Computational

Department of Chemical and Petroleum Engineering, University of Pittsburgh
Ph.D., Chemical Engineering, Cornell University, 1992
Summary:

The Johnson group tackles fundamental problems over a wide range of subject areas using state-of-the-art atomistic modeling methods. Current projects include CO2 capture through the following methods:

  • Selective adsorption in metal organic frameworks (MOFs).
  • Catalytic nanoparticles on amorphous supports.
  • Multiscale modeling proton-exchange membrane (PEM) based fuel cells.  
  • Hydrogen storage in metal hydrides.
  • Absorption into ionic liquids, including ionic liquids that react chemically with CO2.
  • Physical absorption of CO2 into liquid sorbents.
  • Chemical capture involving carbamate forming amines.
  • Solid-state reactions involving carbonates and bicarbonates.

Tools we use in our studies include Kohn-Sham density functional theory, first principles quantum mechanics methods, classical equilibrium and non-equilibrium molecular dynamics, and Monte Carlo simulation techniques.

Most Cited Publications
  1. "The Lennard-Jones equation of state revisited," J. Karl Johnson, John A. Zollweg & Keith E. Gubbins, Molecular Physics 78, 591 (1993)
  2. "Microporous Metal Organic Materials:  Promising Candidates as Sorbents for Hydrogen Storage," Long Pan, Michelle B. Sander, Xiaoying Huang, Jing Li, Milton Smith, Edward Bittner, Bradley Bockrath, and J. Karl JohnsonJ. Am. Chem. Soc. 126, 1308 (2004)
  3. "Rapid Transport of Gases in Carbon Nanotubes," Anastasios I. Skoulidas, David M. Ackerman, J. Karl Johnson, and David S. Sholl, Phys. Rev. Lett. 89, 185901 (2002)
  4. "Molecular simulation of hydrogen adsorption in single-walled carbon nanotubes and idealized carbon slit pores," Qinyu Wang and J. Karl JohnsonJ. Chem. Phys. 110, 577 (1999)
  5. "Adsorption of Gases in Metal Organic Materials:  Comparison of Simulations and Experiments," Giovanni Garberoglio, Anastasios I. Skoulidas, and J. Karl JohnsonJ. Phys. Chem. B 109, 13094 (2005)
Recent Publications
  1. "Toward Understanding the Kinetics of CO2 Capture on Sodium Carbonate."  Tianyi Cai, J Karl Johnson, Ye Wu, Xiaoping Chen.  ACS applied materials and interfaces (2019)
  2. "Graphamine: Amine-Functionalized Graphane for Intrinsic Anhydrous Proton Conduction." A Bagusetty, J Livingston, and JK JohnsonJournal of Phys. Chem. C 123.3. (2018)
  3. "Energy Efficient Formaldehyde Synthesis by Direct Hydrogenation of Carbon Monoxide in Functionalized Metal-Organic Frameworks."  Lin Li, Sen Zhang, Johathan P Ruffley, and J Karl JohnsonACS Sustainable Chemistry and Engineering 7.2. (2018)
  4. "TiH2 as a Dynamic Additive for Improving the De/Rehydrogenation Properties of MgH2: A Combined Experimental and Theoretical Mechanistic Investigation," Ashish Bhatnagar, J. Karl Johnson, M. A. Shaz, and O. N. Srivastava, J. Phys. Chem. C 122, 21248 (2018).
  5. "The effect of topology in Lewis pair functionalized metal organic frameworks on CO2 adsorption and hydrogenation,"Jingyun Ye, Lin Li and J. Karl Johnson, Catal. Sci. Technol.(2018)
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Personal | Department
Department of Chemistry and Biochemistry, Duquesne University
Ph.D., Physical Chemistry, Purdue University, 1985
Summary:

Research in the laboratory consists of the development and application of computational methods in collaboration with experimental research laboratories. Our research interests fall into the areas of computational biophysics and computational material sciences.

