Marcela Madrid

Senior Computational Scientist


Marcela holds a Ph.D. in Physics from the Instituto Balseiro, Univ. Nacional de Cuyo and was a post-doctoral fellow at Stanford University. She is currently the Co-Investigator on the Anton 2 project at the PSC.

Research Interests

Ab initio and molecular dynamics simulations of bimolecular systems, high performance computing.

Selected publications

Ribone SR, Schenfeld EM, Madrid M, Pierini AB, Quevedo MA. Evaluation and synthesis of AZT prodrugs with optimized chemical stabilities: experimental and theoretical analyses. New J. Chem.. 2016; 40:2383; doi: 10.1039/C5NJ03002A.

Akli L, Alameda J, Gordon SI, Madrid M, Rivera L. XSEDE Training: Achieving Access and Inclusion. Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale. 2016; (Art. 55):DOI: 10.1145/2949550.2949586.

Ribone SR, Leen V, Madrid M, Dehaen W, Daelemans D, Pannecouque C, Briñón MC. Synthesis, biological evaluation and molecular modeling of 4,6-diarylpyrimidines and diarylbenzenes as novel non-nucleosides HIV-1 reverse transcriptase inhibitors. Eur J Med Chem. 2012 Dec;58:485-92. doi: 10.1016/j.ejmech.2012.10.036.

Wierzbinski E, de Leon A, Yin X, Balaeff A, Davis KL, Rapireddy S, Venkatramani R, Keinan S, Ly DH, Madrid M, Beratan DN, Achim C, Waldeck DH. Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes. J Am Chem Soc. 2012 Jun 6;134(22):9335-42. doi: 10.1021/ja301677z.

Ribone SR, Quevedo MA, Madrid M, Briñón MC. Rational approaches for the design of effective human immunodeficiency virus type 1 nonnucleoside reverse transcriptase inhibitors. J Chem Inf Model. 2011 Jan 24;51(1):130-8. doi: 10.1021/ci1001636.

He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C. The structure of a gamma-modified peptide nucleic acid duplex. Mol Biosyst. 2010 Sep;6(9):1619-29. doi: 10.1039/c002254c.

Yeh JI, Shivachev B, Rapireddy S, Crawford MJ, Gil RR, Du S, Madrid M, Ly DH. Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization. J Am Chem Soc. 2010 Aug 11;132(31):10717-27. doi: 10.1021/ja907225d.

Goicochea J, Madrid M, Amon C. Thermal Properties of Bulk Silicon Based on the Determination of Relaxation Times using Molecular Dynamics. Journal of heat transfer. 2010; 132(10):102401/1.

He W, Hatcher E, Balaeff A, Beratan DN, Gil RR, Madrid M, Achim C. Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations. J Am Chem Soc. 2008 Oct 8;130(40):13264-73. doi: 10.1021/ja800652h.

Zhou Z, Madrid M, Evanseck JD, Madura JD. Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase. J Am Chem Soc. 2005 Dec 14;127(49):17253-60. doi: 10.1021/ja053973d.

Dilek I, Madrid M, Singh R, Urrea CP, Armitage BA. Effect of PNA backbone modifications on cyanine dye binding to PNA-DNA duplexes investigated by optical spectroscopy and molecular dynamics simulations. J Am Chem Soc. 2005 Mar 16;127(10):3339-45. doi: 10.1021/ja045145a.

Zhou Z, Madrid M, Madura JD. Docking of non-nucleoside inhibitors: neotripterifordin and its derivatives to HIV-1 reverse transcriptase. Proteins. 2002 Dec 1;49(4):529-42. doi: 10.1002/prot.10233.

Kurnikov I, Tong G, Madrid M, Beratan D. Hole Size and Energetics in Double Helical DNA: Competition Between Quantum Delocalization and Solvation Localization. The journal of physical chemistry. B. 2002; 106:7.

Madrid M, Lukin JA, Madura JD, Ding J, Arnold E. Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding. Proteins. 2001 Nov 15;45(3):176-82. doi: 10.1002/prot.1137. 

Zubrzycki I, Xu Y, Madrid M, Tang P. Molecular Dynamics Simulations of a Fully Hydrated Dimyristoylphosphatidylcholine Membrane in Liquid-crystalline Phase. The Journal of chemical physics. 2000; 112:3437.

Kim HW, Shen TJ, Sun DP, Ho NT, Madrid M, Ho C. A novel low oxygen affinity recombinant hemoglobin (alpha96val–> Trp): switching quaternary structure without changing the ligation state. J Mol Biol. 1995 May 12;248(4):867-82. doi: 10.1006/jmbi.1995.0267.

Kim HW, Shen TJ, Sun DP, Ho NT, Madrid M, Tam MF, Zou M, Cottam PF, Ho C. Restoring allosterism with compensatory mutations in hemoglobin. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11547-51. doi: 10.1073/pnas.91.24.11547.


Poetry, literature, languages.