Autonomous DNA computing machine based on photochemical gate transition

We report the construction of a one-pot autonomous DNA computing machine based on photochemical gate transition (photocleavage, hybridization, and photoligation), and we performed binary digit additions using this machine. In our method, both photochemical DNA manipulations previously reported, photoligation via 5-carboxyvinyldeoxyuridene (cvU) containing ODN and photocleavage via carbazole-modified ODN, were employed. The binary digit additions were autonomously carried out by one-time irradiation at 366 nm in the single test tube. The fluorescence readout by the DNA chip was in good agreement with the correct answer of binary digit additions. We believe that this system is easily applicable to correlation analysis between SNPs as well as other binary digit processing, such as subtraction.     

Self-modeling curve resolution (SMCR) analysis of near-infrared (NIR) imaging data of pharmaceutical tablets

The idea of quality by design (QbD) has been proposed in pharmaceutical field. QbD is a systematic approach to control the product performance based on the scientific understanding of the product quality and its manufacturing process. In the present study, near-infrared (NIR) imaging is utilized as a tool to achieve this concept. A practical use of a chemometrics technique called self-modeling curve resolution (SMCR) is demonstrated with NIR imaging analysis of pharmaceutical tablets containing two ingredients, a soluble active ingredient, pentoxifylline (PTX), and an insoluble excipient, palmitic acid. Concentration profiles obtained by SMCR reveal that the homogenous distribution of chemical ingredients strongly depends on the grinding time and that its process plays a central role in quantitative control, say sustained-release of PTX. In addition, pure component spectra by SMCR indicate a sequential change of specific NIR peak intensities following the increase of the grinding time. The spectra change shows a molecular structure change related to its crystallinity during grinding process. Accordingly, this study clearly demonstrates that NIR imaging combined with SMCR can be a powerful tool to reveal chemical or physical mechanism induced by the manufacturing process of pharmaceutical products and that it may be a solid solution for QbD of pharmaceutical products.     

Pressure generation to 50 GPa in Kawai-type multianvil apparatus using newly developed tungsten carbide anvils

A pressure generation test for Kawai-type multianvil apparatus (KMA) has been made using second-stage anvils of a newly developed ultra-hard tungsten carbide composite. Superb performance of the new anvil with significantly less plastic deformation was confirmed as compared to those commonly used for the KMA experiments. A maximum pressure of ～48?GPa was achieved using the new anvils with a truncation edge length (TEL) of 1.5?mm, based on in situ X-ray diffraction measurements. Further optimization of materials and sizes of the pressure medium/gasket should lead to pressures even higher than 50?GPa in KMA using this novel tungsten carbide composite, which may also be used for expansion of the pressure ranges in other types of high pressure apparatus operated in large volume press.     

An attrition game on a network ruled by Lanchester’s square law

We consider two-person zero-sum attrition games in which an attacker and a defender are in combat with each other on a network. The attacker marches from a starting node to a destination node, hoping that the initial members survive the march. The defender deploys his forces on arcs in order to intercept the attacker. If the attacker encounters the defender on an arc, the attacker incurs casualties according to Lanchester’s square law. We consider two models: a one-shot game in which the two players have no information about their opponents, and a two-stage game in which both players have some information about their opponents. For both games, the payoff is defined as the number of survivors for the attacker. The attacker’s strategy is to choose a path, and the defender’s is to deploy the defending forces on arcs. We propose a numerical algorithm, in which nonlinear programming is embedded, to derive the equilibrium of the game.     

Direct observation of substrate-enzyme complexation by surface forces measurement

The substrate-enzyme complexation of heptaprenyl diphosphate synthase was directly investigated using colloidal probe atomic force microscopy (AFM) and a quartz crystal microbalance (QCM) in order to obtain new insights into the molecular mechanism of the enzyme reaction. This enzyme is composed of two dissociable subunits that exhibit a catalytic activity only when they are associated together in the presence of a cofactor, Mg2+, and a substrate, farnesyl diphosphate (FPP). The QCM measurement revealed that FPP was preferentially bound to subunit II in the presence of Mg2+, while the AFM measurement showed that the adhesive force between the subunits was observed only in the presence of both Mg2+ and FPP. This is the first direct demonstration of the specific interaction involved in the enzyme reaction. The dependence of the Mg2+ concentration on the specific interaction between subunits I and II well agreed with that on the enzyme activity of heptaprenyl diphosphate synthase. This indicated that the observed adhesive forces were indeed involved in the catalytic reaction of this enzyme. On the basis of these results, we discussed the processes involved in the substrate-enzyme complexation. The first, the substrate FPP bound to subunit II using Mg2+, followed by the formation of the subunit I-FPP-Mg2+-subunit II complex. Our study showed a very useful methodology for examining the elemental processes of biological reactions such as an enzyme reaction.     

