Diblock copolymer lamellae on sinusoidal and fractal surfaces

A scaling analysis of equilibrium orientation of diblock copolymer molecules on fractal surfaces and a brief comparison with a particular experiment is presented in this paper. This work is motivated by a recent experimental finding that a diblock copolymer film of polystyrene-PMMA, when deposited on a rough substrate, can orient its lamellae from a parallel to a perpendicular configuration depending on the topographical characteristics of the substrate surface. It was found that the RMS height itself is not enough to effect the equilibrium configuration, but the fractal dimension of the surface is also important. In general, the orientation of lamellae is a function of the the power spectral density (PSD) curves of the underlying substrate surface. Assuming the diblock lamellae to behave like an Alexander-deGennes brush, we obtain the free energy expressions for this brush in both parallel and perpendicular orientations in various asymptotic regimes. Comparison of their free energy expressions predicts the equilibrium configuration. By examining the PSD curves and using our scaling results, we are able to qualitatively explain some aspects of the experimental observations regarding the equilibrium orientation of the diblock copolymer lamellae on rough surfaces.     

Metric and multidimensional scaling: efficient tools for clustering molecular conformations

The application of metric and multidimensional scaling to conformer ensembles was demonstrated in this work. An automated process was devised to cluster and assign group memberships and cluster representatives. The method allows rapid clustering, leading to intuitive results that can be visually inspected. Multidimensional scaling was found to be superior to metric scaling for clustering conformers. The performance of different hierarchical clustering algorithms was compared using multidimensional plots, and the group average method was found to perform best.     

Effect of scaling on class modeling with the simca method

The first step in multivariate analysis is almost always the scaling of the variables. The pattern recognition technique SIMCA provides the possibility of scaling the variables over all the objects of the training set (classical scaling), or only over the objects belonging to the same group (separate scaling). The former method of scaling is the more used. The effect of separate scaling on the classification of objects with SIMCA is investigated for a data set consisting of the percentage distribution of fatty acids in olive oils originating from two neighbouring regions in Italy. It is shown that separate scaling has a beneficial effect on the classification.     

Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution

A computational framework is presented for the continuum modeling of cellular biomolecular diffusion influenced by electrostatic driving forces. This framework is developed from a combination of state-of-the-art numerical methods, geometric meshing, and computer visualization tools. In particular, a hybrid of (adaptive) finite element and boundary element methods is adopted to solve the Smoluchowski equation (SE), the Poisson equation (PE), and the Poisson-Nernst-Planck equation (PNPE) in order to describe electrodiffusion processes. The finite element method is used because of its flexibility in modeling irregular geometries and complex boundary conditions. The boundary element method is used due to the convenience of treating the singularities in the source charge distribution and its accurate solution to electrostatic problems on molecular boundaries. Nonsteady-state diffusion can be studied using this framework, with the electric field computed using the densities of charged small molecules and mobile ions in the solvent. A solution for mesh generation for biomolecular systems is supplied, which is an essential component for the finite element and boundary element computations. The uncoupled Smoluchowski equation and Poisson-Boltzmann equation are considered as special cases of the PNPE in the numerical algorithm, and therefore can be solved in this framework as well. Two types of computations are reported in the results: stationary PNPE and time-dependent SE or Nernst-Planck equations solutions. A biological application of the first type is the ionic density distribution around a fragment of DNA determined by the equilibrium PNPE. The stationary PNPE with nonzero flux is also studied for a simple model system, and leads to an observation that the interference on electrostatic field of the substrate charges strongly affects the reaction rate coefficient. The second is a time-dependent diffusion process: the consumption of the neurotransmitter acetylcholine by acetylcholinesterase, determined by the SE and a single uncoupled solution of the Poisson-Boltzmann equation. The electrostatic effects, counterion compensation, spatiotemporal distribution, and diffusion-controlled reaction kinetics are analyzed and different methods are compared.     

The structural stability principle and branching points on multidimensional potential energy surfaces

The chemically interesting potential energy surfaces (PES) are considered on which the conditions underlying application of structural stability principle and Morse inequalities are violated. The possibility of treatment of singular branching points on a PES slope in terms of intrinsic reaction curves (IRC) is discussed.     