Some our current research projects involve, studying the transport mechanism of neurotransmitter sodium symporter proteins, where we are simulating in vivo conditions using molecular dynamics simulations to observe changes in conformation of proteins upon substrate transport. We are researching computer-aided drug design by applying free energy calculations to elucidate intermolecular interactions of various substrates and inhibitors with monoamine transporters. We are investigating conformational properties of polyglutamine peptide systems by applying molecular dynamics, using the metadynmics sampling algorithm, to explore the conformational free energy landscape of polyglutamine peptides in solvent. We are involved in the electronic structure calculations of extended solids, where we are applying computational methods to investigate and predict physicochemical properties of materials. We are also studying smart materials such as hydrogels of PNIPAM.

In the past, we have studied antifreeze proteins at ice/water interfaces and interaction of N-acetylglucosamine with chitnase. The folding of small peptides in salt solution, and structure, function, and dynamics of monoamine transporters have been studied as well.

Dr. Madura is also one of the primary authors to the Brownian dynamics program UHBD, which is used to calculate the diffusion-controlled rate-constants for biomolecular encounters.

Most Cited Publications
  1. "Comparison of simple potential functions for simulating liquid water," William L. Jorgensen, Jayaraman Chandrasekhar, and Jeffry D. Madura, Roger W. Impey and Michael L. Klein, J. Chem. Phys. 79, 926 (1983)
  2. "Optimized intermolecular potential functions for liquid hydrocarbons," William L. Jorgensen, Jeffry D. Madura, Carol J. Swenson, J. Am. Chem. Soc. 106, 6638 (1984)
  3. "Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew," Hans W. Horn, William C. Swope, and Jed W. Pitera, Jeffry D. Madura and Thomas, J. Dick Greg, L. Hura, Teresa Head-Gordon, J. Chem. Phys.120, 9665 (2004)
  4. "Temperature and size dependence for Monte Carlo simulations of TIP4P water," William L. Jorgensen & Jeffry D. MaduraMolecular Physics 56, 1381 (1985)
  5. "Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program," Jeffry D. Madura, James M. Briggs, Rebecca C. Wade, Malcolm E. Davis, Brock A. Luty, Andrew Ilin, Jan Antosiewicz, Michael K. Gilson, Babak Bagheri, L.Ridgway Scott, J.Andrew McCammon, Computer Physics Communications 91, 57 (1995)
Recent Publications
  1. "Polyglutamine Fibrils: New Insights into Antiparallel β-sheet Conformational Preference and Side Chain Structure," David Punihaole, Riley J Workman, Zhenmin Hong, Jeffry D Madura, Sanford A Asher, J. Phys. Chem. B 120, 3012 (2016)
  2. "2-Substituted 3β-Aryltropane Cocaine Analogs Produce Atypical DAT Inhibitor Effects Without Inducing Inward-Facing DAT Conformations," Weimin C. Hong, Theresa A. Kopajtic, Lifen Xu, Stacey A. Lomenzo, Bernandie Jean, Jeffry D. Madura, Christopher K. Surratt, Mark L. Trudell and Jonathan L. Katz, J Pharmacol Exp Ther 356, 624 (2016)
  3. "Human alpha1 Glycine Receptor Allostery as Identified by State-Dependent Crosslinking Studies," Michael Cascio, Rathna J Veeramachaneni, Jeffry MaduraBiophysical Journal 110, 201a (2016)
  4. "Crosslinking/MS Studies of Cholesterol Interactions with Human alpha1 Glycine Receptor," Nicholas Ferraro, Emily Benner, Jeffry Madura, Michael Cascio, Biophysical Journal 110, 355a (2016)
  5. "Computational Investigation of the Transport Mechanism of Neurotransmitter Sodium Symporters using a Physiological Ion Gradient," Emily M Benner, Jeffry D MaduraBiophysical Journal 3, 626a (2016)

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