Skip to main content

Open Research Areas in Distance Geometry

  • Chapter
  • First Online:
Open Problems in Optimization and Data Analysis

Part of the book series: Springer Optimization and Its Applications ((SOIA,volume 141))

Abstract

Distance geometry is based on the inverse problem that asks to find the positions of points, in a Euclidean space of given dimension, that are compatible with a given set of distances. We briefly introduce the field, and discuss some open and promising research areas.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Direct problems may not be all that easy: see Erdős’ unit distances and distinct distances problems [63].

  2. 2.

    Another, and possibly better, candidate is the Graph Isomorphism problem [12, 13].

  3. 3.

    See, e.g., https:en.wikipedia.org/wiki/Classification_of_manifolds.

References

  1. Aaronson, S.: Is P versus NP formally independent? Bulletin of the EATCS 81, Computational Complexity Column (2003)

    Google Scholar 

  2. Abbott, T.: Generalizations of Kempe’s universality theorem. Master’s thesis, MIT (2008)

    Google Scholar 

  3. Alexandrov, A.: Convex Polyhedra (in Russian). Gosudarstv. Izdat. Tekhn.-Theor. Lit., Moscow (1950)

    Google Scholar 

  4. Alfakih, A.: Universal rigidity of bar frameworks in general position: a Euclidean distance matrix approach. In: Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds.) Distance Geometry: Theory, Methods, and Applications, pp. 3–22. Springer, New York (2013)

    Chapter  MATH  Google Scholar 

  5. Alizadeh, F.: Interior point methods in semidefinite programming with applications to combinatorial optimization. SIAM J. Optim. 5(1), 13–51 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  6. Allender, E., Beals, R., Ogihara, M.: The complexity of matrix rank and feasible systems of linear equations. Comput. Complex. 8, 99–126 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  7. Alves, R., Cassioli, A., Mucherino, A., Lavor, C., Liberti, L.: Adaptive branching in iBP with Clifford algebra. In: Andrioni, A., Lavor, C., Liberti, L., Mucherino, A., Maculan, N., Rodriguez, R. (eds.) Proceedings of the workshop on Distance Geometry and Applications. Universidade Federal do Amazonas, Manaus (2013)

    Google Scholar 

  8. Alves, R., Lavor, C.: Geometric algebra to model uncertainties in the discretizable molecular distance geometry problem. Adv. Appl. Clifford Algebr. 27, 439–452 (2017)

    Article  MathSciNet  MATH  Google Scholar 

  9. Alves, R., Lavor, C., Souza, C., Souza, M.: Clifford algebra and discretizable distance geometry. Adv. Appl. Clifford Algebr. 25(4), 925–942 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  10. Asimow, L., Roth, B.: The rigidity of graphs. Trans. Am. Math. Soc. 245, 279–289 (1978)

    Article  MathSciNet  MATH  Google Scholar 

  11. Asimow, L., Roth, B.: The rigidity of graphs II. J. Math. Anal. Appl. 68, 171–190 (1979)

    Article  MathSciNet  MATH  Google Scholar 

  12. Babai, L.: Automorphism groups, isomorphism, reconstruction. In: Graham, R., Grötschel, M., Lovász, L. (eds.) Handbook of Combinatorics, vol. 2, pp. 1447–1540. MIT Press, Cambridge, MA (1996)

    Google Scholar 

  13. Babai, L.: Graph isomorphism in quasipolynomial time. Technical Report 1512.03547v2, arXiv (2016)

    Google Scholar 

  14. Bahr, A., Leonard, J., Fallon, M.: Cooperative localization for autonomous underwater vehicles. Int. J. Robot. Res. 28(6), 714–728 (2009)

    Article  Google Scholar 

  15. Barvinok, A.: Problems of distance geometry and convex properties of quadratic maps. Discret. Comput. Geom. 13, 189–202 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  16. Barvinok, A.: Measure concentration in optimization. Math. Program. 79, 33–53 (1997)

