Joel A Pedersen


Profile Summary

The Pedersen research group studies physicochemical and biophysical processes affecting the behavior of nanoparticles, biomolecules, and organic contaminants in terrestrial and aquatic environments. The group’s research emphasizes mechanistic studies of the interaction of these contaminants at environmental interfaces. Current research topics include molecular scale interactions of engineered nanoparticles with biomolecules and cell surfaces, transformation of nanomaterials in the environment, the processes governing the environmental transmission of prion diseases, and the uptake of polar and ionizable organic contaminants (particularly pharmaceuticals and personal care product ingredients) by plants.



Christl, I.; Ruiz, M.; Schmidt, J. R.; Pedersen, J. A. Clarithromycin and tetracycline binding to soil humic acid in the absence and presence of calcium. Environ. Sci. Technol. 2016, 50 (in press). 

Chesney, A. R.; Booth, C. J.; Lietz, C. B.; Li, L.; Pedersen, J. A. Peroxymonosulfate rapidly inactivates the disease-associated prion protein. Environ. Sci. Technol.2016, 50, 7095-7105.

Miller, E.L.; Nason, S.L.; Karthikeyan, K.G.; Pedersen, J. A. Root uptake of pharmaceuticals and personal care products. Environ. Sci. Technol. 2016, 50, 525-541.

Melby, E.S.; Mensch, A.; Lohse, S.E.; Hu, D.; Orr, G.; Murphy, C.J.; Hamers, R. J.; Pedersen, J. A. Formation of supported lipid bilayers containing phase-segregated domains and their interaction with gold nanoparticles. Environ. Sci. Nano 2016, 3, 45-55.

Hang, M.N.; Gunsolus, I.; Wayland, H.; Melby, E.S.; Mensch, A.; Doğangün, M.; Geiger, F.M.; Pedersen, J. A.; Haynes, C.L.; Hamers, R. J. Impact of nanoscale lithium nickel cobalt manganese oxide (NMC) on the bacterium Shewanella oneidensis MR-1. Chem. Mater. 2016, 28, 1092-1100.

Cui, Q.; Hernandez, R.; Mason, S. E.; Pedersen, J. A.; Geiger, F. M. Mini-review. Sustainable nanotechnology: Opportunities and challenges for theoretical/computational studies. J. Phys. Chem. B2016, 120 (in press). 

Troiano, J. M.; Kuech, T. R.; Vartanian, A. M.; Torelli, M. M.; Sen, A.; Jacob, L. M.; Hamers, R. J.; Murphy, C.J.; Pedersen, J. A.; Geiger, F.M. On electronic and charge interference in second harmonic generation responses from gold metal nanoparticles at supported lipid bilayers. J. Phys. Chem. C 2016, 120 (in press).

Kuech, T.R.; Hamers, R.J.; Pedersen, J.A. Chemical transformations of metal, metal oxide, and metal chalcogenide nanomaterials in the environment. In Engineered Nanoparticles and the Environment: Biophysicochemical Processes and Biotoxicity; Xing, B.; Vectis, C.D.; Senesi, N. (eds.); Wiley-IUPAC Series on Biophysico-chemical Processes in Environmental Systems, Vol. 4.; 2016 (in press)


Jacobson, K.H.; Gunsulos, I.L; Kuech, T.R.; Troiano, J.M.; Melby, E.S.; Lohse, S.E.; Hu, D.; Chrisler, W.B.; Murphy, C.J.; Orr, G.; Geiger, F.M.; Haynes, C.L.; Pedersen, J.A. Lipopolysaccharide density and structure governs the extent and distance of nanoparticle interaction with actual and model bacterial outer membranes. Environ. Sci. Technol. 201549, 10642-10650.

Doğangün, M.; Hang, M.N.; Troiano, J.M.; McGeachy, A.; Melby, E.S.; Pedersen, J.A.; Hamers, R.J.; Geiger, F.M. LiCoO2-induced bilayer asymmetry observed by sum frequency generation. ACS Nano 2015, 9, 8755–8765.

Murphy, C.J.; Vartanian, A.; Geiger, F.H.; Hamers, R.J.; Pedersen, J.A.; Cui, Q.; Haynes, C.L.; Carlson, E.; Hernandez, R.; Klaper, R.D.; Orr, G.; Rosenzweig, Z. Outlook: Biological responses to engineered nanomaterials: Needs for the next decade. ACS Central Science 2015, 1, 117-123

Geiger, F.M.; Pedersen, J.A. How open is open access? J. Phys. Chem. Lett. 2015, 6, 1246-1248. 

