Students working with the cluster

Publications

Supercomputing Research at UW-Eau Claire

UWEC has maintained its commitment to high-impact learning practices with an emphasis on undergraduate research. Students (highlighted) and their mentor collaborators are continuously exploring newer problems, studying together, and publishing their findings.

To see how supercomputing has continuously pushed forward research, check out all of the following publications since 2012 that have used our campus resources:

2024

  • Conformational fluidity of intrinsically disordered proteins in crowded environment: a molecular dynamics simulation study

    Shult, C., Gunderson, K., Coffey, S. J., McNally, B., Brandt, M., Smith, L., Steczynski, J., Olerich, E. R., Schroeder, S. E., Severson, N. J., Hati, S., & Bhattacharyay, S. (2024). Conformational fluidity of intrinsically disordered proteins in crowded environment: a molecular dynamics simulation study. In Journal of Biomolecular Structure and Dynamics (pp. 1–13). Informa UK Limited. https://doi.org/10.1080/07391102.2024.2404531

  • High-performance computing in undergraduate education at primarily undergraduate institutions in Wisconsin: Progress, challenges, and opportunities

    Hebert, J., Hratisch, R., Gomes, R., Kunkel, W., Marshall, D., Ghosh, A., Doss, I., Ma, Y., Stedman, D., Stinson, B., Varghese, A., Mohr, M., Rozario, P., & Bhattacharyya, S. (2024). High-performance computing in undergraduate education at primarily undergraduate institutions in Wisconsin: Progress, challenges, and opportunities. In Education and Information Technologies. Springer Science and Business Media LLC. https://doi.org/10.1007/s10639-024-12582-6 

  • Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects

    Liebau, J., Laatsch, B. F., Rusnak, J., Gunderson, K., Finke, B., Bargender, K., Narkiewicz-Jodko, A., Weeks, K., Williams, M. T., Shulgina, I., Musier-Forsyth, K., Bhattacharyya, S., & Hati, S. (2024). Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase Via Crowding and Confinement Effects. In Biochemistry (Vol. 63, Issue 13, pp. 1621–1635). American Chemical Society (ACS). https://doi.org/10.1021/acs.biochem.3c00719

2023

  • Insights into the Mechanism of Tryptophan Fluorescence Quenching due to Synthetic Crowding Agents: A Combined Experimental and Computational Study

    Fossum, C. J., Johnson, B. O. V., Golde, S. T., Kielman, A. J., Finke, B., Smith, M. A., Lowater, H. R., Laatsch, B. F., Bhattacharyya, S., & Hati, S. (2023). Insights into the Mechanism of Tryptophan Fluorescence Quenching due to Synthetic Crowding Agents: A Combined Experimental and Computational Study. ACS Omega. American Chemical Society (ACS). https://doi.org/10.1021/acsomega.3c06006 

  • Inter-institutional Resource Sharing in Undergraduate HPC Education: Interviews with University Administrators

    Ghosh, A., Kunkel, W., Varghese, A., Ma, Y., Gomes, R., Bhattacharyya, S., Mohr, M., Doss, I., & Hebert, J. (2023). Inter-institutional Resource Sharing in Undergraduate HPC Education. In Proceedings of the 54th ACM Technical Symposium on Computer Science Education V. 1 (pp. 848–853). SIGCSE 2023: The 54th ACM Technical Symposium on Computer Science Education. ACM. https://doi.org/10.1145/3545945.3569784 

  • Jet-Cooled Phosphorescence Excitation Spectrum of the T1(n,π*) ← S0 Transition of 4H-Pyran-4-one

    Parsons, S. W., Hucek, D. G., Mishra, P., Plusquellic, D. F., Zwier, T. S., & Drucker, S. (2023). Jet-Cooled Phosphorescence Excitation Spectrum of the T1(n,π*) ← S0 Transition of 4H-Pyran-4-one. The Journal of Physical Chemistry A. American Chemical Society (ACS). https://doi.org/10.1021/acs.jpca.3c01059

  • Polyethylene Glycol 20k. Does It Fluoresce?

