217 results on '"Distance constraints"'
Search Results
2. Adaptive Fixed-Time Safety Concurrent Control of Vehicular Platoons with Time-Varying Actuator Faults under Distance Constraints
- Author
-
Wei Liu, Zhongyang Wei, Yuchen Liu, and Zhenyu Gao
- Subjects
vehicular platoon ,fixed-time sliding mode control ,distance constraints ,Nussbaum function ,symmetric barrier Lyapunov function ,time-varying actuator fault directions ,Mathematics ,QA1-939 - Abstract
This paper investigates the fault-tolerant control problem for vehicular platoons with time-varying actuator fault directions and distance constraints. A bias constraint function is introduced to convert the asymmetric constraints into symmetric ones, based on which a unified barrier Lyapunov function (BLF) method is proposed to ensure distance constraints. Further, an adaptive fixed-time fault-tolerant controller in the context of a sliding mode control technique is proposed, wherein a new Nussbaum function is adopted to address the effects of unknown time-varying actuator fault directions. It is proved that both individual vehicle stability and string stability can all be guaranteed, and the effectiveness of the proposed algorithm is verified through numerical simulations.
- Published
- 2024
- Full Text
- View/download PDF
3. Geometric Optimization of Distributed MIMO Radar Systems With Spatial Distance Constraints
- Author
-
Yao Wang, Shixing Yang, Tao Zhou, and Na Li
- Subjects
Distributed MIMO radar ,geometric optimization ,distance constraints ,radar surveillance performance ,particle swarm optimization ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
We consider a geometric optimization problem of distributed multi-input multi-output (MIMO) radar systems with widely separated radar nodes in this article. The aim is to maximize the radar surveillance performance in a given area of interest by adjusting the node positions, while satisfying practical spatial distance constraints among radar nodes. Typical constraints can be, for example, the maximum distance constraints between nodes and fusion centers (FCs) due to limited communication and the minimum distance constraints to ensure a better system spatial diversity. To achieve this goal, we first derive an analytical expression for a weighted coverage ratio (WCR) metric to evaluate the system surveillance performance. Then, using the WCR metric as the objective function, we formulate a spatial constrained geometric optimization problem for three typical MIMO radar system architectures, each of which has a unique expression of distance constraints. However, the formulated optimization problem is computationally intractable for practical scenarios due to its high dimensionality, non-convexity and especially the complex spatial constraints. To solve this problem, we propose an enhanced particle swarm optimization (PSO) algorithm, and different from the standard PSO, the particles of the proposed enhanced PSO can properly consider the distance constraints within themselves during swarm optimization process. Finally, various numerical studies show that the proposed method can effectively maximize the surveillance performance while satisfying the complex distance constraints.
- Published
- 2020
- Full Text
- View/download PDF
4. Two-Stage Discrete Mechanical Modelin Three-Dimensional Spacefor Garmentsimulation
- Author
-
Luo Xuan, Jiang Gaoming, and Cong Honglian
- Subjects
garment simulation ,mechanical model ,distance constraints ,Textile bleaching, dyeing, printing, etc. ,TP890-933 - Abstract
This paper focuses on the better performance between the garment simulation result and the simulation speed. For simplicity and clarity, a notation “PART” is defined to indicate the areas between the garment and the human body satisfying some constraints. The discrete mechanical model can be achieved by the two-stage process. In the first stage, the garment can be divided into several PARTs constrained by the distance. In the second stage, the mechanical model of each PART is formulated with a mathematical expression. Thus, the mechanical model of the garment can be obtained. Through changing the constrained distance, the simulation result and the simulation speed can be observed. From the variable distance, a desired value can be chosen for an optimal value. The results of simulations and experiments demonstrate that the better performance can be achieved at a higher speed by saving runtime with the acceptable simulation results and the efficiency of the proposed scheme can be verified as well.
- Published
- 2019
- Full Text
- View/download PDF
5. An indoor spatial accessible area generation approach considering distance constraints.
- Author
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Yang, Lina, Bi, Hongru, Yao, Xiaojing, and Chen, Wei
- Subjects
- *
GEOGRAPHIC spatial analysis , *BUFFER zones (Ecosystem management) , *GEOMETRIC modeling , *DISTANCES , *GENERATIONS , *DATA modeling - Abstract
Indoor objects' accessible area generation considering distance constraints is of important realistic significance for spatial analysis. To the best of our knowledge, few studies have been conducted on indoor accessible area generation considering distance constraints. And because of different spatial characteristics between indoor and outdoor environment, the commonly used approach in outdoor space is not suitable for indoor space. In this paper, based on the hybrid spatial data model of geometric and symbolic model, an accessible area generation approach considering distance constraints for indoor environment is proposed by improving traditional spatial buffer zone generation technique. The buffer zone generation with a predefined distance around indoor objects within their located subspace is executed first; then, based on the indoor spatial connectivity, buffer generation around exit points is successively executed in its next connected subspaces until the distance decreases to zero. The merge of these generated buffer zones is the result of accessible area generation with a predefined distance constraint. During the process, two kinds of spatial search strategies, depth-first search and breadth-first search, are presented. Two sets of experiments are conducted to validate the correctness and efficiency of the proposed approach. Results show that the approach can be effectively used to solve the problem of indoor objects' accessible area generation with distance constraints. Moreover, the potential use, as well as the limitation of the proposed approach is discussed in this paper. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
6. The p-Dispersion Problem with Distance Constraints
- Author
-
Nikolaos Ploskas and Kostas Stergiou and Dimosthenis C. Tsouros, Ploskas, Nikolaos, Stergiou, Kostas, Tsouros, Dimosthenis C., Nikolaos Ploskas and Kostas Stergiou and Dimosthenis C. Tsouros, Ploskas, Nikolaos, Stergiou, Kostas, and Tsouros, Dimosthenis C.
- Abstract
In the (maxmin) p-dispersion problem we seek to locate a set of facilities in an area so that the minimum distance between any pair of facilities is maximized. We study a variant of this problem where there exist constraints specifying the minimum allowed distances between the facilities. This type of problem, which we call PDDP, has not received much attention within the literature on location and dispersion problems, despite its relevance to real scenarios. We propose both ILP and CP methods to solve the PDDP. Regarding ILP, we give two formulations derived from a classic and a state-of-the-art model for p-dispersion, respectively. Regarding CP, we first give a generic model that can be implemented within any standard CP solver, and we then propose a specialized heuristic Branch&Bound method. Experiments demonstrate that the ILP formulations are more efficient than the CP model, as the latter is unable to prove optimality in reasonable time, except for small problems, and is usually slower in finding solutions of the same quality than the ILP models. However, although the ILP approach displays good performance on small to medium size problems, it cannot efficiently handle larger ones. The heuristic CP-based method can be very efficient on larger problems and is able to quickly discover solutions to problems that are very hard for an ILP solver.
- Published
- 2023
- Full Text
- View/download PDF
7. AN EFFECTIVE METAHEURISTIC FOR MULTIPLE TRAVELING REPAIRMAN PROBLEM WITH DISTANCE CONSTRAINTS.
- Author
-
Ha-Bang BAN, Duc-Nghia NGUYEN, and Kien NGUYEN
- Subjects
METAHEURISTIC algorithms ,DISTANCES ,NEIGHBORHOODS ,PARTICLE swarm optimization - Abstract
Multiple Traveling Repairman Problem with Distance Constraints (MTRPD) is an extension of the NP-hard Multiple Traveling Repairman Problem. In MTRPD, a fleet of identical vehicles is dispatched to serve a set of customers with the following constraints. First, each vehicle's travel distance is limited by a threshold. Second, each customer must be visited exactly once. Our goal is to find the visiting order that minimizes the sum of waiting times. To solve MTRPD we propose to combine the Insertion Heuristic (IH), Variable Neighborhood Search (VNS), and Tabu Search (TS) algorithms into an effective two-phase metaheuristic that includes a construction phase and an improvement phase. In the former phase, IH is used to create an initial solution. In the latter phase, we use VNS to generate various neighborhoods, while TS is employed to mainly prohibit from getting trapped into cycles. By doing so, our algorithm can support the search to escape local optima. In addition, we introduce a novel neighborhoods' structure and a constant time operation which are efficient for calculating the cost of each neighboring solution. To show the efficiency of our proposed metaheuristic algorithm, we extensively experiment on benchmark instances. The results show that our algorithm can find the optimal solutions for all instances with up to 50 vertices in a fraction of seconds. Moreover, for instances from 60 to 80 vertices, almost all found solutions fall into the range of 0.9%--1.1% of the optimal solutions' lower bounds in a reasonable duration. For instances with a larger number of vertices, the algorithm reaches good-quality solutions fast. Moreover, in a comparison to the state-of-the-art metaheuristics, our proposed algorithm can find better solutions. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
8. Two-Stage Discrete Mechanical Modelin Three-Dimensional Space for Garment Simulation.
- Author
-
Luo, Xuan, Jiang, Gaoming, and Cong, Honglian
- Subjects
MECHANICAL models ,CLOTHING & dress ,HUMAN body - Abstract
This paper focuses on the better performance between the garment simulation result and the simulation speed. For simplicity and clarity, a notation "PART" is defined to indicate the areas between the garment and the human body satisfying some constraints. The discrete mechanical model can be achieved by the two-stage process. In the first stage, the garment can be divided into several PARTs constrained by the distance. In the second stage, the mechanical model of each PART is formulated with a mathematical expression. Thus, the mechanical model of the garment can be obtained. Through changing the constrained distance, the simulation result and the simulation speed can be observed. From the variable distance, a desired value can be chosen for an optimal value. The results of simulations and experiments demonstrate that the better performance can be achieved at a higher speed by saving runtime with the acceptable simulation results and the efficiency of the proposed scheme can be verified as well. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
