The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode analysis for multiple scales on a high-resolution protein data set using various cutoff radii to define the residues considered to be interacting, or the extent of cooperativity of their motions. These scales include the residue-, atomic-, proton-, and explicit solvent-levels. Interestingly, atomic, proton, and explicit solvent level calculations all provide similar results at the same cutoff value, with the computed mean-square fluctuations showing only a slightly higher correlation (0.61) with the experimental temperature factors from crystallography than the results of the residue-level coarse-graining. The qualitative behavior of each level of coarse graining is similar at different cutoff values. The correlations between these fluctuations and the number of internal contacts improve with increased cutoff values. Our results demonstrate that atomic level elastic network models provide an improved representation for the collective motions of proteins compared to the coarse-grained models.     

Highly Recyclable and Tough Elastic Vitrimers from a Defined Polydimethylsiloxane Network

Despite intensive research on sustainable elastomers, achieving elastic vitrimers with significantly improved mechanical properties and recyclability remains a scientific challenge. Herein, inspired by the classical elasticity theory, we present a design principle for ultra-tough and highly recyclable elastic vitrimers with a defined network constructed by chemically crosslinking the pre-synthesized disulfide-containing polydimethylsiloxane (PDMS) chains with tetra-arm polyethylene glycol (PEG). The defined network is achieved by the reduced dangling short chains and the relatively uniform molecular weight of network strands. Such elastic vitrimers with the defined network, i.e., PDMS-disulfide-D, exhibit significantly improved mechanical performance than random analogous, previously reported PDMS vitrimers, and even commercial silicone-based thermosets. Moreover, unlike the vitrimers with random network that show obvious loss in mechanical properties after recycling, those with the defined network enable excellent thermal recyclability. The PDMS-disulfide-D also deliver comparable electrochemical signals if utilized as substrates for electromyography sensors after the recycling. The multiple relaxation processes are revealed via a unique physical approach. Multiple techniques are also applied to unravel the microscopic mechanism of the excellent mechanical performance and recyclability of such defined network.     

Partitioning technique procedure revisited: Formalism and first application to atomic problems

Usually the partitioning technique (PT) has been studied under two aspects: (i) as a numerical tool for solving secular equations of high order, and (ii) as a theoretical method related to the infinite‐order perturbation theory and the iteration–variation methods. Here it is shown that there exists a form of the PT equations which allows us to determine explicitly the spectrum and eigenstates of the Hamiltonian operator for different forms of potentials without the utilization of perturbative expansions or iterative equations of the type E=f(E). As a first application of the new approach, we consider the hydrogen‐atom in strong magnetic fields (B ~ 10⁹ G). This revised version was published online in July 2006 with corrections to the Cover Date.     

基于弹性网络模型的麦芽糖转运蛋白功能残基的识别

基于弹性网络模型的热力学方法, 识别出麦芽糖转运蛋白质体系中的关键残基, 探讨了麦芽糖转运蛋白内长程协同效应, 研究结果有助于更好地理解该转运体系发挥生物学功能的分子机制.     

Imidazolium-Based Ionic Network as a Robust Heterogeneous Catalyst in Synthesis of Phenacyl Derivatives

A new imidazolium-based poly(ionic liquid) has been synthesized and used as a robust heterogeneous catalyst for the preparation of phenacyl derivatives by an S_N2 reaction of different phenacyl bromides with a broad range of nucleophiles. The products are obtained in high yields under mild conditions. The catalyst can be recycled efficiently.

     

Energetic Contribution to the Elastic Force in Polyphenylmethylsiloxane Networks

Abstract

Energetic contribution to the total elastic force in polyphenylmethylsiloxane networks has been measured in order to elucidate the influence of the phenyl group on chain con -formational mobility. A value of 0.20 ± 0.03 for f_e /f was found.     

Elastic properties of crosslinked poly(vinyl alcohol) gels: Network topology

Current network theory exhibits inconsistencies which show up particularly clearly in deformation of networks prepared by crosslinking a polymer in solution. A check of theory can be obtained if one knows precisely the number of crosslinks in the network and if a range of deformations is applied to the network. In an effort to explore this problem we have examined the relation of shear modulus to crosslink density, primary molecular weight, and polymer concentration for a series of poly(vinyl alcohol) gels at low to intermediate concentrations. Aqueous poly(vinyl alcohol) solutions were crosslinked to form infinite networks using terephthalaldehyde. We find a large discrepancy with these poly(vinyl alcohol) gels between measured shear modulus and that calculated from classical elasticity theory assuming quantitative reaction of crosslinking. The ratio of measured to calculated modulus is independent of crosslink density for a given primary molecular weight and concentration. It shows linear dependence on polymer concentration prior to crosslinking and extrapolates to a critical concentration which is consistent with the effective sizes of the polymer molecules.     

