HOME People Articles Projects Positions Address Movies More Back to Di Nola       Alfredo Di Nola  -  List of publications 2011   139. A. Magliano, M. Anselmi and A. Di Nola Molecular dynamics study of aggregation of amyloidogenic peptides in explicit water . Int. J. Quantum Chem. 2011 Accepted. 138. M. Anselmi, A. Di Nola and A. Amadei Kinetics of Carbon Monoxide migration and binding in solvated Neuroglobin as revealed by Molecular Dynamics Simulations and Quantum Mechanical Calculations. J. Phys. Chem. B 115(10) 2436-2446 (2011). 137. I. Daidone, A. Di Nola and J. C. Smith Molecular origin of Gerstmann-Straussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophys. J. 100, 3000-3007 (2011). 136. Massimiliano Anselmi, Tommaso Eliseo, Laura Zanetti-Polzi, Maria Rosaria Fullone, Vincenzo Fogliano, Alfredo Di Nola, Maurizio Paci and Ingeborg Grgurina Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle: a circular dichroism and NMR spectroscopy combined with molecular dynamics study in octane. Biochim. Biophys. Acta-Biomembranes 1808(9),2102-2110 (2011). 135. I. Daidone,  A.Magliano, A. Di Nola,  G. Mignogna, M.M Clarkson, A.R. Lizzi, A. Oratore, F. Mazza Structural investigation into the bovine Lactoferricin antimicrobial activity by Circular Dichroism and Molecular Dynamics simulations. Biometals 24(2) 259-268 (2011). 134. L. Zanetti-Polzi, I. Daidone, M. Anselmi, M. Aschi, G. Carchini, A. Di Nola and A. Amadei Analysis of infrared spectra of b-hairpin peptides as derived from molecular dynamics simulations. J. Phys. Chem B 115, 11872-11878 (2011). 133. M. Anselmi, A. Di Nola and A. Amadei The effects of the L29F mutation on ligand migration kinetics in crystallized Myoglobin as revealed by Molecular Dynamics simulations. Proteins: Structure, Function, and Bioinformatics 79, 867-879 (2011).     2010   132. P. D'Angelo, S. Della Longa, A. Arcovito, M. Anselmi, A. Di Nola and G. Chillemi Dynamic investigation of protein metal active site: the interplay of XANES and molecular dynamics simulations. J. Am. Chem. Soc. 132(42), 14901-14909 (2010). 131. A. Amadei, I. Daidone, A. Di Nola and M. Aschi Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. Curr Opin Struc Biol 20, 1-7 (2010). 130. I. Daidone, M. Aschi, L. Zanetti-Polzi, A. Di Nola and  A. Amadei On the origin of IR spectral changes upon protein folding. Chem. Phys. Lett. 488(4-6), 213-218 (2010). 129. A. Merlino; A. Vergara; F. Sica; M. Aschi, A. Amadei; A. Di Nola and L. Mazzarella Free Energy Profile for CO Binding to Separated Chains of Human and Trematomus Newnesi Hemoglobin: Insights from MD Simulations and Perturbed Matrix Method. J. Phys. Chem. B ,  114 (20),  7002-7008 (2010). 128. D. Mastrogiovanni, M. Anselmi, A. E. Miele, G. Boumis, F. Angelucci, A. Di Nola, M. Brunori and A. Belleli Combining crystallography and molecular dynamics: the case of Schistosoma mansoni phospholipid glutathione peroxidase. Proteins: Structure, Function, and Bioinformatics  78(2),259-270 (2010). 2009   127. M. D'Abramo, M. Aschi, A. Di Nola and A. Amadei The Kinetics of Carbon Monoxide migration and binding in solvated Myoglobin as revealed by Molecular Dynamics simulations. J. Phys. Chem. B 113, 16346-16353 (2009). 126. A. Tarquini, P.  Marracino, F. Apollonio, M. Liberti, G. d'Inzeo, A. Amadei and A. Di Nola Theoretical and computational characterization of the thermodynamic effects of external fields in dilute ionic solutions. IJLSS Accepted (2009). 125. L. Zanetti-Polzi, M. Anselmi, M. D'Alessandro, A. Amadei and A. Di Nola Structural, thermodynamic and kinetic properties of Gramicidin analogue GS6 studied by molecular dynamics simulations and statistical mechanics.   