    Laatsch, B. F., Brandt, M., Finke, B., Fossum, C. J., Wackett, M. J., Lowater, H. R., Narkiewicz-Jodko, A., Le, C. N., Yang, T., Glogowski, E. M., Bailey-Hartsel, S. C., Bhattacharyya, S., & Hati, S. (2023). Polyethylene Glycol 20k. Does It Fluoresce? ACS Omega (Vol. 8, Issue 15, pp. 14208–14218). American Chemical Society (ACS). https://doi.org/10.1021/acsomega.3c01124

2022

  • Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations

    Wozney, A. J., Smith, M. A., Abdrabbo, M., Birch, C. M., Cicigoi, K. A., Dolan, C. C., Gerzema, A. E. L., Hansen, A., Henseler, E. J., LaBerge, B., Leavens, C. M., Le, C. N., Lindquist, A. C., Ludwig, R. K., O’Reilly, M. G., Reynolds, J. H., Sherman, B. A., Sillman, H. W., Smith, M. A., Snortheim, M. J., Svaren, L. M., Vanderpas, E. C., Voon, A., Wackett, M. J., Weiss, M. M., Hati, S., & Bhattacharyya, S. (2022). Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations. The Protein Journal. https://doi.org/10.1007/s10930-022-10065-6 

  • Pre-Existing Oxidative Stress Creates a Docking-Ready Conformation of the SARS-CoV-2 Receptor-Binding Domain

    Fossum, C. J., Laatsch, B. F., Lowater, H. R., Narkiewicz-Jodko, A. W., Lonzarich, L., Hati, S., & Bhattacharyya, S. (2022). Pre-Existing Oxidative Stress Creates a Docking-Ready Conformation of the SARS-CoV-2 Receptor-Binding Domain. ACS Bio & Med Chem Au, 2(1), 84–93. https://doi.org/10.1021/acsbiomedchemau.1c00040 (Featured On Cover)

2021

  • Structural and energetic properties of OC–BX3 complexes: unrealized potential for bond-stretch isomerism

    Munos, J. A.; Lowney, D. T.; and Phillips J. A.Structural and energetic properties of OC–BX3 complexes: unrealized potential for bond-stretch isomerism, Phys. Chem. Chem. Phys., 2021, 23, 14678-14686 (DOI: https://doi.org/10.1039/D1CP02230J).

2020

  • Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase

    Hu,Q. H.; Williams, M.; Shulgina, I.; Fossum, C.; Weeks, K.; Adams, L.; Reinhardt, C. R.; Musier-Forsyth, K.; Hati, S.; and Bhattacharyya, S. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase ACS Catal., 2020, 10, 10229-10242 (DOI: https://doi.org/10.1021/acscatal.0c02381).

  • Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase

    Zajac, J.; Anderson, H.; Adams, L.; Wangmo, D.; Suhail, S.; Almen, A.; Berns, L.; Coerber, B.; Dawson, L.; Hunger, A.; Jehn, J.; Johnson, J.; Plack, N.; Strasser, S.; Williams, M.; Bhattacharyya, S; and Hati, S. Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase Protein J., 2020, 39, 542-553. (DOI: https://doi.org/10.1007/s10930-020-09910-3).  

  • Impact of Thiol–Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor

    Hati, S. and Bhattacharyya, S. Impact of Thiol–Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor, ACS Omega, 2020, 6, 16292–16298 (DOI: 10.1021/acsomega.0c02125).

  • Structural and energetic properties of RMX3-NH3 complexes

    Phillips, J. A.; Ley, A. R.; Treacy, P. W.; Wahl, B. W.; Zehner, B. C.;  Donald, K. J.; Gillespie, S. Structural and energetic properties of RMX3‐NH3 complexes Int. J. Quan. Chem. 2020, 120, e26383. (DOI: https://doi.org/10.1002/qua.26383).

2019

  • Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase

    Adams, L. A.; Andrews, R. J.; Hu, Q. H.; Schmit, H. L.; Hati, S.; Bhattacharyya, S., Crowder-induced Conformational Ensemble Shift in Escherichia Coli Prolyl-tRNA Synthetase. Biophys. J., 2019, 17, 1269-1284 (DOI:10.1016/j.bpj.2019.08.033).

