Publications


Academic PublicationsPostersTheses



Academic Publications


Probing Additive Loading in the Lamellar Phase of a Nonionic Surfactant: Gibbs Ensemble Monte Carlo Simulations using the SDK Force Field

Minkara, M. S.; Lindsey, R. K.; Hembree, R. H.; Venteicher, C. L.; Jamadagni, S. N.; Eike, D. M.; Ghobadi, A. F.; Koenig, P. H.; Siepmann, J. I. Probing Additive Loading in the Lamellar Phase of a Nonionic Surfactant: Gibbs Ensemble Monte Carlo Simulations using the SDK Force Field. Langmuir 2018, 34 (28), 8245–8254.


Monte Carlo Simulations Probing the Liquid/Vapor Interface of Water/Hexane Mixtures

Minkara, M. S.; Josephson, T.; Venteicher, C. L.; Chen, J. L.; Stein, D. J.; Peters, C. J.; Siepmann, J. I., Monte Carlo Simulations Probing the Liquid/Vapor Interface of Water/Hexane Mixtures. Manuscript accepted for publication in Molecular Physics


Gibbs Ensemble Monte Carlo Simulations Probing the Miscibility Gap in Water/Hydrogen Mixtures at High Temperatures and Pressures

Bunner, C. E.; Minkara, M. S.; Siepmann, J. I., Gibbs Ensemble Monte Carlo Simulations Probing the Miscibility Gap in Water/Hydrogen Mixtures at High Temperatures and Pressures. In preparation


A New DPD Equation of State for Homo-polymers

Minkara, M. S.; Hembree, R. H.; Jamadagni, S. N.; GhobadiFomeshi, A. F.; Eike, D. M.; Koenig P. H.; Siepmann J. I., A New DPD Equation of State for Homo-polymers. In preparation


Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study

Minkara, M. S.; Weaver, M. N.; Merz, K. M. Jr. Effect of 10.5 M Aqueous Urea on Helicobacter pylori Urease: A Molecular Dynamics Study. Biochemistry 2015, 54 (26), 4121-4130.


Implementation of Protocols to Enable Doctoral Training in Physical and Computational Chemistry of a Blind Graduate Student

Minkara, M. S.; Weaver, M. N.; Gorske, J.; Bowers, C. R.; Merz, K. M. Jr. Implementation of Protocols to Enable Doctoral Training in Physical and Computational Chemistry of a Blind Graduate Student. Chem. Educ. 2015, 92 (8), 1280–1283.


Reduction of Urease Activity by Interaction with the Flap Covering Active Site

Macomber, L.; Minkara, M. S.; Hausinger, R.P.; Merz, K. M. Jr. Reduction of Urease Activity by Interaction with the Flap Covering Active Site. Chem. Inf. Model. 2015, 55, 354-361.


Molecular Dynamics Study of Helicobacter pylori Urease

Minkara, M. S.; Ucisik, M. N.; Weaver, M. N.; Merz, K. M. Jr. Molecular Dynamics Study of Helicobacter pylori Urease. Chem. Theory Comput. 2014, 10, 1852-1862.


Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

Kreienkamp, A. B.; Liu, L. Y.; Minkara, M. S.; Knepley, M. G.; Bardhan, J. P.; Radhakrishnan, M. L.  Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding. Molecular Based Mathematical Biology 2013, 1, 124-150.


Multiple Drugs and Multiple Targets: An Analysis of the Electrostatic Determinants of Binding Between Non-nucleoside HIV-1 Reverse Transcriptase (RT) Inhibitors and Variants of HIV-1 RT

Minkara, M. S.; Davis, P. H.; Radhakrishnan; M. L. Multiple Drugs and Multiple Targets: An Analysis of the Electrostatic Determinants of Binding Between Non-nucleoside HIV-1 Reverse Transcriptase (RT) Inhibitors and Variants of HIV-1 RT. Proteins 2012, 80, 573-590.

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Posters

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Theses

Design of a Novel Inhibitor for Helicobacter pylori Urease

Minkara, M. S.; Design of a Novel Inhibitor for Helicobacter pylori Urease. Thesis. University of Florida, 2015. Gainesville: 2015. UFDC. Web.

Analyzing the Binding of Nevirapine and Rilpivirine to HIV-1 Reverse Transcriptase through Computationally Derived Charge Optimization

Minkara, M. S.; Analyzing the Binding of Nevirapine and Rilpivirine to HIV-1 Reverse Transcriptase through Computationally Derived Charge Optimization. Thesis. Wellesley College, 2009. Wellesley: 2009. WCDC. Web.

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