Biopolymers 91(12),1154-1160 (2009). 124. M. D'Abramo, R. Caminiti, A. Di Nola and A. Amadei What can we learn by comparing experimental and theoretical-computational X-ray scattering data? J. Mol. Liq. 144(1-2), 9-12 (2009). 2008     123. M. Pellegrino, F. Apollonio, M. Liberti, A. Amadei, A. Di Nola and G. D'Inzeo Molecular simulations of biochemical processes in presence of a MW signal. 2008 IEEE International Symposium on Antennas and Propagation and USNC/URSI National Radio Science Meeting, APSURSI, art. no. 4619666 (2008). 122.   D. Narzi, I. Daidone, A. Amadei and A. Di Nola Protein folding pathways revealed by essential dynamics sampling. J.Chem. Theory Comput. 4(11), 1940-1948 (2008). 121.   M. Anselmi, M. Brunori, B. Vallone and A. Di Nola Molecular dynamics simulation of the Neuroglobin crystal: comparison with the simulation in solution. Biophys. J. 95, 4157-4162 (2008). 120.   A. Amadei, M. Aschi and A. Di Nola Statistical mechanical modeling of chemical reactions in condensed phase systems. In Challenges and advances in Computational Chemistry and Physics, Vol. 6, Solvation Effects on Molecules and Biomolecules, 191-213 S. Canuto ed. Springer (2008). 119. M. D'Abramo, A. Di Nola, M. Aschi and A. Amadei Theoretical characterization of temperature and density dependence of liquid water electronic excitation energy: Comparison with recent experimental data. J. Chem. Phys. 128, 021103 (2008). 118.   M. Anselmi, A. Di Nola and A. Amadei The kinetics of ligand migration in crystallized Myoglobin as revealed by molecula dynamics simulations. Biophys. J. 94, 4277-4281 (2008). 117.   Francesca Apollonio, Andrea Amadei, Micaela Liberti, Massimiliano Aschi, Monica Pellegrino, Maira D'Alessandro, Marco D'Abramo, Alfredo Di Nola, Guglielmo d'Inzeo Mixed Quantum-Classical Methods for Molecular Simulations of Biochemical Reactions with Microwave Fields: the Case Study of Myoglobin. IEEE T  Microw. Theory  56(11), 2511-2519 (2008). 116.   F. Noe', I. Daidone, J. C. Smith, A. Di Nola and A. Amadei Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation J. Phys. Chem. B, 112(35), 11155-11163 (2008). 115.   Massimiliano Aschi, Maira D'Alessandro, Monica Pellegrino, Alfredo Di Nola, Marco D'Abramo and Andrea Amadei Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state. Theor. Chem. Acc. 119(5-6), 469-476 (2008). 114.   M. D'Alessandro, A. Di Lella, M. Aschi, A. Di Nola and A. Amadei Theoretical characterization of structural and energetical properties of water clusters, by means of a simple polarizable water Hamiltonian. J. Mol. Liq.142(1), 111-117 (2008). 2007   113.   Isabella Daidone_ , Martin Ulmschneider_ , Alfredo Di Nola_ , Andrea Amadei _ and Jeremy C. Smith Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc. Natl. Acad. Sci. U S A. 104, 15230-15235 (2007). 112. C. Leggio, M. Anselmi, A. Di Nola, L. Galantini, A. Jover, F. Meijide, N. V. Pavel, V. H. Soto Tellini and J. V. Tato Study on the structure of host-guest supramolecular polymers. Macromolecules 40(16), 5899-5906 (2007). 111. A. Amadei, M. D'Abramo, A. Di Nola, A. Arcadi, G. Cerichelli and M. Aschi Theoretical study of intramolecular charge transfer pi-conjugated oligomers. Chem. Phys. Lett. 434(4-6), 194-199 (2007). 110. A. Amadei, M. D'Abramo, I. Daidone, M. D'Alessandro, A. Di Nola and M. Aschi Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the haem carbon monoxide binding-unbinding reaction in myoglobin. Theor. Chem. Acc. 117(5-6), 637-647 (2007). 109.   M. B. Ulmschneider, J. P. Ulmschneider, M.S.P. Sansonm and A. Di Nola A generalized Born implicit membrane representation compared to experimental insertion free energies. Biophys. J. 92, 2338-2349 (2007). 108.   