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Additional Constraints (additional + constraint)
Selected AbstractsTransition from Batch to Continuous Operation in Bio-Reactors: A Model Predictive Control Approach and ApplicationTHE CANADIAN JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2007Prashant Mhaskar Abstract This work considers the problem of determining the transition of ethanol-producing bio-reactors from batch to continuous operation and subsequent control subject to constraints and performance considerations. To this end, a Lyapunov-based non-linear model predictive controller is utilized that stabilizes the bio-reactor under continuous mode of operation. The key idea in the predictive controller is the formulation of appropriate stability constraints that allow an explicit characterization of the set of initial conditions from where feasibility of the optimization problem and hence closed-loop stability is guaranteed. Additional constraints are incorporated in the predictive control design to expand on the set of initial conditions that can be stabilized by control designs that only require the value of the Lyapunov function to decay. Then, the explicit characterization of the set of stabilizable initial conditions is used in determining the appropriate time for which the reactor must be run in batch mode. Specifically, the predictive control approach is utilized in determining the appropriate batch length that achieves stabilizable values of the state variables at the end of the batch. Application of the proposed method to the ethanol production process using Zymomonas mobilis as the ethanol producing micro-organism demonstrates the effectiveness of the proposed model predictive control strategy in stabilizing the bio-reactor. Ce travail porte sur le problème de la détermination de la transition entre le fonctionnement discontinu et continu pour des bioréacteurs produisant de l'éthanol et sur le contrôle subséquent lorsque ceux-ci sont soumis à des contraintes et des considérations de performance. À cette fin, on utilise un contrôleur prédictif par modèles non linéaires de type Lyapunov qui stabilise le bioréacteur lorsqu'il est en mode de fonctionnement continu. L'idée maîtresse dans le contrôleur prédictif est la formulation de contraintes de stabilité appropriées qui permettent une caractérisation explicite du jeu des conditions initiales à partir de laquelle la faisabilité du problème d'optimisation et donc la stabilité en boucle fermée sont garanties. Des contraintes additionnelles sont introduites dans la conception du contrôle prédictif pour étendre le jeu de conditions initiales qui peuvent être stabilisées par la conception du contrôle qui requiert seulement que la valeur de la fonction de Lyapunov diminue. Ensuite, la caractérisation explicite du jeu des conditions initiales stabilisables est utilisée dans la détermination de la durée de fonctionnement adéquate pour laquelle le réacteur doit fonctionner en mode discontinu. Spécifiquement, on utilise la méthode de contrôle prédictif dans la détermination de la longueur discontinue appropriée qui réalise les valeurs stabilisables des variables d'état à la fin du mode discontinu. L'application de la méthode proposée au procédé de production de l'éthanol utilisant Zymomonas mobilis comme microorganisme produisant de l'éthanol, démontre l'efficacité de la stratégie de contrôle prédictif de modèles proposée pour stabiliser le bioréacteur. [source] Towards Holonomic Control of Janus Particles in Optomagnetic TrapsADVANCED MATERIALS, Issue 47 2009Randall M. Erb A novel "dot" Janus particle is presented, which is compatible with optical traps and magnetic fields, allowing for direct control over five of the particle's degrees of freedom. With an additional constraint of the final sixth degree of freedom, this system represents the highest control ever achieved over freely suspended colloids, opening up the possibility for novel applications in intermolecular force measurement, microfluidics, and self-assembly. [source] A second-order homogenization procedure for multi-scale analysis based on micropolar kinematicsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 12 2007Ragnar Larsson Abstract The paper presents a higher order homogenization scheme based on non-linear micropolar kinematics representing the macroscopic variation within a representative volume element (RVE) of the material. On the microstructural level the micro,macro kinematical coupling is introduced as a second-order Taylor series expansion of the macro displacement field, and the microstructural displacement variation is gathered in a fluctuation term. This approach relates strongly to second gradient continuum formulations, presented by, e.g. Kouznetsova et al. (Int. J. Numer. Meth. Engng 2002; 54:1235,1260), thus establishing a link between second gradient and micropolar theories. The major difference of the present approach as compared to second gradient formulations is that an additional constraint is placed on the higher order deformation gradient in terms of the micropolar stretch. The driving vehicle for the derivation of the homogenized macroscopic stress measures is the