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

Poster for Liquid-Liquid and Liquid-Vapor Interfacial Tension and Preferential Adsorption for Water SLASH Oil-MixturesPoster for Vapor-liquid and Liquid-liquid Equilibria for a Langmuir Monolayer of Pentadecanoic Acid: A Monte Carlo StudyMonte Carlo Studies of Vapor-Liquid EquilibriaPoster for Probing Electrostatic Interaction between Amino Acids and Urea using ab initio CalculationsPoster for Molecular Dynamics Study of Helicobacter pylori Urease in 150 Millimolar Aqueous NH4ClPoster for Effect of 10.5M Aqueous Urea on Helicobacter pylori Urease: Molecular Dynamics StudyPoster for Molecular Dynamics Study of Helicobacter pylori UreasePoster for Probing Electrostatic Interactions between Amino Acids and Urea using ab initio CalculationsPoster for Improving the Binding of Nevirapine and Rilpivirine to HIV-1 Reverse Transcriptase through Computationally Derived Charge Optimization

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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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