  • Modeling Reaction Energies and Exploring Noble Gas Chemistry in the Physical Chemistry Laboratory

    Phillips, J. A., Modeling Reaction Energies and Exploring Noble Gas Chemistry in the Physical Chemistry Laboratory, in ACS Monograph Series “Using Computations to Teach Chemical Concepts”, 2019, vol 1312, Chapter 4, 33-50 (DOI: 10.1021/bk-2019-1312.ch004).

  • Triplet and Singlet (n,π*) Excited States of 4H-Pyran-4-one Characterized by Cavity Ringdown Spectroscopy and Quantum-Chemical Calculations

    Sessions, A. G.; McDonnell, M. P.; Christianson, D. A.; Drucker, S., Triplet and Singlet (N,Pi*) Excited States of 4H-Pyran-4-One Characterized by Cavity Ringdown Spectroscopy and Quantum-Chemical Calculations. J. Phys. Chem. A 2019, 123, 6269-6280. (DOI: 10.1021/acs.jpca.9b04238).

2018

  • Cyclic Changes in Active Site Polarization and Dynamics Drive the “Ping-pong” Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations

    Reinhardt, C. R.; Hu, Q. H.; Bresnahan, C. G.; Hati, S.; Bhattacharyya, S., Cyclic Changes in Active Site Polarization and Dynamics Drive the “Ping-Pong” Kinetics in Nrh:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations. ACS Catal. 2018, 8,  12015-12029. (DOI: 10.1021/acscatal.8b04193).

  • Integrating Research into the Curriculum: A Low-Cost Strategy for Promoting Undergraduate Research

    Hati, S.; Bhattacharyya, S., Integrating Research into the Curriculum: A Low-Cost Strategy for Promoting Undergraduate Research. in ACS Symposium Series "Best Practices for Supporting and Expanding Undergraduate Research in Chemistry", 2018, 119-141. (DOI:10.1021/bk-2018-1275.ch008).

  • On the interactions of nitriles and fluoro-substituted pyridines with silicon tetrafluoride: Computations and thin film IR spectroscopy

    Hora, N. J.; Wahl, B. M.; Soares, C.; Lara, S. A.; Lanska, J. R.; Phillips, J. A., On the Interactions of Nitriles and Fluoro-Substituted Pyridines with Silicon Tetrafluoride: Computations and Thin Film IR Spectroscopy”, J. Molec. Struct. 2018, 1157, 679. (DOI:10.1016/j.molstruc.2017.12.039).

2017

  • Cavity Ringdown Spectrum of 2‑Cyclohexen-1-one in the CO/Alkenyl CC Stretch Region of the S1(n, π*) − S0 Vibronic Band System

    Mooneyham, A. E.; McDonnell, M. P.; Drucker, S., Cavity Ringdown Spectrum of 2‑Cyclohexen-1-one in the CO/Alkenyl CC Stretch Region of the S1(n, π*) − S0 Vibronic Band System, J. Phys. Chem. A 2017, 121, 2343.

  • Structural and Energetic Properties of Haloacetonitrile–BCl3 Complexes: Computations and Matrix-IR Spectroscopy

    Phillips, J. A.; Dansforth, D. A.; Hora, N. J.; Lanska, J. R.; Waller, A. W., Structural and Energetic Properties of Haloacetonitrile–BCl3 Complexes: Computations and Matrix-IR Spectroscopy. J. Phys. Chem. A 2017, 121, 9252-9261. (DOI: 10.1021/acs.jpca.7b09715).

  • Structural and energetic properties of nitrile–BX3 complexes: substituent effects and their impact on condensed-phase sensitivity

    Waller, A. W.; Weissa, N. M.; Decato, D. A.; Phillips, J. A., Structural and Energetic Properties of Nitrile – BX3Complexes: Substituent Effects and their Impact on Condensed-Phase Sensitivity.  J. Molec. Struct. 2017, 1130, 984. 