M. Anselmi, M. Aschi, A. Di Nola and A. Amadei Theoretical characterization of Carbon Monoxide vibrational spectrum in Sperm Whale Myoglobin distal pocket. Biophys. J. 92, 3442-3447 (2007). 107.   M. D'Abramo, M. Aschi, F. Marinelli, A. Di Nola and A. Amadei Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water. J. Mol. Struc.-Theochem. 811(1-3), 197-201 (2007). 106.   Jakob P. Ulmschneider, Martin P. Ulmschneider and Alfredo Di Nola. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins: Structure, Function, and Bioinformatics 69(2), 297-308 (2007). 105.   M. Anselmi, M. Brunori, B. Vallone and A. Di Nola Molecular dynamics simulation of deoxy and carboxy murine Neuroglobin in water. Biophys. J. 93, 434-441(2007). 2006     104.   D. Floeck, G. Rossetti, I. Daidone, A. Amadei and A. Di Nola Aggregation of small peptides studied by Molecular Dynamics simulations. Proteins: Structure, Function, and Bioinformatics 65(4), 914-921 (2006). 103.   J. Ulmschneider, M. Ulmschneider and A. Di Nola Monte Carlo versus Molecular Dynamics for all-atom polypeptide folding simulations. J. Phys. Chem. B 110(33); 16733-16742 (2006). 102.   Costantino Zazza, Andrea Amadei, Nico Sanna, Andrea Grandi, Giovanni Chillemi, Alfredo Di Nola, Marco D'Abramo and Massimiliano Aschi Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution. Phys. Chem. Chem. Phys. 8, 1385-1393 (2006). 101.   M. D'Abramo, M. Aschi, A. Di Nola and A. Amadei On the importance of configurational sampling in theoretical calculation of electronic properties of complex molecular systems: acetone in water. Chem. Phys. Lett. 424(4-6), 289-294 (2006). 100. M. D'Abramo, M. C. Rinaldi, A. Bozzi, G. Mignogna, A. Di Nola, A. Amadei and M. Aschi Conformational behaviour of Temporin A and Temporin L in aqueous solution: a computational/experimental study. Biopolymers, 81(3), 215-224, (2006). 99. A. Amadei, M. D'Alessandro, M. Paci, A. Di Nola and M. Aschi On the Effect of a Point Mutation on the Reactivity of CuZn Superoxide Dismutase: A Theoretical Study. J. Phys. Chem. B 110(14),7538-7544 (2006). 98. D. Floeck, S. Colacino, G. Colombo and A. Di Nola Misfolding of the Amyloid beta-peptide: A Molecular Dynamics Study. Proteins: Structure, Function, and Bioinformatics 62, 183-192 (2006). 97. M.Aschi , M. D'Abramo, F. Ramondo, I. Daidone, M. D'Alessandro, A. Di Nola and A. Amadei Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde. J. Phys. Org. Chem.  19, 518-530 (2006). 96. M. B. Ulmschneider, M. S. P. Sansom and A. Di Nola Evaluating tilt angles of trans-membrane helices: comparison of computational and NMR techniques. Biophys. J. 90 1650-1660 ( 2006) 2005     95. D. Floeck and A. Di Nola Molecular dynamics studies of protein and peptide misfolding. The FEBS Journal 272 370 (2005) 94. I. Daidone, M. D'Abramo, A. Di Nola and A. Amadei Theoretical characterization of alpha-helix and beta-hairpin folding kinetics. J.Am.Chem.Soc. 127(42),   14825 - 14832  (2005). 93. G. Brancato, A. Di Nola, V. Barone and A. Amadei A mean field approach for molecular simulations of fluid systems. J. Chem. Phys.122, 154109 (2005). 92. C. Bossa, A. Amadei, I. Daidone, M. Anselmi, M. Brunori, B. Vallone and A. Di Nola. Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and cavities dynamics. Biophys. J. 89, 465-474 (2005). 91. M. D'Alessandro, F. Marinelli, M. D'Abramo, M. Aschi, A. Di Nola and A. Amadei . Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study. J. Chem. Phys. 122, 124507 (2005). 90. A. Amadei, F. Marinelli, M. D'Abramo, M. D'Alessandro, M. Anselmi, A. Di Nola and M. Aschi Theoretical modeling of vibro-electronic quantum states in complex molecular systems: solvated carbon monoxide, a test case. J. Chem. Phys. 122, 124506 (2005). 