Resource page for chimera's theoretical biophysics research activity

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Researchers involved:

Andrea De Martino
Daniele De Martino (postdoc)
Francesca Dipatti (postdoc)
Matteo Figliuzzi (Phd student)
Stefania Lamartina (postdoc)
Enzo Marinari
Giorgio Parisi
Federico Ricci Tersenghi
Alessandro Seganti (Phd student)

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Biological articles (most recent first), with related material

• Optimal flux states, reaction replaceability and response to knockouts in the human red blood cell, submitted (2009)
  
  • preprint
  • stoichiometric matrices (single .tar.gz file incl. input and output matrices)
  • optimal flux configurations (a single .tar.gz file with large samples for the healthy rbc and for various enzyme deficiencies)
  • a C code to compute optimal fluxes
  • enumeration of alternative paths for replaceable metabolic conversions
  • a C code implementing Johnson's algorithm to compute replaceabilities
  • related theory: see 1 through 4 below
• Identifying essential genes in E. coli from a metabolic optimization principle, PNAS 106 2607 (2009)
  
  • preprint, published version with supplementary material
  • stoichiometric matrices after leaf removal, reversibility included (1035 reactionsx625 metabolites, single .tar.gz file incl. input and output matrices)
  • list of the 625 metabolites, ordered as in the stoichiometric matrices
  • related theory: see 1, 2 and 4 below

Related theory papers (most recent first)

• [5] A.C.C. Coolen, A. De Martino and A. Annibale, 2009 [preprint]
  Constrained Markovian dynamics of random graphs
  Properties of a Markov chain that explores the space of graphs satisfying a given set of constraints (general theory)
• [4] A. De Martino, C. Martelli and F. Massucci, EPL 85 38007 (2009) [preprint, published version]
  On the role of conserved moieties in shaping the robustness and production capabilities of reaction networks
  Same as 1, with conserved metabolic pools
• [3] V. Van Kerrebroeck and E. Marinari, Phys. Rev. Lett. 101 098701 (2008) [preprint, published version]
  Ranking Vertices or Edges of a Network by Loops: A New Approach
  Ranking of vertices and edges based on the distribution of cycles in directed graphs, compared to other known ranking measures.
• [2] A. De Martino, C. Martelli, R. Monasson and I. Perez Castillo, JSTAT P05012 (2007) [preprint, published version]
  Von Neumann's expanding model on random graphs
  Numerical (via minover) and analytical (via cavity) solution of the Von Neumann problem on random graphs
• [1] A. De Martino and M. Marsili, JSTAT L09003 (2005) [preprint, published version]
  Typical properties of optimal growth in the Von Neumann expanding model for large random economies
  Solution (via replicas) of the Von Neumann problem for a fully connected random input-output network