Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini‐protein,chignolin

The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time‐scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini‐protein, chignolin, and automatically sampled the native structure (C_α root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long‐time 1‐µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape. © 2015 Wiley Periodicals, Inc.     

Polyaniline‐Induced CH Arylation of Arenes with Arenediazonium Salts

A reduced form of polyaniline has been shown to induce direct arylation of an arenediazonium salt with an arene (Gomberg–Bachmann reaction) to give the cross‐coupling product in moderate to good yields under mild conditions. Various arenediazonium salts and arenes, including heteroarenes such as furans, thiophenes, and pyrroles, are employed for the reaction. The most favorable combination of substrates is an electron‐poor arenediazonium salt with an electron‐rich heteroarene. Investigation of the mechanism by reactions with radical scavengers and experiments on kinetic isotope effects indicated the occurrence of a radical chain reaction initiated by one‐electron reduction of an arenediazonium salt by the polyaniline. Only 1 mol % (based on aniline tetramer) of the polyaniline is required for the cross‐coupling reaction to occur. This reaction proceeds under metal‐free conditions and with no need for photonic activation.     

Olefin Polymerization Catalyzed by Double‐Decker Dipalladium Complexes: Low Branched Poly(α‐Olefin)s by Selective Insertion of the Monomer Molecule

Dipalladium complexes of a cyclic bis(diimine) ligand with a double‐decker structure catalyze polymerization of ethylene and α‐olefins and copolymerization of ethylene with 1‐hexene. The polymerization of 1‐hexene yields a polymer that is mainly composed of the hexamethylene unit formed by 2,1‐insertion of the monomer into the palladium–carbon bond, followed by chain‐walking (6,1‐insertion). The polymerization of 4‐methyl‐1‐pentene proceeds by 2,1‐insertion with a selectivity of 92–97 %, and affords the polymer with methyl and 2‐methylhexyl branches. 2,1‐Insertion occurs selectively in all of the polymerization reactions of α‐olefins catalyzed by the dipalladium complexes. Ethylene polymerization with the catalyst at 100 °C lasts over 24 h, whereas the monopalladium–diimine catalyst loses its activity within 8 h at 60 °C. Polyethylene obtained by the dipalladium catalyst is less‐branched and has a higher molecular weight compared to that of the monopalladium catalyst under the same conditions. Copolymerization of ethylene with 1‐hexene affords solid products with melting points and molecular weights that vary depending on the polymerization time, suggesting formation of a block and/or gradient copolymer.     

Preparation of phthalocyanine-bound myristoyl celluloses for photocurrent generation system

The influences of two structural modifications on the photocurrent generation performance of the Langmuir–Blodgett (LB) film of the 6-O-phthalocyaninyl cellulose derivative were investigated. These structural modifications were the substituent groups at the O-2 and O-3 positions, and the central metal of the phthalocyanine moiety. Specifically, 6-O-Zn/phthalocyaninyl- (8a) and Pd/phthalocyaninyl (8b) -2,3-di-O-myristoylcelluloses were prepared instead of 6-O-Zn/phthalocyaninyl-2,3-di-O-myristylcellulose (2). The LB monolayer film of compound 8a on an indium thin oxide electrode showed higher photocurrent generation performance than that of compound 2. This suggested that myristoyl groups (C-14 acyl groups) were more beneficial to photocurrent generation than myristyl groups (C-14 alkyl groups), as the substituent at the O-2 and O-3 positions. The LB monolayer film of compound 8b showed photocurrent generation from 500 to 700 nm, although a blue-shift in the Q-band maximum was observed. The photocurrent generation performance of compound 8b was significantly higher than that of compound 8a. This indicated that Pd was more beneficial to photocurrent generation than Zn. The film of compound 8b prepared by the horizontal lifting method showed better photocurrent generation performance than that prepared by the vertical dipping method. Consequently, compound 8b is a complementary material to the porphyrin-appended cellulose derivative (1) for photocurrent generation system.     

Multi-period resource allocation for estimating project costs in competitive bidding

Central European Journal of Operations Research - In competitive bidding for project contracts, contractors estimate the cost of completing a project and then determine the bid price. Accordingly,...     