    MathSciNet  MATH  Google Scholar 

  17. Basu, S., Pollack, R., Roy, M.F.: Algorithms in Real Algebraic Geometry. Springer, New York (2006)

    MATH  Google Scholar 

  18. Beeker, N., Gaubert, S., Glusa, C., Liberti, L.: Is the distance geometry problem in NP? In: Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds.) Distance Geometry: Theory, Methods, and Applications, pp. 85–94. Springer, New York (2013)

    Chapter  MATH  Google Scholar 

  19. Benedetti, R., Risler, J.J.: Real algebraic and semi-algebraic sets. Hermann, Paris (1990)

    MATH  Google Scholar 

  20. Berger, B., Kleinberg, J., Leighton, T.: Reconstructing a three-dimensional model with arbitrary errors. J. ACM 46(2), 212–235 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  21. Billinge, S., Duxbury, P., Gonçalves, D., Lavor, C., Mucherino, A.: Assigned and unassigned distance geometry: applications to biological molecules and nanostructures. 4OR 14, 337–376 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  22. Biswas, P., Ye, Y.: Semidefinite programming for ad hoc wireless sensor network localization. In: Proceedings of the 3rd International Symposium on Information Processing in Sensor Networks (IPSN04), pp. 46–54. ACM, New York, NY (2004)

    Google Scholar 

  23. Blum, L., Shub, M., Smale, S.: On a theory of computation and complexity over the real numbers: NP-completeness, recursive functions, and universal machines. Bull. Am. Math. Soc. 21(1), 1–46 (1989)

    Article  MathSciNet  MATH  Google Scholar 

  24. Blumenthal, L.: A Modern View of Geometry. Freeman & C., San Francisco (1961)

    MATH  Google Scholar 

  25. Bollobás, B.: Random Graphs. Cambridge Studies in Advanced Mathematics, vol. 73. Cambridge University Press, Cambridge (2001)

    Google Scholar 

  26. Borcea, C., Streinu, I.: Geometric auxetics. Proc. R. Soc. A 471(2184), 20150033 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  27. Borg, I., Groenen, P.: Modern Multidimensional Scaling, 2nd edn. Springer, New York (2010)

    MATH  Google Scholar 

  28. Bourgain, J.: On Lipschitz embeddings of finite metric spaces in Hilbert space. Isr. J. Math. 52(1–2), 46–52 (1985)

    Article  MathSciNet  MATH  Google Scholar 

  29. Bowers, J., Bowers, P.: A Menger redux: embedding metric spaces isometrically. Am. Math. Mon. 124(7), 621–636 (2017)

    Article  MATH  Google Scholar 

  30. Bürgisser, P., Clausen, M., Shokrollahi, M.: Algebraic Complexity Theory. Grundlehren der mathematischen Wissenschaften, vol. 315. Springer, Berlin (1997)

    Book  MATH  Google Scholar 

  31. Burkard, R., Dell’Amico, M., Martello, S.: Assignment Problems. SIAM, Providence, RI (2009)

    Book  MATH  Google Scholar 

  32. Cassioli, A., Bordeaux, B., Bouvier, G., Mucherino, A., Alves, R., Liberti, L., Nilges, M., Lavor, C., Malliavin, T.: An algorithm to enumerate all possible protein conformations verifying a set of distance constraints. BMC Bioinf. 16, 23 (2015)

    Article  Google Scholar 

  33. Cauchy, A.L.: Sur les polygones et les polyèdres. J. de l’École Polytech. 16(9), 87–99 (1813)

    Google Scholar 

  34. Cayley, A.: A theorem in the geometry of position. Camb. Math. J. II, 267–271 (1841)

    Google Scholar 

  35. Cheung, H., Kwok, T., Lau, L.: Fast matrix rank algorithms and applications. J. ACM 60(5), 31:1–31:25 (2013)

    Article  MathSciNet  MATH  Google Scholar 

  36. Cobham, A.: The intrinsic computational difficulty of functions. In: Bar-Hillel, Y. (ed.) Logic, Methodology and Philosophy of Science, pp. 24–30. North-Holland, Amsterdam (1965)

