Computational Chemical Physics Group

Exploring Nature With Computer Simulations


The research activity has resulted in 89 papers published in peer review journals (8 cover pages), 3 book chapters and two theses. The papers have more than 2000 total number of citations and an average of 25 citations per publication with a total h-index of 30 (source: Scholar Google Aug. 2016).



  1. Roccatano, E. Sarukhanyan, R. Zangi. Adsorption Mechanism of an Antimicrobial Peptide to Single-Walled Carbon Nanotubes: a Molecular Dynamics Study. J. Chem. Phys., 146, 074703 (2017). COVER PAGE.



  1. Karki, S. Samanta, D. Roccatano. Molecular Properties of Astaxanthin in Water/Ethanol Solutions from Computer Simulations. JPC B, J. Phys. Chem. B, 120, 9322−9328 (2016).
  2. Zangi and D. Roccatano. Strings-to-Rings Transition and Anti-parallel Dipole Alignment in Two-Dimensional Methanols. Nano Lett., 16(5), 3142-7, (2016).
  3. Verma, D. Holtmann, U. Schwaneberg, D. Roccatano. Unraveling binding effects of Cobalt(II)-Sepulchrate with the Monooxygenase P450BM-3 Heme Domain using Molecular Dynamics Simulations. J. Chem. Theory Comput., 12 (1),  353-363   (2016).
  4. V. Shivange, D. Roccatano, U. Schwaneberg. Iterative key-residues interrogation of a phytase with thermostability increasing substitutions identified in directed evolution. Applied Microbiology and Biotechnology, 100(1), 227-242, (2016).



  1. Roccatano. Structure, dynamics and function of the Monooxygenase P450 BM3: Insights from Computer Simulations Studies. Invited review. Journal of Physics: Condensed Matter. 7, 273102, (2015).
  2. Sarukhanyan, G. Milano, D. Roccatano. Cosolvent, Ions and Temperature Effects on the Structural Properties of Cecropin A- Magainin 2 Hybrid Peptide in Solutions. Biopolymers, 103(1), 1-14, (2015).



  1. Sarukhanyan, A. De Nicola, D. Roccatano, T. Kawakatsu, G. Milano. Spontaneous Insertion of Carbon Nanotube Bundles inside Biomembranes: a Hybrid Particle-Field Coarse-Grained Molecular Dynamics Study. Chem. Phys. Lett. 595, 156–166, (2014).
  2. Sarukhanyan, G. Milano, D. Roccatano. Coating Mechanisms of Single-Walled Carbon Nanotube by Linear Polyether Surfactants: Insights from Computer Simulations. J. Phys. Chem. C. 118 (31),18069–18078, (2014).
  3. De Nicola, Y. Zhao, T. Kawakatsu, S. Hezaveh, D. Roccatano, G. Milano. Micellar Drug Nanocarriers and Biomembranes: How do they interact? PCCP. 16(11), 5093-5105, (2014).
  4. Verma, U. Schwaneberg, D. Roccatano. Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations. Biopolymers. 101(3), 197-209, (2014). COVER PAGE.
  5. Li, D. Roccatano, M. Lorenz, R. Martinez, U. Schwaneberg. Insights on activity and stability of subtilisin E towards guanidinium chloride and sodium dodecyl sulfate. Journal of biotechnology. 169, 87–94, (2014).




  1. Samanta, S. Hezaveh, and D. Roccatano. Theoretical Study of Binding and Permeation of Ether-Based Polymers through Interfaces. J. Phys. Chem. B. 117 (47), 14723–14731, (2013).
  2. Shehzad, S. Panneerselvam, M. Linow, M. Bocola, D. Roccatano, J. Mueller-Dieckmann, M. Wilmanns, U. Schwaneberg. P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation. Chem. Commun. 49, 4694-4696, (2013).
  3. Samanta, D. Roccatano. Interaction of Curcumin with PEO-PPO-PEO block copolymers: A molecular dynamics study. J. Phys. Chem. B., 117(11), 3250-3257 (2013).
  4. Z. Cekic, A. Magnusson, U. Schwaneberg, D. Roccatano, J. Schrader, D. Holtmann. A computational protocol to predict suitable redox mediators for substitution of NAD(P)H in P450 monooxygenases. J. of Catalysis B. 88, 47–51, (2013).
  5. Verma, U. Schwaneberg, D. Roccatano. Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3. JCTC, 9 (1), 96–105, (2013).


