GPU acceleration of many-body perturbation theory methods in MOLGW with OpenACC

Quasiparticle self-consistent many-body perturbation theory (MBPT) methods that update both eigenvalues and eigenvectors can calculate the excited-state properties of molecular systems without depending on the choice of starting points. However, those methods are computationally intensive even on modern multi-core central processing units (CPUs) and thus typically limited to small systems. Many-core accelerators such as graphics processing units (GPUs) may be able to boost the performance of those methods without losing accuracy, making starting-point-independent MBPT methods applicable to large systems. Here, we GPU accelerate MOLGW, a Gaussian-based MBPT code for molecules, with open accelerators (OpenACC) and achieve speedups of up to $$ over 32 open multi-processing (OpenMP) CPU threads.     

Thermal instability of HfO2 on InP structure with ultrathin Al2O3 interface passivation layer

We studied the thermal stability of HfO₂ on an InP structure when an Al₂O₃ interface passivation layer (PL) was introduced. In contrast to the thick (～4 nm) Al₂O₃‐PL, an almost complete disappearance of the thin (～1 nm) Al₂O₃‐PL was observed after a post‐deposition anneal at 600 °C. Based on various chemical and electrical analyses, this was attributed to the intermixing of the thin Al₂O₃‐PL with HfO₂, which might have been accompanied by the out‐diffusion of a substantial amount of substrate elements. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The geometry of SO(n)\SO0(n, 1)

Consider the Lie group SO₀(n, 1) with the left-invariant metric coming from the Killing-Cartan form. The maximal compact subgroup SO(n) of the isometry group acts from the left and right. This paper studies the geometry of the quotient space of the homogeneous submersion SO₀(n, 1) → SO(n)\SO₀(n, 1). It is a cohomogeneity one manifold, which can be expressed as a warped product. Its group of isometries, geodesics, and sectional curvatures are calculated.     

Preparation of a core-shell type MBHA resin and its application for solid-phase peptide synthesis

MBHA (4-methylbenzhydrylamine) resin has been extensively used as a solid support for the synthesis of peptide amides. Herein, we prepared the core-shell-type MBHA resin by benzotriazole-catalyzed amidoalkylation and partial hydrolysis. The core-shell structure of the MBHA resin was confirmed by two-photon microscopy and its synthetic performance in solid-phase peptide synthesis (SPPS) was evaluated.     

In Situ Formation of Gold Nanoparticles within a Polymer Particle and Their Catalytic Activities in Various Chemical Reactions

Composite materials consisting of nanoscale gold particles and protective polymer shells were designed and tested as catalysts in various chemical reactions. Initially, the systematic incorporation of multiple gold nanoparticles into a poly(N-isopropylacrylamide) particle was achieved by an in situ method under light irradiation. The degree of gold nanoparticle loading, along with the structural and morphological properties, was examined as a function of the amount of initial gold ions and reducing agent. As these gold nanoparticles were physically-embedded within the polymer particle in the absence of strong interfacial interactions between the gold nanoparticles and polymer matrix, the readily-accessible surface of the gold nanoparticles with a highly increased stability allowed for their use as recyclable catalysts in oxidation, reduction, and coupling reactions. Overall, the ability to integrate catalytically-active metal nanoparticles within polymer particles in situ allows for designing novel composite materials for multi-purpose catalytic systems.     

Surface‐Independent and Oriented Immobilization of Antibody via One‐Step Polydopamine/Protein G Coating: Application to Influenza Virus Immunoassay

For the construction of high‐performance biosensor, it is important to interface bioreceptors with the sensor surface densely and in the optimal orientation. Herein, a simple surface modification method that can optimally immobilize antibodies onto various kinds of surfaces is reported. For the surface modification, a mixture of polydopamine (PDA) and protein G was employed. PDA is a representative mussel‐inspired polymer, and protein G is an immunoglobulin‐binding protein that enables an antibody to have an optimal orientation. The surface characteristics of PDA/Protein G mixture‐coated substrates are analyzed and the PDA/protein G ratio is optimized to maximize the antibody binding efficiency. Moreover, the antibody‐immobilized substrates are applied to the detection of influenza viruses with the naked eye, providing a detection limit of 2.9 × 10³ pfu mL^‐1. Importantly, the several substrates (glass, SiO₂, Si, Al₂O₃, polyethylene terephthalate, polyethylene, polypropylene, and paper) can be modified by simple incubation with the mixture of PDA/protein G, and then the anti‐influenza A H1N1 antibodies can be immobilized on the substrates successfully. Regardless of the substrate, the influenza viruses are detectable after the sandwich immunoreaction and silver enhancement procedure. It is anticipated that the developed PDA/protein G coating method will extend the range of applicable materials for biosensing.     