89. Giorgio Colombo, Isabella Daidone, Ehud Gazit, Andrea Amadei, and Alfredo Di Nola Molecular dynamics simulation of the aggregation of the core recognition motif of the islet amyloid polypeptide in explicit water. Proteins: Structure, Function, and Bioinformatics 59(3) 519-527 (2005). 88. D. Roccatano, G. Sbardella, G. Amicosante, M. Aschi, C. Bossa, A. Di Nola and F. Mazza Dynamical Aspects of  TEM-1 β-Lactamase Probed by Molecular Dynamics. J. Comp.-Aided Molecular Design 19 329-340 (2005) . 87. I. Daidone, A. Amadei and A. Di Nola Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water. Proteins: Structure, Function, and Bioinformatics 59(3) 510-518 (2005). 86. M. Aschi, M. D'Abramo, C. Di Teodoro, A. Di Nola and A. Amadei Theoretical characterization of liquid water electronic excitation. ChemPhysChem. 6(1), 53-58 (2005). 85. M. Ulmschneider, M.S.P. Sanson and A. Di Nola Properties of Integral Membrane Protein Structures: Derivation of an Implicit Membrane Potential. Proteins: Structure, Function, and Bioinformatics 59(2) 252-265 (2005). 84. M. Aschi, M. D'Abramo, C. Di Teodoro, A. Di Nola and A. Amadei Calculation of the Optical Rotatory Dispersion of solvated alanine by means of the Perturbed Matrix Method Chem. Phys. Lett. 402, 559-563 (2005). 83. M. D'Abramo, M. D'Alessandro, A. Di Nola, D. Roccatano and A. Amadei Characterization of liquid behaviour by means of local density fluctuations. J. Mol. Liq. 117, 17-21 (2005). 2004     82. D. Floeck, I. Daidone and A. Di Nola A Molecular Dynamics Study of Acylphosphatase in aggregation promoting conditions: The Influence of TFE/water solvent. Biopolymers. 75, 491 - 496 (2004) . 81. V. M. Coiro , A. Di Nola, M. A. Vanoni, M. Aschi, A. Coda , B. Curti and D. Roccatano Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Protein Sci. 13, 2979 - 2991 (2004). 80. M. D'Alessandro, M. Aschi, M. Paci, A. Di Nola and A. Amadei Theoretical modeling of enzyme reactions chemistry: the electron transfer of the reduction mechanism in CuZn Superoxide Dismutase. J. Phys. Chem. B 108(41) 16255-16260 (2004). 79. D. Roccatano, A. Di Nola and A. Amadei A theoretical model for folding/unfolding thermodynamics of single domain proteins based on the quasi-Gaussian entropy theory. J. Chem. Phys. 108(18), 5756-5762 (2004). 78. C. Bossa, M. Anselmi, D. Roccatano, A. Amadei, B. Vallone, M. Brunori and A. Di Nola Extended molecular dynamics simulation of the Carbon Monoxide migration in sperm whale Myoglobin Biophys. J. 86, 3855-3862 (2004). 77. I. Daidone, F. Simona, D. Roccatano, R. A. Broglia, G. Tiana, G. Colombo and A. Di Nola Beta-Hairpin conformation of fibrillogenic peptides: Structure and alpha-to-beta transition mechanism revealed by molecular dynamics simulations. Proteins: Structure, Function, and Genetics. 57(1), 198- 204 (2004). 76. M. Aschi, C. Zazza, R. Spezia, C. Bossa, A. Di Nola, M. Paci and A. Amadei Conformational fluctuations and electronic properties in Myoglobin. J. Comput. Chem. 7, 974-984 (2004). 2003     75. I. Daidone, A. Amadei, D. Roccatano and A. Di Nola Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophys. J. 85, 2865-2871 (2003). 74. R. Spezia, M. Aschi, A. Di Nola, M. Di Valentin, D. Carbonera and A. Amadei The effect of protein conformational flexibility on the electronic properties of a chromophore. Biophys. J. 84, 2805-2813 (2003). 73. M. F. Gerini, D. Roccatano, E. Baciocchi and A. Di Nola Molecular dynamics simulation of Lignine peroxidase in solution. Biophys. J. 84, 3883-3893 (2003). 72. D. Roccatano, I. Daidone, M.-A. Ceruso, C. Bossa and A. Di Nola Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys. J. 84,1876-1883 (2003) 71. M.