  1. Verma, U. Schwaneberg, D. Roccatano. Computer-aided directed protein evolution: a review of server, database and tools for protein engineering. Computational and Structural Biotechnology Journal. 2(3), e201209008, (2012).
  2. Hezaveh, A. De Nicola, G. Milano, D. Roccatano. Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer Using Coarse-Grained Molecular Dynamics Simulations. J. Phys. Chem B. 116 (49), 14333–14345, (2012).
  3. J. Ruff, J. Marienhagen, R. Verma, D. Roccatano, H.-G. Genieser, P. Niemann, A.V. Shivange, U. Schwaneberg. dRTP and dPTP a complementary nucleotide couple for Sequence Saturation Mutagenesis (SeSaM). J. Mol. Cat. B: Enzymatic. 84, 40–47, (2012).
  4. Kuper, K.L. Tee, M. Wilmanns, D. Roccatano, U. Schwaneberg, T. S. Wong. The role of active site Phe87 in modulating the organic co-solvent tolerance of cytochrome P450 BM3 monooxygenase. Acta Crystallographica Section F. F68, 1013-1017, (2012).
  5. Karki, D. Gabel, D. Roccatano. A water solvation model of dodecaborate clusters. Inorg. Chem. 51 (9), 4894–4896 (2012).
  6. Verma, U. Schwaneberg, D. Roccatano. MAP2.03D: A Sequence/Structure Based Server for Protein Engineering. ACS Synthetic Biology. 1 (4), 139, (2012).
  7. Li, D. Roccatano, M. Lorenz, U. Schwaneberg. Directed evolution of subtilisin E into a chaophilic protease with high activity and stability in guanidinium chloride and SDS. ChemBioChem. 13(5), 691, (2012).
  8. Hezaveh, S. Samanta, G. Milano, D. Roccatano. Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents. J. Chem. Phys. 136, 124901 (2012).
  9. Samanta, S. Hezaveh, G. Milano, D. Roccatano. Diffusion of 1,2-Dimethoxyethane and 1,2-Dimethoxypropane through Phosphatidylcholine Bilayers: A Molecular Dynamics Study. J. Phys. Chem. B, 116 (17), pp 5141–5151 (2012). COVER PAGE.
  10. De Nicola, Y. Zhao, T. Kawakatsu, Roccatano and G. Milano. Validation of a Hybrid Particle-Field Coarse-Grained Model for DPPC in Non-Lamellar Phases. Theo. Chem. Act. 131, 1167 (2012).



  1. Hezaveh, S. Samanta, G. Milano, D. Roccatano. Structure and dynamics of 1,2-dimethoxyethane and 1,2-dimethoxypropane in aqueous and non-aqueous solutions: A molecular dynamics study. J. Chem. Phys., 135, 164501, (2011). COVER PAGE.
  2. De Nicola, Y. Zhao, T. Kawakatsu, D. Roccatano and G. Milano. Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids. JTCC, 7 (9), 2947–2962 (2011).
  3. V. Shivange, A. Serwe, A. Denning, D. Roccatano, S. Haefner, and U. Schwaneberg. Directed evolution of Yersinia mollaretii phytase. Applied Microbiology and Biotechnology. 95 (2), 405-418 (2011).
  4. Karki, A. Materny, D. Roccatano. Study of structural and dynamic properties of liquid phenyltrimethoxysilane. PCCP, 13, 11864-11871, (2011).
  5. Mundhada, J. Marienhagen, A. Scacioc, A. Schenk, D. Roccatano, U. Schwaneberg. SeSaM-Tv-II generates a protein sequence space which is unobtainable by epPCR. ChemBioChem (2011), 12 (10), 1595-1601, (2011).
  6. Martinez, U. Schwaneberg, D. Roccatano. Temperature Effects on Dynamics of Psychrophilic Protease S41 and its Thermostable Mutants in Solution. PEDS, 24, 533-544, (2011).
  7. Karki and D. Roccatano. Molecular Dynamics Simulation Study of Chlorophyll a in Different Organic Solvents. J. Chem. Theory Comput., 7 (4), 1131–1140, (2011).



