Document Type : Original Article
Authors
1 PhD student at Sharif University of Technology
2 Department of Physics, Sharif University of Technology
Abstract
On an atomistic scale, free energy calculations are important for our understanding of biological processes, which provides an insight to grasp the various mechanisms. Over the years, many computational methods have been developed to calculate free energy differences such as geometrical (e.g. umbrella sampling) and alchemical methods. In this work, we present alchemical-free energy methods, thermodynamic integration (TI) and free energy perturbation (FEP), to investigate polarization effect of paclitaxel drug. Then, we have compared our simulation studies using TI, FEP, and Hamiltonian replica exchange FEP from the perspective of computational cost and accuracy.
Keywords
- Free energy difference "
- " Molecular dynamics simulation "
- " Free energy perturbation "
- " Thermodynamic integration "
- " Solvation free energy
Main Subjects
- D A McQuarrie and J D Simon, “Physical chemistry: a molecular approach” University science books Sausalito CA )1997.(
- S Park, et al., The Journal of Chemical Physics 119 (2003) 3559.
- C Jarzynski, Physical Review Letters 78 )1997( 2690.
- J Kästner, Wiley Interdisciplinary Reviews: Computational Molecular Science 1 (2011( 932.
- G M Torrie and J P Valleau, Journal of Computational Physics 23 )1977( 187.
- P Virnau and M Müller, The Journal of Chemical Physics 120 )2004( 10925.
- W L Jorgensen and L L Thomas, Journal of Chemical Theory and Computation 4 (2008) 869.
- T Straatsma and H Berendsen, The Journal of Chemical Physics 89 )1988( 5876.
- J Wereszczynski and J A McCammon, “Computational Drug Discovery and Design “ Springer (2012(.
- A Groso, et al., Particle and Fibre Toxicology 7 (2010) 1.
- B Fadeel, et al., Nature Nanotechnology 13) 2018( 537.
- K Thomas, et al., Toxicological Sciences 92 )2006( 23.
- K Schirmer, R Behra, and L Sigg, “Ecotoxicological aspects of nanomaterials in the aquatic environment” Pan Stanford Publishing (2013(.
- S Lin, et al., Advanced Material 30, 17 (2018) 1705691.
- J Lee, S Mahendra, and P J Alvarez, ACS Nano 4 )2010( 3580.
- C Chipot, P A Kollman, and D A Pearlman, Journal of Computational Chemistry 17)1996 (1112.
- J Kästner, et al., Journal of Chemical Theory and Computation 2 )2006( 452.
- W Jiang and B Roux, Journal of Chemical Theory and Computation 6 )2010(
- N Lu, J K Singh, and D A Kofke, The Journal of Chemical Physics 118 (2003( 2977.
- N Lu, D A Kofke, and T B Woolf, Journal of Computational Chemistry 25 )2004 (28.
- F Deflorian, et al., Journal of Chemical Information and Modeling 60, 11 (2020) 5563.
- M Zacharias, et al., Biochemistry 32, 29 (1993) 7428.
- Frisch, M. et al. “Gaussian 09, Revision d. 01” Gaussian )2009(.
- B Mennucci, et al., The Journal of Physical Chemistry A 106 )2002( 6102.
- D Van Der Spoel, et al., Journal of Computational Chemistry 26 )2005( 1701.
- S Miyamoto and P A Kollman, Journal of Computational Chemistry 13 )1992( 952.
- B Hess, et al., Journal of Computational Chemistry 18 )1997( 1463.
- S Jo, et al., Biophysical Journal 97 )2009( 50.
- T Darden, D York, and L Pedersen, The Journal of Chemical Physics 98 (1993) 10089.
- U Essmann,. et al., The Journal of Chemical Physics 103 )1995 (8577.