Hill,Mandel condition, postulating the equivalence of microscopic and macroscopic (homogenized) virtual work. Thereby, the resulting homogenization procedure yields not only a stress tensor, conjugated to the micropolar stretch tensor, but also the couple stress tensor, conjugated to the micropolar curvature tensor. The paper is concluded by a couple of numerical examples demonstrating the size effects imposed by the homogenization of stresses based on the micropolar kinematics. Copyright © 2006 John Wiley & Sons, Ltd. [source] Credit cards scoring with quadratic utility functionsJOURNAL OF MULTI CRITERIA DECISION ANALYSIS, Issue 4-5 2002Vladimir Bugera Abstract The paper considers a general approach for classifying objects using mathematical programming algorithms. The approach is based on optimizing a utility function, which is quadratic in indicator parameters and is linear in control parameters (which need to be identified). Qualitative characteristics of the utility function, such as monotonicity in some variables, are included using additional constraints. The methodology was tested with a ,credit cards scoring' problem. Credit scoring is a way of separating specific subgroups in a population of objects (such as applications for credit), which have significantly different credit risk characteristics. A new feature of our approach is incorporating expert judgments in the model. For instance, the following preference was included with an additional constraint: ,give more preference to customers with higher incomes.' Numerical experiments showed that including constraints based on expert judgments improves the performance of the algorithm. Copyright © 2003 John Wiley & Sons, Ltd. [source] Dielectric Response of Aramid Fiber-Reinforced PEEKMACROMOLECULAR CHEMISTRY AND PHYSICS, Issue 16 2002Nina Korbakov Abstract Dielectric spectroscopy was applied for the first time to aramid fiber-reinforced PEEK, wherein the effect of the fiber on the dielectric response was examined for both amorphous and crystalline poly(ether ether ketone) (PEEK) over wide temperature and frequency ranges. Whereas the temperature behavior of the dielectric losses of the materials exhibited the typical , and , processes of PEEK, the specific effect of the fibers in the crystalline PEEK was revealed in shifting the , process to a higher temperature. The unique effect of the fibers was expressed by a significantly higher activation energy and lower dielectric strength for the , relaxation, reflecting a higher constraint level that is imposed by the fiber. It is proposed that this additional constraint is associated with fiber generated transcrystallinity. Scanning electron micrograph of transverse fracture surface of crystallized unidirectional aramid fiber-reinforced PEEK. [source] Size variation and mating success in the stag beetle, Lucanus cervusPHYSIOLOGICAL ENTOMOLOGY, Issue 3 2006DEBORAH J. HARVEY Abstract The stag beetle, Lucanus cervus, is Britain's largest beetle, with a patchy distribution in southern England. The literature suggests that it displays exceptional size variation, particularly in the males, but no analysis of size inequality has ever been conducted. In the present study, stag beetle adults are measured and allometric relationships derived between various parameters and total body length. Most of the specimens found each year are fragments and head width can be used as a good predictor of total body length in each sex. Body size differs between years and between localities and male beetles show a greater degree of size inequality than females. However, L. cervus does not show greater inequality in size than many other beetle species and populations of males are composed of a relatively large number of small individuals. These males are not at a disadvantage in mating because it is the ratio of male : female size that determines mating success. Very large males are less successful in mating and it is suggested that lack of mating success may act as an additional constraint on mandible size in this species. Size variation is most likely caused by variation in larval food resources, coupled with variation in local climatic conditions. [source] Interacting bosons in an optical latticeANNALEN DER PHYSIK, Issue 8 2008C. Moseley Abstract A strongly interacting Bose gas in an optical lattice is studied using a hard-core interaction. Two different approaches are introduced, one is based on a spin-1/2 Fermi gas with attractive interaction, the other one on a functional integral with an additional constraint (slave-boson approach). The relation between fermions and hard-core bosons is briefly discussed for the case of a one-dimensional Bose gas. For a three-dimensional gas we identify the order parameter of the Bose-Einstein condensate through a Hubbard-Stratonovich transformation and treat the corresponding theories within a mean-field approximation and with Gaussian fluctuations. This allows us to evaluate the phase diagram, including the Bose-Einstein condensate and the Mott insulator, the density-density correlation function, the static structure factor, and the quasiparticle excitation spectrum. The role of quantum and thermal fluctuations are