9. Isogeometric shape optimization on triangulations.
- Author
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Wang, Cunfu, Xia, Songtao, Wang, Xilu, and Qian, Xiaoping
- Subjects
- *
ISOGEOMETRIC analysis , *TRIANGULATION , *STRUCTURAL optimization , *POISSON'S ratio , *PARAMETERIZATION - Abstract
The paper presents a Bézier triangle based isogeometric shape optimization method. Bézier triangles are used to represent both the geometry and physical fields. For a given physical domain defined by B-spline boundary, a coarse Bézier triangular parameterization is automatically generated. This coarse mesh is used to maintain parameterization quality and move mesh by solving a pseudo linear elasticity problem. Then a fine mesh for isogeometric analysis is generated from the coarse mesh through degree elevation and refinement. As the fine mesh retains the same geometric map as the coarse mesh, we can guarantee mesh validity with the coarse mesh only. This bi-level mesh allows us to achieve high numerical accuracy of isogeometric analysis and lower computational cost on mesh validity control and mesh movement. Due to the use of B-spline boundary, the optimized shape can be compactly represented with a relatively small number of optimization variables. Due to the use Bézier triangles, this shape optimization method is applicable to structures of complex topology and allows for local refinement for analysis. By representing the squared distance between two Bézier curves as a Bézier form, a distance check scheme is also introduced to prevent intersections of design boundaries and control the thickness of structural connections. Numerical examples on minimal compliance design and design of negative Poisson ratios are presented to demonstrate the efficacy of the proposed method. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
10. Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging
- Author
-
Lei Liu and Changbong Hyeon
- Subjects
Distance constraints ,AcademicSubjects/SCI00010 ,Polycomb-Group Proteins ,Computational biology ,Biology ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Animals ,Epigenetics ,030304 developmental biology ,Epigenesis ,Regulation of gene expression ,0303 health sciences ,Models, Genetic ,Gene regulation, Chromatin and Epigenetics ,Chromosome ,Superresolution ,Chromatin ,Chromosomes, Insect ,Molecular Imaging ,Genetic Techniques ,Drosophila ,Target gene ,030217 neurology & neurosurgery - Abstract
The accessibility of target gene, a factor critical for gene regulation, is controlled by epigenetic fine-tuning of chromatin organization. While there are multiple experimental techniques to study change of chromatin architecture with its epigenetic state, measurements from them are not always complementary. A qualitative discrepancy is noted between recent super-resolution imaging studies, particularly on Polycomb-group protein repressed domains in Drosophila cell. One of the studies shows that Polycomb-repressed domains are more compact than inactive domains and are segregated from neighboring active domains, whereas Hi-C and chromatin accessibility assay as well as the other super-resolution imaging studies paint a different picture. To examine this issue in detail, we analyzed Hi-C libraries of Drosophila chromosomes as well as distance constraints from one of the imaging studies, and modeled different epigenetic domains by employing a polymer-based approach. According to our chromosome models, both Polycomb-repressed and inactive domains are featured with a similar degree of intra-domain packaging and significant intermixing with adjacent active domains. The epigenetic domains explicitly visualized by our polymer model call for extra attention to the discrepancy of the super-resolution imaging with other measurements, although its precise physicochemical origin still remains to be elucidated.
- Published
- 2020
11. Perancangan Sistem Pelaporan Absensi Asrama Melalui Whatsapp
- Author
-
Edrick Christian Warasiwa and Elmor Benedict Wagiu
- Subjects
Medical education ,Distance constraints ,Information transmission ,Human life ,Attendance ,Information system ,Student attendance ,Psychology ,Educational institution - Abstract
Teknologi informasi dan komunikasi saat ini banyak menyentuh aspek-aspek kehidupan manusia sehari-hari. Dengan semakin berkembangnya teknologi maka banyak kegiatan yang semakin dipermudah penggunaan, pencatatan, dan pelaporannya. Universitas Advent Indonesia (UNAI) adalah sebuah institusi pendidikan yang menggunakan sistem informasi untuk pencatatan dan pelaporan dalam banyak hal, salah satunya adalah pencatatan dan pelaporan absensi kegiatan-kegiatan di asrama. Sistem informasi ini dapat diakses oleh mahasiswa dan juga orangtua/wali. Akan tetapi para orangtua/wali mahasiswa ingin mendapatkan informasi tersebut dengan cepat tanpa harus masuk ke dalam sistem informasi tersebut. Maka dari itu tujuan dari penelitian ini adalah: (1) mempermudah penyampaian informasi absensi kepada orang tua /wali yang anak-anaknya tinggal di asrama selama perkuliahan di Uiversitas Advent Indonesia, (2) melakukan efisiensi penggunaan kertas untuk pembuatan surat laporan dan pencatatan absensi, dan (3) menghilangkan kendala jarak dalam penyampaian informasi. Adapun kesimpulan dari penelitian ini adalah: (1) Sistem peringatan absensi asrama menggunakan WhatsApp memberikan kemudahan kepada Kepala Asrama dalam menyampaikan informasi kehadiran mahasiswa kepada orang tua mahasiswa, (2) Sistem ini memberikan kemudahan dalam menyampaikan informasi dalam jumlah yang banyak dengan waktu bersamaan.
- Published
- 2020
12. Geometric Optimization of Distributed MIMO Radar Systems With Spatial Distance Constraints
- Author
-
Na Li, Yao Wang, Tao Zhou, and Shixing Yang
- Subjects
Mathematical optimization ,Optimization problem ,General Computer Science ,Computer science ,MIMO ,02 engineering and technology ,law.invention ,0203 mechanical engineering ,law ,0202 electrical engineering, electronic engineering, information engineering ,General Materials Science ,Radar ,radar surveillance performance ,020301 aerospace & aeronautics ,particle swarm optimization ,Node (networking) ,General Engineering ,Swarm behaviour ,Particle swarm optimization ,020206 networking & telecommunications ,Antenna diversity ,Metric (mathematics) ,Distributed MIMO radar ,geometric optimization ,lcsh:Electrical engineering. Electronics. Nuclear engineering ,lcsh:TK1-9971 ,distance constraints - Abstract
We consider a geometric optimization problem of distributed multi-input multi-output (MIMO) radar systems with widely separated radar nodes in this article. The aim is to maximize the radar surveillance performance in a given area of interest by adjusting the node positions, while satisfying practical spatial distance constraints among radar nodes. Typical constraints can be, for example, the maximum distance constraints between nodes and fusion centers (FCs) due to limited communication and the minimum distance constraints to ensure a better system spatial diversity. To achieve this goal, we first derive an analytical expression for a weighted coverage ratio (WCR) metric to evaluate the system surveillance performance. Then, using the WCR metric as the objective function, we formulate a spatial constrained geometric optimization problem for three typical MIMO radar system architectures, each of which has a unique expression of distance constraints. However, the formulated optimization problem is computationally intractable for practical scenarios due to its high dimensionality, non-convexity and especially the complex spatial constraints. To solve this problem, we propose an enhanced particle swarm optimization (PSO) algorithm, and different from the standard PSO, the particles of the proposed enhanced PSO can properly consider the distance constraints within themselves during swarm optimization process. Finally, various numerical studies show that the proposed method can effectively maximize the surveillance performance while satisfying the complex distance constraints.
- Published
- 2020
13. Conformational Entropy of an Ideal Cross-Linking Polymer Chain
- Author
-
Donald J. Jacobs, Dennis R. Livesay, and Oleg K. Vorov
- Subjects
Conformational entropy ,Mayer expansion ,distance constraints ,cross-linking ,hydrogen bonds ,network rigidity ,protein stability ,Science ,Astrophysics ,QB460-466 ,Physics ,QC1-999 - Abstract
We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cross-links are sharply peaked over the temperature range of interest, and, are well approximated as statistically weighted Dirac delta-functions that enforce distance constraints. All geometrical deformations consistent with a set of distance constraints are integrated over. Exact results for a contiguous series of connected loops are employed to substantiate the validity of a previous phenomenological distance constraint model that describes protein thermodynamics successfully based on network rigidity.
- Published
- 2008
- Full Text
- View/download PDF
14. Sensor Localization from Distance and Orientation Constraints.
- Author
-
Porta, Josep M., Rull, Aleix, and Thomas, Federico
- Abstract
The sensor localization problem can be formalized using distance and orientation constraints, typically in 3D. Local methods can be used to refine an initial location estimation, but in many cases such estimation is not available and a method able to determine all the feasible solutions from scratch is necessary. Unfortunately, existing methods able to find all the solutions in distance space can not take into account orientations, or they can only deal with one- or two-dimensional problems and their extension to 3D is troublesome. This paper presents a method that addresses these issues. The proposed approach iteratively projects the problem to decrease its dimension, then reduces the ranges of the variable distances, and back-projects the result to the original dimension, to obtain a tighter approximation of the feasible sensor locations. This paper extends previous works introducing accurate range reduction procedures which effectively integrate the orientation constraints. The mutual localization of a fleet of robots carrying sensors and the position analysis of a sensor moved by a parallel manipulator are used to validate the approach. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
15. Quasi-phi-functions and optimal packing of ellipses.
- Author
-
Stoyan, Y., Pankratov, A., and Romanova, T.