Complex morphogenesis of surfaces: theory and experiment on coupling of reaction-diffusion patterning to growth

Reaction-diffusion theory for pattern formation is considered in relation to processes of biological development in which there is continuous growth and shape change as each new pattern forms. This is particularly common in the plant kingdom, for both unicellular and multicellular organisms. In addition to the feedbacks in the chemical dynamics, there is then another loop linking size and shape changes with the reaction-diffusion patterning of growth controllers in the growing region. In studies by computation, the codes must incorporate, alongside the usual solvers of the partial differential dynamic equations, a versatile growth code, to express any kind of shape change. We have found that regulation of shape change in particular ways (e.g. to make narrow-angle branchings) demands new features in our chemical mechanisms. Our growth algorithm is for a surface growing tangentially, but moving outward and changing shape to accommodate the extra area. This is potentially applicable both to the tunica layer of multicellular plant meristems and to the growing tip of the cell surface, e.g. in the morphogenesis of single-celled chlorophyte algae which display branching processes: whorl formation in Acetabularia (Dasycladales) and repeated dichotomous branching in Micrasterias (Desmidiaceae). For computational studies, a hemispherical shell is a reasonable idealization of the initial shape. We describe results of two types of study: (1) Pattern formation by three reaction-diffusion models, with contrasted nonlinearities, on the hemispherical shell, particularly to find conditions for robust formation of annular pattern or pattern for dichotomous branching, both of which are common in plants. (2) Sequential dichotomous branchings in a system growing and changing in shape from the hemispherical start.     

Vibrational recognition of adsorption sites for CO on platinum and platinum-ruthenium surfaces

We have studied the vibrational properties of CO adsorbed on platinum and platinum-ruthenium surfaces using density-functional perturbation theory within the Perdew-Burke-Ernzerhof generalized-gradient approximation. The calculated C-O stretching frequencies are found to be in excellent agreement with spectroscopic measurements. The frequency shifts that take place when the surface is covered with ruthenium monolayers are also correctly predicted. This agreement for both shifts and absolute vibrational frequencies is made more remarkable by the frequent failure of local and semilocal exchange-correlation functionals in predicting the stability of the different adsorption sites for CO on transition metal surfaces. We have investigated the chemical origin of the C-O frequency shifts introducing an orbital-resolved analysis of the force and frequency density of states, and assessed the effect of donation and backdonation on the CO vibrational frequency using a GGA+molecular U approach. These findings rationalize and establish the accuracy of density-functional calculations in predicting absolute vibrational frequencies, notwithstanding the failure in determining relative adsorption energies, in the strong chemisorption regime.     

Total luminescence spectroscopy with pattern recognition for classification of edible oils

Total luminescence spectroscopy combined with pattern recognition has been used to discriminate between four different types of edible oils, extra virgin olive (EVO), non-virgin olive (NVO), sunflower (SF) and rapeseed (RS) oils. Simplified fuzzy adaptive resonance theory mapping (SFAM), traditional back propagation (BP) and radial basis function (RBF) neural networks provided 100% classification for 120 samples, SFAM was found to be the most efficient. The investigation was extended to the adulteration of percentage v/v SF or RS in EVO at levels from 5% to 90% creating a total of 480 samples. SFAM was found to be more accurate than RBF and BP for classification of adulterant level. All misclassifications for SFAM occurred at the 5% v/v level resulting in a total of 99.375% correctly classified oil samples. The percentage of adulteration may be described by either RBF network (2.435% RMSE) or a simple Euclidean distance relationship of the principal component analysis (PCA) scores (2.977% RMSE) for v/v RS in EVO adulteration.     

Spontaneous formation of fractal structures on triglyceride surfaces with reference to their super water-repellent properties

Alkylketene dimer (AKD), a kind of wax, has been known to form fractal surfaces spontaneously and show super water-repellency. Such formation of water-repellent and fractal surfaces was also found in this work for triglycerides. Since the crystal phase transitions of these waxes were well studied, we studied the formation of their fractal surfaces through contact angle measurements, differential scanning calorimetry (DSC), and X-ray diffraction (XRD). From time-dependent contact angle measurements, it was found that the formation of super water-repellent surfaces with fractal structures occurred spontaneously also on the triglyceride surfaces at different temperatures. The freshly solidified triglyceride surfaces were almost transparent, and their initial contact angles of water were close to 110 degrees. The surfaces then became rough and clouded after being incubated for a certain time at a specified temperature. The super water-repellent surfaces were quite rough and showed fractal structures with the dimension of ca. 2.2 calculated from the scanning electron microscopic (SEM) images by the box-counting method. The phase transformation from a metastable state to a stable cystalline one after the solidification from the melt of triglycerides was clearly observed by DSC and XRD measurements. The fractal crystalline structures and the super water-repellency resulted from this phase transformation and the crystal growth. Ensuring the initial sample solidified into the metastable state and curing the surface at an appropriate temperature are key factors for the successful preparation of fractal triglyceride surfaces by the solidification method.     

Surfactant adsorption on solid surfaces: recognition between heterogeneous surfaces and adsorbed surfactant aggregates

We study the possibility of the recognition of surface heterogeneities with surfactant adsorption by performing Monte Carlo simulations. It is found that when each patch size of a heterogeneous surface is capable of being commensurate with the size of aggregates adsorbed on the constituent homogeneous surfaces, the adsorption isotherm of the system will display both adsorption characteristics for each homogeneous surface. Otherwise, one or more adsorption characteristics will be spoiled or destroyed. Therefore, the adsorption isotherm of surfactants on a heterogeneous surface provides a signal of recognition.     

