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Design Methods (design + methods)
Kinds of Design Methods Selected AbstractsAdaptive Design Methods in Clinical Trials by Shein-Chung Chow, Mark ChangINTERNATIONAL STATISTICAL REVIEW, Issue 2 2007C.M. O'Brien No abstract is available for this article. [source] Adaptive Design Methods in Clinical TrialsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 1 2008Angela Wade No abstract is available for this article. [source] ,Eosinophilic Fungal Rhinosinusitis': A Common Disorder in Europe?THE LARYNGOSCOPE, Issue 2 2003Hannes Braun MD Abstract Objectives/Hypothesis The traditional criteria for the diagnosis of allergic fungal sinusitis include chronic rhinosinusitis, "allergic mucin" (mucus containing clusters of eosinophils), and detection of fungi by means of histological examination or culture. In 1999, a group of Mayo Clinic researchers, with a novel method of mucus collection and fungal culturing technique, were able to find fungi in 96% of patients with chronic rhinosinusitis. Immunoglobulin E,mediated hypersensitivity to fungal allergens was not evident in the majority of their patients. Because the presence of eosinophils in the allergic mucin, not a type I hypersensitivity, is probably the common denominator in the pathophysiology of allergic fungal sinusitis, the Mayo Clinic group proposed a change in terminology from allergic fungal sinusitis to eosinophilic fungal rhinosinusitis. Using new techniques of culturing fungi from nasal secretion, as well as preservation and histological examination of mucus, we investigated the incidence of "eosinophilic fungal rhinosinusitis" in our patient population. Study Design Methods In an open prospective study nasal mucus from patients with chronic rhinosinusitis as well as from healthy volunteers was cultured for fungi. In patients, who underwent functional endoscopic sinus surgery, nasal mucus was investigated histologically to detect fungi and eosinophils within the mucus. Results Fungal cultures were positive in 84 of 92 patients with chronic rhinosinusitis (91.3%). In all, 290 positive cultures grew 33 different genera, with 3.2 species per patient, on average. Fungal cultures from a control group of healthy volunteers yielded positive results in 21 of 23 (91.3%). Histologically, fungal elements were found in 28 of 37 patients (75.5%) and eosinophilic mucin in 35 of 37 patients (94.6%). Neither fungi nor eosinophils were present in 2 of 37 patients (5.4%). Conclusions Our data show that the postulated criteria of allergic fungal sinusitis are present in the majority of patients with chronic rhinosinusitis. Either those criteria will be found to be invalid and need to be changed or, indeed, "eosinophilic fungal rhinosinusitis" exists in the majority of patients with chronic rhinosinusitis. Based on our results, fungi and eosinophilic mucin appear to be a standard component of nasal mucus in patients with chronic rhinosinusitis. [source] Adaptive Design Methods in Clinical Trials.BIOMETRICAL JOURNAL, Issue 5 2009Chang, M. (2007)., S. C. No abstract is available for this article. [source] Adaptive Design Methods in Clinical Trials by S.-C.BIOMETRICS, Issue 1 2008M. Chang No abstract is available for this article. [source] Book Review: Protein,Ligand Interactions,From Molecular Recognition to Drug Design Methods.CHEMBIOCHEM, Issue 11 2003Edited by Hans-Joachim Böhm, Gisbert Schneider No abstract is available for this article. [source] A program for the design of linear time invariant control systems: CDMCADCOMPUTER APPLICATIONS IN ENGINEERING EDUCATION, Issue 3 2004M. Koksal Abstract Coefficient Diagram Method (CDM) is a new method proposed for the analysis and design of linear time-invariant control systems. The control system design by this method results with satisfactory stability, time response and robustness properties compatible with, and in most cases better than, the ones obtained by the other present design methods. In this study, the design procedure described in the literature for CDM is improved so that a systematic and easy tool with understandable sufficient detail is presented. A visual toolbox, which can be used efficiently both for education and research, is obtained based on the procedure presented by using MATLAB. © 2004 Wiley Periodicals, Inc. Comput Appl Eng Educ 12: 165,174, 2004; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20011 [source] Proportional-Integral-Plus Control of an Intelligent ExcavatorCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 1 2004Jun Gu Previous work using LUCIE was based on the ubiquitous PI/PID control algorithm, tuned on-line, and implemented in a rather ad hoc manner. By contrast, the present research utilizes new hardware and advanced model-based control system design methods to improve the joint control and so provide smoother, more accurate movement of the excavator arm. In this article, a novel nonlinear simulation model of the system is developed for MATLAB/SIMULINK©, allowing for straightforward refinement of the control algorithm and initial evaluation. The PIP controller is compared with a conventionally tuned PID algorithm, with the final designs implemented on-line for the control of dipper angle. The simulated responses and preliminary implementation results demonstrate the feasibility of the approach. [source] Spectral analysis and design approach for high force-to-volume extrusion damper-based structural energy dissipationEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 2 2008Geoffrey W. Rodgers Abstract