    Google Scholar 

  37. Connelly, R.: A counterexample to the rigidity conjecture for polyhedra. Publications Mathématiques de l’IHES 47, 333–338 (1978)

    Article  MATH  Google Scholar 

  38. Cook, S.: The complexity of theorem-proving procedures. In: ACM Symposium on the Theory of Computing, STOC, pp. 151–158. ACM, New York (1971)

    Google Scholar 

  39. Coope, I.: Reliable computation of the points of intersection of n spheres in \(\mathbb {R}^n\). Aust. N. Z. Ind. Appl. Math. J. 42, C461–C477 (2000)

    Google Scholar 

  40. Costa, V., Mucherino, A., Lavor, C., Cassioli, A., Carvalho, L., Maculan, N.: Discretization orders for protein side chains. J. Glob. Optim. 60, 333–349 (2014)

    Article  MathSciNet  MATH  Google Scholar 

  41. Cremona, L.: Le figure reciproche nella statica grafica. G. Bernardoni, Milano (1872)

    Google Scholar 

  42. Cremona, L.: Elementi di calcolo grafico. Paravia, Torino (1874)

    Google Scholar 

  43. Crippen, G.: An alternative approach to distance geometry using l distances. Discret. Appl. Math. 197, 20–26 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  44. Cucuringu, M.: Asap – an eigenvector synchronization algorithm for the graph realization problem. In: Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds.) Distance Geometry: Theory, Methods, and Applications, pp. 177–196. Springer, New York (2013)

    Chapter  Google Scholar 

  45. Cucuringu, M., Singer, A., Cowburn, D.: Eigenvector synchronization, graph rigidity and the molecule problem. Inf. Inference J IMA 1, 21–67 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  46. Dakić, T.: On the turnpike problem. Ph.D. thesis, Simon Fraser University (2000)

    Google Scholar 

  47. D’Ambrosio, C., Ky, V.K., Lavor, C., Liberti, L., Maculan, N.: New error measures and methods for realizing protein graphs from distance data. Discrete Comput. Geom. 57(2), 371–418 (2017)

    Article  MathSciNet  MATH  Google Scholar 

  48. D’Ambrosio, C., Liberti, L.: Distance geometry in linearizable norms. In: Nielsen, F., Barbaresco, F. (eds.) Geometric Science of Information. Lecture Notes in Computer Science, vol. 10589, pp. 830–838. Springer, Berlin (2017)

    Chapter  MATH  Google Scholar 

  49. Dekkers, A., Aarts, E.: Global optimization and simulated annealing. Math. Program. 50, 367–393 (1991)

    Article  MathSciNet  MATH  Google Scholar 

  50. Dias, G., Liberti, L.: Diagonally dominant programming in distance geometry. In: Cerulli, R., Fujishige, S., Mahjoub, R. (eds.) International Symposium in Combinatorial Optimization. Lecture Notes in Computer Science, vol. 9849, pp. 225–236. Springer, New York (2016)

    MATH  Google Scholar 

  51. Doherty, L., Pister, K., El Ghaoui, L.: Convex position estimation in wireless sensor networks. In: Twentieth Annual Joint Conference of the IEEE Computer and Communications Societies. INFOCOM, vol. 3, pp. 1655–1663. IEEE, Piscataway (2001)

    Google Scholar 

  52. Dokmanić, I., Parhizkar, R., Ranieri, J., Vetterli, M.: Euclidean distance matrices: Essential theory, algorithms and applications. IEEE Signal Process. Mag. 1053–5888, 12–30 (2015)

    Article  Google Scholar 

  53. Donald, B.: Algorithms in Structural Molecular Biology. MIT Press, Boston (2011)

    Google Scholar 

  54. Dong, Q., Wu, Z.: A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances. J. Glob. Optim. 22, 365–375 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  55. Du, H., Alechina, N., Stock, K., Jackson, M.: The logic of NEAR and FAR. In: Tenbrink, T., et al. (eds.) COSIT. Lecture Notes in Computer Science, vol. 8116, pp. 475–494. Springer, Cham (2013)

