On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

1. D’Hollander, E. H., J. J. Dongarra, I. Foster, L. Grandinetti, G. R. Jouber t. Transition of HpcTowards Exascale Computing (Advances in Parallel COmputing), IOS Press, 2013, p. 232.Search in Google Scholar

2. Alder, B., T. Wainwright. Studies in Molecular Dynamics. I. General Method. - J. Chem. Phys., Vol. 31, 1959, No 2, 459.10.1063/1.1730376Search in Google Scholar

3. Tuckerman, M., G. Martyn a. Understanding Modern Molecular Dynamics Methods: Techniques and Applications. - J. Phys. Chem., Vol. 104, 2000, No 2, pp. 159-178. 10.1021/jp992433ySearch in Google Scholar

4. Poghosyan, A. H., L. H. Arsenyan, H. V. Astsatry a n. Dynamic Features of Complex Systems: A Molecular Simulation Study. - Modeling and Optimization in Science and Technologies. Vol. 2, 2014, pp. 117-121.10.1007/978-3-319-01520-0_14Search in Google Scholar

5. Poghosyan, A. H., H. V. Astsatryan, A. A. Shahinya n. Parallel Peculiarities and Performance of GROMACS Package on HPC Platforms. - International Journal of Scientific and Engineering Research, Vol. 4, 2013, No 12, pp. 1755-1761.Search in Google Scholar

6. Karapetian, A. T., Z. A. Grigoryan, Y. S. Mamasakhlisov, M. V. Minasyants, P. O. Vardevan y a n. Theoretical Treatment of Helix-Coil Transition of Complexes DNA with Two Different Ligands Having Different Binding Parameters. - Journal of Biomolecular Structure and Dynamics, Vol. 34, 2016, No 1, pp. 201-205.10.1080/07391102.2015.1010584Search in Google Scholar

7. Otzen, D. E. Protein-Surfactant Interactions: A Tale of Many States. - Biochim. Biophys. Acta, Vol. 1814, 2011, No 5, pp. 562-591.Search in Google Scholar

8. Jones, M. N. A Theoretical Approach to the Binding of Amphipathic Molecules to Globular Proteins. - Biochem. J., Vol. 151, 1975, No 1, pp. 109-114.10.1042/bj1510109Search in Google Scholar

9. Ivnitski, D., I. AbdelHamid, P. Atanasov, E. Wilkins. Biosensors for Detection of Pathogenic Bacteria. - Biosensors and Bioelectronics, Vol. 14, 1999, No 7, pp. 599-624.10.1016/S0956-5663(99)00039-1Search in Google Scholar

10. Gao, Y., L. K. Wolf, R. M. Georgiad i s. Secondary Structure Effects on DNA Hybridization Kinetics: A Solution Versus Surface Comparison. - Nucleic Acids Res., Vol. 34, 2006, No 11, pp. 3370-3377.10.1093/nar/gkl422148888416822858Search in Google Scholar

11. Morrison, L. E., L. M. Stols. Sensitive Fluorescence-Basedthermodynamic and Kinetic Measurements of DNA Hybridization in Solution. - Biochemistry, Vol. 32, 1993, No 12, pp. 3095-3104.10.1021/bi00063a0228457571Open DOISearch in Google Scholar

12. Azam, M. S., J. M. Gibbs- Davis. Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy. - Analyt. Chem., Vol. 85, 2013, No 17, pp. 8031-8038.10.1021/ac401009u23927789Search in Google Scholar