- Subjects
PACKING problem (Mathematics) ,COMBINATORIAL packing & covering ,CUTTING stock problem ,PACKING for shipment ,MATHEMATICAL models - Abstract
We further develop our phi-function technique for solving Cutting and Packing problems. Here we introduce quasi-phi-functions for an analytical description of non-overlapping and containment constraints for 2D- and 3D-objects which can be continuously rotated and translated. These new functions can work well for various types of objects, such as ellipses, for which ordinary phi-functions are too complicated or have not been constructed yet. We also define normalized quasi-phi-functions and pseudonormalized quasi-phi-functions for modeling distance constraints. To show the advantages of our new quasi-phi-functions we apply them to the problem of placing a given collection of ellipses into a rectangular container of minimal area. We use radical free quasi-phi-functions to reduce it to a nonlinear programming problem and develop an efficient solution algorithm. We present computational results that compare favourably with those published elsewhere recently. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
16. Symmetry in Sphere-Based Assembly Configuration Spaces.
- Author
-
Sitharam, Meera, Vince, Andrew, Wang, Menghan, and Bóna, Miklós
- Subjects
- *
MOLECULAR self-assembly , *SYMMETRY (Physics) , *ISOMORPHISM (Crystallography) , *ENTROPY , *CHEMICAL kinetics - Abstract
Many remarkably robust, rapid and spontaneous self-assembly phenomena occurring in nature can be modeled geometrically, starting from a collection of rigid bunches of spheres. This paper highlights the role of symmetry in sphere-based assembly processes. Since spheres within bunches could be identical and bunches could be identical, as well, the underlying symmetry groups could be of large order that grows with the number of participating spheres and bunches. Thus, understanding symmetries and associated isomorphism classes of microstates that correspond to various types of macrostates can significantly increase efficiency and accuracy, i.e., reduce the notorious complexity of computing entropy and free energy, as well as paths and kinetics, in high dimensional configuration spaces. In addition, a precise understanding of symmetries is crucial for giving provable guarantees of algorithmic accuracy and efficiency, as well as accuracy vs. efficiency trade-offs in such computations. In particular, this may aid in predicting crucial assembly-driving interactions. This is a primarily expository paper that develops a novel, original framework for dealing with symmetries in configuration spaces of assembling spheres, with the following goals. (1) We give new, formal definitions of various concepts relevant to the sphere-based assembly setting that occur in previous work and, in turn, formal definitions of their relevant symmetry groups leading to the main theorem concerning their symmetries. These previously-developed concepts include, for example: (i) assembly configuration spaces; (ii) stratification of assembly configuration space into configurational regions defined by active constraint graphs; (iii) paths through the configurational regions; and (iv) coarse assembly pathways. (2) We then demonstrate the new symmetry concepts to compute the sizes and numbers of orbits in two example settings appearing in previous work. (3) Finally, we give formal statements of a variety of open problems and challenges using the new conceptual definitions. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
17. An indoor spatial accessible area generation approach considering distance constraints
- Author
-
Xiaojing Yao, Lina Yang, Hongru Bi, and Wei Chen
- Subjects
Distance constraints ,010504 meteorology & atmospheric sciences ,Computer science ,Real-time computing ,0211 other engineering and technologies ,General Earth and Planetary Sciences ,02 engineering and technology ,01 natural sciences ,021101 geological & geomatics engineering ,0105 earth and related environmental sciences ,Computer Science Applications - Abstract
Indoor objects’ accessible area generation considering distance constraints is of important realistic significance for spatial analysis. To the best of our knowledge, few studies have been conducte...
- Published
- 2019
18. An MIP formulation for the open location‐routing problem considering the topological characteristic of the solution‐paths
- Author
-
Eliana Mirledy Toro, Ramón Alfonso Gallego, and Mauricio Granada
- Subjects
Imagination ,Thesaurus (information retrieval) ,Distance constraints ,Theoretical computer science ,Linear programming ,Computer Networks and Communications ,Location routing ,Computer science ,media_common.quotation_subject ,Search engine ,Hardware and Architecture ,Software ,Information Systems ,media_common - Published
- 2019
19. Three-dimensional dust mapping of 12 supernovae remnants in the Galactic anticentre
- Author
-
Bingqiu Chen, Bin Yu, Albert A. Zijlstra, and Biwei Jiang
- Subjects
Physics ,Distance constraints ,Molecular cloud ,Extinction (astronomy) ,FOS: Physical sciences ,Astronomy and Astrophysics ,Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Supernova ,Distribution (mathematics) ,Astrophysics - Solar and Stellar Astrophysics ,Cover (topology) ,Space and Planetary Science ,Astrophysics of Galaxies (astro-ph.GA) ,Continuum (set theory) ,Solar and Stellar Astrophysics (astro-ph.SR) - Abstract
We present three dimensional (3D) dust mapping of 12 supernova remnants (SNRs) in the Galactic anti-center (Galactic longitude $l$ between 150\degr\ and 210\degr) based on a recent 3D interstellar extinction map. The dust distribution of the regions which cover the full extents in the radio continuum for the individual SNRs are discussed. Four SNRs show significant spatial coincidences between molecular clouds (MCs) revealed from the 3D extinction mapping and the corresponding radio features. The results confirm the interactions between these SNRs and their surrounding MCs. Based on these correlations, we provide new distance estimates of the four SNRs, G189.1+3.0 (IC443, $d=1729^{+116}_{-94} \rm \,pc$), G190.9-2.2 ($d=1036^{+17}_{-81} \rm \,pc$), G205.5+0.5 ($d=941^{+96}_{-94}$ or $1257^{+92}_{-101} \rm \,pc$) and G213.0-0.6 ($d=1146^{+79}_{-80} \rm \,pc$). In addition, we find indirect evidences of potential interactions between SNRs and MCs for three other SNRs. New distance constraints are also given for these three SNRs., Comment: 14 pages, 13 figures, accepted for publication in MNRAS
- Published
- 2019
20. Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies
- Author
-
Andrew Keller, James E. Bruce, Juan D. Chavez, and Kevin C. Felt
- Subjects
Models, Molecular ,0301 basic medicine ,Distance constraints ,030102 biochemistry & molecular biology ,Protein Conformation ,Chemistry ,Protein Data Bank (RCSB PDB) ,Proteins ,Fraction (chemistry) ,General Chemistry ,Plasma protein binding ,Biochemistry ,Interactome ,Article ,03 medical and health sciences ,Cross-Linking Reagents ,030104 developmental biology ,In vivo ,Protein Interaction Mapping ,Biophysics ,Quality check ,Protein Interaction Maps ,Databases, Protein ,Whole cell ,Protein Binding - Abstract
Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intra-protein cross-links can arise from proteins in isolation, inter-protein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of inter-protein to intra-protein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for all interacting complex subunits. Here we determine the theoretical number of possible inter- and intra-protein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of inter-protein cross-links in large scale in vivo cross-linking studies. We show how the maximum fraction can guide interpretation of reported inter-protein fractions with respect to the extent of sample protein binding, comparing whole cell and lysate cross-linked samples as an example. We also demonstrate how an observation of inter-protein cross-link fractions greater than the maximum value can result from the presence of false positive cross-links which are predominantly inter-protein, their number estimable from the observed surplus fraction of inter-protein cross-links.
- Published
- 2019
21. Solving the open vehicle routing problem with capacity and distance constraints with a biased random key genetic algorithm
- Author
-
Valeria Soto-Mendoza, Ricardo Reyes, E. Ruiz, and Alvaro Ernesto Ruiz Barbosa
- Subjects
Mathematical optimization ,Distance constraints ,021103 operations research ,General Computer Science ,Computer science ,0211 other engineering and technologies ,General Engineering ,02 engineering and technology ,Vehicle routing problem ,Genetic algorithm ,0202 electrical engineering, electronic engineering, information engineering ,Key (cryptography) ,Benchmark (computing) ,020201 artificial intelligence & image processing - Abstract
This paper presents a biased random-key genetic algorithm designed to solve the open vehicle routing problem with capacity and distance constraints. Consider a depot from which vehicles depart to deliver goods demanded by clients. Every client is served by one vehicle that is part of a homogeneous fleet. The vehicles initiate their routes at the depot and finish them after servicing the last client without returning to the depot. The problem’s objective function is to minimize the total distance traveled by the vehicles while respecting the capacity and maximum distance constraints. The potential applications in real life scenarios make this problem relevant among other vehicle routing problems. Three sets of benchmark problems from the literature are used to test the proposed algorithm. The obtained results show the algorithm’s good performance since the best-known solutions for 16 of the 30 instances were improved.