-A. Ceruso, A. Grottesi and A. Di Nola Long distance effects of mutations in cytochrome c551 from Pseudomonas aeruginosa. Proteins: Structure, Function, and Genetics 50, 222-229 (2003). 2002     70. M. D'Alessandro, M. D'Abramo, G. Brancato, A. Di Nola and A. Amadei Statistical mechanics and thermodynamics of simulated ionic solutions. J. Phys.Chem. B 106 (45) 11843-11848 ( 2002). 69. R. Spezia, M. Aschi A. Di Nola and A. Amadei Extension of the Perturbed Matrix Method: application to a water molecule. Chem. Phys. Lett. 365, 450-456 (2002). 68. M. Aschi, D. Roccatano, F. Mazza, A. Di Nola, C. Gallina, E. Gavuzzo, G. Pochetti, M. Pieper and H. Tschesche Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S-3 and S '(3) subsites in the interaction with a phosphonate inhibitor. J. Comp.-Aided Molecular Design 16(3), 213-225 (2002). 67. A. Merlino, L. Vitagliano, M.-A. Ceruso, A. Di Nola, and L. Mazzarella Global and Local Motions in Ribonuclease A: a Molecular Dynamics Study. Biopolymers 65(4), 274-283 (2002). 66. M. Aschi, F. Mazza and A. Di Nola Cation-pi interactions between ammonium ion and aromatic rings: an energy decomposition study. J. Mol. Struct. THEOCHEM 587, 177-188 (2002). 65. A. Amadei, M. Aschi, R. Spezia and A. Di Nola A first principles polarizable water model for molecular simulations: application to water dimer. J. Mol. Liq. 101, 181-198 (2002). 64. A. Amadei, M.E.F. Apol, G. Brancato and A. Di Nola Theoretical equations of state for temperature and electro-magnetic field dependence of fluid systems, based on the quasi-Gaussian entropy theory. J. Chem. Phys. 116 (11), 4437-4449 (2002). 63. M.E.F. Apol, A. Amadei and A. Di Nola Statistical mechanics and thermodynamics of magnetic and dielectric systems based on magnetization and polarization fluctuations: application of the quasi-Gaussian entropy theory. J. Chem. Phys. 116 (11), 4426-4436 (2002). 62. A. Grottesi, M.-A. Ceruso, A. Colosimo and A. Di Nola Molecular dynamics study of a hyperthermophilic and a mesophilic Rubredoxin. Proteins: Structure, Function, and Genetics 46 (3), 287-294 (2002). 2001     61. M. Aschi, R. Spezia, A. Di Nola and A. Amadei A first-principle method to model perturbed electronic wavefunctions: the effect of an external homogeneous field. Chem. Phys. Lett. 344(3-4), 374-380 (2001). 60. A. Amadei, B. Iacono, S. Grego, G. Chillemi, E.M.F. Apol, E. Paci, M. Delfini and A. Di Nola On the use of  the quasi-Gaussian entropy theory in systems of polyatomic flexible molecules. J. Phys Chem., 105(9), 1834-1844 (2001). 2000     59. A. Amadei, G. Chillemi, M. Ceruso, A. Grottesi and A. Di Nola Molecular dynamics simulations with constrained roto-translational motions: theoretical basis and statistical mechanics consistency. J. Chem. Phys.,   112(1), 9-23 (2000). 1999     58. S. Barè, V.M. Coiro, A. Scaloni, A. Di Nola, M. Paci, A.L. Segre and A. Ballio Conformations in solution of the fuscopeptins, phytotoxic metabolites of Pseudomonas fuscovaginae. Eur. J. Biochem. 266, 484-492 (1999). 57. M. F. E. Apol, A. Amadei, H. J. C. Berensen and A. Di Nola Derivation of thermal equations of state for quantum systems using the quasi-Gaussian entropy theory. J. Chem .Phys.  111(10), 4431-4441 (1999). 56. M. A. Ceruso, A. Grottesi and A. Di Nola Effects of core packing on the structure, function and dynamics of a four-helix-bundle protein ROP. Proteins: Structure, Function, and Genetics 36(4), 436-446 (1999). 55. A. Amadei, M. A. Ceruso and A. Di Nola On the convergence of the conformational coordinates basis set obtained by essential dynamics analysis of proteins molecular dynamics simulations. Proteins: Structure, Function, and Genetics 36(4), 419-424 (1999). 