  1. Zhu, R. Verma, D. Roccatano, Y. Ni, Z.-H. Sun, U. Schwaneberg. A Potential Antitumor Drug (Arginine Deiminase) Reengineered for Efficient Operation under Physiological Conditions. ChemBioChem 11 (5), 691–697, (2010). COVER PAGE.
  2. Zhu, K. L. Tee, D. Roccatano, B. Sonmez, Y. Ni, Z.-H. Sun, U. Schwaneberg. Directed evolution of a potential anti-tumor drug (arginine deiminase) for increased activity at physiological pH. ChemBioChem 11 (5), 691–697, (2010).
  3. V. Shivange, U. Schwaneberg, D. Roccatano. Conformational dynamics of active site loop in Escherichia coli phytase. Biopolymers. 93(11), 994–1002, (2010). COVER PAGE.


  1. Roccatano. Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions Current Peptide and Peptide Science. 9(4), 407-426, (2008).
  2. Onaca, P. Sarkar, D. Roccatano, T. Friedrich, B. Hauer, M. Grzelakowski, A. Gueven, M. Fioroni, U. Schwaneberg. Functionalized nano compartments (Synthosomes) with a reduction-triggered system.. Angew. Chem. Int. Ed., 47(37), 7029-7031, (2008).
  3. Nazor, S. Dannennmann, R. Obeg Adjei, Y. B. Fordjour, T. I. Ghampson, M. Blanusa, D. Roccatano, U. Schwaneberg. Laboratory evolution of P450 BM3 for mediated electron transfer yields and activity-improved & reductase-independent variant. Protein Eng. Des. Sel., 21(1), 29-35, (2008).
  4. L. Tee, D. Roccatano, S. Stolte, J. Arning, B. Jastorff, U. Schwaneberg. Ionic liquid as cosolvent for biotransformation catalyzed by P450 BM-3. Green Chem., 10, 117-123, (2008).
  5. S. Wong, D. Roccatano, K. L. Tee, A. Schrenk, M. Breuer, B. Hauer, U. Schwaneberg. Transversion-enriched sequence saturation mutagenesis (SeSaM-Tv+): A random mutagenesis method with consecutive nucleotide exchanges that complements the bias of error-prone PCR. Biotechnology Journal, 3(1), 74-82, (2008).


  1. S. Wong, Danilo Roccatano, U. Schwaneberg. Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain Biotechnology Journal, 2, 133-142 (2007).
  2. Kuper, T. S. Wong, D. Roccatano M. Wilmanns, U. Schwaneberg. Understanding the mechanism of organic co-solvent inactivation in heme monooxygenase P450 BM-3 JACS, 129, 5786-5787 (2007).
  3. Roccatano, A. Barthel, M. Zacharias. Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulations. Biopolymers, 85, 401-421, (2007).
  4. Roccatano, H. Sahoo, M. Zacharias, W. M. Nau. Temperature dependence of looping rates in a short peptide J. Chem. Phys B, 111, 2639-2646 (2007).
  5. Sahoo, D. Roccatano, A. Henning and W. M. Nau. A 10 Å spectroscopic ruler applied to short polyprolines. JACS, 129, 9762-9772 (2007).
  6. S. Wong, D. Roccatano, U. Schwaneberg. Steering directed protein evolution: strategies to manage combinatorial complexity of mutant libraries., Environmental Microbiology, 9(11), 2645-2659, (2007).
  7. S. Wong, D. Roccatano, U. Schwaneberg. Challenges of the genetic code for exploring sequence space in directed protein evolution. Biocatalysis and Biotransformation, 25(2-4), 229-241, (2007).