Origin of the vertebrate visual cycle: III. Distinct distribution of RPE65 and beta-carotene 15,15'-monooxygenase homologues in Ciona intestinalis

We previously identified three genes that encode putative visual cycle proteins that are homologues of retinal G-protein coupled receptor (Ci-opsin3), cellular retinaldehyde-binding protein (Ci-CRALBP) and beta-carotene 15,15'-monooxygenase (Ci-BCO) in the ascidian Ciona intestinalis. Ci-opsin3 and Ci-CRALBP are localized in both ocellus photoreceptor cells and surrounding non-photoreceptor cells in the brain vesicle of the larva. In the present study, we investigated the possible role and evolutionary origin of the BCO/RPE65 family in the visual cycle by analyzing Ci-BCO localization by immunohistochemistry and by identifying a novel gene that encodes a homologue of retinal pigment epithelium-specific 65 kDa protein (Ci-RPE65) in C. intestinalis. In situ hybridization and expressed sequence tag (EST) profiles consistently suggest that Ci-RPE65 is not significantly expressed in the ocellus and brain vesicle of the larva. Ci-RPE65 is expressed in the neural complex, a photoreceptor organ of the adult ascidian, at a level comparable to that of Ci-opsin3 and Ci-CRALBP. Ci-RPE65 is also expressed in various adult tissues, including the gill, body wall and intestine, suggesting that Ci-RPE65 plays a role in addition to that in the visual cycle. In contrast, Ci-BCO is predominantly localized in ocellus photoreceptor cells of the larva. The larval visual cycle seems to use Ci-opsin3 as a photo-isomerase. Our results also suggest that the RPE65-dependent visual cycle is used in the adult photoreceptors of a primitive chordate.     

Effect of Acid Treatment of Montmorillonite on “Support‐Activator” Performance to Support Metallocene for Propylene Polymerization Catalyst

This work is focused on montmorillonite (MMT)‐based “support‐activators” (S‐As) for the metallocene‐catalyzed propylene polymerization. This catalyst was previously industrialized; however, for further technological advances, the activation mechanism is investigated. The chemical and morphological requirements of the S‐A are surveyed using both commercially available raw clay minerals (non‐acid‐treated) and acid‐treated clay minerals. The S‐A possessing strong‐acid sites (pK a < ?8.2) gives a highly active catalyst. Acid treatment of MMT induces morphological changes as well as the formation of strong acid sites. Based on pore size distribution analysis and atomic force microscopy observations, it is concluded that the strong acid sites are located in the small pores around the edge of the clay mineral (not in the interlayer), where the structure is disordered by the acid treatment.

     

Synthesis of nano-polycrystalline diamond from glassy carbon at pressures up to 25 GPa

ABSTRACT

Nano-polycrystalline diamond (NPD) with various grain sizes has been synthesized from glassy carbon at pressures 15–25?GPa and temperatures 1700–2300°C using multianvil apparatus. The minimum temperature for the synthesis of pure NPD, below which a small amount of compressed graphite was formed, significantly increased with pressure from ～1700°C at 15?GPa to ～1900°C at 25?GPa. The NPD having grain sizes less than ～50?nm was synthesized at temperatures below ～2000°C at 15?GPa and ～2300°C at 25?GPa, above which significant grain growth was observed. The grain size of NPD decreases with increasing pressure and decreasing temperature, and the pure NPD with grain sizes less than 10?nm is obtained in a limited temperature range around 1800–2000°C, depending on pressure. The pure NPD from glassy carbon is highly transparent and exhibits a granular nano-texture, whose grain size is tunable by selecting adequate pressure and temperature conditions.     

Quantum proton transfer in hydrated sulfuric acid clusters: a perspective from semiempirical path integral simulations

We have carried out path-integral molecular dynamics simulations for hydrated sulfuric acid clusters to understand acid-dissociation and hydrogen-bonded structural rearrangement processes in these clusters from a quantum mechanical viewpoint. The simulations were performed using the PM6 semiempirical electronic structure level whose parameters were modified on the basis of the specific reaction parameters strategy so that relative energies of optimized structures, as well as water binding energies reproduce ab initio and density-functional theory calculations. We have found that the acid dissociation processes, first and second deprotonation, effectively occur in a hydrated cluster with a specific cluster size. The mechanisms of the proton-transfer processes were analyzed in detail and it was found that the distance between O in sulfuric acid and O in the proton-accepting water is playing an important role. We also found that the water coordination number of the poton-accepting water is important in the proton-transfer processes.     

Nonadiabatic electron wavepacket dynamics of molecules in an intense optical field: an ab initio electronic state study

A theory of quantum electron wavepacket dynamics that nonadiabatically couples with classical nuclear motions in intense optical fields is studied. The formalism is intended to track the laser-driven electron wavepackets in terms of the linear combination of configuration-state functions generated with ab initio molecular orbitals. Beginning with the total quantum Hamiltonian for electrons and nuclei in the vector potential of classical electromagnetic field, we reduce the Hamiltonian into a mixed quantum-classical representation by replacing the quantum nuclear momentum operators with the classical counterparts. This framework gives equations of motion for electron wavepackets in an intense laser field through the time dependent variational principle. On the other hand, a generalization of the Newtonian equations provides a matrix form of forces acting on the nuclei for nonadiabatic dynamics. A mean-field approximation to the force matrix reduces this higher order formalism to the semiclassical Ehrenfest theory in intense optical fields. To bring these theories into a practical quantum chemical package for general molecules, we have implemented the relevant ab initio algorithms in it. Some numerical results in the level of the semiclassical Ehrenfest-type theory with explicit use of the nuclear kinematic (derivative) coupling and the velocity form for the optical interaction are presented.