Francesco Rao Research Lab

32. The quest for self-consistency in hydrogen-bond definitions
Prada-Gracia, D; Shevchuk, R; Rao, F†.
arXiv:1305.3060

31. Consensus for the Fip35 folding mechanism?
Berezovska, A; Prada-Gracia, D; Rao, F†.
arXiv:1304.5903

30. Lattice Boltzmann implementation of the three-dimensional Ben-Naim potential for water-like fluids. Moradi, N; Greiner, A; Rao, F, Succi S.
J. Chem. Phys. 138, 124105 (2013)

29. Quantum physics and biology
Levi, F; Mostarda, S; Rao, F†; Mintert, F†.
submitted

28. Structure-dynamics relationship in coherent transport through disordered systems
Mostarda, S; Levi, F; Mintert, F†; Rao, F†.
arXiv:1302.2449

27. Accounting for the kinetics in order parameter analysis: lessons from theoretical models and a disordered peptide
Berezovska, A; Prada-Gracia, D; Mostarda, S; Rao, F†.
J. Chem. Phys. 137, 194101 (2012) [cover page]
> A tutorial on the methodology introduced in the paper

26. Is ion channel selectivity mediated by confined water?
Prada-Gracia, D; Rao, F†.
arXiv:1207.6953

25. Towards a microscopic description of the free-energy landscape of water. Prada-Gracia, D; Shevchuk, R; Hamm, P; Rao, F†. J. Chem. Phys. 137, 144504 (2012)

24. Microsecond long atomistic simulation of supercooled water.
Shevchuk, R; Rao, F†. J. Chem. Phys. 137, 036101 (2012)

23. Water structure-forming capabilities are temperature shifted for different models. Shevchuk, R; Prada-Gracia, D; Rao, F†.
J. Phys. Chem. B, 116, 7538 (2012)

22. Beyond the binding site: the role of the b2-b3 loop and extra-domain structures in PDZ domains. Mostarda, S; Gfeller, D; Rao, F†. Plos Comp. Bio., 8, e1002429 (2012)

21. Thermodynamics and kinetics of large-time-step molecular dynamics. Rao, F†; Spichty, M. J. Comp. Chem., 33, 475-483 (2012)

20. Three-Dimensional Infrared Spectroscopy of Isotope-Substituted Liquid Water Reveals Heterogeneous Dynamics. Garrett-Roe, S; Perakis, F; Rao, F; Hamm, P. J. Phys. Chem. B, 115, 6976-6984 (2011)

19. Protein Inherent Structures by Different Minimization Strategies. Rao, F. J. Comp. Chem., 32, 1113-1116 (2011)

18. Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces. Seeber, M; Felline, A; Raimondi, F; Muff, S; Friedman, R; Rao, F; Caflisch, A; Fanelli, F. J. Comp. Chem., 32, 1183-1194 (2011)

17. Structural Inhomogeneity of Water by Complex Network Analysis. Rao, F†; Garrett-Roe, S; Hamm, P. J. Phys. Chem. B, 114, 15598-15604 (2010)

16. Local Transition Gradients Indicating the Global Attributes of Protein Energy Landscapes. Rao, F. J. Phys. Chem. Lett., 1, 1580-1583 (2010)

15. Protein dynamics investigated by inherent structure analysis. Rao, F†; Karplus, M. Proc. Natl. Acad. Sci. USA, 107, 9152-9157 (2010)

14. Computational Screening of Rhodopsin Mutations Associated with Retinitis Pigmentosa. Felline, A; Seeber, M; Rao, F; Fanelli, F. J. Chem. Theor. Comp., 5, 2472-2485 (2009)

13. On the rich-club effect in dense and weighted networks. Zlatic, V.; Bianconi, G.; Diaz-Guilera, A.; Garlaschelli, D.; Rao, F.; Caldarelli, G.. E. Phys. J. B, 67, 271-275 (2009)

12. Taxonomy and clustering in collaborative systems: The case of the on-line encyclopedia Wikipedia. Capocci, A.; Rao, F.; Caldarelli, G.. Europhys. Lett., 81, 28006 (2008)

11. Wordom: a program for efficient analysis of molecular dynamics simulations. Seeber, M; Cecchini, M; Rao, F; Settanni, G; Caflisch, A. Bioinf., 23, 2625-2627 (2007)

10. Uncovering the topology of configuration space networks. Gfeller, D; Morton de Lachapelle, D; De Los Rios, P; Caldarelli, G; Rao, F†. Phys. Rev. E, 76, 026113 (2007)

9. Complex network analysis of free-energy landscapes. Gfeller, D.; De Los Rios, P.; Caflisch, A.; Rao, F†. Proc. Natl. Acad. Sci. USA, 104, 1817-1822 (2007)

8. Local modularity measure for network clusterizations. Muff, S; Rao, F; Caflisch, A. Phys. Rev. E, 72, 056107 (2005)

7. Estimation of protein folding probability from equilibrium simulations. Rao, F; Settanni, G; Guarnera, E; Caflisch, A. J. Chem. Phys., 122, 184901 (2005)

6. phi-Value analysis by molecular dynamics simulations of reversible folding. Settanni, G; Rao, F; Caflisch, A. Proc. Natl. Acad. Sci. USA, 102, 628-633 (2005)

5. Replica exchange molecular dynamics simulations of amyloid peptide aggregation. Cecchini, M; Rao, F; Seeber, M; Caflisch, A. J. Chem. Phys., 121, 10748-10756 (2004)

4. The protein folding network. Rao, F; Caflisch, A. J. Mol. Biol., 342, 299-306 (2004)

3. Frequency-domain study of alpha relaxation in the random orthogonal model. Rao, F; Crisanti, A; Ritort, F. Phil. Mag., 84, 1389-1395 (2004)

2. Replica exchange molecular dynamics simulations of reversible folding. Rao, F; Caflisch, A. J. Chem. Phys., 119, 4035-4042 (2003)

1. Frequency-domain study of relaxation in a spin glass model for the structural glass transition. Rao, F; Crisanti, A; Ritort, F. Europhys. Lett., 62, 869-875 (2003)

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