Catalytic spatiotemporal thermal patterns during CO oxidation on cylindrical surfaces: experiments and simulations

Dynamics of spatiotemporal thermal patterns during the catalytic CO oxidation over Pd supported on a glass-fiber catalytic cloth rolled into a tube of 20 mm diameter and 80 mm length has been studied in a continuous flow reactor by IR thermography. A specially designed aluminum mirror built in the reactor provided image of the entire surface of the horizontally held catalytic tube. With flow in the main axial direction and through the tube surface, we observed periodic motions of a pulse, which was born downstream and propagated upstream. The temperature pulse motion was accompanied by conversion oscillations of CO2. With flow in the main axial direction, parallel to the surface, we observed a stationary hot zone after an oscillatory transient. These patterns can be simulated with a plug-flow-reactor-like heterogeneous reactor model that incorporates previously determined kinetic and transport parameters.     

Adsorption and freezing of diblock copolymers on stripe-patterned surfaces: a scaling analysis

We present the results of scaling analysis of diblock copolymers adsorbed on stripe-patterned surfaces of various widths. Our previous studies [K. Sumithra and E. Straube, J. Chem. Phys. 125, 154701 (2006)] show that the adsorption of diblock copolymer on patterned surfaces yields two peaks in the specific heat capacity, thereby indicating two transition. In the current study, we characterize these two transitions. The scaling of the adsorption energy data proves that the first peak in the heat capacity curve is, in fact, associated with the adsorption transition. We found that for this transition the classical scaling laws are obeyed and that the critical crossover exponent is unaltered with respect to the case of homogeneous polymers. However, we found a change in the scaling exponent in the case of parallel component of the radius of gyration. It is evident from the scaling analysis of the parallel component of the radius of gyration that the chain is stretched along the direction of the stripes. The scaling plot shows, for (square root )/Nnu, an exponent of approximately 0.55 which is much different from that expected of a self-avoiding chain (nud=2-nu)/phi which is 0.25. The observed value is closer to an exponent of (nud=1-nu)/phi=0.69, for a completely stretched chain in one dimension. The perpendicular component of the radius of gyration shows deviation from the power law and the slope is steeper than the expected value of -2. We have also defined an order parameter to characterize the second transition and have found that it corresponds to a freezing transition where there are only a few dominant conformations. The perpendicular component of the radius of gyration also supports this information.     

Self-complementary recognition of supramolecular urea-aminotriazines in solution and on surfaces

The recognition of self-complementary quadruple urea-aminotriazine (UAT)-based hydrogen-bonded arrays was investigated in solution and at surfaces. For this purpose, an UAT-based donor-acceptor-donor-acceptor (DADA) array and complementary receptors were synthesized. Two-dimensional proton nuclear magnetic resonance ((1)H NMR) measurements in CDCl(3) pointed at an intramolecular hydrogen-bond stabilization of the UAT, which promotes a planar molecular geometry and, thereby, results in a significant stabilization of the dimeric complex. The bond strength of the UAT dimers at surfaces was determined by atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS) in hexadecane. The UAT receptor was immobilized on gold surfaces using an ultrathin layer of ethylene glycol terminated lipoic acid and isocyanate chemistry. The layers obtained and the reversible self-complementary recognition were thoroughly characterized with contact angle measurements, grazing angle Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and AFM. Loading rate-dependent SMFS measurements yielded a barrier width x(β) and a bond lifetime at zero force t(off)(0) of 0.29 ± 0.02 nm and 100 ± 80 ms, respectively. The value of the corresponding off-rate constant k(off) suggests a substantially larger value of the dimerization constant compared to theoretical predictions, which is fully in line with the additional intramolecular hydrogen-bond stabilization detected in solution by (1)H NMR spectroscopy.     

Nonclassical critical indices in the statistical theory of liquids and equations of state with regular and scaling components

Nonclassical critical indices γ = 9/8 and β = 3/8 obtained in works using the statistical theory of liquids are used to approximate data on the isothermal compressibility of ⁴He and SF₆ on critical isochores and binodals, and on the shape of a binodal. The ratio of asymptotic compressibility coefficients Γ ₀ ⁺ /Γ ₀ ^? on critical isochores and binodals is determined from experiments using statistical theory and it is shown that Γ ₀ ⁺ /Γ ₀ ^? coincides with the magnitude of this ratio for linear scaling model with γ = 9/8 and β = 3/8 indices. Highly accurate P-ρ-T data on ⁴He and SF₆ are approximated at these values of the indices using new combined equations of state that include regular and scaling components. The advantage of describing of P-ρ-T data in this manner, compared to describing them with the same equations of state using the critical indices of the three-dimensional Ising model, is demonstrated.     