    Google Scholar 

  56. Duxbury, P., Granlund, L., Juhas, P., Billinge, S.: The unassigned distance geometry problem. Discret. Appl. Math. 204, 117–132 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  57. Edmonds, J.: Paths, trees and flowers. Can. J. Math. 17, 449–467 (1965)

    Article  MathSciNet  MATH  Google Scholar 

  58. Erdős, P., Renyi, A.: On the evolution of random graphs. Publ. Math. Inst. Hung. Acad. Sci. 5, 17–61 (1960)

    Google Scholar 

  59. Eren, T., Goldenberg, D., Whiteley, W., Yang, Y., Morse, A., Anderson, B., Belhumeur, P.: Rigidity, computation, and randomization in network localization. In: IEEE INFOCOM, pp. 2673–2684 (2004)

    Google Scholar 

  60. Euler, L.: Continuatio fragmentorum ex adversariis mathematicis depromptorum: II Geometria, 97. In: Fuss, P., Fuss, N. (eds.) Opera postuma mathematica et physica anno 1844 detecta, vol. I, pp. 494–496. Eggers & C., Petropolis (1862)

    Google Scholar 

  61. Fréchet, M.: Sur quelques points du calcul fonctionnel. Rendiconti del Circolo Matematico di Palermo 22, 1–74 (1906)

    Article  MATH  Google Scholar 

  62. Garey, M., Johnson, D.: Computers and Intractability: A Guide to the Theory of NP-Completeness. Freeman and Company, New York (1979)

    MATH  Google Scholar 

  63. Garibaldi, J., Iosevich, A., Senger, S.: The Erdős Distance Problem. Student Mathematical Library, vol. 56. American Mathematical Society, Providence (2011)

    Google Scholar 

  64. Gluck, H.: Almost all simply connected closed surfaces are rigid. In: Dold, A., Eckmann, B. (eds.) Geometric Topology. Lecture Notes in Mathematics, vol. 438, pp. 225–239. Springer, Berlin (1975)

    Chapter  Google Scholar 

  65. Gödel, K.: On the isometric embeddability of quadruples of points of r 3 in the surface of a sphere. In: Feferman, S., Dawson, J., Kleene, S., Moore, G., Solovay, R., van Heijenoort J. (eds.) Kurt Gödel: Collected Works, vol. I, pp. (1933b) 276–279. Oxford University Press, Oxford (1986)

    Google Scholar 

  66. Gortler, S., Healy, A., Thurston, D.: Characterizing generic global rigidity. Am. J. Math. 132(4), 897–939 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  67. Graver, J., Servatius, B., Servatius, H.: Combinatorial Rigidity. American Mathematical Society, Providence, RI (1993)

    Book  MATH  Google Scholar 

  68. Grünbaum, B., Shephard, G.: Lectures on lost mathematics. Technical Report EPrint Collection – Mathematics [112], University of Washington (2010)

    Google Scholar 

  69. Havel, T., Wüthrich, K.: An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J. Mol. Biol. 182(2), 281–294 (1985)

    Article  Google Scholar 

  70. Havel, T., Kuntz, I., Crippen, G.: The theory and practice of distance geometry. Bull. Math. Biol. 45(5), 665–720 (1983)

    Article  MathSciNet  MATH  Google Scholar 

  71. Hendrickson, B.: Conditions for unique graph realizations. SIAM J. Comput. 21(1), 65–84 (1992)

    Article  MathSciNet  MATH  Google Scholar 

  72. Heron: Metrica, vol. I. Alexandria (∼100AD)

    Google Scholar 

  73. Hoang, T.: On the complexity of some problems in linear algebra. Ph.D. thesis, Universität Ulm (2003)

    Google Scholar 

  74. Indyk, P., Naor, A.: Nearest neighbor preserving embeddings. ACM Trans. Algorithms 3(3), Art. 31 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  75. Jackson, B., Jordán, T.: Connected rigidity matroids and unique realization of graphs. J. Comb. Theory Ser. B 94, 1–29 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  76. Jackson, B., Jordán, T.: Graph theoretic techniques in the analysis of uniquely localizable sensor networks. In: Mao, G., Fidan, B. (eds.) Localization Algorithms and Strategies for Wireless Sensor Networks: Monitoring and Surveillance Techniques for Target Tracking, pp. 146–173. IGI Global, Hershey (2009)