Troiano, J.M.; Olenick, L.L.; Kuech, T.R.; Melby, E.S.; Hu, D.; Lohse, S.E.; Mensch, A.C.; Doğangün, M.; Vartanian, A.M.; Torelli, M.; Ehimiaghe, E.; Walter, S.R.; Fu, L.; Wang, F.; Orr, G.; Murphy, C.J.; Hamers, R.J.; Pedersen, J.A.; Geiger; F.M. Direct probes of 4-nm diameter gold nanoparticles interacting with supported lipid bilayers. J. Phys. Chem. C 2015119, 534–546.

Carlson, C.M.; Schneider, J.R.; Pedersen, J.A.; Heisey, D.M.; Johnson, C.J. Experimental infection meadow voles (Microtus pennsylvanicus) with sheep scrapie. Can. J. Vet. Res. 201579, 68-73.


Mori, T.; Hamers, R.J.; Pedersen, J.A.; Cui, Q. Integrated Hamiltonian Sampling: A simple and versatile method for free energy simulations and conformational sampling. J. Phys. Chem. B 2014, 118, 8210-8220. doi: 10.1021/jp501339t

Kim, M.-S.; Louis, K.M.; Pedersen, J.A.; Hamers, R.J.; Peterson, R.E.; Heideman, W. Using citrate-functionalized TiO2 nanoparticles to study the effect of particle size on zebrafish embryo toxicity. Analyst 2014, 139, 964-972. doi: 10.1039/C3AN01966G

Greiner, E.; Kumar, K.; Sumit, M.; Guiffre, A.; Pedersen, J.A.; Sahai, N. Adsorption of L-glutamic acid and L-aspartic acid on γ-Al2O3Geochim. Cosmochim. Acta 2014, 133, 142-155. doi: 10.1016/j.gca.2014.01.004

Smith, C.B.; Booth, C.J.; Wadzinsky, T.; Legname, G.; Chappell, R.; Johnson, C.J.; Pedersen, J.A. Humic substances interfere with detection of pathogenic prion protein. Soil Biol. Biochem. 2014, 68, 309-316.

Bishop, L.M.; Tillman, A.S.; Geiger, F.M.; Haynes, C.L.; Klaper, R.D.; Murphy, C.J.; Orr, G.; Pedersen, J.A.; DeStefano, L.; Hamers, R.J. Blogging as a tool to enhance graduate students’ written communication skills. J. Chem. Ed. 2014, 91, 1600-1605.

Pedersen, J.A. Prion diseases. Chapter 4 in Creating Life from Life: Biotechnology and Science Fiction; Berne, R.W. (Ed.); Pan Stanford Press, 2014. ISBN-10: 9814463582, ISBN-13: 978-9814463584.


Wiecinski, P.N.; Metz, K.M.; Peterson, R.E.; Heideman, W.; Hamers, R.J.; Pedersen, J.A. Toxicity of oxidatively degraded quantum dots. Environ. Sci. Technol. 2013, 47, 9132-9139. doi: 10.1021/es304987r

Jacobson, K.H.; Kuech, T.R.; Pedersen, J.A. Attachment of pathogenic prion protein to model mineral surfaces. Environ. Sci. Technol. 2013, 47, 6925-6934. doi: 10.1021/es3045899

Bar-Ilan, O.; Chuang, C.C.; Schwahn, D.J.; Yang, S.; Joshi, S.; Pedersen, J.A.; Hamers, R.J.; Peterson, R.E.; Heideman, W. TiO2 nanoparticle exposure spanning zebrafish development: photo-dependent toxicity at parts per billion concentrations. Environ. Sci. Technol. 2013, 47, 4726-4733. doi: 10.1021/es304514r

Yang, S.; Louis, K.; Heideman, W.; Hamers, R.J.; Peterson, R.E.; Pedersen, J.A. Influence of humic acid on titanium dioxide nanoparticle toxicity to developing zebrafish. Environ. Sci. Technol. 2013, 47, 4718-4725. doi: 10.1021/es3047334

Mori, T.; Hamers, R.J.; Pedersen, J.A.; Cui, Q. An explicit consideration of desolvation is critical to binding free energy calculations of charged molecules at ionic surfaces. J. Chem. Theo. Comp. 2013, 9, 5059-5069.