  1. S. Wong, D. Roccatano, M. Zacharias, U. Schwaneberg. A statistical analysis of current random mutagenesis methods for directed protein evolution. J. Mol. Biol., 355, 858-871 (2006). COVER PAGE.
  2. Schenk, T. S. Wong, D. Roccatano, B. Hauer, U. Schwaneberg. SeSaM (Sequence Saturation Mutagenesis): Eine Methode zur Sättigungsmutagenese eines Genes. Biospectrum, 3, 277-279(2006).
  3. Pal, G. Milano, D. Roccatano. Synthetic polymers and biomembranes. How do they interact? : Atomistic molecular dynamics simulation study of PEO in contact with DMPC lipid bilayer. J. Phys. Chem. B., 110, 26170-26179 (2006).
  4. Sahoo, D. Roccatano, M. Zacharias, W. M. Nau. Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 Å Domain. JACS, 128, 8118-8119 (2006).
  5. Roccatano, T. S. Wong, U. Schwaneberg, M. Zacharias. Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study., Biopolymers, 83, 467-476 (2006). COVER PAGE.


  1. D’Abramo, M. D’Alessandro, A. Di Nola, D. Roccatano, A. Amadei. Characterization of liquid behavior by means of local density fluctuations. J. Mol. Liq., 117, 17-21 (2005).
  2. Di Teodoro, M. Aschi, A. Amadei, D. Roccatano, F. Malatesta, L. Ottaviano. Conformational and electronic properties of a microperoxidase in aqueous solution: A computational study. ChemPhysChem, 6, 681-689 (2005).
  3. Pal, D. Roccatano, H. Weiss, H. Keller, F. Müller-Plathe. Molecular dynamics simulation of water near structured hydrophobic surfaces: interfacial energies. ChemPhysChem, 6, 1641-1649, (2005).
  4. Roccatano, T. S. Wong, U. Schwaneberg, M. Zacharias. Structural and dynamical properties of cytochrome P450 BM3 in pure water and in DMSO/water mixture. Biopolymers, 78, 259-267 (2005).
  5. Roccatano, G. Sbardella, M. Aschi, G. Amicosante, C. Bossa, A. Di Nola, F. Mazza. Dynamical aspect of TEM-1 β-lactamase. J. Comp. Aided Mol. Des., 19, 329-340 (2005).
  6. Roccatano, M. Fioroni, G. Colombo, M. Zacharias. Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study. Prot. Sci., 14, 2582-2589 (2005).
  7. S. Wong, N. Wu, D. Roccatano, M. Zacharias and U. Schwaneberg. Sensitive assay for laboratory evolution of hydroxylases toward aromatic and heterocyclic compounds. J. Biomol. Screen, 10, 246-252 (2005). COVER PAGE.