High force-to-volume extrusion damping devices can offer significant energy dissipation directly in structural connections and significantly reduce seismic response. Realistic force levels up to 400,kN have been obtained experimentally validating this overall concept. This paper develops spectral-based design equations for their application. Response spectra analysis for multiple, probabilistically scaled earthquake suites are used to delineate the response reductions due to added extrusion damping. Representative statistics and damping reduction factors are utilized to characterize the modified response in a form suitable for current performance-based design methods. Multiple equation regression analysis is used to characterize reduction factors in the constant acceleration, constant velocity, and constant displacement regions of the response spectra. With peak device forces of 10% of structural weight, peak damping reduction factors in the constant displacement region of the spectra are approximately 6.5,×, 4.0,×, and 2.8,× for the low, medium, and high suites, respectively. At T,=,1,s, these values are approximately 3.6,×, 1.8,×, and 1.4,×, respectively. The maximum systematic bias introduced by using empirical equations to approximate damping reduction factors in design analyses is within the range of +10 to ,20%. The seismic demand spectrum approach is shown to be conservative across a majority of the spectrum, except for large added damping between T,=,0.8 and 3.5,s, where it slightly underestimates the demand up to a maximum of approximately 10%. Overall, the analysis shows that these devices have significant potential to reduce seismic response and damage at validated prototype device force levels. Copyright © 2007 John Wiley & Sons, Ltd. [source] Pure aluminium shear panels as dissipative devices in moment-resisting steel framesEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 7 2007G. De Matteis Abstract The use of energy dissipation systems for the seismic control of steel structures represents a valid alternative to conventional seismic design methods. The seismic devices currently employed are mostly based on the metallic yielding technology due to the large feasibility and efficiency they can provide. Within this context, in the current paper an innovative solution based on the adoption of low-yield-strength pure aluminium shear panels (SPs) for seismic protection of steel moment-resisting frames is proposed and investigated. In order to prove the effectiveness of the system, a wide numerical study based on both static and dynamic non-linear analyses has been carried out, considering a number of different frame-to-shear panel combinations, aiming at assessing the effect of the main influential parameters on the seismic response of the structure. The obtained results show that the contribution provided by aluminium SPs is rather significant, allowing a remarkable improvement of the seismic performance of the structure in terms of stiffness, strength and ductility, with the possibility to strongly limit the damage occurring in the members of moment-resisting frames. In particular, it is clearly emphasized that the stiffening effect provided by SPs allows a more rational design procedure to be adopted, since the serviceability limit state check does not lead to unavoidable and uneconomical increase of the size of main structural members. Copyright © 2007 John Wiley & Sons, Ltd. [source] On the accuracy of simplified methods for the analysis of isolated bridgesEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 3 2001P. Franchin Abstract To foster the use of seismic isolation in structures, existing guidelines strive to formulate design methods which are simple and accessible to non-specialized engineers. On the other hand, not all of the simplifying provisions adopted by the norms can be said to have been adequately tested to provide a consistent level of accuracy. The study attempts, in particular, to elucidate three aspects related to the methods of analysis for linear or linearized isolated bridges on which little or no advice can be found in the norms. The first one is about the way one has to account for the fact that damping matrices of isolated bridges are never of proportional type. The present study demonstrates, through a number of typical applications, that classical modal analysis, using real modes and the diagonal terms of the modal damping matrices, still provide a fully acceptable approximation. The second and third aspects are related to the use of linearization expressions extended to the analysis of hyperstatic bridges. Parametric analyses conducted in the study show that none of the formulas in current use gives satisfactory results for both the displacement and the force responses, a requirement for a reliable design of an isolated bridge. How to use the equivalent linear parameters, and in particular the isolators equivalent damping ratios, in the context of a modal analysis, is treated next. This problem is seldom if ever mentioned in the norms where at most a formula is given for constructing modal damping ratios based on the damping ratios of the isolators. A rational, approximate procedure is discussed in this paper, applicable to all types of structures with non-proportional damping, which in the case of bridges can be shown to reduce to the expression provided in the Japanese bridge design guidelines. Copyright © 2001 John Wiley & Sons, Ltd. [source] A design for robust power system stabilizer by means of H, control and particle swarm