    Chapter  Google Scholar 

  77. Jacobs, D., Thorpe, M.: Generic rigidity percolation. Phys. Rev. Lett. 75(22), 4051–4054 (1995)

    Article  Google Scholar 

  78. Johnson, D.: The NP-completeness column: an ongoing guide. J. Algorithms 3, 182–195 (1982)

    Article  MathSciNet  MATH  Google Scholar 

  79. Johnson, W., Lindenstrauss, J.: Extensions of Lipschitz mappings into a Hilbert space. In: Hedlund, G. (ed.) Conference in Modern Analysis and Probability. Contemporary Mathematics, vol. 26, pp. 189–206. American Mathematical Society, Providence (1984)

    Chapter  Google Scholar 

  80. Karp, R.: Reducibility among combinatorial problems. In: Miller, R., Thatcher, W. (eds.) Complexity of Computer Computations. IBM Research Symposia, vol. 5, pp. 85–104. Plenum, New York (1972)

    Chapter  Google Scholar 

  81. Khoo, Y.: Protein structural calculation from NMR spectroscopy. Ph.D. thesis, Princeton University (2016)

    Google Scholar 

  82. Krislock, N., Wolkowicz, H.: Explicit sensor network localization using semidefinite representations and facial reductions. SIAM J. Optim. 20, 2679–2708 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  83. Kuratowski, C.: Quelques problèmes concernant les espaces métriques non-séparables. Fundamenta Mathematicæ 25, 534–545 (1935)

    Article  MATH  Google Scholar 

  84. Laman, G.: On graphs and rigidity of plane skeletal structures. J. Eng. Math. 4(4), 331–340 (1970)

    Article  MathSciNet  MATH  Google Scholar 

  85. Laurent, M.: Polynomial instances of the positive semidefinite and Euclidean distance matrix completion problems. SIAM J. Matrix Anal. Appl. 22(3), 874–894 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  86. Laurent, M.: Matrix completion problems. In: Floudas, C., Pardalos, P. (eds.) Encyclopedia of Optimization, 2nd edn., pp. 1967–1975. Springer, New York (2009)

    Chapter  Google Scholar 

  87. Lavor, C.: On generating instances for the molecular distance geometry problem. In: Liberti, L., Maculan, N. (eds.) Global Optimization: from Theory to Implementation, pp. 405–414. Springer, Berlin (2006)

    Chapter  Google Scholar 

  88. Lavor, C., Liberti, L., Maculan, N.: Molecular distance geometry problem. In: Floudas, C., Pardalos, P. (eds.) Encyclopedia of Optimization, 2nd edn., pp. 2305–2311. Springer, New York (2009)

    Google Scholar 

  89. Lavor, C., Lee, J., Lee-St. John, A., Liberti, L., Mucherino, A., Sviridenko, M.: Discretization orders for distance geometry problems. Optim. Lett. 6, 783–796 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  90. Lavor, C., Liberti, L., Maculan, N., Mucherino, A.: The discretizable molecular distance geometry problem. Comput. Optim. Appl. 52, 115–146 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  91. Lavor, C., Liberti, L., Maculan, N., Mucherino, A.: Recent advances on the discretizable molecular distance geometry problem. Eur. J. Oper. Res.219, 698–706 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  92. Lavor, C., Liberti, L., Mucherino, A.: The interval Branch-and-Prune algorithm for the discretizable molecular distance geometry problem with inexact distances. J. Glob. Optim. 56, 855–871 (2013)