- Published
- 2019
22. Optimizing the spatial assignment of schools through a random mechanism towards equal educational opportunity: A resemblance approach
- Author
-
Teqi Dai, Cong Liao, and Shaoya Zhao
- Subjects
Distance constraints ,Operations research ,Computer science ,Heuristic ,Mechanism (biology) ,Ecological Modeling ,Node (networking) ,Geography, Planning and Development ,0211 other engineering and technologies ,Primary education ,021107 urban & regional planning ,02 engineering and technology ,Variance (accounting) ,Urban Studies ,Beijing ,Probability distribution ,021101 geological & geomatics engineering ,General Environmental Science - Abstract
Although it is generally agreed that public primary education should be equally available to all, a spatial disparity of educational opportunity exists worldwide, for wealthy families can acquire residential locations with better access to the best schools. Random allocation of school places is considered to be an effective approach for breaking such spatial linkages. This study addresses the problem of achieving the optimal spatial equality of educational opportunity by re-assigning school places to demand nodes using a combined mechanism that introduces a random allocation into a proximity-based system. This study proposes the use of a probability distribution for a full description of educational opportunity. A new spatial allocation optimization model towards equal educational opportunity with the maximum school travel distance constraints and capacities constraints was developed to maximize the resemblance between the probability distributions across demand nodes (RES-based model). This model was applied to a case study of primary school allocation in the Shijingshan District of Beijing, China, and was resolved in a heuristic way. The solution was compared with those provided by a capacitated proximity-based model and a model also using the random mechanism but measuring educational opportunity by expectation values (VAR-based model). It was found that the introducing of random mechanism could significantly improve the spatial equality of educational opportunity with a significant loss of spatial efficiency. In addition, the solution provided by the RES-based model was quite different to that provided by the VAR-based model. An improvement in the resemblance of demand node probability distributions might lead to an increase in the variance of expectations. The resemblance approach proposed in this study may also be applied to the optimization of other random objectives.
- Published
- 2019
23. Two-Stage Discrete Mechanical Modelin Three-Dimensional Spacefor Garmentsimulation
- Author
-
Xuan Luo, Honglian Cong, and Gaoming Jiang
- Subjects
010302 applied physics ,Computer science ,Chemical technology ,ComputerApplications_COMPUTERSINOTHERSYSTEMS ,TP1-1185 ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,mechanical model ,garment simulation ,Control theory ,0103 physical sciences ,General Materials Science ,Stage (hydrology) ,0210 nano-technology ,distance constraints - Abstract
This paper focuses on the better performance between the garment simulation result and the simulation speed. For simplicity and clarity, a notation “PART” is defined to indicate the areas between the garment and the human body satisfying some constraints. The discrete mechanical model can be achieved by the two-stage process. In the first stage, the garment can be divided into several PARTs constrained by the distance. In the second stage, the mechanical model of each PART is formulated with a mathematical expression. Thus, the mechanical model of the garment can be obtained. Through changing the constrained distance, the simulation result and the simulation speed can be observed. From the variable distance, a desired value can be chosen for an optimal value. The results of simulations and experiments demonstrate that the better performance can be achieved at a higher speed by saving runtime with the acceptable simulation results and the efficiency of the proposed scheme can be verified as well.
- Published
- 2019
24. Street-Level Geolocation Based on Router Multilevel Partitioning
- Author
-
Ruixiang Li, Xiangyang Luo, Fan Zhao, Rui Xu, and Zhu Ma
- Subjects
Router ,Service (systems architecture) ,Distance constraints ,delay-distance correlation ,General Computer Science ,service range calculation ,business.industry ,Computer science ,Real-time computing ,IP geolocation ,General Engineering ,Internet hosting service ,Object (computer science) ,Geographic distribution ,Geolocation ,General Materials Science ,multilevel partitioning of routers ,Granularity ,lcsh:Electrical engineering. Electronics. Nuclear engineering ,business ,lcsh:TK1-9971 - Abstract
The high-precision geolocation of Internet hosts plays an important role in many applications, such as online advertising and deception detection. The existing typical high-precision geolocation algorithms usually utilize single-hop or relative delay to geolocate an Internet host at street-level granularity. However, it is difficult to accurately measure the single-hop or relative delay within a city. This challenge sometimes results in large geolocation errors. To solve this problem, a street-level geolocation algorithm based on router multilevel partitioning is proposed. Unlike existing typical algorithms, the proposed algorithm makes a credible hypothesis that each router has a relatively stable service object for a period of time. By analyzing the connection between routers and landmarks, the possible geographic service ranges of routers are inferred from the geographic distribution of landmarks. Then, distance constraints arising from routers' service ranges are formed to estimate the geographic location of the target IP. Theoretical analysis of the geolocation error shows that the maximum and average errors of the proposed algorithm are less than those of existing typical algorithms. The proposed algorithm is evaluated by geolocating a total of 12,152 target IP addresses located in four cities in different regions. The experimental results show that, compared with the existing typical street-level geolocation algorithms SLG and NC-Geo, the average median error of the proposed algorithm decreases from 4.735 km and 3.776 km to 3.25 km, representing error reductions of approximately 31.36% and 13.96%, respectively.
- Published
- 2019
25. An Effective Metaheuristic for Multiple Traveling Repairman Problem with Distance Constraints
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Due Nghia Nguyen, Kien Nguyen, and Ha Bang Ban
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Mathematical optimization ,Heuristic (computer science) ,Computer science ,General Engineering ,insertion heuristic ,Tabu search ,Set (abstract data type) ,Range (mathematics) ,Local optimum ,tabu search ,Benchmark (computing) ,variable neighborhood search ,Metaheuristic ,Traveling repairmen problem ,distance constraints ,Variable neighborhood search - Abstract
Multiple Traveling Repairman Problem with Distance Constraints (MTRPD) is an extension of the NP-hard Multiple Traveling Repairman Problem. In MTRPD, a fleet of identical vehicles is dispatched to serve a set of customers with the following constraints. First, each vehicle's travel distance is limited by a threshold. Second, each customer must be visited exactly once. Our goal is to find the visiting order that minimizes the sum of waiting times. To solve MTRPD we propose to combine the Insertion Heuristic (IH), Variable Neighborhood Search (VNS), and Tabu Search (TS) algorithms into an effective two-phase metaheuristic that includes a construction phase and an improvement phase. In the former phase, IH is used to create an initial solution. In the latter phase, we use VNS to generate various neighborhoods, while TS is employed to mainly prohibit from getting trapped into cycles. By doing so, our algorithm can support the search to escape local optima. In addition, we introduce a novel neighborhoods’ structure and a constant time operation which are efficient for calculating the cost of each neighboring solution. To show the efficiency of our proposed metaheuristic algorithm, we extensively experiment on benchmark instances. The results show that our algorithm can find the optimal solutions for all instances with up to 50 vertices in a fraction of seconds. Moreover, for instances from 60 to 80 vertices, almost all found solutions fall into the range of 0.9 %-1.1 % of the optimal solutions' lower bounds in a reasonable duration. For instances with a larger number of vertices, the algorithm reaches good-quality solutions fast. Moreover, in a comparison to the state-of-the-art metaheuristics, our proposed algorithm can find better solutions.
- Published
- 2019
26. Rapid determination of quaternary protein structures in complex biological samples
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Lotta Happonen, Simon Hauri, Hamed Khakzad, Johan Teleman, Johan Malmström, Lars Malmström, University of Zurich, and Malmström, Johan
- Subjects
0301 basic medicine ,Distance constraints ,530 Physics ,Science ,General Physics and Astronomy ,1600 General Chemistry ,Genetics and Molecular Biology ,Peptide ,02 engineering and technology ,Computational biology ,Mass spectrometry ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Protein structure ,1300 General Biochemistry, Genetics and Molecular Biology ,Tandem Mass Spectrometry ,Humans ,Protein Structure, Quaternary ,lcsh:Science ,chemistry.chemical_classification ,Chromatography, Reverse-Phase ,Multidisciplinary ,General Chemistry ,Blood Proteins ,021001 nanoscience & nanotechnology ,3100 General Physics and Astronomy ,Healthy Volunteers ,Recombinant Proteins ,Molecular Docking Simulation ,030104 developmental biology ,Cross-Linking Reagents ,chemistry ,Docking (molecular) ,10231 Institute for Computational Science ,Multiprotein Complexes ,General Biochemistry ,Protein quaternary structure ,lcsh:Q ,0210 nano-technology ,Surface protein ,Protein structure modeling ,Algorithms ,Software - Abstract
The understanding of complex biological systems is still hampered by limited knowledge of biologically relevant quaternary protein structures. Here, we demonstrate quaternary structure determination in biological samples using a combination of chemical cross-linking, high-resolution mass spectrometry and high-accuracy protein structure modeling. This approach, termed targeted cross-linking mass spectrometry (TX-MS), relies on computational structural models to score sets of targeted cross-linked peptide signals acquired using a combination of mass spectrometry acquisition techniques. We demonstrate the utility of TX-MS by creating a high-resolution quaternary model of a 1.8 MDa protein complex composed of a pathogen surface protein and ten human plasma proteins. The model is based on a dense network of cross-link distance constraints obtained directly in a mixture of human plasma and live bacteria. These results demonstrate that TX-MS can increase the applicability of flexible backbone docking algorithms to large protein complexes by providing rich cross-link distance information from complex biological samples., Protein structure determination in complex biological samples is still challenging. Here, the authors develop a computational modeling-guided cross-linking mass spectrometry method, obtaining a high-resolution model of a 1.8 MDa protein assembly from cross-links detected in a mixture of human plasma and bacteria.
