Publications
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 EQUATION OF STATE FOR HOMO-POLYMERS IN DISSIPATIVE PARTICLE DYNAMICS

Minkara, M. S.; Hembree, R. H.; Jamadagni, S. N.; Ghobadi, A. F.; Eike, D. M.; Siepmann, J. I., A New Equation of State for Homo-polymers in Dissipative Particle Dynamics. J. Chem. Phys. Accepted for publication

MONTE CARLO SIMULATIONS PROBING THE LIQUID/VAPOUR INTERFACE OF WATER/HEXANE MIXTURES: ADSORPTION THERMODYNAMICS, HYDROPHOBIC EFFECT, AND STRUCTURAL ANALYSIS

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: Adsorption Thermodynamics, Hydrophobic Effect, and Structural Analysis. Mol. Phys. 2018, 116, 3283.

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, 8245.

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, 4121.

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, 1280.

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.

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.

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..

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.

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.