The three-dimensional model of Dictyostelium discoideum racE based on the human rhoA-GDP crystal structure

The three-dimensional structure of racE was modeled using several homologous small G proteins, and the best model obtained using the human rhoA as modeling template is reported. The three-dimensional fold of the racE model is remarkably similar to the cellular form of human ras p21 crystal structure. Its secondary structure consists of six alpha-helices, six beta-strands and three 3(10) helices. The model retains its secondary structure after a 300 K, 300 ps molecular dynamics (MD) simulation. Important domains of the protein include its effector loop (residues 34-46), the insertion domain (residues 121-136), and the polybasic motif (between 210 and 220) not modeled in the current structure. The effector loop is inherently flexible and the structure docked with GDP exhibits the effector loop moving significantly closer to the nucleotide binding pocket, forming a tighter complex with the bound GDP. The mobility of the effector loop is conferred by a single residue 'hinge' point at residue 34Asp, also allowing the Switch I region, immediately preceding the effector loop, to be equally mobile. In comparison, the Switch II region shows average mobility. The insertion domain is highly flexible, with the insertion taking the form of a helical domain, with several charged residues forming a complex charged interface over the entire insertion region. While the GDP moiety is loosely held in the active site, the metal cation is extensively co-ordinated. The critical residue 38Thr exhibits high mobility, and is seen interacting directly with the metal ion at a distance of 2.64 A, and indirectly via an intervening water molecule. 64Gln, a key residue involved in GTP hydrolysis in ras, is seen facing the beta-phosphate group and the metal ion. Certain residues (i.e. 51Asn, 38Thr and 65Glu) exhibit unique characteristics and these residues, together with 158Val, may play important roles in the maintenance of the protein's integrity and function. There is strong consensus of secondary structural elements between models generated using various templates, such as h-rac1, h-rhoA and h-cdc42 bound to RhoGDI, all sharing only 50-55% sequence identity with racE, which suggests that this model is in all probability an accurate prediction of the true tertiary structure of racE.     

A three-dimensional motion model of loads on the lumbar spine: I. Model structure

Traditionally most biomechanical models that are used to estimate the loading experienced by the spine during work focus on static, two-dimensional representations of the work. However, most work tasks impose loads on the lumbar spine under dynamic, three-dimensional conditions. The objective of this study was to describe the structure and logic of a model that is capable of producing estimates of spine loading under three-dimensional motion conditions. This model is intended for use primarily under laboratory conditions. The model was designed initially for workplace simulation in which the trunk is moving under symmetric and asymmetric constant velocity lifting conditions. Future embellishments may enable the model to be used under free dynamic conditions. The model predicts lumbar spine compression, shear, and torsional forces as well as trunk torque production continuously throughout the exertion. This information may be compared with spine tolerance limits so that the risk of causing a vertebral end-plate microfracture by workplace requirements could be determined.     

Computational methods for a three-dimensional model of the petroleum-discovery process

A discovery-process model devised by Drew, Schuenemeyer, and Root can be used to predict the amount of petroleum to be discovered in a basin from some future level of exploratory effort: the predictions are based on historical drilling and discovery data. Because marginal costs of discovery and production are a function of field size, the model can be used to make estimates of future discoveries within deposit size classes. The modeling approach is a geometric one in which the area searched is a function of the size and shape of the targets being sought. A high correlation is assumed between the surface-projection area of the fields and the volume of petroleum. To predict how much oil remains to be found, the area searched must be computed, and the basin size and discovery efficiency must be estimated. The basin is assumed to be explored randomly rather than by pattern drilling. The model may be used to compute independent estimates of future oil at different depth intervals for a play involving multiple producing horizons. We have written FORTRAN computer programs that are used with Drew, Schuenemeyer, and Root's model to merge the discovery and drilling information and perform the necessary computations to estimate undiscovered petroleum. These program may be modified easily for the estimation of remaining quantities of commodities other than petroleum.     