    Article  MathSciNet  MATH  Google Scholar 

  93. Lavor, C., Alves, R., Figuereido, W., Petraglia, A., Maculan, N.: Clifford algebra and the discretizable molecular distance geometry problem. Adv. Appl. Clifford Algebr. 25, 925–942 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  94. Lavor, C., Firer, M., Martinez, J.M., Liberti, L.: Preface. Int. Trans. Oper. Res. 23(5), 841 (2016)

    Article  Google Scholar 

  95. Lavor, C., Liberti, L., Donald, B., Worley, B., Bardiaux, B., Malliavin, T., Nilges, M.: Minimal NMR distance information for rigidity of protein graphs. Discret. Appl. Math. https://doi.org/10.1016/j.dam.2018.03.071

  96. Lemke, P., Skiena, S., Smith, W.: Reconstructing sets from interpoint distances. In: Aronov, B., et al. (eds.) Discrete and Computational Geometry. Algorithms and Combinatorics, vol. 25, pp. 597–631. Springer, Berlin (2003)

    Google Scholar 

  97. Liberti, L. (ed.): Proceedings of the DIMACS Workshop on Distance Geometry Theory and Applications (DGTA16) (2016)

    Google Scholar 

  98. Liberti, L., Lavor, C.: Six mathematical gems in the history of distance geometry. Int. Trans. Oper. Res. 23, 897–920 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  99. Liberti, L., Vu, K.: Barvinok’s naive algorithm in distance geometry. Oper. Res. Lett. 46, 476–481, 2018

    Article  MathSciNet  Google Scholar 

  100. Liberti, L., Lavor, C., Maculan, N.: A branch-and-prune algorithm for the molecular distance geometry problem. Int. Trans. Oper. Res. 15, 1–17 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  101. Liberti, L., Lavor, C., Mucherino, A., Maculan, N.: Molecular distance geometry methods: from continuous to discrete. Int. Trans. Oper. Res. 18, 33–51 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  102. Liberti, L., Lavor, C., Mucherino, A.: The discretizable molecular distance geometry problem seems easier on proteins. In: Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds.) Distance Geometry: Theory, Methods, and Applications, pp. 47–60. Springer, New York (2013)

    Chapter  MATH  Google Scholar 

  103. Liberti, L., Lavor, C., Alencar, J., Abud, G.: Counting the number of solutions of kDMDGP instances. In: Nielsen, F., Barbaresco, F. (eds.) Geometric Science of Information. Lecture Notes in Computer Science, vol. 8085, pp. 224–230. Springer, New York (2013)

    Chapter  MATH  Google Scholar 

  104. Liberti, L., Lavor, C., Maculan, N., Mucherino, A.: Euclidean distance geometry and applications. SIAM Rev. 56(1), 3–69 (2014)

    Article  MathSciNet  MATH  Google Scholar 

  105. Liberti, L., Masson, B., Lavor, C., Lee, J., Mucherino, A.: On the number of realizations of certain Henneberg graphs arising in protein conformation. Discrete Appl. Math. 165, 213–232 (2014)

    Article  MathSciNet  MATH  Google Scholar 

  106. Liberti, L., Swirszcz, G., Lavor, C.: Distance geometry on the sphere. In: Akiyama, J., et al. (eds.) JCDCG2. Lecture Notes in Computer Science, vol. 9943, pp. 204–215. Springer, New York (2016)

    Google Scholar 

  107. Linial, N., London, E., Rabinovich, Y.: The geometry of graphs and some of its algorithmic applications. In: Proceedings of the Symposium on Foundations of Computer Science. FOCS, vol. 35, pp. 577–591. IEEE, Piscataway (1994)

    Google Scholar 

  108. Linial, N., London, E., Rabinovich, Y.: The geometry of graphs and some of its algorithmic applications. Combinatorica 15(2), 215–245 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  109. Locatelli, M.: Simulated annealing algorithms for global optimization. In: Pardalos, P., Romeijn, H. (eds.) Handbook of Global Optimization, vol. 2, pp. 179–229. Kluwer Academic Publishers, Dordrecht (2002)

