Publications
Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences
Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences

MS Minkara, OA Erickson, RB Cole, JM Isaacs…

Science Advances, 2023

Elucidating the enhanced binding affinity of a double mutant SP-D with trimannose on the influenza A virus using molecular dynamics
Data for all: Tactile graphics that light up with picture-perfect resolution
Data for all: Tactile graphics that light up with picture-perfect resolution

Minkara, M.; Koone, J.C.; Dashnaw, C.M.; Alonzo, E.; Iglesias, M.A.;Patero, K.S.; Lopez, J.; Zhang, S.Y.; Zechmann, B.; Cook, N. …

Science Advances, 2022

Nonane and Hexanol Adsorption in the Lamellar Phase of a Nonionic Surfactant: Molecular Simulations and Comparison to Ideal Adsorbed Solution Theory
Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences
Virtually the same? Evaluating the effectiveness of remote undergraduate research experiences

MS Minkara, OA Erickson, RB Cole, JM Isaacs…

bioRxiv, 2022

'How do we do this at a distance?!' A descriptive study of remote undergraduate research programs during COVID-19
“How do we do this at a distance?!” A descriptive study of remote undergraduate research programs during COVID-19

OA Erickson, RB Cole, JM Isaacs, S Alvarez-Clare…

CBE Life Sciences Education, 2022

The Influence of a Blind Professor in a Bioengineering Course
The Influence of a Blind Professor in a Bioengineering Course

Greenvall, B.R., Tiano, A.L., Chandani, A. et al. The Influence of a Blind Professor in a Bioengineering Course.

Biomed Eng Education 1, 245–258 (2021).

Partial Molar Properties From Molecular Simulation Using Multiple Linear Regression
Partial Molar Properties From Molecular Simulation Using Multiple Linear Regression

Josephson, T. R.; Singh, R.; Minkara, M. S.; Fetisov, E. O.; Siepmann, J. I. Partial molar properties from molecular simulation using multiple linear regression

Mol. Phys. 2019, 117, 3589.

A New Equation of State for Homo-Polymers in Dissipative Particle Dynamics
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. 2019, 150, 124104.

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

Monte Carlo Simulations Probing the Liquid/Vapour Interface of Water/Hexane Mixtures: Adsorption Thermodynamics, Hydrophobic Effect, and Structural Analysis
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.

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

J.Chem. Educ. 2015, 92, 1280.

Reduction of Urease Activity by Interaction With the Flap Covering Active Site
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.

J. Chem. Inf. Model. 2015, 55, 354.

Molecular Dynamics Study of Helicobacter Pylori Urease
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.

J. Chem. Theory Comput. 2014, 10, 1852.

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Analysis of Fast Boundary-Integral Approximations for Modeling Electrostatic Contributions of Molecular Binding
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.

Mol. Based Math. Biol. 2013, 1, 124.

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

Proteins 2012, 80, 573.

Analyzing Electrostatic Determinants of Affinity and Promiscuity in the HIV-1 Reverse Transcriptase System Using Charge Optimization
Current
Postdoctoral
Graduate
Undergraduate

Minkara, M. S.; Design of a Novel Inhibitor for Helicobacter pylori Urease.

Thesis. University of Florida, 2015. Gainesville: 2015. UFDC. Web.

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.