- Published
- 2019
27. On the Distance-Constrained Close Enough Arc Routing Problem
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Miguel Reula, Isaac Plana, Ángel Corberán, and José M. Sanchis
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Mathematical optimization ,Information Systems and Management ,General Computer Science ,Close-enough ,Computer science ,Heuristic (computer science) ,0211 other engineering and technologies ,02 engineering and technology ,Management Science and Operations Research ,Industrial and Manufacturing Engineering ,Set (abstract data type) ,Rural Postman ,0502 economics and business ,Distance constraints ,Routing ,050210 logistics & transportation ,021103 operations research ,Heuristic ,05 social sciences ,Branch and cut ,Modeling and Simulation ,Benchmark (computing) ,Routing (electronic design automation) ,MATEMATICA APLICADA ,Arc routing ,Automatic meter reading ,Street network - Abstract
[EN] Arc routing problems consist basically of finding one or several routes traversing a given set of arcs and/or edges that must be serviced. The Close-Enough Arc Routing Problem, or Generalized Directed Rural Postman Problem, does not assume that customers are located at specific arcs, but can be serviced by traversing any arc of a given subset. Real-life applications include routing for meter reading, in which a vehicle equipped with a receiver travels a street network. If the vehicle gets within a certain distance of a meter, the receiver collects its data. Therefore, only a few streets which are close enough to the meters need to be traversed. In this paper we study the generalization of this problem to the case in which a fleet of vehicles is available. This problem, the Distance-Constrained Close Enough Arc Routing Problem, consists of finding a set of routes with minimum total cost such that their length does not exceed a maximum distance. In this article, we propose a new formulation for the Distance-Constrained Close Enough Arc Routing Problem and present some families of valid inequalities that we use in a branch-and-cut algorithm for its solution. Extensive computational experiments have been performed on a set of benchmark instances and the results are compared with those obtained with other heuristic and exact methods., This work was supported by the Spanish Ministerio de Ciencia, Innovacion y Universidades (MICIU) and Fondo Social Europeo (FSE) through project PGC2018-099428-B-I00. The authors want to thank the comments and suggestions done by two anonymous referees that have contributed to improve the content and readability of the article.
- Published
- 2021
28. Kinematic calibration of a six-axis serial robot using distance and sphere constraints.
- Author
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Joubair, Ahmed and Bonev, Ilian
- Subjects
- *
KINEMATICS of machinery , *ROBOTS , *PARAMETER estimation , *SIMULATION methods & models , *NOISE measurement - Abstract
This paper describes a kinematic calibration method developed to improve the accuracy of a six-axis serial industrial robot in a specific target workspace, using distance and sphere constraints. A simulation study demonstrates the ability of the calibration approach to identify the kinematic parameters, regardless of measurement noise. Experimental validation shows that the robot's accuracy inside the target workspace is significantly improved by reducing the mean and maximum distance errors from 0.698 to 0.086 mm and from 1.321 to 0.127 mm, respectively. The experimental data are collected using a Renishaw precision touch probe mounted on the flange of a FANUC LR Mate 200iC and a special triangular plate with three datum 2-in spheres 300 mm apart. The calibration method uses an optimization model based on fitting several probed positions on spheres and minimizing the residual of the spheres' center-to-center distances. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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29. Maximum feasible subsystems of distance geometry constraints
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Maurizio Bruglieri, Roberto Cordone, Leo Liberti, Politecnico di Milano (Politecnico di Milano), Dipartimento di Informatica, Università degli Studi di Milano, Italy (UNIMI), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)
- Subjects
Systematic error ,MINLP ,Distance constraints ,021103 operations research ,Control and Optimization ,Applied Mathematics ,experimental error formulation ,0211 other engineering and technologies ,02 engineering and technology ,Interval (mathematics) ,[INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO] ,Management Science and Operations Research ,systematic error formulation ,Distance geometry ,Computer Science Applications ,Protein conformation ,protein folding, experimental error formulation, systematic error formulation ,protein folding ,Euclidean geometry ,Protein conformation, MINLP, Diagonally dominant programming ,Algorithm ,Diagonally dominant programming ,ComputingMilieux_MISCELLANEOUS ,Mathematics - Abstract
We study the problem of satisfying the maximum number of distance geometry constraints with minimum experimental error. This models the determination of the shape of proteins from atomic distance data which are obtained from nuclear magnetic resonance experiments and exhibit experimental and systematic errors. Experimental errors are represented by interval constraints on Euclidean distances. Systematic errors occur from a misassignment of distances to wrong atomic pairs: we represent such errors by maximizing the number of satisfiable distance constraints. We present many mathematical programming formulations, as well as a “matheuristic” algorithm based on reformulations, relaxations, restrictions and refinement. We show that this algorithm works on protein graphs with hundreds of atoms and thousands of distances.
- Published
- 2021
30. One-dimensional multi-agent optimal control with aggregation and distance constraints: Qualitative properties and mean-field limit
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Marco Cirant and Annalisa Cesaroni
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Mean field limit ,Distance constraints ,Density constraints ,Finite agent optimal control ,Mean-field optimal control ,Γ-convergence ,Applied Mathematics ,General Physics and Astronomy ,Statistical and Nonlinear Physics ,Optimal control ,Applied mathematics ,Mathematical Physics ,Mathematics - Published
- 2021
31. Sensor Localization from Distance and Orientation Constraints
- Author
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Josep M. Porta, Aleix Rull, and Federico Thomas
- Subjects
localization ,sensor networks ,distance constraints ,orientation constraints ,Distance Geometry ,Chemical technology ,TP1-1185 - Abstract
The sensor localization problem can be formalized using distance and orientation constraints, typically in 3D. Local methods can be used to refine an initial location estimation, but in many cases such estimation is not available and a method able to determine all the feasible solutions from scratch is necessary. Unfortunately, existing methods able to find all the solutions in distance space can not take into account orientations, or they can only deal with one- or two-dimensional problems and their extension to 3D is troublesome. This paper presents a method that addresses these issues. The proposed approach iteratively projects the problem to decrease its dimension, then reduces the ranges of the variable distances, and back-projects the result to the original dimension, to obtain a tighter approximation of the feasible sensor locations. This paper extends previous works introducing accurate range reduction procedures which effectively integrate the orientation constraints. The mutual localization of a fleet of robots carrying sensors and the position analysis of a sensor moved by a parallel manipulator are used to validate the approach.
- Published
- 2016
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32. Symmetry in Sphere-Based Assembly Configuration Spaces
- Author
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Meera Sitharam, Andrew Vince, Menghan Wang, and Miklós Bóna
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sphere assembly ,configuration space ,stratification ,distance constraints ,Cayley geometry ,entropy ,kinetics ,pathways ,Mathematics ,QA1-939 - Abstract
Many remarkably robust, rapid and spontaneous self-assembly phenomena occurring in nature can be modeled geometrically, starting from a collection of rigid bunches of spheres. This paper highlights the role of symmetry in sphere-based assembly processes. Since spheres within bunches could be identical and bunches could be identical, as well, the underlying symmetry groups could be of large order that grows with the number of participating spheres and bunches. Thus, understanding symmetries and associated isomorphism classes of microstates that correspond to various types of macrostates can significantly increase efficiency and accuracy, i.e., reduce the notorious complexity of computing entropy and free energy, as well as paths and kinetics, in high dimensional configuration spaces. In addition, a precise understanding of symmetries is crucial for giving provable guarantees of algorithmic accuracy and efficiency, as well as accuracy vs. efficiency trade-offs in such computations. In particular, this may aid in predicting crucial assembly-driving interactions. This is a primarily expository paper that develops a novel, original framework for dealing with symmetries in configuration spaces of assembling spheres, with the following goals. (1) We give new, formal definitions of various concepts relevant to the sphere-based assembly setting that occur in previous work and, in turn, formal definitions of their relevant symmetry groups leading to the main theorem concerning their symmetries. These previously-developed concepts include, for example: (i) assembly configuration spaces; (ii) stratification of assembly configuration space into configurational regions defined by active constraint graphs; (iii) paths through the configurational regions; and (iv) coarse assembly pathways. (2) We then demonstrate the new symmetry concepts to compute the sizes and numbers of orbits in two example settings appearing in previous work. (3) Finally, we give formal statements of a variety of open problems and challenges using the new conceptual definitions.