Booth, C.J.; Johnson, C.J.; Pedersen, J.A. Microbial and enzymatic inactivation of prions in soil environments. Soil Biol. Biochem. 2013, 59, 1-15. doi: 10.1016/j.soilbio.2012.12.016

Johnson, C.J.; Gilbert, PUPA; Albrecht, M.; Baldwin, K.L.; Pedersen, J.A.; Aiken, J.M.; McKenzie, D. Low copper and high manganese levels in prion plaques. Viruses 2013, 5, 654-662. doi:10.3390/v5020654


Tomaszewski, J.E.; Madliger, M.; Pedersen, J.A.; Schwarzenbach, R.P.; Sander, M. Adsorption of insecticidal Cry1Ab protein to humic substances. 2. Influence of humic and fulvic acid charge and polarity characteristics. Environ. Sci. Technol. 2012, 46, 9932-9940. doi: 10.1021/es302248u

Gao, J.; Hedman, C.; Liu, C.; Guo, T.; Pedersen, J.A. Transformation of sulfamethazine by manganese oxide in aqueous solution. Environ. Sci. Technol. 2012, 46, 2642-2651. doi: 10.1021/es202492h

Bishop, L.M.; Yeager, J.C.; Chen, X.; Wheeler, J.N.; Torelli, M.D.; Benson, M.C.; Burke, S.D.; Pedersen, J.A.; Hamers, R.J. A citric acid-derived ligand for modular functionalization of metal oxide surfaces via “click” chemistry. Langmuir 201228, 1322-1329. doi: 10.1021/la204145t

Sturm, R.M.; Kreitinger, G.; Booth, C.J.; Smith, L.M.; Pedersen, J.A.; Li, L. Absolute quantification of prion protein (90-231) using stable isotope-labeled chymotryptic peptide standards in a LC-MRM AQUA workflow. J. Am. Soc. Mass. Spectr. 201223, 1522-1533. doi: 10.1007/s13361-012-0411-1

Johnson, C.J.; Aiken, J.M.; McKenzie, D.; Samuel, M.D.; Pedersen, J.A. Highly efficient amplification of chronic wasting disease agent by protein misfolding cyclic amplification with beads (PMCAb). PLoS ONE 20127, e35383. doi: 10.1371/journal.pone.0035383

Walters, R.H.; Jacobson, K.H.; Pedersen, J.A.; Murphy, R.M. Analysis of the elongation kinetics of polyglutamine peptide fibrils: A quartz crystal microbalance with dissipation study. J. Molec. Biol. 2012421, 329-347. doi: 10.1016/j.jmb.2012.03.017

Bar-Ilan, O.; Louis, K.; Yang, S.; Pedersen, J.A.; Hamers, R.J.; Peterson, R.E.; Heideman, W. ­­­ Titanium dioxide nanoparticles produce phototoxicity in the developing zebrafish. Nanotoxicol. 20126, 670-679. doi: 10.3109/17435390.2011.604438

Pedersen, J.A.; Somerville, R. Why and how are TSEs sometimes spread via environmental routes? In Decontamination of Prions; Deslys, J.-P.; Pocchiari, M.; Reisner, D.; Somerville, R. (eds); Düsseldorf University Press: Düsseldorf, Germany, 2012; 19-37.


Sibley, S.D.; Goldberg, T.L.; Pedersen, J.A. Detection of known and novel adenoviruses in cattle wastes by using broad-spectrum primers. Appl. Environ. Microbiol. 201177, 5001-5008. doi: 10.1128/AEM.00625-11

Smith, C.B.; Booth, C.M.; Pedersen, J.A. Fate of prions in soils: A review. J. Environ. Qual. 2011, 40, 449-461. doi: 10.2134/jeq2010.0412

Pedersen, J.A.; Simpson, M.A.; Bockheim, J.G. Kumar, K. Characterization of soil organic carbon in drained thaw lake basins of arctic Alaska by NMR and FTIR photoacoustic spectroscopy. Org. Geochem. 201142, 947-954. doi: 10.1016/j.orggeochem.2011.04.003

Johnson, C.J.; McKenzie, D.; Pedersen, J.A.; Aiken, J.M. Meat and bone meal and mineral feed additives may increase the risk of oral prion disease transmission. J. Toxicol. Environ. Health A 201174, 161-166. doi: 10.1080/15287394.2011.529066


