Topological Elements Research Articles

Consequences of binding an S-adenosylmethionine analogue on the structure and dynamics of the thiopurine methyltransferase protein backbone.

In humans, the enzyme thiopurine methyltransferase (TPMT) metabolizes 6-thiopurine (6-TP) medications, commonly used for immune suppression and for the treatment of hematopoietic malignancies. Genetic polymorphisms in the TPMT protein sequence accelerate intracellular degradation of the enzyme through an ubiquitylation and proteasomal-dependent pathway. Research has led to the hypothesis that these polymorphisms destabilize the native structure of TPMT, resulting in the formation of misfolded or partially unfolded states, which are subsequently recognized for intracellular degradation. Addition of the cosubstrate, S-adenosylmethionine (SAM), prevents degradation of the TPMT polymorphs in experimental assays, presumably by stabilizing the native structure. Using a bacterial orthologue of TPMT from Pseudomonas syringae, we have used NMR spectroscopy to describe the consequences of binding sinefungin, a SAM analogue, on the structure and dynamics of the TPMT protein backbone. NMR chemical shift mapping experiments localize sinefungin to a highly conserved site in classical methyltransferases. Distal chemical shift changes involving the presumed active site cover imply indirect conformational changes induced by sinefungin, which may play a role in substrate recognition or the catalytic mechanism. Analysis of protein backbone dynamics based on NMR relaxation reveals a combination of complementary effects. Whereas the peripheral, inserted structural elements of the TPMT topology are conformationally stabilized by the presence of sinefungin, a consistent increase in backbone mobility is observed for the central, conserved structural elements. The potential implications for the structural and dynamic effects of binding sinefungin for the catalytic mechanism of the enzyme and the stabilization of the degradation-susceptible TPMT polymorphs are discussed.

Mathematical representation of feature conversion for CAD/CAM system integration

Automatic generation of machining information from a design system has been the research focus in feature-based CAD/CAPP/CAM applications for many years. Design data from a CAD model cannot be directly used in a CAPP system due to the difficulties arising from different feature viewpoints in each application and in various feature representations. To create a process-planning model automatically using machine features, feature mapping or conversion is the key issue to solve this problem. This paper addresses the problem of how to convert the design feature representation into machining feature representation in a mathematical model. Design features in the design domain are represented by a set of faces of each feature geometry and a set of attributes such as dimensions and material feature. Machining features in the manufacturing domain are represented by a number of faces and relationships between these faces that are meaningful for the process/machining operations. Using a mathematical description of the feature mapping process, machining features can be deduced and formed by the Set Operation, and the difficult problem of feature interaction can be described mathematically and converted in theory. On the basis of feature representations in the design and manufacturing domains, the mathematical model of feature mapping is represented by a mapping function g d−m which is a synthesis function of the process mapping functions g 1 and g 2. The first function, g 1, extracts the topological elements of a feature from a design model, and forms its own face model which including an interactive feature topological elements. The second function, g 2, groups these extracted elements into a machining feature according to the geometrical relationship between these elements and matches them with the pre-defined machining features. Examples are given in this paper to show the procedure of the feature mapping process. A feature-based CAD/CAPP/CAM integration system is described with the help of the formulation and representation of machining features.

