are dimension-one instead of codimension-one. Our main result is that the space of such laminations is compact. This in turn is based on the result that crossing, in the sense of Scott-Swarup, is an open condition. Our construction is based on Hatcher's normal form for spheres in the model manifold.

Defect-Free Hyperbranched Polydithioacetal via Melt Polymerization

Degree of branching (DB) describes the level of structural perfection of a hyperbranched polymer when compared to its defect-free analogue, namely the dendrimer. The strategy most commonly used to achieve high DB values, specifically while using AB(2) type self-condensations, is to design an AB2 monomer wherein the reaction of the first B-group leads to an enhancement of the reactivity of the second one. In the present study, we show that an AB2 monomer carrying a dimethylacetal unit and a thiol group undergoes a rapid self-condensation in the melt under acid-catalysis to yield a hyperbranched polydithioacetal with no linear defects. NMR studies using model systems reveal that the intermediate monothioacetal is relatively unstable under the polymerization conditions and transforms rapidly to the dithioacetal; because this second step occurs irreversibly during polymer formation, it leads to a defect-free hyperbranched polydithioacetal. TGA studies of the polymerization process provided some valuable insights into the kinetics of polymerization. An additional virtue of this approach is that the numerous terminal dimethylacetal groups are very labile and can be quantitatively transformed by treatment with a variety of functional thiols; the terminal dimethylacetals were, thus, reacted with various thiols, such as dodecanethiol, benzyl mercaptan, ethylmercaptopropionate, and so on, to demonstrate the versatility of these systems as sulfur-rich hyperscaffolds to anchor different kinds of functionality on their periphery.

Tunable device properties of free-standing inorganic/organic flexible hybrid structures obtained by exfoliation

We report the fabrication of free-standing flexible inorganic/organic hybrid structures by exfoliating ZnO nanostructured films from the flat indium tin oxide (ITO)/silicon/sapphire substrates using poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS). Strong interaction between ZnO and PEDOT: PSS and the thermomechanical response of PEDOT: PSS are the key issues for the exfoliation to prevail. The performance of the free-standing hybrid structures as rectifiers and photodetectors is better as compared to ITO supported hybrid structures. It is also shown that device properties of hybrid structures can be tuned by using different electrode materials. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729550]

Conflict-Free Coloring for Rectangle Ranges Using O(n.382) Colors

Given a set of points P ⊆ R2, a conflict-free coloring of P w.r.t. rectangle ranges is an assignment of colors to points of P, such that each nonempty axisparallel rectangle T in the plane contains a point whose color is distinct from all other points in P ∩ T . This notion has been the subject of recent interest and is motivated by frequency assignment in wireless cellular networks: one naturally would like to minimize the number of frequencies (colors) assigned to base stations (points) such that within any range (for instance, rectangle), there is no interference. We show that any set of n points in R2 can be conflict-free colored with O(nβ∗+o(1)) colors in expected polynomial time, where β∗ = 3−√5 2 < 0.382.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (similar to 80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

Sensitivity of polyvinylidene fluoride films to mechanical vibration modes and impact after optimizing stretching conditions

The β-phase of polyvinylidene fluoride (PVDF) is well known for its piezoelectric properties. PVDF films have been developed using solvent cast method. The films thus produced are in α-phase. The α-phase is transformed to piezoelectric β-phase when the film is hot-stretched with various different stretching factors at various different temperatures. The films are then characterized in terms of their mechanical properties and surface morphological changes during the transformation from α- to β-phases by using X-ray diffraction, differential scanning calorimeter, Raman spectra, Infrared spectra, tensile testing, and scanning electron microscopy. The films showed increased crystallinity with stretching at temperature up to 80°C. The optimum conditions to achieve β-phase have been discussed in detail. The fabricated PVDF sensors have been tested for free vibration and impact on plate structure, and its response is compared with conventional piezoelectric wafer type sensor. The resonant and antiresonant peaks in the frequency response of PVDF sensor match well with that of lead zirconate titanate wafer sensors. Effective piezoelectric properties and the variations in the frequency response spectra due to free vibration and impact loading conditions are reported. POLYM. ENG. SCI., 2012. © 2012 Society of Plastics Engineers.