- Published
- 2016
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33. Clustering of LRGs in the DECaLS DR8 Footprint: Distance Constraints from Baryon Acoustic Oscillations Using Photometric Redshifts
- Author
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Jeffrey A. Newman, Robert Blum, Enrique Gaztanaga, Rongpu Zhou, Francisco Prada, Chia-Hsun Chuang, Martin Landriau, Yong-Seon Song, Ashley J. Ross, and Srivatsan Sridhar
- Subjects
Distance constraints ,Cosmology and Nongalactic Astrophysics (astro-ph.CO) ,010504 meteorology & atmospheric sciences ,FOS: Physical sciences ,Library science ,Astrophysics::Cosmology and Extragalactic Astrophysics ,Astronomy & Astrophysics ,7. Clean energy ,01 natural sciences ,Atomic ,Physical Chemistry ,law.invention ,Telescope ,Photometry ,Particle and Plasma Physics ,Observatory ,law ,Large-scale structure of the universe ,0103 physical sciences ,User Facility ,Nuclear ,010303 astronomy & astrophysics ,0105 earth and related environmental sciences ,Astroparticle physics ,Physics ,Molecular ,Astronomy and Astrophysics ,Cosmology ,13. Climate action ,Space and Planetary Science ,High-redshift galaxies ,astro-ph.CO ,Christian ministry ,National laboratory ,Distance measure ,Astronomical and Space Sciences ,Astrophysics - Cosmology and Nongalactic Astrophysics ,Fermi Gamma-ray Space Telescope ,Physical Chemistry (incl. Structural) - Abstract
A photometric redshift sample of luminous red galaxies (LRGs) obtained from the DECam Legacy Survey (DECaLS) is analyzed to probe cosmic distances by exploiting the wedge approach of the two-point correlation function. Although the cosmological information is highly contaminated by the uncertainties existing in the photometric redshifts from the galaxy map, an angular diameter distance can be probed at the perpendicular configuration in which the measured correlation function is minimally contaminated. An ensemble of wedged correlation functions selected up to a given threshold based on having the least contamination was studied in previous work (Sridhar & Song 2019) using simulations, and the extracted cosmological information was unbiased within this threshold. We apply the same methodology for analyzing the LRG sample from DECaLS, which will provide the optical imaging for targeting two-thirds of the Dark Energy Spectroscopic Instrument footprint and measure the angular diameter distances at z = 0.69 and z = 0.87 to be and with a fractional error of 4.77% and 6.09%, respectively. We obtain a value of H 0 = 66.58 ± 5.31 km s-1 Mpc-1, which supports the H 0 measured by all other baryon acoustic oscillation results and is consistent with the ΛCDM model. © 2020. The American Astronomical Society. All rights reserved.., The Photometric Redshifts for the Legacy Surveys (PRLS) catalog used in this paper was produced thanks to funding from the U.S. Department of Energy Office of Science, Office of High Energy Physics, via grant DE-SC0007914. The Legacy Surveys consist of three individual and complementary projects: the Dark Energy Camera Legacy Survey (AST-0950945 Michigan, the National Optical Astronomy Observatory, the University of Nottingham, the Ohio State UniversityDECaLS; NOAO Proposal ID 2014B-0404; PIs: David Schlegel and Arjun Dey), the Beijing-Arizona Sky Survey (BASS; NOAO Proposal ID 2015A-0801; PIs: Zhou Xu and Xiaohui Fan), and the Mayall z-band Legacy Survey (MzLS; NOAO Proposal ID 2016A-0453; PI: Arjun Dey). DECaLS, BASS, and MzLS together include data obtained, respectively, at the Blanco telescope, Cerro Tololo InterAmerican Observatory, the National Optical Astronomy Observatory (NOAO); the Bok telescope, Steward Observatory, University of Arizona; and the Mayall telescope, Kitt Peak National Observatory, NOAO. The Legacy Surveys project is honored to be permitted to conduct astronomical research on Iolkam Du'ag (Kitt Peak), a mountain with particular significance to the Tohono O'odham Nation. This project used data obtained with the Dark Energy Camera (DECam), which was constructed by the Dark Energy Survey (DES) collaboration. Funding for the DES Projects has been provided by the U.S. Department of Energy, the U.S. National Science Foundation, the Ministry of Science and Education of Spain, the Science and Technology Facilities Council of the United Kingdom, the Higher Education Funding Council for England, the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, the Kavli Institute of Cosmological Physics at the University of Chicago, the Center for Cosmology and AstroParticle Physics at the Ohio State University, the Mitchell Institute for Fundamental Physics and Astronomy at Texas A&M University, Financiadora de Estudos e Projetos, Fundacao Carlos Chagas Filho de Amparo, Financiadora de Estudos e Projetos, Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico and the Ministerio da Ciencia, Tecnologia e Inovacao, the Deutsche Forschungsgemeinschaft and the Collaborating Institutions in the Dark Energy Survey. The Collaborating Institutions are Argonne National Laboratory, the University of California at Santa Cruz, the University of Cambridge, Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas-Madrid, the University of Chicago, University College London, the DES-Brazil Consortium, the University of Edinburgh, the Eidgenossische Technische Hochschule (ETH) Zurich, Fermi National Accelerator Laboratory, the University of Illinois at UrbanaChampaign, the Institut de Ciencies de l'Espai (IEEC/CSIC), the Institut de Fisica d'Altes Energies, Lawrence Berkeley National Laboratory, the Ludwig-Maximilians Universitat Munchen and the associated Excellence Cluster Universe, the University of Michigan, the National Optical Astronomy Observatory, the University of Nottingham, the Ohio State University, the University of Pennsylvania, the University of Portsmouth, SLAC National Accelerator Laboratory, Stanford University, the University of Sussex, and Texas A&M University. The Legacy Survey team makes use of data products from the Near-Earth Object Wide-field Infrared Survey Explorer (NEOWISE), which is a project of the Jet Propulsion Laboratory/California Institute of Technology. NEOWISE is funded by the National Aeronautics and Space Administration. The Legacy Surveys imaging of the DESI footprint is supported by the Director, Office of Science, Office of High Energy Physics of the U.S. Department of Energy under Contract No. DE-AC02-05CH1123; by the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility under the same contract; and by the U.S. National Science Foundation, Division of Astronomical Sciences under Contract No. AST-0950945 to NOAO.
- Published
- 2020
34. Assur Decompositions of Direction-Length Frameworks
- Author
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Anthony Nixon
- Subjects
Discrete mathematics ,Universal joint ,Distance constraints ,Spanning tree ,Computer science ,law ,Realisation ,Rigidity (psychology) ,Graph ,law.invention - Abstract
A bar-joint framework is a realisation of a graph consisting of stiff bars linked by universal joints. The framework is rigid if the only bar-length preserving continuous motions of the joints arise from isometries. A rigid framework is isostatic if deleting any single edge results in a flexible framework. Generically, rigidity depends only on the graph and we say an Assur graph is a pinned isostatic graph with no proper pinned isostatic subgraphs. Any pinned isostatic graph can be decomposed into Assur components which may be of use for mechanical engineers in decomposing mechanisms for simpler analysis and synthesis. A direction-length framework is a generalisation of bar-joint framework where some distance constraints are replaced by direction constraints. We initiate a theory of Assur graphs and Assur decompositions for direction-length frameworks using graph orientations and spanning trees and then analyse choices of pinning set.
- Published
- 2020
35. Predicting helix pair structure from fuzzy contact maps.
- Author
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Kuo, Tony C.Y. and Glasgow, Janice
- Subjects
FUZZY systems ,MATHEMATICAL mappings ,FUZZY logic ,INFORMATION retrieval ,MATHEMATICAL bounds ,SMOOTHNESS of functions - Abstract
Highlights: [•] We incorporate fuzzy logic to create fuzzy contact maps for helix pairs. [•] Similar distance map regions to a query are retrieved based on fuzzy contact map similarity. [•] Retrieved distance map regions are used to predict a distance map using bound smoothing. [•] The EMBED algorithm is used on the predicted distance map to obtain 3D structure. [•] We obtain good structures at various levels of noise. [Copyright &y& Elsevier]
- Published
- 2014
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- View/download PDF
36. Improving identification of in-organello protein-protein interactions using an affinity-enrichable, isotopically coded, and mass spectrometry-cleavable chemical crosslinker
- Author
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Chris Meisinger, Elena L. Rudashevskaya, Christoph H. Borchers, F.-Nora Vögtle, Yassene Mohammed, Evgeniy V. Petrotchenko, Albert Sickmann, and Karl A.T. Makepeace
- Subjects
0303 health sciences ,Distance constraints ,Chemistry ,030302 biochemistry & molecular biology ,technology, industry, and agriculture ,macromolecular substances ,Mass spectrometry ,Biochemistry ,Electron transport chain ,Crosslinking reagent ,Analytical Chemistry ,Protein–protein interaction ,03 medical and health sciences ,Identification (information) ,Reagent ,Organelle ,Biophysics ,Molecular Biology ,030304 developmental biology - Abstract
An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonstrated improvements in the application of the CLMS technique, in terms of the detection, acquisition, and identification of crosslinker-modified peptides. This approach was evaluated on intact yeast mitochondria, and the results showed that hundreds of unique protein- protein interactions could be identified on an organelle proteome-wide scale. Both known and previously unknown protein-protein interactions were identified. These interactions were assessed based on their known sub-compartmental localizations. Additionally, the identified crosslinking distance constraints are in good agreement with existing structural models of protein complexes involved in the mitochondrial electron transport chain.
- Published
- 2020
37. A Hybrid Grasshopper Optimization Algorithm Applied to the Open Vehicle Routing Problem
- Author
-
Irma D. García-Calvillo, Efraín Ruiz-y-Ruiz, Jaime Pérez-Terrazas, and Valeria Soto-Mendoza
- Subjects
0209 industrial biotechnology ,Distance constraints ,Mathematical optimization ,lcsh:T55.4-60.8 ,Computer science ,02 engineering and technology ,Travelling salesman problem ,lcsh:QA75.5-76.95 ,Theoretical Computer Science ,020901 industrial engineering & automation ,Vehicle routing problem ,0202 electrical engineering, electronic engineering, information engineering ,lcsh:Industrial engineering. Management engineering ,Local search (optimization) ,grasshopper optimization algorithm ,Computer Science::Information Theory ,Numerical Analysis ,Optimization algorithm ,business.industry ,open vehicle routing problem ,Computational Mathematics ,Computational Theory and Mathematics ,Benchmark (computing) ,Combinatorial optimization ,020201 artificial intelligence & image processing ,combinatorial optimization ,lcsh:Electronic computers. Computer science ,business ,optimization ,Decoding methods - Abstract
This paper presents a hybrid grasshopper optimization algorithm using a novel decoder and local search to solve instances of the open vehicle routing problem with capacity and distance constraints. The algorithm&rsquo, s decoder first defines the number of vehicles to be used and then it partitions the clients, assigning them to the available routes. The algorithm performs a local search in three neighborhoods after decoding. When a new best solution is found, every route is locally optimized by solving a traveling salesman problem, considering the depot and clients in the route. Three sets containing a total of 30 benchmark problems from the literature were used to test the algorithm. The experiments considered two cases of the problem. In the first, the primary objective is to minimize the total number of vehicles and then the total distance to be traveled. In the second case, the total distance traveled by the vehicles is minimized. The obtained results showed the algorithm&rsquo, s proficient performance. For the first case, the algorithm was able to improve or match the best-known solutions for 21 of the 30 benchmark problems. For the second case, the best-known solutions for 18 of the 30 benchmark problems were found or improved by the algorithm. Finally, a case study from a real-life problem is included.