  1. Bossa, M. Anselmi, D. Roccatano, A. Amadei, B. Vallone, M. Brunori, A. Di Nola. Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin. Bioph. J., 86, 3855-3862 (2004).
  2. M. Coiro, A. Di Nola, M. A. Vanoni, M. Aschi, A. Coda, D. Roccatano. Molecular dynamics simulation of interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Prot. Sci., 13, 2979-2991 (2004).
  3. Daidone, F. Simona, D. Roccatano, R. A. Broglia, G. Tiana, G. Colombo, A. Di Nola. β-hairpin conformation of fibrillogenic peptides: structure and α/β transition revealed by molecular dynamics simulations. PROTEINS: Struct., Funct. and Bioinf., 57, 198-204 (2004).
  4. Daidone, D. Roccatano, S. Hayward. Investigating the accessibility of the closed and open domain conformations of citrate synthase using essential dynamics sampling. J. Mol. Biol., 339, 515-525 (2004).
  5. Roccatano, A. Di Nola, A. Amadei. A theoretical model for the folding/unfolding thermodynamics of single-domain proteins, based on the quasi-Gaussian entropy theory. J. Phys. Chem. B, 108, 5756-5762 (2004).
  6. Roccatano, W. M. Nau, M. Zacharias. Structural and dynamics properties of CAGQW peptide in water: a molecular dynamics simulation study using different force fields. J. Phys. Chem. B, 118, 18734-18742 (2004).


  1. Colombo, G. M. S. De Mori, D. Roccatano. Interplay between hydrophobic cluster and loop propensity in β-hairpin formation: a mechanistic study. Prot. Sci., 12, 538-550 (2003).
  2. Daidone, D. Roccatano, A. Amadei, A. Di Nola. Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Bioph. J., 85, 2865-2871 (2003).
  3. Fioroni, K. Burger, A. E. Mark, D. Roccatano. The influence of trifluoromethyl groups on the miscibility of fluorinated alcohols with water: a molecular dynamics simulation study of 1,1,1-trifluoro-propan-2-ol and its aqueous solution. J. Phys. Chem. B, 107, 4855-4861 (2003).
  4. Fioroni, K. Burger, D. Roccatano. Chiral discrimination in 1,1,1-trifluoro-propan-2-ol: a molecular dynamics study. J. Chem. Phys., 119, 1-8 (2003).
  5. F. Gerini, D. Roccatano, E. Baciocchi, A. Di Nola. Molecular dynamics simulation of lignin peroxidase. Bioph. J., 84, 3883-3893 (2003).
  6. Roccatano, I. Daidone, M. A. Ceruso, C. Bossa, A. Di Nola. Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Bioph. J., 84, 1876-1883 (2003).


  1. Aschi, D. Roccatano, A. Di Nola, C. Gallina, E. Gavuzzo, G. Pochetti, M. Pieper, H. Tschesche, F. Mazza. Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S and S’ subsites in the interaction with a phosphonate inhibitor. J. Comp. Aided Mol. Des., 16, 213-225 (2002).
  2. Colombo, D. Roccatano, A. E. Mark. Folding and stability of the three-stranded β-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins: Struct., Funct., Genet., 46, 380-392 (2002).
  3. Roccatano, G. Colombo, M. Fioroni, A. E. Mark. Mechanism by which 2,2,2-trifluorethanol/water mixtures stabilize secondary structure formation in peptides: A molecular dynamics study. Proc. Natl. Acad. Sci., 99, 12179-12184 (2002).


  1. Fioroni, K. Burger, A. E. Mark, D. Roccatano. Model of 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular dynamics simulations. J. Phys. Chem. B, 105, 10967-10975 (2001).
  2. Roccatano, A. E. Mark, S. Hayward. Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. J.Mol.Biol., 310, 1039-1053 (2001).
  3. Fioroni, K. Bruger, A. E. Mark, D. Roccatano. A new 2,2,2-trifluorethanol model for molecular dynamics simulations. J. Phys. Chem. B, 104, 12347-12354 (2000).


  1. Mangoni, D. Roccatano, A. Di Nola. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulations. Proteins: Struct., Funct., Genet., 35, 153-162 (1999).
  2. Roccatano, A. Amadei, A. Di Nola, H. J. C. Berendsen. A molecular dynamics study of the 41-56 β-hairpin from B1 domain of Protein G. Protein Sci., 8, 2130-2143 (1999).