studied in detail for both approaches, where we find good agreement with the Gross-Pitaevskii equation and with the Bogoliubov approach in the dilute regime. In the dense regime, which is characterized by the phase transition between the Bose-Einstein condensate and the Mott insulator, we discuss a renormalized Gross-Pitaevskii equation. This equation can describe the macroscopic wave function of the Bose-Einstein condensate in the dilute regime as well as close to the transition to the Mott insulator. Finally, we compare the results of the attractive spin-1/2 Fermi gas and those of the slave-boson approach and find good agreement for all physical quantities. [source] New constraints from the H, line for the temperature of the transiting planet host star OGLE-TR-10,ASTRONOMISCHE NACHRICHTEN, Issue 6 2008M. Ammler-von Eiff Abstract The spectroscopic analysis of systems with transiting planets gives strong constraints on planetary masses and radii as well as the chemical composition of the systems. The properties of the system OGLE-TR-10 are not well-constrained, partly due to the discrepancy of previous measurements of the effective temperature of the host star. This work, which is fully independent from previous works in terms of data reduction and analysis, uses the H, profile in order to get an additional constraint on the effective temperature. We take previously published UVES observations which have the highest available signal-to-noise ratio for OGLE-TR-10. A proper normalization to the relative continuum is done using intermediate data products of the reduction pipeline of the UVES spectrograph. The effective temperature then is determined by fitting synthetic H, profiles to the observed spectrum. With a result of Teff = 6020 ± 140 K, the H, profile clearly favours one of the previous measurements. The H, line is further consistent with dwarf-like surface gravities as well as solar and super-solar metallicities previously derived for OGLE-TR-10. The H, line could not be used to its full potential, partly because of the varying shape of the UVES échelle orders after flat field correction. We suggest to improve this feature when constructing future spectrographs. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] High-pressure mineral assemblage in granitic rocks from continental units, Alpine Corsica, FranceGEOLOGICAL JOURNAL, Issue 1 2006Alessandro Malasoma Abstract The Popolasca,Francardo area of northern Corsica contains an assemblage of continental tectonic units affected by an Alpine deformation. In one of these units, Unit II, previously regarded as weakly metamorphosed, a metamorphic mineral assemblage characterized by sodic amphibole, phengite, quartz, albite and epidote has been found in an aplite dyke that cuts the dominant granitoids. Peak-metamorphic temperature and pressure conditions of 300,370°C and 0.50,0.80,GPa, respectively, have been determined. This finding indicates that a continuous belt of continental slices, characterized by high-pressure, low-temperature metamorphism of Tertiary age, extends from the Tenda Massif in the north to the Corte area in the south, thus placing additional constraints on the tectonic evolution of Alpine Corsica. Copyright © 2005 John Wiley & Sons, Ltd. [source] Vadose Zone Flow Model Uncertainty as Conditioned on Geophysical DataGROUND WATER, Issue 2 2003Andrew Binley An approach to estimating the uncertainty in model descriptions based on a landscape space to model space mapping concept is described. The approach is illustrated by an application making use of plot scale geophysical estimates of changes in water content profiles to condition a model of recharge to the Sherwood Sandstone Aquifer in the United Kingdom. It is demonstrated that the mapping is highly uncertain and that many different parameter sets give acceptable simulations of the observations. Multiple profile measurements over time offer only limited additional constraints on the mapping. The resulting mapping weights may be used to evaluate uncertainty in the predictions of vadose zone flow dynamics for the site. [source] A survey on vertex coloring problemsINTERNATIONAL TRANSACTIONS IN OPERATIONAL RESEARCH, Issue 1 2010Enrico Malaguti Abstract This paper surveys the most important algorithmic and computational results on the Vertex Coloring Problem (VCP) and its generalizations. The first part of the paper introduces the classical models for the VCP, and discusses how these models can be used and possibly strengthened to derive exact and heuristic algorithms for the problem. Computational results on the best performing algorithms proposed in the literature are reported. The second part of the paper is devoted to some generalizations of the problem, which are obtained by considering additional constraints [Bandwidth (Multi) Coloring Problem, Bounded Vertex Coloring Problem] or an objective function with a special structure (Weighted Vertex Coloring Problem). The extension of the models for the classical VCP to the considered problems and the best performing algorithms from the literature, as well as the corresponding computational results, are reported. [source] Charge derivatization by 4-sulfophenyl isothiocyanate