optimization methodELECTRONICS & COMMUNICATIONS IN JAPAN, Issue 8 2008Yoshifumi Zoka Abstract This paper proposes two types of PSS design methods that take into account robustness for comparably large power systems. The first one is a design method based on , control theory and the second one is a parameter determination method for a standard PSS by using Particle Swarm Optimization (PSO). In order to deal with large-scale systems, a reduced model is developed to get the target system which preserves major oscillation modes only. The major oscillation modes are selected by using the residue concept, and the PSS is designed based on the target system. In order to verify effectiveness, the proposed methods are compared with the other previously proposed method based on a Genetic Algorithm (GA) through many numerical simulations. © 2008 Wiley Periodicals, Inc. Electron Comm Jpn, 91(8): 34,43, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecj.10132 [source] A simulation study comparing different experimental designs for estimating uptake and elimination ratesENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2006Bryan R. Bell Abstract The design of ecotoxicological studies requires decisions about the number and spacing of exposure groups tested, the number of replications, the spacing of sampling times, the duration of the study, and other considerations. For example, geometric spacing of sampling times or toxicant concentrations is often used as a default design. Optimal design methods in statistics can suggest alternative spacing of sampling times that yield more precise estimates of regression coefficients. In this study, we use a computer simulation to explore the impact of the spacing of sampling times and other factors on the estimation of uptake and elimination rate constants in an experiment addressing the bioaccumulation of a contaminant. Careful selection of sampling times can result in smaller standard errors for the parameter estimates, thereby allowing the construction of smaller, more precise confidence intervals. Thus, the effort invested in constructing an optimal experimental design may result in more precise inference or in a reduction of replications in an experimental design. [source] ON THE ORIGIN OF MODULAR VARIATIONEVOLUTION, Issue 8 2002Hod Lipson Abstract We study the dynamics of modularization in a minimal substrate. A module is a functional unit relatively separable from its surrounding structure. Although it is known that modularity is useful both for robustness and for evolvability (Wagner 1996), there is no quantitative model describing how such modularity might originally emerge. Here we suggest, using simple computer simulations, that modularity arises spontaneously in evolutionary systems in response to variation, and that the amount of modular separation is logarithmically proportional to the rate of variation. Consequently, we predict that modular architectures would appear in correlation with high environmental change rates. Because this quantitative model does not require any special substrate to occur, it may also shed light on the origin of modular variation in nature. This observed relationship also indicates that modular design is a generic phenomenon that might be applicable to other fields, such as engineering: Engineering design methods based on evolutionary simulation would benefit from evolving to variable, rather than stationary, fitness criteria, as a weak and problem-independent method for inducing modularity. [source] Technical basis on structural fire resistance design in building standards law of JapanFIRE AND MATERIALS, Issue 2-4 2004Kazunori Harada Abstract Structural fire resistance design method came into effect due to the revision of Japan's building code (building standards law of Japan) in June 2001. The method includes standard methods to calculate (1) fire exposure to structural elements, (2) temperature rise of steel and RC elements during fire exposure and (3) structural end points such as ultimate steel temperature for buckling of columns, bending failure of beams and so on. This paper discusses the technical basis for design methods especially focused on steel framed buildings. The calculated values by design equations were compared with experimental values in order to examine the redundancies implied. In the final stage, all the redundancies were combined by Monte-Carlo method and first-order moment method (AFORM). Target safety index and corresponding partial safety factors were discussed. Copyright © 2004 John Wiley & Sons, Ltd. [source] System design in normative and actual practice: A comparative study of cognitive task allocation in advanced manufacturing systemsHUMAN FACTORS AND ERGONOMICS IN MANUFACTURING & SERVICE INDUSTRIES, Issue 2 2004Sotiris Papantonopoulos The Human Factors Engineering approach to human-machine system design is based largely on normative design methods. This article suggests that the scope of Human Factors Engineering shall be extended to the descriptive study of system design in actual practice by the application of theoretical frameworks that emphasize the role of the system-design practitioner and organization in the design process. A comparative study of system design in normative and actual practice was conducted in the design of cognitive task allocation in a Flexible Manufacturing System (FMS) cell. The study showed that the designers' allocation decisions were influenced strongly by factors related to their own design practices, yet exogenous to the tasks to be