Gao, J.; Pedersen, J.A. Sorption of sulfonamide antimicrobial agents to humic-clay complexes. J. Environ. Qual. 2010, 39,228-235. doi: 10.2134/jeq2008.0274

Seyfried, E.E.; Newton, R.J.; Rubert, K.F., IV; Pedersen, J.A.; McMahon, K.D. Diversity of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline. Microb. Ecol. 201059, 799-807. doi: 10.1007/s00248-009-9624-7

Jacobson, K.H.; Lee, S.; Somerville, R.A.; McKenzie, D.; Benson, C.H.; Pedersen, J.A. Pathogenic prion protein transport through soils. J. Environ. Qual. 2010, 39, 1145-1152.doi: 10.2134/jeq2009.0137

Adkin, A.L.; Matthews, D.; Hope, J.; Maddison, B.C.; Somerville, R.A.; Pedersen, J. Risk of escape of prions in gaseous emissions from on-farm processing vessels. Vet. Rec. 2010167, 28-29. doi: 10.1136/vr.c3158

Lowry, G.V.; Holtze, E.M.; Bernhardt, E.S.; Dionysiou, D.D.; Pedersen, J.A.; Wiesner, M.R.; Xing, B. Environmental occurrence, behavior and ecological effects of engineered nanomaterials. J. Environ. Qual. 2010, 39, 1867-1874. doi: 10.2134/jeq2010.0297

Oleson T.A.; Sahai, N.; Pedersen, J.A. Electrostatic effects on deposition of multiple phospholipid bilayers at oxide surfaces. J. Colloid Interface Sci. 2010352, 327-36. doi: 10.1016/j.jcis.2010.08.057


Jacobson, K.H.; Lee, S.; McKenzie, D.; Benson, C.H.; Pedersen, J.A. Transport of the pathogenic prion protein through landfill materials. Environ. Sci. Technol. 2009, 43, 2022-2028. doi: 10.1021/es802632d

Metz, K.M.; Magham, A.N.; Bierman, M.J.; Jin, S.; Hamers, R.J.; Pedersen, J.A. Engineered nanomaterial transformation under oxidative environmental conditions: Development of an in vitro biomimetic assay. Environ. Sci. Technol. 200943, 1598-1604. doi: 10.1021/es802217y

King Heiden, T.C.; Wiecinski, P.N.; Magham, A.N.; Metz, K.M.; Nesbit, D.; Pedersen, J.A.; Hamers, R.J.; Heideman, W.; Peterson, R.E. Quantum dot nanotoxicity assessment using the zebrafish embryo. Environ. Sci. Technol. 200943, 1605-1611. doi: 10.1021/es801925c

Wiecinski, P.N.; Metz, K.M.; Mangham, A.N.; Jacobson, K.H.; Hamers, R.J.; Pedersen, J.A. Gastrointestinal biodurability of engineered nanomaterials: Development of an in vitro assay. Nanotoxicol. 20093, 202-214. doi: 10.1080/17435390902859556

Liang, C.; Pedersen, J.A.; Balser, T.C. Aminoglycoside antibiotics may interfere with microbial amino sugar analysis. J. Chromatogr. A 20091216, 5296-5301. doi: 10.1016/j.chroma.2009.05.010

Russo, F.; Johnson, C.J.; Johnson, C.J.; McKenzie, D.; Aiken, J.M.; Pedersen, J.A. Degradation of the pathogenic prion protein by a manganese mineral found in soils. J. Gen. Virol. 200990, 275-280. doi: 10.1099/vir.0.003251-0

Johnson, C.J.; Gilbert, P.U.P.A.; McKenzie, D.; Pedersen, J.A.; Aiken, J.M. Ultraviolet-ozone treatment reduces levels of disease-associated prion protein and prion infectivity. BMC Res. Notes 20092, 121-125


Sibley, S.D.; Pedersen, J.A. Interaction of the macrolide antimicrobial clarithromycin with dissolved humic acid. Environ. Sci. Technol. 2008, 42, 422-428. doi: 10.1021/es071467d

Bialk, H.M.; Pedersen, J.A. NMR investigation of enzymatic coupling of sulfonamide antimicrobials with humic substances. Environ. Sci. Technol. 2008, 42, 106-112. doi: 10.1021/es070779d