The InP-HEMT IC Technology for 40-Gbit/s Optical Communications

We present the outline of the InP HEMT IC technology. This technology realizes InP HEMT digital ICs for 40-Gbit/s optical fiber communication systems through the integration of 0.1-μm-gate-length HEMTs, vertical diodes, capacitors, and WSiN resistors with two level interconnections. This paper describes the high-speed digital IC circuit design and fabrication in InP HEMT technology for 40-Gbit/s/channel optical communication systems. Some results on InP HEMTs' reliability are also covered. Basic circuit design techniques utilizing SCFL topology and fundamental circuit elements of the selector and D-type flip-flop are discussed in detail. The basic digital ICs of MUX, D-FF, and DEMUX ICs fabricated with 0.1-μm-gate InP HEMTs successfully operated up to 50 Gbit/s in the packaged modules. These IC modules offer large speed margins for the 43-Gbit/s OTU-3 data rate. In order to develop cost-effective optical transmitters and receivers, we designed a PLL-based CDR with a full-rate architecture. The fully monolithic integrated CDR exhibited error-free operation for 231-1 PRBS data signal at the OTU-3 bit rate of 43.0184 Gbit/s. Four-bit MUX and DEMUX ICs are other key components, and could be implemented by using InP HEMT technology. Additionally, we describe InP-IC fabrication technology with two-level inter-connection. This is already fully matured for 40-Gbit/s SSI fabrication. The uniform FET characteristics and high-yield passive component fabrication technologies support this degree of maturity. InP HEMT lifetime is 107 hours at l00°C. These results prove the InP HEMT IC fabrication technology presented here, to be highly reliable. These investigation show that robust performance and yield when realizing SSI and MSI 40-Gbit/s functions.

Statistical analysis and simulation of indoor single-phase low voltage power-line communication channels on the basis of multipath propagation

With regard to emerging utilization of the HF band for power-line communication applications, narrowband statistical characteristics of corresponding fading channels along single-phase electric networks are being investigated. By the reasonable two-conductor transmission line approach for cabling components, a model giving channel transfer functions on account of multi-path propagation is proposed Appropriate assumptions based on indoor electric networks' topology are adopted concerning scattering points' spatial allocation, by which amplitudes are demonstrated to follow the lognormal distribution, whereas the normal distribution is extracted for arrival times. For this theoretical treatment, a suitable definition of the term path is introduced, inferred by reflection points discrete spatial distribution. Verification of statistical modelling is established, involving inventory through simulation. During the simulating process, a well applicable cable transmission-line model is used, and the configuration of a bus having numerous transverse branches connected in parallel is considered, which forms the fundamental topological element for electric networks. Simulation results show remarkable compliance with the behaviour theoretically anticipated, and the model proposed herein seems to precisely describe the power delay profile of indoor single-phase power-line communication channels in the HF spectral area.

Hydrophobic Hydration of the Protein,-Attraction between Actin Molecules through Excluded Volume Effect.

One of the interactions between macromolecules is the attractive force through the excluded volume effect. We studied the attraction between the molecules of muscle protein, actin, from the following two points by using the extended scaled particle theory (XSPT). I) we verified the basic assumption used in the XSPT that topological elements which determine the analytical expression of the excluded volume are almost unchanged through the scaling down of the solute molecule in the thought experiment. Results of the computational geometry method (α-shape method) showed that this assumption is valid even in the case of the actin molecule. II) we calculated the attraction between actin monomer molecules, G-actin. Calculated differences of the values of the attraction potential of two macromolecules between at contact and at one macromolecule apart by the XSPT is almost the same as those by the Asakura-Oosawa theory.

Toward a Meta-Model for Computational Engineering

Geometric modeling and finite element analysis have matured in recent decades. Both methods are used extensively in engineering design. However, the link between geometric modeling, physical modeling and finite element analysis is currently cumbersome, error-prone, and ad-hoc. Topological domain modeling provides the missing link. In this paper, we propose a combined topological modeling and finite element modeling method that allows not only topological modeling, but also promotes geometric and physical modeling, by providing a topological base space for the definition of finite element meshes, fields, and the definition and solution of boundary value problems. We call the method the Constructive Topological Domain Method (CTDM). In this method, Primitive Topological Domains (PTDs), each possessing a natural coordinate space, are combined in multiple n-dimensional Cartesian coordinate spaces, called charts, using generalizations of Boolean set operations, to create Constructed Topological Domains (CTDs) capable of acting as the base spaces of fiber bundles. The charts are glued together to create an atlas, within which the CTD is defined. The fiber of the bundle may describe, in addition to geometry, physical fields like density, stress, and temperature. Finite element meshes may be defined upon each of the PTDs from which the CTD is constructed, enabling the definition and solution of boundary value problems, thus avoiding the difficult and messy problem of creating a single finite element mesh to represent the entire CTD. A modified finite element method, to handle the individually meshed PTDs, is described. The boundary conditions may be specified as analytical or as finite element-based fields upon each of the PTDs. The CTDM appears to be a promising approach to robust mathematical and computational modeling of physical objects. Simple examples are presented.