  1. Roccatano, R. Bizzarri, G. Chillemi, N. Sanna, A. Di Nola. Development of a parallel molecular dynamics code on SIMD computers: An algorithm for the use of the pair list criterion. J. Comp. Chem., 19, 685-694 (1998).
  2. Roccatano, A. Amadei, M. E. F. Apol, A. Di Nola, 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).
  3. Roccatano, H. J. C. Berendsen, P. D’Angelo. Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended X-ray absorption fine structure spectroscopy: A case study of Sr in methanol solution. J. Chem. Phys., 108, 9487-9497 (1998).


  1. Amadei, D. Roccatano, M. E. F. Apol, H. J. C. Berendsen, A. Di Nola. Prediction of the liquid-vapor equilibrium pressure using the Quasi-Gaussian entropy theory. J. Chem. Phys., 105, 7022-7025 (1996).
  2. D’Angelo, N. V. Pavel, H. F. Nolting, D. Roccatano. Multielectron excitations at the L-edges of barium in aqueous solution. Phys. Rev. B, 54, 12129-12138 (1996).


  1. Di Nola, E. Gavuzzo, F. Mazza, G. Pochetti, D. Roccatano. Internal β-turn hydration: crystallographic evidence and molecular dynamics simulation. J. Phys. Chem., 99, 9625-9631 (1995).
  2. D’Angelo, A. Di Nola, A. Filipponi, N. V. Pavel, D. Roccatano. An extended X-ray adsorption fine structure study of aqueous solutions. J. Chem. Phys., 100, 985-994 (1994).
  3. Di Nola, D. Roccatano, H. J. C. Berendsen. Molecular dynamics simulation of the docking of substrates to proteins. Proteins: Struct., Funct., Genet., 19, 174-182 (1994).




  1. Verma, U. Schwaneberg, D. Roccatano. The Mutagenesis Assistant Program. Methods in Molecular Biology. E. Gillam, D. Ackerley and J. Copp Eds. (2014).
  2. Roccatano. Computer simulations study of biomolecules in non-aqueous solutions. Invited book chapter in Advances in Protein and Peptide Sciences. (2013), Vol. 1, Ed. Ben M. Dunn. Bentham Science Publisher.
  3. Roccatano. Theoretical Study of Nanostructured Biopolymers using Molecular Dynamics Simulations: a Practical Introduction. Book chapter in “Nanostructured Soft Matter: Experiment, Theory, Simulation and Perspectives”. Edited by A. V Zvelindovsky. Springer monograph (2007).



  1. Roccatano. Studio di sistemi molecolari complessi mediante l’uso di tecniche avanzate di Dinamica Molecolare. PhD Thesis (in Italian): Advisor: Prof. A. Di Nola, University of Rome “La Sapienza”, 1998.
  2. Roccatano. Determinazione della struttura dello Cu(II) aquatrisimidazolo solfato mediante dinamica molecolare e spettroscopia XANES. Tesi di Laurea, equivalent to a Master Thesis (in Italian). Advisors: Prof. A. Di Nola and Prof. M. Barteri, University of Rome “La Sapienza”, Italy, 1992.



  1. Bossa, M. A. Ceruso, R. Spezia, V. M. Coiro, D. Roccatano, A. Di Nola. Opening and closure of flaps in HIV-1 protease. A flip-flap mechanism suggested by molecular dynamics simulations. Ital. J. Biochem., 52, 91 (2002).
  2. Mazza, G. Amicosante, M. Aschi, D. Roccatano. Molecular dynamics simulations of the β-lactamase TEM-1. Ital. J. Biochem., 52, 109 (2002).
  3. Roccatano, A. Amadei, A. Di Nola, H. J. C Berendsen. Study of a β-hairpin forming peptide in aqueous solution using molecular dynamics simulations. Journal of Bioscience, 24/S1, 49 (1999).
  4. Mangoni, D. Roccatano, A. Di Nola. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulations. Journal of Bioscience, 24/S1, 69 (1999).



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