    Chapter  MATH  Google Scholar 

  110. Lovász, L., Yemini, Y.: On generic rigidity in the plane. SIAM J. Algebraic Discrete Methods 3(1), 91–98 (1982)

    Article  MathSciNet  MATH  Google Scholar 

  111. Mahajan, M., Sarma, J.: On the complexity of matrix rank and rigidity. Theory Comput. Syst. 46, 9–26 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  112. Matoušek, J.: Lecture notes on metric embeddings. Technical report, ETH Zürich (2013)

    Google Scholar 

  113. Maxwell, J.: On reciprocal figures and diagrams of forces. Philos. Mag. 27(182), 250–261 (1864)

    Article  Google Scholar 

  114. Maxwell, J.: On the calculation of the equilibrium and stiffness of frames. Philos. Mag. 27(182), 294–299 (1864)

    Article  Google Scholar 

  115. Mehlhorn, K., Sanders, P.: Algorithms and Data Structures. Springer, Berlin (2008)

    MATH  Google Scholar 

  116. Menger, K.: Untersuchungen über allgemeine Metrik. Mathematische Annalen 100, 75–163 (1928)

    Article  MathSciNet  MATH  Google Scholar 

  117. Menger, K.: New foundation of Euclidean geometry. Am. J. Math. 53(4), 721–745 (1931)

    Article  MathSciNet  MATH  Google Scholar 

  118. Milnor, J.: On the Betti numbers of real varieties. Proc. Am. Math. Soc. 15, 275–280 (1964)

    Article  MathSciNet  MATH  Google Scholar 

  119. Moré, J., Wu, Z.: Global continuation for distance geometry problems. SIAM J. Optim. 7(3), 814–846 (1997)

    Article  MathSciNet  MATH  Google Scholar 

  120. Mosek ApS: The mosek manual, Version 7 (Revision 114) (2014). www.mosek.com

  121. Moukarzel, C., Duxbury, P.: Stressed backbone and elasticity of random central-force systems. Phys. Rev. Lett. 75(22), 4055–4059 (1995)

    Article  Google Scholar 

  122. Mucherino, A., Liberti, L., Lavor, C.: MD-jeep: an implementation of a branch-and-prune algorithm for distance geometry problems. In: Fukuda, K., van der Hoeven, J., Joswig, M., Takayama, N. (eds.) Mathematical Software. Lecture Notes in Computer Science, vol. 6327, pp. 186–197. Springer, New York (2010)

    Google Scholar 

  123. Mucherino, A., Lavor, C., Liberti, L.: The discretizable distance geometry problem. Optim. Lett. 6, 1671–1686 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  124. Mucherino, A., Lavor, C., Liberti, L.: Exploiting symmetry properties of the discretizable molecular distance geometry problem. J. Bioinf. Comput. Biol. 10, 1242009(1–15) (2012)

    Article  MATH  Google Scholar 

  125. Mucherino, A., Lavor, C., Liberti, L., Maculan, N. (eds.): Distance Geometry: Theory, Methods, and Applications. Springer, New York (2013)

    MATH  Google Scholar 

  126. Mucherino, A., de Freitas, R., Lavor, C.: Preface. Discrete Appl. Math. 197, 1–2 (2015)

    Article  Google Scholar 

  127. Nilges, M., Clore, G., Gronenborn, A.: Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229(2), 317–324 (1988)

    Article  Google Scholar 

  128. Nilges, M., Gronenborn, A., Brunger, A., Clore, G.: Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27–38 (1988)

    Article  Google Scholar 

  129. Recski, A.: Applications of combinatorics to statics — A survey. Rendiconti del Circolo Matematico di Palermo II(Suppl. 3), 237–247 (1984)

    Google Scholar 

  130. Recski, A.: Applications of combinatorics to statics — a second survey. Discret. Math. 108, 183–188 (1992)

    Article  MathSciNet  MATH  Google Scholar 

  131. Rojas, N.: Distance-based formulations for the position analysis of kinematic chains. Ph.D. thesis, Universitat Politecnica de Catalunya (2012)

    Google Scholar 

  132. Santana, R., Larrañaga, P., Lozano, J.: Side chain placement using estimation of distribution algorithms. Artif. Intell. Med. 39, 49–63 (2007)