allocated. Theoretical frameworks from Design Research were applied to illustrate differences between normative and actual practice of system design. © 2004 Wiley Periodicals, Inc. Hum Factors Man 14: 181,196, 2004. [source] A new saturated/unsaturated model for stormwater infiltration systemsHYDROLOGICAL PROCESSES, Issue 25 2008Dale Browne Abstract Infiltration systems are widely used as an effective urban stormwater control measure. Most design methods and models roughly approximate the complex physical flow processes in these systems using empirical equations and fixed infiltration rates to calculate emptying times from full. Sophisticated variably saturated flow models are available, but rarely applied owing to their complexity. This paper describes the development and testing of an integrated one-dimensional model of flow through the porous storage of a typical infiltration system and surrounding soils. The model accounts for the depth in the storage, surrounding soil moisture conditions and the interaction between the storage and surrounding soil. It is a front-tracking model that innovatively combines a soil-moisture-based solution of Richard's equation for unsaturated flow with piston flow through a saturated zone as well as a reservoir equation for flow through a porous storage. This allows the use of a simple non-iterative numerical solution that can handle ponded infiltration into dry soils. The model is more rigorous than approximate stormwater infiltration system models and could therefore be valuable in everyday practice. A range of test cases commonly used to test soil water flow models for infiltration in unsaturated conditions, drainage from saturation and infiltration under ponded conditions were used to test the model along with an experiment with variable depth in a porous storage over saturated conditions. Results show that the model produces a good fit to the observed data, analytical solutions and Hydrus. Copyright © 2008 John Wiley & Sons, Ltd. [source] Finite elements modelling of the long-term behaviour of a full-scale flexible pavement with the shakedown theoryINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 1 2009Cyrille Chazallon Abstract Rutting, due to permanent deformations of unbound materials, is one of the principal damage modes of low-traffic pavements. Flexible pavement design methods remain empirical; they do not take into account the inelastic behaviour of pavement materials and do not predict the rutting under cyclic loading. A simplified method, based on the concept of the shakedown theory developed by Zarka for metallic structures under cyclic loadings, has been used to estimate the permanent deformations of unbound granular materials subjected to traffic loading. Based on repeated load triaxial tests, a general procedure has been developed for the determination of the material parameters of the constitutive model. Finally, the results of a finite elements modelling of the long-term behaviour of a flexible pavement with the simplified method are presented and compared with the results of a full-scale flexible pavement experiment performed by Laboratoire Central des Ponts et Chaussées. Finally, the calculation of the rut depth evolution with time is carried out. Copyright © 2008 John Wiley & Sons, Ltd. [source] Skin friction features of drilled CIP piles in sand from pile segment analysisINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 7 2008Sungjune Lee Abstract Numerical pile segment analysis is conducted in this study with an advanced soil model to investigate the skin friction behaviour of a drilled Cast-In-Place (CIP) pile installed in sand. Although the interface between the sand and pile is considered rough, thin elements adjacent to the pile are used to include effects of localized shear. Unit weights of fluid concrete and accompanied changes in stress are considered as the effects of pile installation. Changes in effective stresses are the most prominent effect due to pile installation with a change in direction of the major principal stress from the vertical to the radial direction. Shear behaviour of the sand at the interface during the early shear stage is related to the contractive tendency of the sand at small strain levels. Changes in the stress field around the pile with little changes in volumetric strain take place during the early shear stage. Stress redistributions during the early shear stage depend on the direction of the major principal stress before shear. Results of the pile segment analyses for drilled CIP piles show good agreement with design methods. Parametric studies are used to characterize the effects of sand density and pile diameter on the skin friction behaviour of drilled CIP piles. Copyright © 2007 John Wiley & Sons, Ltd. [source] An integrated parameter identification method combined with sensor placement designINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 12 2008Yiqian Li Abstract Material parameter identification based on in situ measurements plays a very important role in engineering. Since noises are inevitable in measurements and the parameter identification is inherently ill posed, it is necessary to consider some methods to stabilize the identification procedure. One choice is properly designing the sensor placement, which has attracted much attention over the past 30 years. Most existing sensor placement design methods are based on certain sensitivity analysis, which commonly requires evaluating Jacobian matrix for given parameters. However, the ,true' values of parameters are unknown