54. D. Roccatano, A. Amadei, A. Di Nola and H. J. C. Berendsen A Molecular dynamics study of the 41-56 beta-hairpin from Protein G B1 domain. Proteins Sci. 8(10),  2130-2143 (1999). 53. A. Amadei, M. E. F. Apol,  G. Chillemi, H.J. C. Berendsen and A. Di Nola Derivation of a general fluid equation of state based on the quasi-Gaussian entropy theory: application to the Lennard-Jones fluid. Molec. Phys. 96(10), 1469-1490 (1999). 52. B. de Groot, A. Amadei, M. Ceruso, M. Paci, A. Di Nola and H.J. C. Berendsen A kinetic model for the internal motions of proteins: diffusion between multiple quasi harmonic wells. Proteins: Structure, Function, and Genetics 35, 283-292 (1999). 51. M. Mangoni, D. Roccatano and A. Di Nola Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulations. Proteins: Structure, Function, and Genetics 35(2), 153-162 (1999). 50. M-A. Ceruso, A. Amadei and A. Di Nola Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues. Protein Sci. 8(1), 147-160 (1999). 1998     49. D. Roccatano, A. Amadei, M. E. F. Apol, A. Di Nola and H.J. C. Berendsen Application of the quasi-Gaussian entropy theory to molecular dynamics simulations of Lennard-Jones fluids. J. Chem Phys. 109, 6358-6363 (1998). 48. V. M. Coiro, A. Ballio, G. Veglia, A.L. Segre, M.  Paci and A. Di Nola Solution conformation of the Pseudomonas syringae MSU 16H phytotoxic lipodepsipeptide pseudomycin A by computer simulations using distance geometry and molecular dynamics from NMR data. Eur. J. Biochem.  257, 443-448 (1998). 47. M. Cirilli, V. M. Coiro, A. Di Nola and F. Mazza Conformation dependent geometry evidenced by molecular dynamics simulation of Ca,a-dialkylated glycines Biopolymers46, 239-244 (1998). 46. A.  Di Nola and A. T.  Brünger Free energy calculations in globular proteins: methods to reduce errors. J. Comput. Chem. 18 (7), 1229-1240 (1998). 45. D. Roccatano, R. Bizzarri, G. Chillemi, N. Sanna and A. Di Nola Development of a parallel molecular dynamics code on SIMD computers: an algorithm for the use of pair list criterion. J. Comput. Chem. 18(7), 685-694 (1998). 1997   44. G. Chillemi, A. Amadei, M. Falcioni, G.Zimatore, A. Desideri and A.  Di Nola The essential dynamics of Cu,Zn Superoxide dismutase: suggestion of intersubunit communication Biophys. J. 73, 1007-1018 (1997). 1996   43. A.  Di Nola and A.  Amadei Simulazioni di dinamica molecolare: principi,  applicazioni,  prospettive e limiti. Atti della Scuola dell'Associazione Italiana di Cristallografia Perugia 9-13 settembre 1996. 42. M.  D'Alagni,  M.  Delfini,  A.  Di Nola,  M.  Eisenberg,  M.  Paci,  L. G.  Roda and G.  Veglia Conformational study of Met-enkephalin-Arg6-Phe7 in the presence of phosphatidylserine vesicles. Eur.  J.  Biochem. 240, 540-549 (1996). 41. A.  Amadei,  M. E. F.   Apol,  D.  Roccatano,  H. J. C.  Berendsen and A.  Di Nola Prediction of the liquid-vapor equilibrium pressure using the quasi-Gaussian entropy theory. J.  Chem Phys.  105, 7022, (1996). 40. A.  Amadei,  M. E. F.   Apol,  A.  Di Nola and H. J. C.  Berendsen The of the quasi gaussian entropy theory J.  Chem.  Phys. 104,1560,  (1996). 39. P.  D'Angelo,  A.  Di Nola,  M.  Mangoni and V.  Pavel An extended x-ray absorption fine structure study by employing mplecular dynamics simulaions: bromine anion in methoanolic solution. J. Chem Phys. 104, 1779-90, (1996). 1995   38. A.  Ballio,  F.  Bossa,  A.  Di Nola,  C.  Manetti,  M.  Paci,  A.  Scaloni and A. L. Segre Solution conformation of the Pseudomonas syringae pv. syringae phytotoxic lipodepsipeptide syringopeptin 25-A. Two-dimensional NMR, distance geometry and molecular dynamics. Eur. J. Biochem.  234, 747-758, (1995). 37. P.  