- Published
- 2020
38. Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling
- Author
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Klykov, Oleg, van der Zwaan, Carmen, Heck, Albert J R, Meijer, Alexander B, Scheltema, Richard A, Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, and Sub Biomol.Mass Spectrometry & Proteom.
- Subjects
Distance constraints ,Protein Conformation ,DSSO ,Computational biology ,030204 cardiovascular system & hematology ,Fibrinogen ,Biochemistry ,Mass Spectrometry ,Fibrin ,fibrin clot ,03 medical and health sciences ,0302 clinical medicine ,Interaction network ,Albumins ,medicine ,Humans ,Dysfibrinogenemia ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,biology ,Chemistry ,cross-linking mass spectrometry ,Thrombosis ,XlinkX ,Biological Sciences ,Clot formation ,medicine.disease ,Models, Structural ,Cross-Linking Reagents ,Mutation ,biology.protein ,fibrinogen ,UniProt ,circulatory and respiratory physiology ,medicine.drug - Abstract
Significance Fibrinogen hexamers are major components of blood clots. After release of fibrinopeptides resulting in fibrin monomers, clot formation occurs through fibrin oligomerization followed by lateral aggregation, packing into fibrin fibers, and consequent branching. Shedding light on fibrin clots by in situ cross-linking mass spectrometry and structural modeling extends our current knowledge of the structure of fibrin with regard to receptor-binding hotspots. Further restraint-driven molecular docking reveals how fibrin oligomers laterally aggregate into clots and uncovers the molecular architecture of the clot to albumin interaction. We hypothesize this interaction is involved in the prevention of clot degradation. Mapping known mutations validates the generated structural model and, for a subset, brings their molecular mechanisms into view., Upon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots which assist in wound healing. Limited insights into their molecular architecture, due to the sheer size and the insoluble character of fibrin clots, have restricted our ability to develop novel treatments for clotting diseases. The, so far resolved, disparate structural details have provided insights into linear elongation; however, molecular details like the C-terminal domain of the α-chain, the heparin-binding domain on the β-chain, and other functional domains remain elusive. To illuminate these dark areas, we applied cross-linking mass spectrometry (XL-MS) to obtain biochemical evidence in the form of over 300 distance constraints and combined this with structural modeling. These restraints additionally define the interaction network of the clots and provide molecular details for the interaction with human serum albumin (HSA). We were able to construct the structural models of the fibrinogen α-chain (excluding two highly flexible regions) and the N termini of the β-chain, confirm these models with known structural arrangements, and map how the structure laterally aggregates to form intricate lattices together with the γ-chain. We validate the final model by mapping mutations leading to impaired clot formation. From a list of 22 mutations, we uncovered structural features for all, including a crucial role for βArg’169 (UniProt: 196) in lateral aggregation. The resulting model can potentially serve for research on dysfibrinogenemia and amyloidosis as it provides insights into the molecular mechanisms of thrombosis and bleeding disorders related to fibrinogen variants. The structure is provided in the PDB-DEV repository (PDBDEV_00000030).
- Published
- 2020
- Full Text
- View/download PDF
39. Mass, height of burst, and source–receiver distance constraints on the acoustic coda phase delay method
- Author
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Arthur J. Rodgers, Daniel C. Bowman, Douglas Seastrand, and Sarah Albert
- Subjects
Distance constraints ,010504 meteorology & atmospheric sciences ,Acoustics and Ultrasonics ,Near and far field ,010502 geochemistry & geophysics ,Geodesy ,01 natural sciences ,Coda ,Acoustic wave propagation ,Arts and Humanities (miscellaneous) ,Air temperature ,Event (particle physics) ,Order of magnitude ,Geology ,0105 earth and related environmental sciences ,Group delay and phase delay - Abstract
This research uses the acoustic coda phase delay method to estimate relative changes in air temperature between explosions with varying event masses and heights of burst. It also places a bound on source-receiver distance for the method. Previous studies used events with different shapes, height of bursts, and masses and recorded the acoustic codas at source-receiver distances less than 1 km. This research further explores the method using explosions that differ in mass (by up to an order of magnitude) and are placed at varying heights. Source-receiver distances also cover an area out to 7 km. Relative air temperature change estimates are compared to complementary meteorological observations. Results show that two explosions that differ by an order of magnitude cannot be used with this method because their propagation times in the near field and their fundamental frequencies are different. These differences are expressed as inaccuracies in the relative air temperature change estimates. An order of magnitude difference in mass is also shown to bias estimates higher. Small differences in height of burst do not affect the accuracy of the method. An upper bound of 1 km on source-receiver distance is provided based on the standard deviation characteristics of the estimates.
- Published
- 2018
40. A GRASP+VND Algorithm for the Multiple Traveling Repairman Problem with Distance Constraints
- Author
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Ban Ha Bang
- Subjects
Distance constraints ,Computer science ,Traveling repairman problem ,GRASP ,0202 electrical engineering, electronic engineering, information engineering ,020206 networking & telecommunications ,020201 artificial intelligence & image processing ,02 engineering and technology ,Algorithm - Abstract
Multiple Traveling Repairman Problem (MTRP) is a class of NP-hard combinatorial optimization problems. In this paper, an other variant of MTRP, also known as Multiple Traveling Repairman Problem with Distance Constraint (MTRPD) is introduced. In MTRPD problem, a fleet of vehicles serve a set of customers. Each vehicle that starts from the depot is not allowed to travel a distance longer than a limit and each customer must be visited exactly once. The goal is to find the order of customer visits that minimizes the sum of waiting time. To the best of our knowledge, the problem has not been studied much previously, even though it is a natural and practical extension of the Traveling Repairman Problem or Multiple Traveling Repairman Problem case. In our work, we propose a metaheuristic algorithm which is mainly based on the principles of Greedy Randomized Adaptive Search Procedure (GRASP) and Variable Neighborhood Descent (VND) to solve the problem. The GRASP is used to build an initial solution which is good enough in construction phase. In a cooperative way, the VND is employed to generate diverse neighborhoods in improvement phase, therefore, it can prevent the search to escape from local optimal. Extensive numerical experiments on benchmark instances show that our algorithm can find the optimal solutions with up to 50 vertices in several instances. For larger instances, our algorithm obtains provably near-optimal solutions, even for large instances.
- Published
- 2018
41. Data obtained from acoustic recording units and from field observer point counts of Tasmanian forest birds are similar but not the same
- Author
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Susan C. Baker, Gregory J. Jordan, Andrew B. Hingston, and Tim Wardlaw
- Subjects
0106 biological sciences ,Distance constraints ,Geography ,010604 marine biology & hydrobiology ,Observer (physics) ,010603 evolutionary biology ,01 natural sciences ,Cartography - Abstract
Acoustic recording units (ARUs) have recently been used in place of field observers to survey birds. To test whether data obtained from ARUs and from point counts by a field observer are directly comparable, we surveyed Tasmanian forest birds using these two methods at exactly the same times and places. Data derived from ARUs were similar to those obtained by the field observer without distance constraints for (a) the total numbers of species detected at each of three points, and (b) both the number and composition of species within each of the 13 5-minute surveys at each point. However, data sets obtained by each method comprised more records of certain species, largely because of calls being detected by one method but not by the other. Additional differences between methods arose because ARUs could not detect birds seen by the field observer that were not calling, and ARUs sometimes led to false positive identifications when the person listening to recordings was unable to distinguish mimetic calls from those of the species being mimicked. Because ARUs appeared to detect many calls from beyond 100 m, their use to survey a particular patch of vegetation requires placement (within the vegetation patch) at distances greater than 100 m from the edge of the patch to prevent the inclusion of calls from non-target vegetation.
- Published
- 2018
42. A matheuristic for the Distance-Constrained Close-Enough Arc Routing Problem
- Author
-
Universitat Politècnica de València. Departamento de Matemática Aplicada - Departament de Matemàtica Aplicada, European Regional Development Fund, Ministerio de Economía y Competitividad, Corberán, A., PLANA, ISAAC, Reula, Miguel, Sanchís Llopis, José María, Universitat Politècnica de València. Departamento de Matemática Aplicada - Departament de Matemàtica Aplicada, European Regional Development Fund, Ministerio de Economía y Competitividad, Corberán, A., PLANA, ISAAC, Reula, Miguel, and Sanchís Llopis, José María
- Abstract
[EN] The Close-Enough Arc Routing Problem, also called Generalized Directed Rural Postman Problem, is an arc routing problem with interesting real-life applications, such as routing for meter reading. In this application, a vehicle with a receiver travels through a series of neighborhoods. If the vehicle gets within a certain distance of a meter, the receiver is able to record the gas, water, or electricity consumption. Therefore, the vehicle does not need to traverse every street, but only a few, in order to be close enough to each meter. In this paper we deal with an extension of this problem, the Distance-Constrained Generalized Directed Rural Postman Problem or Distance-Constrained Close Enough Arc Routing Problem, in which a fleet of vehicles is available. The vehicles have to leave from and return to a common vertex, the depot, and the length of their routes must not exceed a maximum distance (or time). For solving this problem we propose a matheuristic that incorporates an effective exact procedure to optimize the routes obtained. Extensive computational experiments have been performed on a set of benchmark instances and the results are compared with those obtained with an exact procedure proposed in the literature.