2016

  • Analysis of atomic integrals involving explicit correlation factors for the three-electron case. I. Connection to the hypergeometric function

    Leong, C. H.; Porras, I.; King, F. W., Analysis of Atomic Integrals Involving Explicit Correlation Factors for the Three-Electron Case. I. Connection to the Hypergeometric Function. J. Math. Chem. 2016, 54, 1514-1552.

  • Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    Hati, S.; Bhattacharyya, S., Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins. Biochem. Mol. Biol. Educ. 2016, 44, 140-159.

  • Infrared Spectrum of Ch3cn-Hcl in Solid Neon, and Modeling Matrix Effects in CH3CN-HCl and H3N-HCl. J. Molec. Struct

    Weiss, N. M.; Waller, A. W.; Phillips, J. A., Infrared Spectrum of Ch3cn-Hcl in Solid Neon, and Modeling Matrix Effects in CH3CN-HCl and H3N-HCl. J. Molec. Struct. 2016, 1105, 341.

  • Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study

    Reinhardt, C. R.; Jaglinski, T. C.; Kastenschmidt, A. M.; Song, E. H.; Gross, A. K.; Krause, A. J.; Gollmar, J. M.; Meise, K. J.; Stenerson, Z. S.; Weibel, T. J.; Dison, A.; Finnegan, M. R.; Griesi, D. S.; Heltne, M. D.; Hughes, T. G.; Hunt, C. D.; Jansen, K. A.; Xiong, A. H.; Hati, S.; Bhattacharyya, S., Insight into the Kinetics and Thermodynamics of the Hydride Transfer Reactions between Quinones and Lumiflavin: A Density Functional Theory Study. J. Mol. Model. 2016, 22, 199.

  • The Evaluation of Some Four-Electron Correlated Integrals with a Slater Basis Arising in Linear and Nonlinear R12 Theories. J. Phys. B-Atom. Mol. Opt. Phys.

    King, F. W., The Evaluation of Some Four-Electron Correlated Integrals with a Slater Basis Arising in Linear and Nonlinear R12 Theories. J. Phys. B-Atom. Mol. Opt. Phys. 2016, 49, 105001-105010.

2015

  • Characterization of Ch3cn-Bcl3: A Complex with Two Distinct Minima Along the B-N Bond Potential

     Wrass, J. P.; Sadowsky, D.; Bloomgren, K. M.; Cramer, C. J.; Phillips, J. A., Quantum Chemical and Matrix-Ir Characterization of Ch3cn-Bcl3: A Complex with Two Distinct Minima Along the B-N Bond Potential. Phys. Chem. Chem. Phys. 2014, 16, 16480-16491.

  • Comparison of intrinsic dynamics of cytochrome P450 proteins Using Normal Mode Analysis

    Dorner, M. E.; McMunn, R. D.; Bartholow, T. G.; Calhoon, B. E.; Conlon, M. R.; Dulli, J. M.; Fehling, S. C.; Fisher, C. R.; Hodgson, S. W.; Keenan, S. W.; Kruger, A. N.; Mabin, J. W.; Mazula, D. L.; Monte, C. A.; Olthafer, A.; Sexton, A. E.; Soderholm, B. R.; Strom, A. M.; Hati, S., Comparison of Intrinsic Dynamics of Cytochrome P450 Proteins Using Normal Mode Analysis. Protein Sci. 2015, 24, 1495-1507.

  • Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin

    Bresnahan, C. G.; Reinhardt, C. R.; Bartholow, T. G.; Rumpel, J. P.; North, M.; Bhattacharyya, S., Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol. J. Phys. Chem. A 2015, 119, 172-182.

  • Quantum chemical and matrix-IR characterization of CH3CN-BCl3: a complex with two distinct minima along the B-N bond potential

    Wrass, J. P.; Sadowsky, D.; Bloomgren, K. M.; Cramer, C. J.; Phillips, J. A., Quantum Chemical and Matrix-Ir Characterization of Ch3cn-Bcl3: A Complex with Two Distinct Minima Along the B-N Bond Potential. Phys. Chem. Chem. Phys. 2014, 16, 16480-16491.