enhances peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2003Lyuben N. Marekov Abstract High-sensitivity, rapid identification of proteins in proteomic studies normally uses a combination of one- or two-dimensional electrophoresis together with mass spectrometry. The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) have increased its application in recent years. The most common method of ,peptide fingerprinting' often may not provide robust identification. Normally additional sequence information by post-source decay (PSD) MALDI-TOFMS provides additional constraints for database searches to achieve highly confident results. Here we describe a derivatization procedure to facilitate the acquisition of such sequence information. Peptide digests from a skin-expressed protein were modified with 4-sulfophenyl isothiocyanate. The resulting peptides carry a fixed negative charge at the N-terminal end and the resulting PSD spectrum is dominated by C-terminal y-type ions. The sequence information in most cases can be obtained manually or with simple programming tools. Methods of optimizing the procedure and increasing the sensitivity are discussed. Copyright © 2003 John Wiley & Sons, Ltd. [source] Dose escalation of radical radiation therapy in non-small-cell lung cancer using positron emission tomography/computed tomography-defined target volumes: Are class solutions obsolete?JOURNAL OF MEDICAL IMAGING AND RADIATION ONCOLOGY, Issue 2 2008S Everitt Summary This study investigated the maximum theoretical radiation dose that could safely be delivered to 20 patients diagnosed with non-small-cell lung cancer. Two three-dimensional conformal radiation therapy (RT) class-solution techniques (A and B) and an individualized three-dimensional conformal RT technique (C) were compared at the standard dose of 60 Gy (part I). Dose escalation was then attempted for each technique successfully at 60 Gy, constrained by predetermined limits for lung and spinal canal (part II). Part I and part II data were reanalysed to include oesophageal dose constraints (part III). In part I, 60 Gy was successfully planned using techniques A, B and C in 19 (95%), 18 (90%) and 20 (100%) patients, respectively. The mean escalated dose attainable for part II using techniques A, B and C were 76.4, 74 and 97.8 Gy, respectively (P < 0.0005). One (5%) patient was successfully planned for 120 Gy using techniques A and B, whereas four (20%) were successfully planned using technique C. Following the inclusion of additional constraints applied to the oesophagus in part III, the amount of escalated dose remained the same for all patients who were successfully planned at 60 Gy apart from two patients when technique C was applied. In conclusion, individualized three-dimensional conformal RT facilitated greater dose conformation and higher escalation of dose in most patients. With modern planning tools, simple class solutions are obsolete for conventional dose radical RT in non-small-cell lung cancer. Highly individualized conformal planning is essential for dose escalation. [source] Credit cards scoring with quadratic utility functionsJOURNAL OF MULTI CRITERIA DECISION ANALYSIS, Issue 4-5 2002Vladimir Bugera Abstract The paper considers a general approach for classifying objects using mathematical programming algorithms. The approach is based on optimizing a utility function, which is quadratic in indicator parameters and is linear in control parameters (which need to be identified). Qualitative characteristics of the utility function, such as monotonicity in some variables, are included using additional constraints. The methodology was tested with a ,credit cards scoring' problem. Credit scoring is a way of separating specific subgroups in a population of objects (such as applications for credit), which have significantly different credit risk characteristics. A new feature of our approach is incorporating expert judgments in the model. For instance, the following preference was included with an additional constraint: ,give more preference to customers with higher incomes.' Numerical experiments showed that including constraints based on expert judgments improves the performance of the algorithm. Copyright © 2003 John Wiley & Sons, Ltd. [source] Real-time accelerated interactive MRI with adaptive TSENSE and UNFOLD,MAGNETIC RESONANCE IN MEDICINE, Issue 2 2003Michael A. Guttman Abstract Reduced field-of-view (FOV) acceleration using time-adaptive sensitivity encoding (TSENSE) or unaliasing by Fourier encoding the overlaps using the temporal dimension (UNFOLD) can improve the depiction of motion in real-time MRI. However, increased computational resources are required to maintain a high frame rate and low latency in image reconstruction and display. A high-performance software system has been implemented to perform TSENSE and UNFOLD reconstructions for real-time MRI with interactive, on-line display. Images were displayed in the scanner room to investigate image-guided procedures. Examples are shown for normal volunteers and cardiac interventional experiments in animals using a steady-state free precession (SSFP) sequence. In order to maintain adequate image quality for