State-selective frustration as a key driver of allosteric pluripotency

Allosteric pluripotency arises when an allosteric effector switches from agonist to antagonist depending on the experimental conditions. For example, the Rp-cAMPS ligand of Protein Kinase A (PKA) switches from agonist to antagonist as the MgATP concentration increases and/or the kinase substrate affinity or concentration decreases. Understanding allosteric pluripotency is essential to design effective allosteric therapeutics with minimal side effects. Allosteric pluripotency of PKA arises from divergent allosteric responses of two homologous tandem cAMP-binding domains, resulting in a free energy landscape for the Rp-cAMPS-bound PKA regulatory subunit R1a in which the ground state is kinase inhibition-incompetent and the kinase inhibition-competent state is excited. The magnitude of the free energy difference between the ground non-inhibitory and excited inhibitory states (ΔG_R,Gap) relative to the effective free energy of R1a binding to the catalytic subunit of PKA (ΔG_R:C) dictates whether the antagonism-to-agonism switch occurs. However, the key drivers of ΔG_R,Gap are not fully understood. Here, by analyzing an R1a mutant that selectively silences allosteric pluripotency, we show that a major determinant of ΔG_R,Gap unexpectedly arises from state-selective frustration in the ground inhibition-incompetent state of Rp-cAMPS-bound R1a. Such frustration is caused by steric clashes between the phosphate-binding cassette and the helices preceding the lid, which interact with the phosphate and base of Rp-cAMPS, respectively. These clashes are absent in the excited inhibitory state, thus reducing the ΔG_R,Gap to values comparable to ΔG_R:C, as needed for allosteric pluripotency to occur. The resulting model of allosteric pluripotency is anticipated to assist the design of effective allosteric modulators.

The Rp-cAMPS ligand of protein kinase A switches from agonist to antagonist depending on metabolite and proteomic contexts. We show that the state-selective frustration is a key driver of this allosteric pluripotency phenomenon.     

Biodegradable Polycarbonate Synthesis by Copolymerization of Carbon Dioxide with Epoxides Using a Heterogeneous Zinc Complex

As a means for the chemical fixation of carbon dioxide and the synthesis of biodegradable polycarbonates, copolymerizations of carbon dioxide with various epoxides such as cyclohexene oxide (CHO), cyclopetene oxide, 4-vinyl-1-cyclohexene-1,2epoxide, phenyl glycidyl ether, allyl glycidyl ether, propylene oxide, butene oxide, hexene oxide, octene oxide, and 1-chloro-2,3-epoxypropane were investigated in the presence of a double metal cyanide catalyst (DMC). The DMC catalyst was prepared by reacting K₃Co(CN)₆ with ZnCl₂, together with tertiary butyl alcohol and poly(tetramethylene ether glycol) as complexing reagents and was characterized by various spectroscopic methods. The DMC catalyst showed high activity (526.2 g-polymer/g-Zn atom) for CHO/CO₂ (P_CO2 = 140 psi) copolymerization at 80 °C, to yield biodegradable aliphatic polycarbonates of narrow polydispersity (M_w/M_n = 1.67) and moderate molecular weight (M_n = 8900). The DMC catalyst also showed high activities with different CO₂ reactivities for other epoxides to yield various aliphatic polycarbonates with narrow polydispersity.     

Polymerizations of ethylene and styrene initiated with trisiloxane-bridged dinuclear titanium metallocene/MMAO catalyst systems

Two kinds of the trisiloxane-bridged dinuclear titanium metallocene-type complexes were synthesized. They are monocyclopentadienyl and biscyclopentadienyl dinuclear titanocenes with trisiloxane bridges. The above complexes with modified methylaluminoxane (MMAO) cocatalyst initiate the polymerizations of ethylene and styrene to produce high-density polyethylene and syndiotactic polystyrene. In addition, a copolymer of ethylene and styrene was obtained.