Correlation between the fractal dimension of fracture surfaces and fracture toughness for ductile polymer materials

A microcrack-shear band chain model for the fracture of ductile materials is proposed. The fractal dimension (D) of the fracture surfaces is derived and correlated with the fracture toughness (K_Ic) of ductile materials. The fractal dimension of the fracture surface is predicted to have an inverse trend with the fracture toughness. The theoretical results are consistent with the experimental results of some polymers and metals. © 1994 John Wiley & Sons, Inc.     

Micellization of telechelic associative polymers: self-consistent field modeling and comparison with scaling concepts

We present numerical results from self-consistent field calculations on the micellization of telechelic associative polymers and their mono-functional analogues. These results are confronted with relatively simple scaling concepts. The proportionality of the critical micelle concentration (CMC) with the hydrophilic backbone length, as found in the calculations, shows good correspondence with a scaling argument based on the entropic penalty of loop formation. It is also shown that models for the conformation of spherical brushes can be applied to predict the structure of the flowerlike micelles formed by these telechelic polymers. Furthermore, we find good agreement between the numerical dependence of the aggregation number upon both backbone and terminal hydrophobe length and an analytical expression derived from the well-known Daoud-Cotton model by introducing a correction for the finite size of the micellar core.     

Stable isotope-free quantitative shotgun proteomics combined with sample pattern recognition for rapid diagnostics

Mass spectrometry (MS) has become a powerful tool for the quantitative analysis of complex protein samples. A high-throughput strategy for the comparative analysis of multiple protein samples with high complexity becomes more and more important. Two strategies, spectral count and peak intensity, for label-free MS analysis of prefractionated complex mixtures have been described recently to be useful for quantitation. Here we compare both strategies for rapid and quantitative 1-D shotgun LC/MS/MS analyses of highly complex protein mixtures using silica-based monolithic columns. First, we validated linearity and sensitivity of these methods by spiking varying amounts of an internal standard protein in a complex plant protein extract. Secondly, quantitative data of proteins of Medicago truncatula nodules were visualized with independent components analysis using data either obtained from spectral count or peak integration performed with commercial software. Spectral count showed apparent advantages over peak integration because several peptides per protein are automatically averaged, the linear dynamic range of quantitation increases in complex matrices and the number of quantified proteins surpasses the number of proteins using peak integration. Thus, for the need of rapid comparative analysis of highly complex protein samples, spectral count enables sample pattern recognition and identification of biomarkers in nongel based proteomic studies.     

Analytical modeling and thermodynamic analysis of robust superhydrophobic surfaces with inverse-trapezoidal microstructures

A polydimethylsiloxane (PDMS) elastomer surface with perfectly ordered microstructures having an inverse-trapezoidal cross-sectional profile (simply PDMS trapezoids) showed superhydrophobic and transparent characteristics under visible light as reported in our previous work. The addition of a fluoropolymer (Teflon) coating enhances both features and provides oleophobicity. This paper focuses on the analytical modeling of the fabricated PDMS trapezoids structure and thermodynamic analysis based on the Gibbs free energy analysis. Additionally, the wetting characteristics of the fabricated PDMS trapezoids surface before and after the application of the Teflon coating are analytically explained. The Gibbs free energy analysis reveals that, due to the Teflon coating, the Cassie-Baxter state becomes energetically more favorable than the Wenzel state and the contact angle difference between the Cassie-Baxter state and the Wenzel state decreases. These two findings support the robustness of the superhydrophobicity of the fabricated Teflon-coated PDMS trapezoids. This is then verified via the impinging test of a water droplet at a high speed. The dependencies of the design parameters in the PDMS trapezoids on the hydrophobicity are also comprehensively studied through a thermodynamic analysis. Geometrical dependency on the hydrophobicity shows that overhang microstructures do not have a significant influence on the hydrophobicity. In contrast, the intrinsic contact angle of the structural material is most important in determining the apparent contact angle. On the other hand, the experimental results showed that the side angles of the overhangs are critical not for the hydrophobic but for the oleophobic property with liquids of a low surface tension. Understanding of design parameters in the PDMS trapezoids surface gives more information for implementation of superhydrophobic surfaces.     

Recognizing chromatographic peaks with pattern recognition methods III. Application of the algorithm for peak recognition in trace analysis

Summary The application of a newly developed peak recognition algorithm is shown. This algorith is based on the KNN method, one of the pattern recognition methods. It is shown that peaks with a S/N-ratio down to one can be safely recognized. This is also possible if the baseline has not only detector noise, but has other disturbances, e.g., noise signals which are generated by a reaction detector. The recognition ability of the algorithm is demonstrated by a standard chromatogram with three different concentrations and with two different sampling rates. The improvement against the classical algorithm is demonstrated. Some properties of the algorithm are discussed.