Theoretical Characterization of the Long-range Attraction between G-actin Molecules through the Excluded Volume Effect.

One of the interactions between macromolecules is the attractive forcethrough the excluded volume effect. We studied the attraction betweenthe molecules of muscle protein, actin, in the two points by using theextended scaled particle theory (XSPT). I) we verified the basic assumptionused in the XSPT that topological elements which determine the analyticalexpression of the excluded volume are almost unchanged through the scalingdown of the solute molecule in the thought experiment. Results of thecomputational geometry method (α-shape method) showed that thisassumption is valid even in the case of the actin molecule. II) wecalculated the attraction between actin monomer molecules, G-actin.Calculated differences of the values of the attraction potential of twomacromolecules between at contact and at one macromolecule apart by theXSPT is almost the same as those by the Asakura-Oosawa theory.

Structural basis of water-specific transport through the AQP1 water channel.

Water channels facilitate the rapid transport of water across cell membranes in response to osmotic gradients. These channels are believed to be involved in many physiological processes that include renal water conservation, neuro-homeostasis, digestion, regulation of body temperature and reproduction. Members of the water channel superfamily have been found in a range of cell types from bacteria to human. In mammals, there are currently 10 families of water channels, referred to as aquaporins (AQP): AQP0-AQP9. Here we report the structure of the aquaporin 1 (AQP1) water channel to 2.2 A resolution. The channel consists of three topological elements, an extracellular and a cytoplasmic vestibule connected by an extended narrow pore or selectivity filter. Within the selectivity filter, four bound waters are localized along three hydrophilic nodes, which punctuate an otherwise extremely hydrophobic pore segment. This unusual combination of a long hydrophobic pore and a minimal number of solute binding sites facilitates rapid water transport. Residues of the constriction region, in particular histidine 182, which is conserved among all known water-specific channels, are critical in establishing water specificity. Our analysis of the AQP1 pore also indicates that the transport of protons through this channel is highly energetically unfavourable.

Crystallochemical aspects of solid state reactions in mechanically alloyed Al–Cu–Fe quasicrystalline powders

A number of elemental mixtures having initial compositions close to Al 65Cu 23Fe 12 were mechanically alloyed at different energy intensities using a planetary mill. Laboratory X-ray diffraction analysis, differential scanning calorimetry and Mössbauer spectroscopy were used for characterization of the phase and structural state of mechanically alloyed powders after different periods of milling and annealing. Several exothermic effects were found, and these were ascribed to specific solid-state reactions. Quantitative phase analysis was applied in order to identify the mechanism of solid-state reactions taking place in the vicinity of the quasicrystalline phase domain in the Al–Cu–Fe system as a result of mechanical and thermal excitation and homogenization. Metastable intermetallics were identified which possess certain structural and topological elements identical to those found in quasicrystals.

1P090排除体積効果に起因するG-actin間の長距離引力の拡張caled particle理論による計算

One of the interactions between macromolecules is the attractive forcethrough the excluded volume effect. We studied the attraction betweenthe molecules of muscle protein, actin, in the two points by using theextended scaled particle theory (XSPT). I) we verified the basic assumptionused in the XSPT that topological elements which determine the analyticalexpression of the excluded volume are almost unchanged through the scalingdown of the solute molecule in the thought experiment. Results of thecomputational geometry method (α-shape method) showed that thisassumption is valid even in the case of the actin molecule. II) wecalculated the attraction between actin monomer molecules, G-actin.Calculated differences of the values of the attraction potential of twomacromolecules between at contact and at one macromolecule apart by theXSPT is almost the same as those by the Asakura-Oosawa theory.