Prediction of the vibration characteristics of a full-size structure from those of a scale model

The dynamic characteristics of a three-dimensional full-size crane structure are predicted for the system when it is subjected to multiple two-dimensional time-dependent moving loads using the relevant features of a scale model and the associated scaling laws. In order to establish the procedure the dynamic responses of a full-size uniform beam and its scale model, both elastically supported at each end and subjected to a moving force, are investigated. Both free and forced vibration characteristics are used to validate the scaling laws. From the premises established in this example certain derived scaling laws are then applied to the gantry crane problem.     

Comparison of templates for homology model of ρ1 GABAC receptors: More insights to the orthosteric binding site’s structure and functionality

Five sets of ρ1 GABA_C homology models were generated based on X-ray crystal structures of the acetylcholine binding protein (AChBP), the ion channel from Caenorhabditis elegans (GLIC), the ion channel from Erwinia chrysanthemi (ELIC), the homomeric GABA_A β₃ ion channel, and the homomeric α-subunit of glutamate-gated homopentameric chloride channel (GluCl). The GluCl based model was found to the represent the structure of ρ1 GABA_C receptors. The GABA pose docked in the selected best model was confirmed by QM-polarized ligand docking and induced fit docking protocol, and used to study molecular interactions in the ρ1 GABA binding site. The potential interactions of identified residues are discussed. This study identified several residues with potential ligand interactions located on loops F and G with their side chain oriented toward the binding site such as Ser215 and Gln83. The partial agonists muscimol and imidazole-4-acetic acid (I4AA) were docked into the binding site of the most reliable ‘GABA bound’ homology model. The potency and efficacy of these partial agonists in activating recombinant ρ1 receptors were correlated with their docking results. The model predicts that muscimol resembles GABA in the docking pose with similar interactions. However, I4AA has a very different docking pose to GABA and was predicted by the model to form π–π stacking with aromatic residues in the orthosteric binding site. A set of TPMPA bound ρ1 homology models based on the GluClα ‘apo state’ template was built in order to study a competitive antagonist in the ρ1 orthosteric binding site. The results demonstrated the ability of our model to explain most experimental findings and predict potential roles of residues within the orthosteric binding site.     

Simulation of scaling effects of thermal emission from non-isothermal pixels with the typical three-dimensional structure

This paper suggests approaches to simulate scaling effects of thermal emission from non-isothermal pixels with a typical three-dimensional structure. We simulate effective emissivities of various V-shaped valleys by using our Monte Carlo method under the isothermal assumption. An analytical formula of the effective emissivities is derived based on photon rebounding between surfaces in the valleys. The comparison between the simulated and the analytically modelled effective emissivities shows that the analytical formula is highly accurate. After simulating effective emissivities of the V-shaped valley under several non-isothermal conditions, we find that the structure and component temperature difference of a pixel cause the scaling effects of thermal emission of the pixel. The results, therefore, prove that Planck's law has to be corrected for remote sensing to estimate land surface temperature with high accuracy.     

Understanding the final-state control from the standpoint of the model predictive control and its application to a three-dimensional trajectory control problem

Microsystem Technologies - In many motion control problems of mechatronic equipment, the control performance of the final-state of the control period is strictly important for positioning or...     

Applications of structure from motion: a survey

Structure from motion (SfM) has been an active research area in computer vision for decades and numerous practical applications are benefiting from this research. While no previous work has tried to summarize the applications appearing in the literature, this paper deals with a comprehensive overview of recent applications of SfM by classifying them into 10 categories, namely augmented reality, autonomous navigation/guidance, motion capture, hand-eye calibration, image/video processing, image-based 3D modeling, remote sensing, image organization/browsing, segmentation and recognition, and military applications. The goal is to provide insights for researchers to position their work more appropriately in the context of existing techniques, and to perceive both new applications and relevant research problems.     