at that moment, because sensor placement design is carried out before the parameter identification. Consequently, roughly estimated ,true' parameters have to be used and less optimal sensor placement could be obtained. To solve this problem, this paper presents an integrated method in which the parameter identification and sensor placement design are carried out alternatively. The validity of the proposed method is illustrated by two simple academic examples. Then it is implemented to detect damages in a real highway bridge. Copyright © 2007 John Wiley & Sons, Ltd. [source] Robust fault detection and isolation for LPV systems under a sensitivity constraintINTERNATIONAL JOURNAL OF ADAPTIVE CONTROL AND SIGNAL PROCESSING, Issue 1 2009Saverio Armeni Abstract A novel fault detection and isolation (FDI) filter design method is proposed for linear parameter varying (LPV) systems. The LPV system description can be used to approximate the behavior of nonlinear systems and leads to simple nonlinear FDI designs. The main goal here is to obtain residual generator (RG) filters with enhanced fault transmission dc-gains and large ,, nuisance attenuation. This is achieved using bilinear matrix inequality techniques by exploiting the relevant geometrical properties of the affine LPV description. Finally, it is shown by a nonlinear example that the RG filters designed by the proposed method compare well with alternative approaches including direct nonlinear design methods. Copyright © 2008 John Wiley & Sons, Ltd. [source] Design of multichannel MAC protocols for wireless ad hoc networksINTERNATIONAL JOURNAL OF NETWORK MANAGEMENT, Issue 5 2009Shou-Chih Lo Medium access control (MAC) protocols coordinate channel access between wireless stations, and they significantly affect the network throughput of wireless ad hoc networks. MAC protocols that are based on a multichannel model can increase the throughput by enabling more simultaneous transmission pairs in the network. In this paper, we comprehensively compare different design methods for multichannel MAC protocols. We classify existing protocols into different categories according to the channel negotiation strategies they employ. The common problems that may be encountered in multichannel design are discussed. We then propose a hybrid protocol that combines the advantages of the two methods of a common control channel and a common control period. The simulation results show that our proposed protocol can significantly outperform two representative protocols. Copyright © 2008 John Wiley & Sons, Ltd. [source] Full-wave modeling and optimization of Bøifot junction ortho-mode transducersINTERNATIONAL JOURNAL OF RF AND MICROWAVE COMPUTER-AIDED ENGINEERING, Issue 4 2008Jorge A. Ruiz-Cruz Abstract The full-wave design of broadband ortho-mode transducers based on the Bøifot junction has two main aspects: an efficient analysis method and a design process divided into tasks with relatively low computational effort. In the analysis part, a rigorous mode-matching technique has been developed to obtain the generalized admittance matrix of the Bøifot junction. The other elements of the device are also analyzed by mode-matching. With respect to the design, the proposed procedure starts with the optimization of the individual building blocks of the device. Their interaction is also taken into account in a systematic process. The analysis and design methods have been validated with other numerical methods and an experimental prototype. © 2008 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2008. [source] On the optimum pyramidal-horn design methodsINTERNATIONAL JOURNAL OF RF AND MICROWAVE COMPUTER-AIDED ENGINEERING, Issue 6 2006Jing Lu Teo Abstract In this article the optimum pyramidal-horn design methods are considered. The validity of comparing the different methods with respect to design accuracy is examined in light of the fundamental accuracy limits of Schelkonoff's horn-gain formulas. © 2006 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2006. [source] Integrated fault detection and control for LPV systemsINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 3 2009Heng Wang Abstract This paper studies the integrated fault detection and control problem for linear parameter-varying systems. A parameter-dependent detector/controller is designed to generate two signals: residual and control signals that are used to detect faults and simultaneously meet some control objectives. The low-frequency faults and certain finite-frequency disturbances are considered. With the aid of the newly developed linearization techniques, the design methods are presented in terms of solutions to a set of linear matrix inequalities. A numerical example is given to illustrate the effectiveness of the proposed methods. Copyright © 2008 John Wiley & Sons, Ltd. [source] Robust fault estimation of uncertain systems using an LMI-based approachINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 18 2008Euripedes G. Nobrega Abstract General recent techniques in fault detection and isolation (FDI) are based on H, optimization methods to address the issue of robustness in the presence of disturbances, uncertainties and modeling errors. Recently developed linear matrix inequality (LMI) optimization methods are currently used to design controllers and filters, which present several advantages over the Riccati equation-based design methods. This article presents an LMI formulation to design full-order and reduced-order robust H, FDI filters to estimate the faulty input signals in