Predicting Residual Stresses due to Solidification in Cast Plastics

A method is developed for the quantitative prediction of thermally induced residual stresses in polymeric materials. During processing, when the polymeric material is cooling down from an elevated temperature, to room temperature, a strain becomes 'frozen-in' the material. Different cooling processes will cause different amounts of the strain to become frozen-in. The residual stresses are then just a material response to the frozen-in strains at a uniform room temperature, well after processing. A link between thermal history and frozen-in strains is found to be the 'residual' temperature field. The thermo-mechanical response of the material to the applied residual temperature field is identical to the response to frozen-in strains only. By knowing the residual temperature field, the residual stress problem can be considered as a thermal stress problem, which can be solved using various commercial numerical packages. The numerical algorithm for determining the residual temperature field is also presented. It accommodates various elements of the Finite Volume mesh topology as the Finite Volume method is used to carry out the thermo-mechanical analysis. The procedure includes tracking integration paths always orthogonal to the solidification front at any point and numerical integration of frozen-in temperature gradients along them. The application of the method is illustrated by predicting residual stresses in a polymeric plate subjected to controlled cooling conditions.

Multi-volume CAD modeling for heterogeneous object design and fabrication

The current computer-aided technologies in design and product development, the evolution of CAD modeling, and a framework of multi-volume CAD modeling system for heterogeneous object design and fabrication are presented in this paper. The multi-volume CAD modeling system is presented based on nonmanifold topological elements. Material identifications are defined as design attributes introduced along with geometric and topological information at the design stage. Extended Euler operation and reasoning Boolean operations for merging and extraction are executed according to the associated material identifications in the developed multi-volume modeling system for heterogeneous object. An application example and a pseudo-processing algorithm for prototyping of heterogeneous structure through solid free-form fabrication are also described.

A framework for system specification using chains on cell complexes

This paper describes a framework for the specification and manipulation of models of systems. The systems are modelled within this framework using chain models, which permit the specification and manipulation of attributes associated with the topological elements of the systems. The paper provides a formalism which modifies and extends an already-existing formalism, and, also, a practical software kernel with a convenient application programming interface (API). Examples of system specification using the API are given, to illustrate that quite complicated systems can be modelled in a clear and concise way by means of the chain-model approach.

GEOGRAPHICAL INFORMATION SYSTEM & REMOTE SENSING IN BICYCLE PLANNING

This paper presents a new methodology in order to give support to analyse the cyclist routes using a Geographical Information System (GIS) and Remote Sensing (RS). This methodology focus some specific cyclist travels characteristics that usually can not be considered by the measure difficulties. The topological elements such as land slope are identified from digital terrain model defined using GIS. These variables are considered in the definition of the cyclist route. In this context, GIS plays a fundamental role, fulfilling the gap of the transportation models.

Small rings and amorphous tetrahedral carbon

We apply first-principles density-functional calculations to study strain in dense amorphous tetrahedral carbon $(a\ensuremath{-}\mathrm{tC}).$ While the large strain present in small-ring structures, particularly three-member rings, could argue against their existence in $a\ensuremath{-}\mathrm{tC},$ we demonstrate, based on energetic arguments, that strained small (three- and four-member) rings are plausible topological microstructural elements. We present two bulk carbon structures made up entirely of fourfold-coordinated atoms: the first with every atom in one three-member ring, the second with every atom in one four-member ring. Calculations show these bulk ring structures are relatively low in energy, only 0.37 and 0.23 eV/atom above diamond, respectively. This computed strain energy is much less than that present in recent models for $a\ensuremath{-}\mathrm{tC}.$ We examine properties of these structures with the intention to provide benchmark calculations for more approximate models, and to investigate the impact small rings might have on the properties of $a\ensuremath{-}\mathrm{tC}.$ We use a recently developed linear-response algorithm to compute phonon spectra for these ring structures.