Toward the three-dimensional structure and lysophosphatidic acid binding characteristics of the LPA4/p2y9/GPR23 receptor: A homology modeling study

Lysophosphatidic acid (LPA) is a naturally occurring phospholipid that initiates a broad array of biological processes, including those involved in cell proliferation, survival and migration via activation of specific G protein-coupled receptors located on the cell surface. To date, at least five receptor subtypes (LPA_1–5) have been identified. The LPA_1–3 receptors are members of the endothelial cell differentiation gene (Edg) family. LPA₄, a member of the purinergic receptor family, and the recently identified LPA₅ are structurally distant from the canonical Edg LPA_1–3 receptors. LPA₄ and LPA₅ are linked to G_q, G_12/13 and G_s but not G_i, while LPA_1–3 all couple to G_i in addition to G_q and G_12/13. There is also evidence that LPA₄ and LPA₅ are functionally different from the Edg LPA receptors. Computational modeling has provided useful information on the structure–activity relationship (SAR) of the Edg LPA receptors. In this work, we focus on the initial analysis of the structural and ligand-binding properties of LPA₄, a prototype non-Edg LPA receptor. Three homology models of the LPA₄ receptor were developed based on the X-ray crystal structures of the ground state and photoactivated bovine rhodopsin and the recently determined human β₂-adrenergic receptor. Docking studies of LPA in the homology models were then conducted, and plausible LPA binding loci were explored. Based on these analyses, LPA is predicted to bind to LPA₄ in an orientation similar to that reported for LPA_1–3, but through a different network of hydrogen bonds. In LPA_1–3, the ligand polar head group is reported to interact with residues at positions 3.28, 3.29 and 7.36, whereas three non-conserved amino acid residues, S114(3.28), T187(EL2) and Y265(6.51), are predicted to interact with the polar head group in the LPA₄ receptor models.     

HIMADES-1: a hierarchical machine design system based on the structure model for a machine

A structure model is presented which can represent not only the simplified geometry of an individual part but also the whole structure of a machine. The model is derived from observation of the general features of a machine, ie the hierarchy and the topology (connectivity) among parts. The model plays an important role in developing a CAD system to aid designers in the primary design stage, because a general method for representing the whole structure of a machine is needed at that stage. An interactive machine design system named HIMADES-1 has been developed. The data structure of the system is based on the above structure model. The system has some original features, the most distinctive of which is the unified algorithm for dimension matching and motion analysis which reduces design labour in the primary stages of machine design.     

Brain peeling: viewing the inside of a laminar three-dimensional solid

We describe a 3D surface-tracking algorithm that is used to detect the interior laminar surfaces of a solid shell. Each of these surfaces is called a peel. Successive peels may be generated, thus representing the solid shell by its tangential layers. This algorithm is based on voxel surface-tracking methods and solves the problems associated with transforming a surface-tracking algorithm into a brain peeler. We also discuss the properties of the voxel surfaces produced by this algorithm. Using the connectivity properties of these objects, we are able to convert voxel representations into polyhedral representations without human interaction. We illustrate this work with a high-resolution reconstruction of a monkey visual cortex. Additional application domains of this work are in areas in which there is a natural laminar structure to a 3D solid, such as in geophysics (earth strata).Supported by System Development Foundation, AFOSR 85-0341, and the Nathan S. Kline Psychiatric Research Center     

Application of the independent molecule model to elucidate the dynamics of structure I methane hydrate: a second report

Two model systems of methane hydrate are constructed. One has a small cage surrounded by 12 large cages. The other has a large cage surrounded by four small cages and ten large cages. Three different H-bonding network patterns between waters are formed, and three random configurations of methane in each cage are chosen. A new method called the surface water fixed model is presented in which the energy minimum conformations for both model systems are preserved close to the X-ray crystallized structure. With normal mode analysis, we calculated frequencies of 2916.6 cm⁻¹ for a small cage at a centre, 2915.9 cm⁻¹ not at a centre, and 2911.7 cm⁻¹ for a large cage at a centre, and 2911.3 cm⁻¹ not at a centre. These frequencies are in moderate agreement with the corresponding Raman spectra, though not adequate. With our new method, however, it should be possible to improve agreement with the Raman spectra, if a model system vastly larger than the present model systems were constructed.     