interventional procedures, the imaging rate was limited to seven frames per second after an acceleration factor of 2 with a voxel size of 1.8 × 3.5 × 8 mm. Initial experiences suggest that TSENSE and UNFOLD can each improve the compromise between spatial and temporal resolution in real-time imaging, and can function well in interactive imaging. UNFOLD places no additional constraints on receiver coils, and is therefore more flexible than SENSE methods; however, the temporal image filtering can blur motion and reduce the effective acceleration. Methods are proposed to overcome the challenges presented by the use of TSENSE in interactive imaging. TSENSE may be temporarily disabled after changing the imaging plane to avoid transient artifacts as the sensitivity coefficients adapt. For imaging with a combination of surface and interventional coils, a hybrid reconstruction approach is proposed whereby UNFOLD is used for the interventional coils, and TSENSE with or without UNFOLD is used for the surface coils. Magn Reson Med 50:315,321, 2003. Published 2003 Wiley-Liss, Inc. [source] The kinematical structure of gravitationally lensed arcsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2006Ole Möller ABSTRACT In this paper, the expected properties of the velocity fields of strongly lensed arcs behind galaxy clusters are investigated. The velocity profile along typical lensed arcs is determined by ray-tracing light rays from a model source galaxy through parametric cluster toy models consisting of individual galaxies embedded in a dark cluster halo. We find that strongly lensed arcs of high-redshift galaxies show complex velocity structures that are sensitive to the details of the mass distribution within the cluster, in particular at small scales. From fits to the simulated imaging and kinematic data, we demonstrate that reconstruction of the source velocity field is in principle feasible. Two-dimensional kinematic information obtained with integral field units on large ground-based telescopes in combination with adaptive optics will allow the reconstruction of rotation curves of lensed high redshift galaxies. This makes it possible to determine the mass-to-light ratios of galaxies at redshifts z > 1 out to about 2,3 scalelengths with better than ,20 per cent accuracy. We also discuss the possibilities of using two-dimensional kinematic information along the arcs to give additional constraints on the cluster lens mass models. [source] A method for the direct determination of the surface gravities of transiting extrasolar planetsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY: LETTERS (ELECTRONIC), Issue 1 2007John Southworth ABSTRACT We show that the surface gravity of a transiting extrasolar planet can be calculated from only the spectroscopic orbit of its parent star and the analysis of its transit light curve. This does not require additional constraints, such as are often inferred from theoretical stellar models or model atmospheres. The surface gravity of the planet can therefore be measured precisely and from only directly observable quantities. We outline the method and apply it to the case of the first known transiting extrasolar planet, HD 209458b. We find a surface gravity of gp= 9.28 ± 0.15 m s,2, which is an order of magnitude more precise than the best available measurements of its mass, radius and density. This confirms that the planet has a much lower surface gravity than that predicted by published theoretical models of gas giant planets. We apply our method to all 14 known transiting extrasolar planets and find a significant correlation between surface gravity and orbital period, which is related to the known correlation between mass and period. This correlation may be the underlying effect as surface gravity is a fundamental parameter in the evaporation of planetary atmospheres. [source] On the impact of the solution representation for the Internet Protocol Network Design Problem with max-hop constraintsNETWORKS: AN INTERNATIONAL JOURNAL, Issue 2 2004L. De Giovanni Abstract The IP (Internet Protocol) Network Design Problem can be shortly stated as follows. Given a set of nodes and a set of traffic demands, we want to determine the minimum cost capacity installation such that all the traffic is routed. Capacity is provided by means of links of a given capacity and traffic must be loaded on the network according to the OSPF-ECM (Open Shortest Path First,Equal Commodity Multiflow) protocol, with additional constraints on the maximum number of hops. The problem is strongly NP-Hard, and the literature proposes local search-based heuristics that do not take into account max-hop constraints, or assume a simplified OSPF routing. The core in a local search approach is the network loading algorithm for the evaluation of the neighbor solutions costs. It presents critical aspects concerning both computational efficiency and memory requirements. Starting from a tabu search prototype, we show how these aspects deeply impact on the design of a local search procedure, even at the logical level. We present several properties of the related network loading problem, that allow to overcome the critical issues and lead to an