D'Angelo,  A.  Di Nola,  E.  Giglio,  M.  Mangoni and N. V.  Pavel EXAFS study of micelar aggregates of bile acid rubidium salts J.  Phys.  Chem.  99, 5471-80,  (1995). 36. A.  Di Nola,  E.  Gavuzzo,  F.  Mazza and G.  Pochetti Internal b-turn hydration: crystallographic evidence and Molecular Dynamics simulation. J. Phys. Chem. 99, 9625-9631 (1995). 1970-1994   35. P.  D'Angelo,  A.  Di Nola,  A.  Filipponi,  N. V.  Pavel and D.  Roccatano An extended x-ray absorption fine structure study of aqueous solutions by employing molecular dynamics simulations. J.  Chem.  Phys.  100,  985-994,  (1994). 34. A.  Di Nola,  G.  Fabrizi,  D.  Lamba and A. L.  Segre Solution conformation of a pectic acid fragment by 1H NMR and molecular dynamics. Biopolymers, 34,  457-462 (1994). 33. A.  Ballio,  A.  Collina,  A.  Di Nola,  C.  Manetti,  M.  Paci and A. L.  Segre Determination of structure and conformation in solution of Syringotoxin,  a ipodepsipeptide from Pseudomonas Syringae pv. syringae by 2D NMR and molecular dynamics. Structural Chemistry,   5,  43-50 (1994). 32. A.  Di Nola,  D.  Roccatano,  H. J. C.  Berendsen Molecular dynamics simulation of the docking of substrates to proteins. Proteins: Structure, Function, and Genetics, 19, 174-182 (1994). 31. E. Brosio, M. Delfini, A. Di Nola, A. D'Ubaldo and C. Lintas 1H and 23Na NMR relaxation times studiy of pectin solutions and gels. Cell.  Mol.  Biol. ,   6, 583-588,  (1993). 30. E.  Brosio,  A.  Di Nola and B.  Verzegnassi NMR study of seed hydration: effect of pH and ionic strength on water uptake of soaked cowpeas. Cell.  Mol.  Biol. ,  39,  193-198,  (1993). 29. G.  Pagani Zecchini,  M.  Paglialunga Paradisi,  I.  Torrini,  G. Lucente,  E. Gavuzzo,  F. Mazza,  G.  Pochetti,  M.  Paci,  M.  Sette, A.  Di Nola, G.  Veglia,  S. Spisani and S. Traniello Synthesis,  conformation and activity of For-Met-DzLeu-Phe-OMe,  an active analog of chemotactic N-Formyltripeptides. Biopolymers, 33,  437-451 (1993). 28. A.  Di Nola,  E.  Carnovale,  A.  D'Ubaldo,  M.  Fracassi,  E.  Marconi and E. Brosio NMR studies of seed hydration.  in Recent advances in Cellular and Molecular Biology.  Wegmann,  R. J.  and Wegmann,  M. A.  (eds),  Peeters press,  Leuven, Belgium,  1992,   5,   257-284. 27. E.  Marconi,  E.  Carnovale,  A.  Di Nola and  E.  Brosio NMR assessement of water uptake in different vigna seeds. Int.  J.  of Fd.  Sci.  and Technol. ,  1992. 26. E. Brosio, A. Di Nola, M. Fracassi, E. Carnovale and E. Marconi NMR study of seed hydration: the role of the seed anatomical structures in water uptake of soaked cowpeas. Cell.  Mol.  Biol. ,  38,  693-697 (1992). 25. A. Di Nola, A. D'Ubaldo, M. Fracassi and E. Brosio NMR study of seed hydration with deuterated water: dependence of proton signals on hydration level. Cell.  Mol.  Biol. ,  37(1),  9-13(1991). 24. E. Brosio, T. Aureli, A. Di Nola, O.  Scorrano and E. Carnovale An NMR study of the hydration kinetics of cowpeas. Magn. Reson. Med. Biol. ,  4,  5-16 (1990). 23. M.  Delfini,  A.  Di Nola, E.  Carnovale,  E.  Gaggelli,  A.  Lepri and N. Russo 13C NMR study of the natural glycosides Vicine and Convicine. Spectroscopy Letters,  23(5),  657-667 (1990). 22. A.  Di Nola,  E.  Brosio,  M.  Delfini,  F.  Manes and S. Quattrocchi Hydration mechanism study in lettuce seeds by proton NMR relaxation times. Cell.  Mol.  Biol.   34(6),  639-648 (1988). 21. A. Di Nola, H. J. C. Berendsen and O. Edholm Free energy determination of polypeptide conformations generated by molecular dynamics. Macromolecules17(10),  2044 (1984). 20. H. J. C.  Berendsen,  J. P. M.  Postma,  W. F.  Van Gunsteren,  A.  Di Nola  and J. R.  Haak Molecular dynamics with coupling to an external bath. J. Chem. Phys.  81(8),  3684 (1984). 