- Published
- 2019
43. Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in 15N-13C-ILV methyl labeled proteins.
- Author
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Frueh, Dominique, Leed, Alison, Arthanari, Haribabu, Koglin, Alexander, Walsh, Christopher, and Wagner, Gerhard
- Abstract
We present a time-shared 3D HSQC-NOESY experiment that enables one to simultaneously record
13 C- and15 N-dispersed spectra in Ile, Leu and Val (ILV) methyl-labeled samples. This experiment is designed to delineate the two spectra which would otherwise overlap with one another when acquired together. These spectra display nOe correlations in the detected proton dimension, i.e. with maximum resolution. This is in contrast to NOESY-HSQC types of experiments that provide cross-peaks in the indirect dimension with low resolution due to limits in experimental time. The technique is particularly advantageous at high field where even longer experimental times would be required for comparable resolution in NOESY-HSQC experiments. The method is demonstrated at 900 MHz and at 750 MHz on 37 and 31 kDa proteins, respectively. The resolution and time saving provided in this experiment was crucial for solving the structures of these two proteins. [ABSTRACT FROM AUTHOR]- Published
- 2009
- Full Text
- View/download PDF
44. Precoloring extension for 2-connected graphs with maximum degree three
- Author
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Voigt, Margit
- Subjects
- *
GROUP extensions (Mathematics) , *GRAPH coloring , *GRAPH connectivity , *TOPOLOGICAL degree , *GRAPH theory , *MATHEMATICAL analysis , *SET theory - Abstract
Abstract: Let be a simple graph, a list assignment with and an independent subset of the vertex set. Define to be the minimum distance between two vertices of . In this paper it is shown that if is 2-connected with and is not then every precoloring of is extendable to a proper list coloring of provided that . An example shows that the bound is sharp. This result completes the investigation of precoloring extensions for graphs with for all where the precolored set is an independent set. [Copyright &y& Elsevier]
- Published
- 2009
- Full Text
- View/download PDF
45. Approximation algorithms for forests augmentation ensuring two disjoint paths of bounded length
- Author
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Chepoi, Victor, Estellon, Bertrand, and Vaxès, Yann
- Subjects
- *
ALGORITHMS , *ALGEBRA , *FOUNDATIONS of arithmetic , *COMPUTER science - Abstract
Abstract: Given a forest and a positive integer , we consider the problem of finding a minimum number of new edges such that in the augmented graph any pair of vertices can be connected by two vertex-disjoint paths of length . We show that this problem and some of its variants are NP-hard, and we present approximation algorithms with worst-case bounds 6 and 4. These algorithms can be implemented in time. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
- View/download PDF
46. Structural constraints for the Crh protein from solid-state NMR experiments.
- Author
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Gardiennet, Carole, Loquet, Antoine, Etzkorn, Manuel, Heise, Henrike, Baldus, Marc, and Böckmann, Anja
- Abstract
We demonstrate that short, medium and long-range constraints can be extracted from proton mediated, rare-spin detected correlation solid-state NMR experiments for the microcrystalline 10.4 × 2 kDa dimeric model protein Crh. Magnetization build-up curves from cross signals in NHHC and CHHC spectra deliver detailed information on side chain conformers and secondary structure for interactions between spin pairs. A large number of medium and long-range correlations can be observed in the spectra, and an analysis of the resolved signals reveals that the constraints cover the entire sequence, also including inter-monomer contacts between the two molecules forming the domain-swapped Crh dimer. Dynamic behavior is shown to have an impact on cross signals intensities, as indicated for mobile residues or regions by contacts predicted from the crystal structure, but absent in the spectra. Our work validates strategies involving proton distance measurements for large and complex proteins as the Crh dimer, and confirms the magnetization transfer properties previously described for small molecules in solid protein samples. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
47. Solving school bus routing problems through integer programming.
- Author
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Bektaş, T. and Elmastaş, Seda
- Subjects
PROBLEM solving ,ELEMENTARY schools ,SCHOOL buses ,TRANSPORTATION ,INTEGER programming ,LINEAR programming - Abstract
In this paper, an exact solution approach is described for solving a real-life school bus routing problem (SBRP) for transporting the students of an elementary school throughout central Ankara, Turkey. The problem is modelled as a capacitated and distance constrained open vehicle routing problem and an associated integer linear program is presented. The integer program borrows some well-known inequalities from the vehicle routing problem, which are also shown to be valid for the SBRP under consideration. The optimal solution of the problem is computed using the proposed formulation, resulting in a saving of up to 28.6% in total travelling cost as compared to the current implementation. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
48. Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins.
- Author
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Snyder, David, Zhang, Fengli, and Brüschweiler, Rafael
- Abstract
Elucidation of high-resolution protein structures by NMR spectroscopy requires a large number of distance constraints that are derived from nuclear Overhauser effects between protons (NOEs). Due to the high level of spectral overlap encountered in 2D NMR spectra of proteins, the measurement of high quality distance constraints requires higher dimensional NMR experiments. Although four-dimensional Fourier transform (FT) NMR experiments can provide the necessary kind of spectral information, the associated measurement times are often prohibitively long. Covariance NMR spectroscopy yields 2D spectra that exhibit along the indirect frequency dimension the same high resolution as along the direct dimension using minimal measurement time. The generalization of covariance NMR to 4D NMR spectroscopy presented here exploits the inherent symmetry of certain 4D NMR experiments and utilizes the trace metric between donor planes for the construction of a high-resolution spectral covariance matrix. The approach is demonstrated for a 4D
13 C-edited NOESY experiment of ubiquitin. The 4D covariance spectrum narrows the line-widths of peaks strongly broadened in the FT spectrum due to the necessarily short number of increments collected, and it resolves otherwise overlapped cross peaks allowing for an increase in the number of NOE assignments to be made from a given dataset. At the same time there is no significant decrease in the positive predictive value of observing a peak as compared to the corresponding 4D Fourier transform spectrum. These properties make the 4D covariance method a potentially valuable tool for the structure determination of larger proteins and for high-throughput applications in structural biology. [ABSTRACT FROM AUTHOR]- Published
- 2007
- Full Text
- View/download PDF
49. Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry.
- Author
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Jacobsen, Richard B., Sale, Kenneth L., Ayson, Marites J., Novak, Petr, Hong, Joohee, Lane, Pamela, Wood, Nichole L., Kruppa, Gary H., Young, Malin M., and Schoeniger, Joseph S.
- Abstract
Recent work using chemical cross-linking to define interresidue distance constraints in proteins has shown that these constraints are useful for testing tertiary structural models. We applied this approach to the G-protein-coupled receptor bovine rhodopsin in its native membrane using lysine- and cysteine-targeted bifunctional cross-linking reagents. Cross-linked proteolytic peptides of rhodopsin were identified by combined liquid chromatography and FT-ICR mass spectrometry with automated data-reduction and assignment software. Tandem mass spectrometry was used to verify cross-link assignments and locate the exact sites of cross-link attachment. Cross-links were observed to form between 10 pairs of residues in dark-state rhodopsin. For each pair, cross-linkers with a range of linker lengths were tested to determine an experimental distance-of-closest-approach (DCA) between reactive side-chain atoms. In all, 28 cross-links were identified using seven different cross-linking reagents. Molecular mechanics procedures were applied to published crystal structure data to calculate energetically achievable theoretical DCAs between reactive atoms without altering the position of the protein backbone. Experimentally measured DCAs are generally in good agreement with the theoretical DCAs. However, a cross-link between C316 and K325 in the C-terminal region cannot be rationalized by DCA simulations and suggests that backbone reorientation relative to the crystal coordinates occurs on the timescale of cross-linking reactions. Biochemical and spectroscopic data from other studies have found that the C-terminal region is highly mobile in solution and not fully represented by X-ray crystallography data. Our results show that chemical cross-linking can provide reliable three-dimensional structural information and insight into local conformational dynamics in a membrane protein. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
50. Specimen acquisition: ROSEs, gardeners, and gatekeepers
- Author
-
Adele Kraft
- Subjects
Cancer Research ,Distance constraints ,Practice patterns ,business.industry ,030209 endocrinology & metabolism ,Data science ,Variety (cybernetics) ,03 medical and health sciences ,0302 clinical medicine ,Tomography x ray computed ,Oncology ,030220 oncology & carcinogenesis ,Medicine ,Treatment decision making ,Personalized medicine ,business ,Telepathology ,Minimally invasive procedures - Abstract
The use of minimally invasive procedures for diagnosis and treatment decisions means that very often cytological samples are the only material available for testing. Cytology has evolved from a strictly morphological approach to the routine use of immunohistochemistry. The advent of personalized medicine has increased the demand for molecular testing, making rapid on-site evaluation even more relevant. This article presents current rapid on-site evaluation practice patterns in different settings, with a special focus on the variety of professionals involved. Technological advances such as telepathology can help to alleviate distance constraints. This article also provides an overview of telecytopathology, describing challenges to its implementation and how to address them. Issues such as hardware, personnel training, communication, guidelines, validation, use, and future directions are highlighted. Cancer Cytopathol 2017;125(6 suppl):449-54. © 2017 American Cancer Society.
- Published
- 2017
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