Time-Dependent and Sample-to-Sample Variations in Human Plasma Peptidome are Both Minimized Through Use of Protease Inhibitors

Abstract

In the current study, we have developed a method to measure relative peptide stability over time in different blood collection tubes. Reversed-phase chromatography and liquid chromatography–matrix-assisted laser desorption/ionization were performed on three subjects to facilitate a deeper look into the plasma peptidome. The data further support the importance of protease inhibitors in stabilizing plasma samples. Significantly, we have revealed subject-to-subject variability in the intrinsic damage over time that is possible in standard EDTA plasma, with such variations extensively minimized by protease inhibitors. We conclude that protease inhibitors can simultaneously improve time-dependent and individual-dependent preanalytical variables in human plasma samples.     

稳健Madaline网络算法及其在复方制剂分析中的应用

根据常用稳健回归方法的原理,对神经网络算法之一Ｍａｄａｌｉｎｅ网络算法作了改进,建立了稳健Ｍａｄａｌｉｎｅ网络算法。甲硝唑和氯霉素组成的两组分复方制剂的分析结果表明：该法具有较好的稳健性能,其最大奇异点数约占总样本数的５０％,优于Ｍ估计的稳健性能。     

Prediction of Tensile Curves of Rubber Materials by Different Network Models

The paper presents application of rubber elasticity theory to the predictive model of tensile mechanical properties. Poly(methyl methacrylate) was chosen as a model polymer. The input dates were crosslink density and type of chain. The crosslink density was taken from swelling experiment. Two types of chain were analyzed, namely worm like and chain with the realistic function of dihedral potential. Dihedral potential function was derived from molecular model of chain segment. Predictive tensile curve was compared with experimental one. The similarity of potential functions of selective polymers (polypropylene, poly-vinylchloride, poly-vinylalcohol, poly-vinylfluoride, polystyrene) enables to generalize this procedure.     

General Formalism for New Generation Geometrical Model: Application to the Thermodynamics of Liquid Mixtures

In our previous papers, a new geometric model has been proposed for calculating the thermodynamic properties of a multi-component system in terms of the properties of its three sub-binary systems. This new model can overcome the inherent defects of the traditional symmetrical and asymmetrical geometric models. Consequently, it is more reasonable theoretically and more reliable in practical applications. However, calculations using this new model involve a series of integration processes which make it complicated and affects its applications. Since a large number of real systems can be approximately fit through a Redlich–Kister polynomial, in this paper a new formalism is presented for the model, based on the binary Redlich–Kister type parameters. The advantage of this treatment is that the whole integration process is avoided by using algebraic operations, thereby simplifying the calculation.     

Thermodynamic Approach to the Wetting of Solids by Surface-Active Agents: A Supplementary Approach to the Gibbs Formalism

The adsorption of a solute on a solid can be followed by contact angle measurements of a drop of the solution on the solid. The Gibbs isotherm model can be used for quantitative interpretation of wettability variations. Its use in linking the wettability to the adsorption isotherm involves assimilating the Gibbs' planes to the surfaces themselves. Within this framework, these interpretations lead to the conclusion that adsorption of surface-active agents is greater on solid-vapor interfaces than on solid-liquid interfaces, for hydrophilic solids. This is not the only approach. Thermodynamics allows other formalisms, the conclusions of which can be completely different. We present a thermodynamic approach which explicitly reveals relationships between surface tensions and contents of surfaces, without referring to the Gibbs' plane. This permits us to explain the behavior of a drop of surfactant solution put on hydrophilic or hydrophobic solids with conclusions different from those reached using the Gibbs approach. We show that all these thermodynamic approaches are linked; they do not dismiss one another but give different views of the same phenomenon. Copyright 2000 Academic Press.     

