Wu, Z.; Gogonea, V.; Lee, X.; Wagner, M. A.; Li, X.-M.; Huang, Y.; Undurti, A.; May, R. P.; Haertlein, M.; Moulin, M.; Gutsche, I.;  Zaccai, G.; DiDonato, J.; Hazen, S. L. The Double Super Helix model of high density lipoprotein. J. Biol. Chem. 284, 36605-19 (2009).

D. Dogaru, S. Motiu, and V. Gogonea, Inactivation of [FeFe]-Hydrogenase H-cluster by O2. Thermodynamics and frontier molecular orbitals analysis. Int. J. Quant. Chem., 109, 876-89 (2009).

P. K. Biswas and V. Gogonea, A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals. J. Chem. Phys. 129, 154108-13 (2008).

Z. Wu, M. Wagner, L. Zheng, S. Liang, J. Parks, G. Vince, J. Smith, J. Shy, V. Gogonea, S. L. Hazen, The refined structure of nascent HDL reveals a key functional domain for particle maturation and dysfunction. Nat. Struct. Mol. Biol., 14, 861-868 (2007).

S. Motiu, D. Dogaru, and V. Gogonea, Reactivation Pathway of the Hydrogenase H-cluster: Density Functional Theory Study. Int. J. Quant. Chem. Soc. 107(5) 1248-1252 (2007).

A. Ababou , A. van der Vaart , V. Gogonea and K. M. Merz Jr., Interaction Energy Decomposition in Protein-Protein Association: A Quantum Mechanical Study of Barnase-Barstar Complex, Biophys. Chem. 125, 221-236 (2007).

V. Gogonea, J. M. Shy, II, P. K. Biswas, The Electronic Structure, Ionization Potential and Electron Affinity of the Enzyme Cofactor (6R)-5,6,7,8-Tetrahydrobiopterin in Gas Phase, Solution and Protein Environment. J. Phys. Chem. B 110(45): 22861-22871 (2006).

P. K. Biswas, J. Niu, T. Frederico, and V. Gogonea, Numerical simulation and graphical analysis of in-vitro benign tumor growth. Application of single-particle state bosonic matter equation with length scaling. Journal of Molecular Modeling, 12, 641-648 (2006).

P. K. Biswas and V. Gogonea, A regularized and renormalized electrostatic coupling Hamiltonain for hybrid quantum mechanical - molecular mechanical calculations. J. Chem. Phys. 123, 164114 (2005).

T. Orban, M. Kalafatis and V. Gogonea, "Completed Three-Dimensional Model of Human Coagulation Factor Va. Molecular. Dynamics Simulations and Structural Analysis" Biochemistry, 44(39) 13082-13090 (2005).

V. Gogonea, "Potential Energy Surface of the Reaction of Imidazole with Peroxynitrite: A Density Functional Theory Study" Int. J. Quant. Chem., 104, 342-353 (2005).

V. Gogonea, "The Solvent Boundary Potential: A New Approach for Computer Simulation of Large Systems" Inter. Elec. J. Mol. Design, 2, 179-194 (2003).

V. Gogonea, "The QM/MM Method. On overview" Inter. Elec. J. Mol. Design, 1, 173-184 (2002).