Geometric Properties of the Shifted Hypergeometric Functions

We will provide sufficient conditions for the shifted hypergeometric function \(z_2F_1(a,b;c;z)\) to be a member of a specific subclass of starlike functions in terms of the complex parameters a, b and c. For example, we study starlikeness of order \(\alpha ,\) \(\lambda \)-spirallikeness of order \(\alpha \) and strong starlikeness of order \(\alpha .\) In particular, those properties lead to univalence of the shifted hypergeometric functions on the unit disk.     

Nonlinear rheological behavior of a concentrated spherical silica suspension

Linear and nonlinear viscoelastic properties were examined for a 50 wt% suspension of spherical silica particles (with radius of 40 nm) in a viscous medium, 2.27/1 (wt/wt) ethylene glycol/glycerol mixture. The effective volume fraction of the particles evaluated from zero-shear viscosities of the suspension and medium was 0.53. At a quiescent state the particles had a liquid-like, isotropic spatial distribution in the medium. Dynamic moduli G^* obtained for small oscillatory strain (in the linear viscoelastic regime) exhibited a relaxation process that reflected the equilibrium Brownian motion of those particles. In the stress relaxation experiments, the linear relaxation modulus G(t) was obtained for small step strain (0.2) while the nonlinear relaxation modulus G(t, ) characterizing strong stress damping behavior was obtained for large (>0.2). G(t, ) obeyed the time-strain separability at long time scales, and the damping function h() (–G(t, )/G(t)) was determined. Steady flow measurements revealed shear-thinning of the steady state viscosity () for small shear rates (< ^–1; = linear viscoelastic relaxation time) and shear-thickening for larger (>^–1). Corresponding changes were observed also for the viscosity growth and decay functions on start up and cessation of flow, + (t, ) and _– (t, ). In the shear-thinning regime, the and dependence of ₊(t,) and _–(t,) as well as the dependence of () were well described by a BKZ-type constitutive equation using the G(t) and h() data. On the other hand, this equation completely failed in describing the behavior in the shear-thickening regime. These applicabilities of the BKZ equation were utilized to discuss the shearthinning and shear-thickening mechanisms in relation to shear effects on the structure (spatial distribution) and motion of the suspended particles.Dedicated to the memory of Prof. Dale S. Parson     

Experimental study of heat and mass transfer from a horizontal cylinder in downward air-water mist flow with blockage effect

An experimental study was made on convective heat and mass transfer from a horizontal heated cylinder in a downward flow of air-water mist at a blockage ratio of 0.4. The measured local heat transfer coefficients agree fairly well with the authors' numerical solutions obtained previously for the front surface of a cylinder over the ranges mass flow ratio 0–4.5×10⁻², a temperature difference between the cylinder and air 10–43 K, gas Reynolds number (7.9–23)×10³, Rosin-Rammler size parameter 105–168 μm, and dispersion parameter 3.4–3.7. Heat transfer augmentation, two-pahse to single-phase of greater than 19 was attained at the forward stagnation point. For heat transfer in the rear part of the cylinder, an empirical formula is derived by taking into account the dimensionless governing variables, that is, coolant-feed and evaporation parameters.     

Coordination characteristics of trivalent lanthanides and actinides in molten hydrate salts of Ca(NO<Subscript>3</Subscript>)<Subscript>2</Subscript> and CaCl<Subscript>2</Subscript>

Distribution behavior of Ce(III), Am(III), and Cm(III) between tri-n-butyl phosphate solution and molten calcium nitrate hydrate Ca(NO₃)₂·RH₂O or molten calcium chloride hydrate CaCl₂·RH₂O was studied radiochemically. In Ca(NO₃)₂·RH₂O systems, maximum separation factors of Ce and Cm to Am were observed to be 12 (Ce/Am) and 1.7 (Cm/Am). The distribution ratios of these elements increased with the decrease of water activity in the hydrates, and the extractabilities at the water deficient region was less sensitive compared to those at the water abundant region. This trend was similar to the coordination circumstance change observed in electronic absorption spectra of Nd(III) in the hydrates.