efficient solution evaluation. © 2004 Wiley Periodicals, Inc. NETWORKS, VoL. 44(2), 73,83 2004 [source] A GRASP with path-relinking for private virtual circuit routing,NETWORKS: AN INTERNATIONAL JOURNAL, Issue 2 2003Mauricio G. C. Resende Abstract A frame relay service offers virtual private networks to customers by provisioning a set of long-term private virtual circuits (PVCs) between customer endpoints on a large backbone network. During the provisioning of a PVC, routing decisions are made without any knowledge of future requests. Over time, these decisions can cause inefficiencies in the network and occasional offline rerouting of the PVCs is needed. In this paper, the offline PVC routing problem is formulated as an integer multicommodity flow problem with additional constraints and with an objective function that minimizes propagation delays and/or network congestion. We propose variants of a GRASP with path-relinking heuristic for this problem. Experimental results for realistic-size problems are reported, showing that the proposed heuristics are able to improve the solutions found with standard routing techniques. Moreover, the structure of our objective function provides a useful strategy for setting the appropriate value of its weight parameter, to achieve some quality of service (QoS) level defined by a desired balance between propagation delay and delay due to network congestion. © 2003 Wiley Periodicals, Inc. [source] The role of low soil temperature in the inhibition of growth and PSII function during dark chilling in soybean genotypes of contrasting tolerancePHYSIOLOGIA PLANTARUM, Issue 1 2007Abram J. Strauss Dark chilling affects growth and yield of warm-climate crops such as soybean [Glycine max (L.) Merr.]. Several studies have investigated chilling-stress effects on photosynthesis and other aspects of metabolism, but none have compared effects of whole-plant chilling (WPC; shoots and roots) with that of aboveground chilling in legumes. This is important because low root temperatures might induce additional constraints, such as inhibition of N2 fixation, thereby aggravating chilling-stress symptoms. Effects of dark chilling on PSII, shoot growth, leaf ureide content and photosynthetic capacity were studied in two soybean genotypes, Highveld Top (chilling tolerant) and PAN809 (chilling sensitive), in experiments comparing effects of WPC with that of shoot chilling (SC). Both treatments inhibited shoot growth in PAN809 but not Highveld Top. Also, WPC in PAN809 caused a decrease in leaf ureide content followed by severe chlorosis and alterations in O-J-I-P fluorescence-rise kinetics, distinct from SC. A noteworthy difference was the appearance of a ,K peak in the O-J-I-P fluorescence rise in response to WPC. These genotypic and treatment differences also reflected in the degree of inhibition of CO2 assimilation rates. The appearance of a ,K peak, coupled with growth inhibition, reduced ureide content, chlorosis and lower CO2 assimilation rates, provides mechanistic information about how WPC might have aggravated chilling-stress symptoms in PAN809. We introduce a model explaining how chilling soil temperatures might trigger N-limitation in sensitive genotypes and how characteristic changes in O-J-I-P fluorescence-rise kinetics are linked to changes in carbon and nitrogen metabolism. [source] Docking structures of domains into maps from cryo-electron microscopy using local correlationACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2000Alan M. Roseman Accurate maps of large macromolecular complexes can be calculated from cryo-electron micrographs of non-crystalline specimens to resolutions of about 10,Å. A method to dock the atomic structures of domains solved by X-ray crystallography or nuclear magnetic resonance into cryo-EM maps is presented. Domains can be docked independently into large complexes without prior definition of the boundaries. No special symmetry is assumed and the procedure is suitable for general application to almost any system where a cryo-EM map (at 15,Å resolution or better) of a complex has been obtained and the atomic structures of the components are available. This is achieved through use of a real-space density-matching procedure based on local correlation. A complete asymmetric unit search correlating a density object derived from the atomic coordinates and the density of the EM map is performed. The correlation coefficient is calculated locally in real space using only values of the search object and corresponding samples extracted from the EM map which are under the `footprint' of the positioned search object. The procedure has been demonstrated by docking the domains of GroEL from the crystal structure into a cryo-EM map Fourier filtered to 12 or 15,Å resolution. The correct positions were found without applying any additional constraints. A model of the oligomer built from the docked domains compared favourably with the known crystal structure, confirming the validity of the approach. The procedure is designed to facilitate the incorporation of additional constraints on the docking solutions, which could help to dock using lower resolution maps. [source] | ||||||||||||||||||||||||||||