Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.     

Utilization of mathematical programming for public systems: An application to effective formation of integrated regional information networks

This paper concerns a methodological reflection on the multiobjective approach to public systems which involve group decision processes. Particular attention is given to an integrated program of regional systems which include value trade-offs between multiple objectives. Our intention is to combine the judgmental processes with the optimization processes in the soft public systems. A two-layer approach is applied. At the first layer, each regional program is formulated in mathematical programming based on a utility assessment with different regional characteristics. Each subsystem independently reflects its particular concern as a single agent. The dual optimal solutions obtained for each subsystem are treated as an index, or the theoretical prices, representing the value trade-offs among the multiple objectives. At the second layer, an effective formation of interregional cooperation for compromising the conflicting regional interests is examined. Ann-person cooperative game in the characteristic function form is used to evaluate the effectiveness of the cooperation. The characteristic function for the game is derived on the incremental value of the regional benefit after the formation of a cooperation. The nucleolus and the augmented nucleolus as the solution concepts of the cooperative game are used for indicating the effectiveness of the cooperation. Finally using alternative criteria, the results in assessing the best decisions are examined comparatively.     

Sequencing 5‐Hydroxymethyluracil at Single‐Base Resolution

5‐hydroxymethyluracil (5hmU) is formed through oxidation of thymine both enzymatically and non‐enzymatically in various biological systems. Although 5hmU has been reported to affect biological processes such as protein–DNA interactions, the consequences of 5hmU formation in genomes have not been yet fully explored. Herein, we report a method to sequence 5hmU at single‐base resolution. We employ chemical oxidation to transform 5hmU to 5‐formyluracil (5fU), followed by the polymerase extension to induce T‐to‐C base changes owing to the inherent ability of 5fU to form 5fU:G base pairing. In combination with the Illumina next generation sequencing technology, we developed polymerase chain reaction (PCR) conditions to amplify the T‐to‐C base changes and demonstrate the method in three different synthetic oligonucleotide models as well as part of the genome of a 5hmU‐rich eukaryotic pathogen. Our method has the potential capability to map 5hmU in genomic DNA and thus will contribute to promote the understanding of this modified base.     

Low-temperature synthetic route based on the amorphous nature of giant species for preparation of lower valence oxides

We examined low-temperature synthetic route based on the amorphous nature of giant species to succeed to prepare Cs blue bronze (Cs_0.3MoO₃), which has never obtained by usual high-temperature methods, at ca. 680 K. Solid solutions (K_1−xRb_x)_0.28MoO₃ and (Li_1−xNa_x)_0.9Mo₆O₁₇ were also obtained at lower temperatures (ca. 670 K). For the latter system consisting of non-isostructural end members, Li_0.9Mo₆O₁₇-structure type solid solution was formed even when 0.25<x<0.70, unlike the case by the usual high-temperature methods. Metastable mixed oxides Ln₂Mo₃O₉ (Ln=La, Gd) were obtained, but not as single phases.     

Thermochromism and Solvatochromism in Solution

Summary.  The thermochromic behaviour of various coordination compounds in solution is discussed, with a special focus on cyclic diamine chelates. Thermally induced spin-crossover phenomena of iron(II) complexes are also considered. The solvatochromic behaviour of mixed-ligand complexes is presented in detail. Received April 2, 2001. Accepted (revised) April 19, 2001     

Quantum simulation of the t–J model

Computer simulation of a many-particle quantum system is bound to reach the inevitable limits of its ability as the system size increases. The primary reason for this is that the memory size used in a classical simulator grows polynomially whereas the Hilbert space of the quantum system does so exponentially. Replacing the classical simulator by a quantum simulator would be an effective method of surmounting this obstacle. The prevailing techniques for simulating quantum systems on a quantum computer have been developed for purposes of computing numerical algorithms designed to obtain approximate physical quantities of interest. The method suggested here requires no numerical algorithms; it is a direct isomorphic translation between a quantum simulator and the quantum system to be simulated. In the quantum simulator, physical parameters of the system, which are the fixed parameters of the simulated quantum system, are under the control of the experimenter. A method of simulating a model for high-temperature superconducting oxides, the t–J model, by optical control, as an example of such a quantum simulation, is presented.     

Thermally assisted magnetic recording with bit-patterned media to achieve areal recording density beyond 5 Tb/in

Thermally assisted magnetic recording (TAR) with bit-patterned media was investigated by micromagnetic simulation. The media were assumed to be FePt layers. The effective head-field margin as well as the increase in temperature margin and down-track shift margin was investigated. Conditions of the head and medium that lead to a recording density beyond 5 Tb/in² were proposed.     

Thermochromism and Solvatochromism in Solution

 The thermochromic behaviour of various coordination compounds in solution is discussed, with a special focus on cyclic diamine chelates. Thermally induced spin-crossover phenomena of iron(II) complexes are also considered. The solvatochromic behaviour of mixed-ligand complexes is presented in detail.     

Functional zonation of the rat adrenal cortex: the development and maintenance

The adrenal cortex of mammals consists of three concentric zones, i.e., the zona glomerulosa (zG), the zona fasciculata (zF), and the zona reticularis (zR), which secrete mineralocorticoids, glucocorticoids, and adrenal androgens, respectively. In 1994, we identified immunohistochemically a new zone between zG and zF of the rat adrenal gland. The zone appeared to be devoid of any significant endocrine functions specific to adrenocortical zones, therefore, we designated the zone as “undifferentiated cell zone (zU)”. Further, BrdU (5-bromo-2′-deoxyuridine)-incorporating cells (cells in S-phase) were concentrated at the outer region and the inner region of zU, and these cells proliferated and migrated bidirectionally: toward zG centrifugally and toward zF centripetally. We proposed that cells in and around zU are stem/progenitor cells of the rat adrenal cortex, maintaining functional zonation of the adrenal cortex. The view is consistent with observations reported recently that Sonic hedgehog (Shh), an important factor in embryonic development and adult stem cell maintenance, exists in zU of the rat adrenal gland and the Shh-containing cells seem to migrate bidirectionally.     

Novel copper hydride-promoted 1,3-rearrangement of α-allenylcyclopropane systems to methylenecyclopentenes

α-Allenylcyclopropanedicarboxylates, for which a novel synthetic method has been devised by conjugate addition of a copper hydride (Stryker) reagent to α-cyclopropylpropargylic esters, have been newly found to be smoothly converted to methylenecyclopentene derivatives under mild reaction conditions by further treatment with the copper hydride reagent. The mechanistic pathway is discussed.