Phylogenetic analysis of anthropoid relationships

The relationships of anthropoids to other primates are currently debated, as are the relationships among early fossil anthropoids and crown anthropoids. To resolve these issues, data on 291 morphological characters were collected for 57 taxa of living and fossil primates and analyzed using PAUP and MacClade. The dental evidence provides weak support for the notion of an adapid origin for anthropoids, the cranial evidence supports the tarsier–anthropoid hypothesis, and the postcranial evidence supports a monophyletic Prosimii and a monophyletic Anthropoidea. Combining these data into a single data set produces almost universal support for a tarsier–anthropoid clade nested within omomyids.EosimiasandAfrotarsiusare certainly members of this clade, and probably basal anthropoids, although the Shanghuang petrosal may not belong toEosimias. The tree derived from the combined data set resembles the tree derived from the cranial data set rather than the larger dental data set. This may be attributable to relatively slower evolution in the cranial characters. The combined data set shows Anthropoidea to be monophyletic but the features traditionally held to be anthropoid synapomorphies are found to have evolved mosaically. Parapithecines are the sister taxon to crown anthropoids; qatraniines and oligo-pithecids are more distantly related sister taxa. There is support for a relationship of aTarsius+Anthropoidea clade with either washakiines orUintanius. These elements of tree topology remain fairly stable under different assumptions sets, but overall, tree topology is not robust. Previously divergent hypotheses regarding anthropoid relationships are attributable to the use of restricted data sets. This large data set enables the adapid–anthropoid hypothesis to be rejected, and unitesTarsius, Anthropoidea and Omomyiformes within a clade, Haplorhini. However, relationships among these three taxa cannot be convincingly resolved at present.

Automatic 3D surface meshing to address today's industrial needs

An overall automatic surface meshing strategy is presented that details a combination of meshing technologies that together provide for meeting the demands placed on automatic, unstructured meshing in industrial settings. These demands include such issues as robustness, mesh quality, speed, and controllability. The scheme ties together several meshing technologies including advancing front tri meshing, background meshes, tri to quad conversion, constrained Laplacian smoothing, and topological and quality-based element improvement.

A method for the prediction of surface “U”-turns and transglobular connections in small proteins

A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, "U" turns, and assigning the dominant secondary structure of the intervening transglobular blocks in small, single-domain globular proteins has been developed. Since the emphasis of the method is on the prediction of the major topological elements that comprise the global structure of the protein rather than on a detailed local secondary structure description, this approach is complementary to standard secondary structure prediction schemes. Consequently, it may be useful in the early stages of tertiary structure prediction when establishment of the structural class and possible folding topologies is of interest. Application to a set of small proteins of known structure indicates a high level of accuracy. The prediction of the approximate location of the surface turns/loops that are responsible for the change in overall chain direction is correct in more than 95% of the cases. The accuracy for the dominant secondary structure assignment for the linear blocks between such surface turns/loops is in the range of 82%.

Current status, architecture, and future technologies for the International Space Station electric power system

The Electric Power System (EPS) being built for the International Space Station has undergone several significant changes over the last year, as major design decisions have been made for the overall station. While the basic topology and system elements have remained the same, there are important differences in connectivity, assembly sequence, and start-up. The key drivers for these changes in architecture have been the goal to simplify verification, and most significantly, the introduction of extensive Russian participation in the program. Having the Russians join the international community in this project has resulted in an expanded station size, larger crew, and almost doubled the observable surface of the Earth covered by the station. For the power system it has meant additional interfaces for power transfer, and new challenges for solar tracking at the higher inclination orbit. This paper reviews the current architecture and emphasizes the new features that have evolved, as the design for the new, larger station has developed. Additionally, the possible application of developing technology to the station, and other future missions is considered.

A Computationally Efficient Approach to Feature Abstraction in Design-Manufacturing Integration

Design-for-Manufacturing (DFM) analysis saves time and reduces production costs by anticipating manufacturing problems at a product’s design stage. Performing manufacturing analysis of a design created by Computer Aided Design (CAD) systems requires a higher level of geometrical abstraction of its component features. For complicated parts, such as those found in injection molding, this problem becomes very difficult. The current approach presents a computationally efficient approach to converting the basic topological elements used in CAD systems into more abstract geometrical features necessary for DFM analysis. Very large computer models of parts have been subjected to feature recognition using the current system, ManuFEATURE, with significant success.