the presence of uncertainty and model errors. Several cases are examined for nominal and uncertain plants, which consider a weight function for the disturbance and a reference model for the faults. The FDI LMI synthesis conditions are obtained based on the bounded real lemma for the nominal case and on a sufficient extension for the uncertain case. The conditions for the existence of a feasible solution form a convex problem for the full-order filter, which may be solved via recently developed LMI optimization techniques. For the reduced-order FDI filter, the inequalities include a non-convex constraint, and an alternating projections method is presented to address this case. The examples presented in this paper compare the simulated results of a structural model for the nominal and uncertain cases and show that a degree of conservatism exists in the robust fault estimation; however, more reliable solutions are achieved than the nominal design. Copyright © 2008 John Wiley & Sons, Ltd. [source] Linear, parameter-varying control and its application to a turbofan engineINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 9 2002Gary J. BalasArticle first published online: 15 JUL 200 This paper describes application of parameter-dependent control design methods to a turbofan engine. Parameter-dependent systems are linear systems, whose state-space descriptions are known functions of time-varying parameters. The time variation of each of the parameters is not known in advance, but is assumed to be measurable in real-time. Three linear, parameter-varying (LPV) approaches to control design are discussed. The first method is based on linear fractional transformations which relies on the small gain theorem for bounds on performance and robustness. The other methods make use of either a single (SQLF) or parameter-dependent (PDQLF) quadratic Lyapunov function to bound the achievable level of performance. The latter two techniques are used to synthesize controllers for a high-performance turbofan engine. A LPV model of the turbofan engine is constructed from Jacobian linearizations at fixed power codes for control design. The control problem is formulated as a model matching problem in the ,, and LPV framework. The objective is decoupled command response of the closed-loop system to pressure and rotor speed requests. The performance of linear, ,, point designs are compared with the SQLF and PDQLF controllers. Nonlinear simulations indicate that the controller synthesized using the SQLF approach is slightly more conservative than the PDQLF controller. Nonlinear simulations with the SQLF and PDQLF controllers show very robust designs that achieve all desired performance objectives. Copyright © 2002 John Wiley & Sons, Ltd. [source] Toward accurate relative energy predictions of the bioactive conformation of drugsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Keith T. Butler Abstract Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol,1 of a local minimum, with penalties above 2.0kcal mol,1 being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] A novel method for enzyme designJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2009Xiaolei Zhu Abstract Rational design of enzymes is a stringent test of our understanding of protein structure and function relationship, which also has numerous potential applications. We present a novel method for enzyme design that can find good candidate protein scaffolds in a protein-ligand database based on vector matching of key residues. Residues in the vicinity of the active site were also compared according to a similarity score between the scaffold protein and the target enzyme. Suitable scaffold proteins were selected, and the side chains of residues around the active sites were rebuilt using a previously developed side-chain packing program. Triose phosphate isomerase (TIM) was used as a validation test for enzyme design. Selected scaffold proteins were found to accommodate the enzyme active sites and successfully form a good transition state complex. This method overcomes the limitations of the current enzyme design methods that use limited number of protein scaffold and based on the position of ligands. As there are a large number of protein scaffolds available in the Protein Data Band, this method should be widely applicable for various types of enzyme design. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Biologically inspired climbing with a hexapedal robotJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 4-5 2008M. J. Spenko This paper presents an integrated, systems-level view of several novel design and control features associated with the biologically inspired, hexapedal, RiSE (Robots in Scansorial Environments) robot. RiSE is the first legged machine capable of locomotion on both the ground and a variety of vertical building surfaces including brick, stucco, and crushed stone at speeds up to 4 cm/s, quietly and without the use of suction, magnets, or adhesives. It achieves these capabilities through a combination of bioinspired and traditional design methods. This paper describes the design process and specifically addresses body morphology, hierarchical compliance in the legs and feet, and sensing and control systems that enable robust and reliable climbing on difficult surfaces. Experimental results illustrate the effects of various behaviors on climbing performance and demonstrate the robot's ability to climb reliably for long distances. © 2008 Wiley Periodicals, Inc. 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