19. V. Pavone, A. Di Nola, S. Andini, L. Ferrara, B. Di Blasio, E. Benedetti, and P. Pucci Modified calmodulin calcium binding domain III. Solid phase synthesis, purification and 1H n.m.r. characterization Int J Pept Protein Res 23 (5), 454 (1984). 18. P. Fantazzini, L. Lendinara, F. Novello, E. Brosio and A. Di Nola The water proton spin-lattice relaxation time measurements in liver samples from hepatectomized and sham-operated rats. Biochim.  Biophys.  Acta  803,  250 (1984). 17. E. Brosio, G. Altobelli and A.  Di Nola A pulsed low resolution NMR study of water binding to milk proteins. J.  Fd.  Technol.   19,  103 (1984). 16. E. Brosio, G. Altobelli, Shi Yun Yu and A. Di Nola A pulsed low-resolution NMR study of water  binding to powdered milk. J.  Fd.  Technol.  18,  219 (1983). 15. A.  Di Nola and E. Brosio Bound and free water determination by pulsed low-resolution Nuclear Magnetic Resonance: a method for data analysis in presence of  exchange between bound and free water. J.  Fd.  Technol.  18,  125 (1983). 14. E. Brosio and A. Di Nola Pulsed low-resolution nuclear magnetic resonance-an analytical tool in food science. Trends in Analytical Chemistry 1,  284 (1982). 13. A. Di Nola and E. Brosio HELP:a FORTRAN V computer program for obtaining the cartesian coordinates of a single molecule from its chemical formula. J.  Appl.  Cryst.  15,  129 (1982). 12. E. Brosio, F. Conti, A. Di Nola, M. Scalzo and E. Zulli Oil and water determination in emulsions by pulsed low-resolution nuclear magnetic resonance. J.  Amer.  Oil Chem.  Soc.  59,  59 (1982). 11. F. Balestrieri, E. Brosio, F. Conti, A. Di Nola and O. Scorrano Simultaneous determination of oil and water content in olive husk by pulsed low-resolution nuclear magnetic resonance. J.  Fd.  Technol.  16,  629 (1981). 10. E. Brosio, F. Conti, A. Di Nola and S. Sykora Correlation between iodine number and proton relaxation times in maize oil. J.  Fd.  Technol.  16,  67 (1981) 9. E. Brosio, F. Conti. A. Di Nola and S. Sykora A pulsed low-resolution NMR study on crystallization and melting process of cocoa butter. J.  Amer.  Oil Chem.  Soc.  57,  78 (1980). 8. E. Brosio, F. Conti, A. Di Nola, A. L. Kovacs and G. Napolitano A stereochemical model for phospholipids.  III. Molecular conformation and molecular packing of L-O-Phosphatidylserine (PS). Chem.  and Phys.  of Lipids  27,  127 (1980). 7. A. L. Kovacs, E. Brosio, F. Conti, A. Di Nola and G. Napolitano A stereochemical model for phospholipids. II.  Conformational analysis and molecular packing of phosphatidylethanolamine (PE). Chem.  and Phys.  of Lipids  27,  113 (1980). 6. E. Brosio, F. Conti, A. Di Nola and A. L.  Kovacs A stereochemical model for phospholipids. I.  Conformational  energy refinement and molecular packing of L-a-Dipalmitoyl-lecithin (DPL). J.  Theor.  Biol.  67, 319 (1977). 5. A. L. Segre, A. Benedetto, T. Eremenko, P. Volpe, A. Di Nola and F. Conti Free radicals study in cells. Biochim.  Biophys.  Acta 497, 615 (1977). 4. E. Brosio, F. Conti, M. Delfini, A. Di Nola and A. L. Segre Computer simulation of 13C NMR spectra of copolymers. Gazz.  Chim.  Ital.  107, 237 (1977). 3. E. Brosio, F. Conti, M. R. Del Giudice, A. Di Nola and D. Gattegno Conformations of viomycin in solution. Gazz.  Chim.  Ital.  107, 139 (1977). 2. E.  Cappelli,  A.  Di Nola and A. L.  Segre The NMR spectrum of coumarine partially oriented in a nematic  mesophase. Molec.  Phys.  27, 1385 (1974). 1. A.  Di Nola and E.  Giglio Van der Waals interactions and molecular packing in crystals of cubic alpha-nitrogen, orthorombic cyanogen and monoclinic    octachlorocyclobutane. Acta Cryst.  26, 144 (1970).