“Volume‐Preserving” Conformational Rheological Models for Multi‐Component Miscible Polymer Blends Using the GENERIC Formalism

A family of conformational rheological models for multi‐component miscible polymer blends is developed using a modified form of the Poisson bracket formulation. Two conformation tensors called c ₁ and c ₂ are introduced to show the orientation of the first and the second components of a blend, respectively. The mobility tensor and the energy function for each blend component are expressed in terms of these conformation tensors. The interaction effects are also included by energy expressions. The predictions of this family of “volume‐preserving” models are illustrated for a Hookean‐type energy function and several expressions of the modified mobility tensors. The results are illustrated for material functions in transient (start‐up and relaxation) and steady shear flows. The predictions are compared with experimental data taken from the literature for a miscible polymer blend. Study of the model sensitivity to its parameter shows that model predictions can cover a wide range of rheological behavior generally observed for multi‐component miscible polymer blends in steady and transient shear flows.

Experimental data and model predictions for steady shear viscosity for HDPE/LDPE blends.     

New Variations in the Colloidal Route to ErIII@ZnO Nanocrystals and Films

1-propanolic particulate ZnO nanocolloids were co-doped with Er^III ions and various silanes prior to coating. The resulting functionalized sols and sintered films were examined by UV/Vis-, FTIR- and time-resolved NIR-fluorescence spectroscopy. As a result, methyl- and phenyl triethoxysilanes (MTEOS, PTEOS) were found to block the slow ageing of the ZnO sols while the higher substituted silanes did not. Furthermore, film samples prepared from TEOS co-doped Er^III/ZnO sols and sintered at 400°C showed no fluorescence whereas PTEOS co-doping allows to detect the complex NIR-Er^III-fluorescence decay. In the last part of this contribution, the effect of thermal ZnO particle healing on the subsequent co-dopings and NIR-fluorescence dynamics will be discussed. Briefly, with increasing healing temperature the life time of the 1.54 m fluorescence decreases. Interestingly, in ZnO sols healed at 170°C, the erbium acetate precursor is no more soluble which means that the ZnO nanocrystals could not be doped either.     

Variations in electrophoretic tear protein pattern due to contact lens wear

Electrophoresis of tear proteins was used to compare the patterns from tear proteins in contact lens wearers with non-contact lens wearers. Thirty-five non-contact lens wearers and 35 wearers volunteered to enter our study. Both groups aged 20-25 years with no history of eye diseases. Stimulated tear samples were collected using a capillary tube. Total tear protein was measured for each group individually using standard assay methods. The results showed slightly higher total tear protein in the group wearing contact lenses. Some new bands also appeared in the electrophoresis patterns of this group as compared to the control group.     

Elastic waves in quasiperiodic structures

We study the transverse and sagittal elastic waves in different quasiperiodic structures by means of the full transfer-matrix technique and surface Green-function matching method. The quasiperiodic structures follow Fibonacci, Thue-Morse and Rudin-Shapiro sequences, respectively. We consider finite structures having stress-free bounding surfaces and different generation orders, including up to more than 1000 interfaces. We obtain the dispersion relations for elastic waves and spatial localization of the different modes. The fragmentation of the spectrum for different sequences is evident for intermediate generation orders, in the case of transverse elastic waves, whereas, for sagittal elastic waves, higher generation orders are needed to show clearly the spectrum fragmentation. The results of Fibonacci and Thue-Morse sequences exhibit similarities not present in the results of Rudin-Shapiro sequences.     

Elastic excitations in polycarbonate membranes

Brillouin light scattering was used to probe acoustic waves propagating with both longitudinal and transverse polarizations in the surface and the bulk of self‐supported particle track‐etched polycarbonate membranes with 15‐ and 80‐nm nanopores. The recorded scattering line shape at gigahertz frequencies reveals changes in the surface waves of the membranes which are more pronounced for the 80‐nm nanopores despite the low porosity (0.7 and 0.05%). Because the measured elastic constants (1.2 and 6.2 GPa) were found to compare very well with the values for thick polycarbonate film, modifications of the elasto‐optical coefficients and/or the transparency might be the reason for the different scattering line shapes. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3311–3317, 2004     

Spheroidal multipolar expansions for intermolecular energy in crystal theory. I. Formalism

In view of further applications to molecular crystal theory, spheroidal expansion of intermolecular potential involving. anisotropic molecules is investigated, including multipole moments up to octupole. The spheroidal formalism is worked out for the electrostatic potential outside a non-spherica charge distribution as well as for interactions between two anisotropic molecules in the non-overlap assumption. The case where either molecule is axia symmetric is presented as a reduced form of the general formulas displayed.