Microstructure and Texture Evolution in Interstitial-free (IF) Steel processed by Multi-Axial Forging

In this study, severe plastic deformation (SPD) of Ti-bearing interstitial-free steel was carried out by multi-axial forging (MAF) technique. The grain refinement achieved was comparable to that by other SPD techniques. A considerable heterogeneity was observed in the microstructure and texture. Texture of multi-axially forged steels has been evaluated and reported for the first time. The material exhibited a six-fold increase in the yield strength after four cycles of MAF.

Maximum weight independent sets in hole- and dart-free graphs

The Maximum Weight Independent Set (MWIS) problem on graphs with vertex weights asks for a set of pairwise nonadjacent vertices of maximum total weight. The complexity of the MWIS problem for hole-free graphs is unknown. In this paper, we first prove that the MWIS problem for (hole, dart, gem)-free graphs can be solved in O(n(3))-time. By using this result, we prove that the MWIS problem for (hole, dart)-free graphs can be solved in O(n(4))-time. Though the MWIS problem for (hole, dart, gem)-free graphs is used as a subroutine, we also give the best known time bound for the solvability of the MWIS problem in (hole, dart, gem)-free graphs. (C) 2012 Elsevier B.V. All rights reserved.

Carbonization of solvent and capping agent based enhancement in the stabilization of cobalt nanoparticles and their magnetic study

We describe a hybrid synthetic protocol, the solvated metal atom dispersion (SMAD) method, for the synthesis and stabilization of monodisperse amorphous cobalt nanoparticles. By employing an optimized ratio of a weakly coordinating solvent and a capping agent monodisperse colloidal cobalt nanoparticles (2 +/- 0.5 nm) have been prepared by the SMAD method. However, the as-prepared samples were found to be oxidatively unstable which was elucidated by their magnetic studies. Oxidative stability in our case was achieved via a pyrolysis process that led to the decomposition of the organic solvent and the capping agent resulting in the formation of carbon encapsulated cobalt nanoparticles which was confirmed by Raman spectroscopy. Controlled annealing at different temperatures led to the phase transformation of metallic cobalt from the hcp to fcc phase. The magnetic behaviour varies with the phase and the particle size; especially, the coercivity of nanoparticles exhibited strong dependence on the phase transformation of cobalt. The high saturation magnetization close to that of the bulk value was achieved in the case of the annealed samples. In addition to detailed structural and morphological characterization, the results of thermal and magnetic studies are also presented.

Bromenium-Catalysed Tandem Ring Opening/Cyclisation of Vinylcyclopropanes and Vinylcyclobutanes: A Metal-Free 3+2+1]/4+2+1] Cascade for the Synthesis of Chiral Amidines and Computational Investigation

We present a detailed study of a 3+2+1] cascade cyclisation of vinylcyclopropanes (VCP) catalysed by a bromenium species (Brd+?Xd-) generated in situ, which results in the synthesis of chiral bicyclic amidines in a tandem one-pot operation. The formation of amidines involves the ring-opening of VCPs with Br?X, followed by a Ritter-type reaction with chloramine-T and a tandem cyclisation. The reaction has been further extended to vinylcyclobutane systems and involves a 4+2+1] cascade cyclisation with the same reagents. The versatility of the methodology has been demonstrated by careful choice of VCPs and VCBs to yield bicyclo4.3.0]-, -4.3.1]- and -4.4.0]amidines in enantiomerically pure form. On the basis of the experimental observations and DFT calculations, a reasonable mechanism has been put forth to account for the formation of the products and the observed stereoselectivity. We propose the existence of a p-stabilised homoallylic carbocation at the cyclopropane carbon as the reason for high stereoselectivity. DFT studies at B3LYP/6-311+G** and M06-2X/6-31+G* levels of theory in gas-phase calculations suggest the ring-opening of VCP is initiated at the p-complex stage (between the double bond and Br?X). This can be clearly perceived from the solution-phase (acetonitrile) calculations using the polarisable continuum model (PCM) solvation model, from which the extent of the ring opening of VCP was found to be noticeably high. Studies also show that the formation of zero-bridge bicyclic amidines is favoured over other bridged bicyclic amidines. The energetics of competing reaction pathways is compared to explain the product selectivity.