    Article  Google Scholar 

  133. Santana, R., Larrañaga, P., Lozano, J.: Combining variable neighbourhood search and estimation of distribution algorithms in the protein side chain placement problem. J. Heuristics 14, 519–547 (2008)

    Article  MATH  Google Scholar 

  134. Saxe, J.: Embeddability of weighted graphs in k-space is strongly NP-hard. In: Proceedings of 17th Allerton Conference in Communications, Control and Computing, pp. 480–489 (1979)

    Google Scholar 

  135. Schoenberg, I.: Remarks to Maurice Fréchet’s article “Sur la définition axiomatique d’une classe d’espaces distanciés vectoriellement applicable sur l’espace de Hilbert”. Ann. Math. 36(3), 724–732 (1935)

    Article  MathSciNet  MATH  Google Scholar 

  136. Singer, A.: Angular synchronization by eigenvectors and semidefinite programming. Appl. Comput. Harmon. Anal. 30, 20–36 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  137. Sitharam, M., Zhou, Y.: A tractable, approximate, combinatorial 3D rigidity characterization. In: Fifth Workshop on Automated Deduction in Geometry (2004)

    Google Scholar 

  138. Sitharam, M., Vince, A., Cheng, J.: Graph algorithmic characterizations and rank bounds for maximal rank abstract rigidity matroids. Technical Report, Manuscript, University of Florida (2018)

    Google Scholar 

  139. Sljoka, A.: Algorithms in rigidity theory with applications to protein flexibility and mechanical linkages. Ph.D. thesis, York University, Canada (2012)

    Google Scholar 

  140. Souza, M., Lavor, C., Muritiba, A., Maculan, N.: Solving the molecular distance geometry problem with inaccurate distance data. BMC Bioinf. 14(Suppl. 9), S71–S76 (2013)

    Google Scholar 

  141. Tarski, A.: A decision method for elementary algebra and geometry. Technical Report R-109, Rand Corporation (1951)

    Google Scholar 

  142. Tay, T.S., Whiteley, W.: Generating isostatic frameworks. Struct. Topol. 11, 21–69 (1985)

    MathSciNet  MATH  Google Scholar 

  143. Thorpe, M., Duxbury, P. (eds.): Rigidity Theory and Applications. Fundamental Materials Research. Springer, New York (2002)

    Google Scholar 

  144. Wüthrich, K.: Protein structure determination in solution by nuclear magnetic resonance spectroscopy. Science 243, 45–50 (1989)

    Article  Google Scholar 

  145. Wüthrich, K., Billeter, M., Braun, W.: Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J. Mol. Biol. 169, 949–961 (1983)

    Article  Google Scholar 

  146. Yemini, Y.: The positioning problem — a draft of an intermediate summary. In: Proceedings of the Conference on Distributed Sensor Networks, pp. 137–145. Carnegie-Mellon University, Pittsburgh (1978)

    Google Scholar 

  147. Yemini, Y.: Some theoretical aspects of position-location problems. In: Proceedings of the 20th Annual Symposium on the Foundations of Computer Science, pp. 1–8. IEEE, Piscataway (1979)

    Google Scholar 

  148. Young, G., Householder, A.: Discussion of a set of points in terms of their mutual distances. Psychometrika 3(1), 19–22 (1938)

    Article  MATH  Google Scholar 

Download references

Acknowledgements

We are grateful for Ana Flavia Lima for helping to check the manuscript prior to submission. LL was partly supported by the ANR “Bip:Bip” project n. ANR-10-BINF-03-08. CL was partly supported by the Brazilian research agencies FAPESP, CNPq.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Leo Liberti .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Liberti, L., Lavor, C. (2018). Open Research Areas in Distance Geometry. In: Pardalos, P., Migdalas, A. (eds) Open Problems in Optimization and Data Analysis. Springer Optimization and Its Applications, vol 141. Springer, Cham. https://doi.org/10.1007/978-3-319-99142-9_11

Download citation

Publish with us

Policies and ethics