2014

  • Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations

    Strom, A. M.; Fehling, S. C.; Bhattacharyya, S.; Hati, S., Probing the Global and Local Dynamics of Aminoacyl-tRNA Synthetases Using All-Atom and Coarse-Grained Simulations. J. Mol. Model. 2014, 20, 2245.

  • Strictly Conserved Lysine of Prolyl-tRNA Synthetase Editing Domain Facilitates Binding and Positioning of Misacylated tRNA(Pro.)

     Bartholow, T. G.; Sanford, B. L.; Cao, B.; Schmit, H. L.; Johnson, J. M.; Meitzner, J.; Bhattacharyya, S.; Musier-Forsyth, K.; Hati, S., Strictly Conserved Lysine of Prolyl-tRNA Synthetase Editing Domain Facilitates Binding and Positioning of Misacylated Trna(Pro.). Biochemistry 2014, 53, 1059-1068.

  • Structural and Energetic Properties of Acetonitrile–Group IV (A & B) Halide Complexes

    Helminiak, H. M.; Knauf, R. R., Danforth, S. J.; Phillips, J. A. Structural and Energetic Properties of Acetonitrile – Group IV (A & B) Halide Complexes. J. Phys. Chem. A 2014, 118, 4266.

2013

  • Condensed-phase effects on the structural properties of FCH2CN-BF3 and ClCH2CN-BF3: a matrix-isolation and computational study.

    Buchberger, A. R.; Danforth, S. J.; Bloomgren, K. M.; Rohde, J. A.; Smith, E. L.; Gardener, C. C.; Phillips, J. A., Condensed-Phase Effects on the Structural Properties of FCH2CN-BF3 and ClCH2CN-BF3: A Matrix-Isolation and Computational Study. J. Phys. Chem. B 2013, 117, 11687-11696.

  • Lowest triplet (n, π*) electronic state of acrolein: determination of structural parameters by cavity ringdown spectroscopy and quantum-chemical methods

      Hlavacek, N. C.; McAnally, M. O.; Drucker, S., Lowest Triplet (n, p*) Electronic State of Acrolein: Determination of Structural Parameters by Cavity Ringdown Spectroscopy and Quantum-Chemical Calculations. J. Chem. Phys. 2013, 138, 064303.

  • Lowest triplet (n,π*) state of 2-cyclohexen-1-one: characterization by cavity ringdown spectroscopy and quantum-chemical calculations

    McAnally, M. O.; Zabronsky, K. L.; Stupca, D. J.; Phillipson, K.; Pillsbury, N. R.; Drucker, S., Lowest Triplet (n, p*) State of 2-Cyclohexen-1-One: Characterization by Cavity Ringdown Spectroscopy and Quantum-Chemical Calculations. J. Chem. Phys. 2013, 139, 214311.

  • Multiple pathways promote dynamical coupling between catalytic domains in Escherichia coli prolyl-tRNA synthetase.

    Johnson, J. M.; Sanford, B. L.; Strom, A. M.; Tadayon, S. N.; Lehman, B. P.; Zirbes, A. M.; Bhattacharyya, S.; Musier-Forsyth, K.; Hati, S., Multiple Pathways Promote Dynamical Coupling between Catalytic Domains in Escherichia Coli Prolyl-tRNA Synthetase. Biochemistry, 2013, 52, 4399-4412.

2012

  • Role of Coupled-Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases

    Sanford, B.; Cao, B.; Johnson, J. M.; Zimmerman, K.; Strom, A. M.; Mueller, R. M.; Bhattacharyya, S.; Musier-Forsyth, K.; Hati, S., Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-Like Prolyl-tRNA Synthetases. Biochemistry 2012, 51, 2146-2156.

  • Structural and Energetic Properties of Alkylfluoride – BF3 Complexes in the Gas Phase and Condensed-Phase Media

     Knauf, R. R.; Helminiak, H. M.; Wrass, J. P.; Gallert, T. M.; Phillips, J. A. Structural and Energetic Properties of Alkylfluoride – BF3 Complexes in the Gas Phase and Condensed-Phase Media: Computations and Matrix Infrared Spectroscopy. J. Phys. Org. Chem. 2012, 25, 493.