Proton micromachining: a new technique for the production of three-dimensional microstructures

A novel technique for the fabrication of high aspect ratio three-dimensional (3D) microstructures is presented. A suitable resist (e.g. PMMA or SU-8) is exposed using focused MeV (million electron volt) protons in a direct write process to produce 3D microstructures with sub-micrometer feature sizes. By adjusting the energy of the proton beam, the depth of the microstructures can be controlled very accurately (e.g. between 5 and 160 μm). Single layer SU-8, a newly developed, chemically accelerated, negative tone, near UV, photo-resist, has been used in multiple exposures using different proton energies to produce intricate 3D microstructures. The combination of a well controlled exposure depth coupled with the ability to tilt the sample with respect to the beam increases the manufacturing capability, and allows the production of complex microstructures with well defined edges in single layers of resist. Received: 15 July 1999/Accepted: 30 July 1999     

An evaluation of the Mn–Ga system: Phase diagram,crystal structure,magnetism, and thermodynamic properties

The Ni–Mn-Ga alloy system is attractive due to its functional properties with potentials in various applications. However, the fundamental alloy thermodynamics of the binary Mn–Ga system is still lack of investigation. Therefore, a comprehensive evaluation of the Mn–Ga is performed in this work. Different versions of Mn–Ga phase diagrams available in the literature are reviewed. A new version of the Mn–Ga phase diagram is recommended along with possible invariant reactions. The crystal structure, magnetic transition, and thermochemical properties of intermetallic compounds are reviewed by considering available experimental and modeling such as ab initio calculations. In fact, more experimental information on the Mn-rich side is required in order to perform CALPHAD thermodynamic modeling for a reliable database. Further experiments are recommended to study the high-temperature phase equilibria between liquid, (γMn), (δMn) and Mn₂Ga(h), phase reactions between Mn₈Ga₅ and Mn₇Ga₆, and invariant reactions involving the MnGa phase. Nevertheless, the summarized information on phase equilibria, phase diagram, crystallography, magnetic transition temperature, magnetic moment, heat capacity, and enthalpy of formation can support the future thermodynamic investigation of the Mn–Ga system, which is critical for the materials design and discovery of Ni–Mn-Ga alloys.     

The behaviour of US stock prices: Evidence from a threshold autoregressive model

This paper investigates the behaviour of US stock prices using an unrestricted two-regime threshold autoregressive (TAR) model with an autoregressive unit root. The TAR model is applied to monthly stock price (NYSE Common Stocks) data for the US for the period 1964:06 to 2003:04. Amongst our main results, we find that the US stock price is a nonlinear series that is characterized by a unit root process, consistent with the efficient market hypothesis.     

Developing a model to assess the success of e-learning systems: evidence from a manufacturing company in transitional economy

This paper examines the success of an e-learning system in a company from the perspective of employees by using a multimethod approach. For this purpose Moodle learning management system was used. The success of e-learning as an information system was evaluated using four constructs of the updated DeLone and McLean IS success model—system quality, use, user satisfaction and net benefits, and adding one more construct—user performance. In this research a combination of observation and survey as two different research methods was used, which allowed the new measure to be incorporated into the model. Empirical assessment was carried out by exploratory factor analysis, confirmatory factor analysis and structural equation modeling. The research model was found to be valid and reliable. The results provide an expanded understanding of the constructs that measure the success of an e-learning system, helping to more deeply understand the key success dimensions and their interrelationships. The implications of our work were discussed. The DeLone and McLean IS success model applied equally well. However, the use of observation as a method of data collection revealed the weaknesses of the original model.