2023

• Analysis of Swin-UNet vision transformer for Inferior Vena Cava filter segmentation from CT scans

  Gomes, R., Pham, T., He, N., Kamrowski, C., & Wildenberg, J. (2023). Analysis of Swin-UNet vision transformer for Inferior Vena Cava filter segmentation from CT scans. In Artificial Intelligence in the Life Sciences (Vol. 4, p. 100084). Elsevier BV. https://doi.org/10.1016/j.ailsci.2023.100084

• Deep Learning Patch-Based Approach for Hyperspectral Image Classification

  Rozario, P. F., Ruehmann, E., Pham, T., Sun, T., Jensen, J., Jia, H., Yu, Z., & Gomes, R. (2023). Deep Learning Patch-Based Approach for Hyperspectral Image Classification. 2023 IEEE International Conference on Electro Information Technology (eIT). IEEE. https://doi.org/10.1109/eit57321.2023.10187387 

• 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 

• 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

• A Robust Framework for Deep Learning Approaches to Facial Emotion Recognition and Evaluation

  Siddiqui, N., Reither, T., Black, D., Bauer, T., Hanson, M., & Dave, R., (2022). A Robust Framework for Deep Learning Approaches to Facial Emotion Recognition and Evaluation. 2022 Asia Conference on Algorithms, Computing and Machine Learning (CACML). IEEE. https://doi.org/10.1109/cacml55074.2022.00020 

• Abstract No. 144 Automated IVC filter detection from abdominopelvic CT exams using deep learning

  Wildenberg, J., Kamrowski, C., Senor, C., Mohan, P., & Gomes, R. (2022). Abstract No. 144 Automated IVC filter detection from abdominopelvic CT exams using deep learning. Journal of Vascular and Interventional Radiology (Vol. 33, Issue 6, p. S67). https://doi.org/10.1016/j.jvir.2022.03.225 

• Advances in Rechargeable Lithium–Sulfur Batteries

  Ma Y. (2022) Computation and Simulation. In: Manthiram A., Fu Y. (eds) Advances in Rechargeable Lithium–Sulfur Batteries. Modern Aspects of Electrochemistry, vol 59. Springer, Cham. https://doi.org/10.1007/978-3-030-90899-7_10

• Application of Deep Learning to IVC Filter Detection from CT Scans

  Gomes, R., Kamrowski, C., Mohan, P. D., Senor, C., Langlois, J., & Wildenberg, J. (2022). Application of Deep Learning to IVC Filter Detection from CT Scans. Diagnostics, 12(10), 2475. https://doi.org/10.3390/diagnostics12102475

• Application of Feature Selection and Deep Learning for Cancer Prediction Using DNA Methylation Markers

  Gomes, R., Paul, N., He, N., Huber, A. F., & Jansen, R. J. (2022). Application of Feature Selection and Deep Learning for Cancer Prediction Using DNA Methylation Markers. Genes, 13(9). https://doi.org/10.3390/genes13091557

• 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)

• The 2020 Global Stock Market Crash: Endogenous or Exogenous?

  Song R.; Shu M.; and Zhu W. The 2020 Global Stock Market Crash: Endogenous or Exogenous?, Physica A: Statistical Mechanics and its Applications, 2022, 585, 126425, (DOI: https://doi.org/10.1016/j.physa.2021.126425).

2021

• A scalable deep learning framework for breast cancer prediction using DNA methylation data

  Gomes, R.; He, N.; Huber, A.; Jansen, R.; and Paul, N. A scalable deep learning framework for breast cancer prediction using DNA methylation data. American Society of Human Genetics 2021, 2021, (View Poster).

• Limited evidence for a positive relationship between hybridization and diversification across seed plant families

  Mitchell, N. and Whitney, K.D. Limited evidence for a positive relationship between hybridization and diversification across seed plant families. Evolution, 2021, 75, 1966-1982. (DOI: https://doi.org/10.1111/evo.14291).

• Named Entity Recognition in Unstructured Medical Text Documents

  Pearson, C.; Seliya, N.; and Dave, R. Named Entity Recognition in Unstructured Medical Text Documents. 2021 International Conference on Electrical, Computer and Energy Technologies (ICECET), 1–6, 2021 (DOI: https://doi.org/10.1109/ICECET52533.2021.9698694)

• 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).

• The 2021 Bitcoin Bubbles and Crashes—Detection and Classification

  Shu M.; Song R.; and Zhu W. The 2021 Bitcoin Bubbles and Crashes—Detection and Classification, Stats, 2021, 4(4), 950-970, (DOI: https://doi.org/10.3390/stats4040056).

• The ‘COVID’ crash of the 2020 U.S. Stock market

   Shu M.; Song R.; and Zhu W. The ‘COVID’ Crash of the 2020 U.S. Stock Market, The North-American Journal of Economics and Finance, 2021, 58, 101497, (DOI: https://doi.org/10.1016/j.najef.2021.101497).

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).

• Lithiation and Delithiation Processes in Lithium–Sulfur Batteries from Ab Initio Molecular Dynamics Simulations

  Arneson, C.; Wawrzyniakowski, Z. D.; Postlewaite, J. T.; Ma, Y., Lithiation and Delithiation Processes in Lithium–Sulfur Batteries from Ab Initio Molecular Dynamics Simulations. J. Phys. Chem. C 2018, 122, 8769-8779. (DOI:10.1021/acs.jpcc.8b00478).

• Mixture is better: enhanced electrochemical performance of phenyl selenosulfide in rechargeable lithium batteries

  Guo, W.; Bhargav, A.; Ackerson, J. D.; Cui, Y.; Ma, Y.; Fu, Y., Mixture Is Better: Enhanced Electrochemical Performance of Phenyl Selenosulfide in Rechargeable Lithium Batteries. Chemical Communications 2018, 54, 8873-8876. (DOI: 10.1039/c8cc04076a).

• 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.