Hinckley, G.T.; Johnson, C.J.; Jacobson, K.H.; McKenzie, D.; Aiken, J.M.; McMahon, K.D.; Pedersen, J.A. Persistence of pathogenic prion protein during simulated wastewater treatment processes. Environ. Sci. Technol. 200842, 5254-5259. doi: 10.1021/es703186e


Johnson, C.J.; Pedersen, J.A.; Chappell, R.J.; McKenzie, D.; Aiken, J.M. Oral transmissibility of prion disease is enhanced by binding to soil particles. PLoS Pathogens 20073, 874-881 (e93). doi: 10.1371/journal.ppat.0030093

Bialk, H.M.; Hedman, C.; Castillo, A.; Pedersen, J.A. Laccase-mediated Michael addition of 15N-sulfapyridine to a model humic constituent. Environ. Sci. Technol. 200741, 3593-3600. doi: 10.1021/es0617338

Ma, X.; Benson, C.H.; McKenzie, D; Aiken, J.M.; Pedersen, J.A. Adsorption of pathogenic prion protein to quartz sand. Environ. Sci. Technol. 200741, 2324-2330. doi: 10.1021/es062122i

Gu, C.; Karthikeyan, K.G.; Sibley, S.D.; Pedersen, J.A. Complexation of the antibiotic tetracycline with humic acid. Chemosphere 200766, 1494-1501. doi: 10.1016/j.chemosphere.2006.08.028

Soliman, M.; Pedersen, J.A.; Park, H.; Castaneda-Jimenez, A.; Stenstrom, M.K; Suffet, I.H. Human pharmaceuticals, antioxidants and plasticizers in wastewater treatment plant and water reclamation plant effluents. Wat. Environ. Res. 200779, 156-167. doi: 10.2175/106143006X111961


Johnson, C.J.; Phillips, K.E.; Schramm, P.T.; McKenzie, D.; Aiken, J.M.; Pedersen, J.A. Prions adhere to soil minerals and remain infectious. PLoS Pathogens 20062, 296-302 (e32). doi: 10.1371/journal.ppat.0020032

Rubert, K.F., IV; Pedersen, J.A. Kinetics of oxytetracycline reaction with a hydrous manganese oxide. Environ. Sci. Technol. 200640, 7216-7221. doi: 10.1021/es060357o

Pedersen, J.A.; Yeager, M.A.; Suffet, I.H. Organophosphorus insecticides in agricultural and residential runoff: Field observations and implications for Total Maximum Daily Load development. Environ. Sci. Technol. 200640, 2120-2127. doi: 10.1021/es051677v

Schramm, P.T.; Johnson, C.J.; Mathews, N.E.; McKenzie, D.; Aiken, J.M.; Pedersen, J.A. Potential role of soil in the transmission of prion disease. Medical Mineralogy and Geochemistry. Rev. Mineral. Geochem. 2006, 64, 135-152. doi: 10.2138/rmg.2006.64.5

Pedersen, J.A.; McMahon, K.D.; Benson, C.H. Prions: Novel pathogens of environmental concern? J. Environ. Eng. 2006132, 967-969. doi: 10.1061/(ASCE)0733-9372(2006)132:9(967)


Gao, J.; Pedersen, J.A. Adsorption of sulfonamide antimicrobial agents to clay minerals. Environ. Sci. Technol. 2005, 39, 9509-9516. doi: 10.1021/es050644c

Bialk, H.M.; Simpson, A.J.; Pedersen, J.A. Cross-coupling of sulfonamide antimicrobial agents to model humic constituents. Environ. Sci. Technol. 2005, 39, 4436-4473. doi: 10.1021/es0500916

Pedersen, J.A.; Soliman, M.A.; Suffet, I.H. Human pharmaceuticals, hormones and personal care product ingredients in runoff from agricultural fields irrigated with treated wastewater. J. Agric. Food Chem. 200553, 1625-1632. doi: 10.1021/jf049228m

Rose, P.E.; Pedersen, J.A. Fate of oxytetracycline in streams receiving aquaculture discharges: Model simulations. Environ. Toxicol. Chem. 2005, 24, 40-50. doi: 10.1897/03-640.1

Prior to 2005

Soliman, M.A.; Pedersen, J.A.; Suffet, I.H. Rapid gas chromatography-mass spectrometry screening method for human pharmaceuticals, hormones, antioxidants and plasticizers in water. J. Chromatogr. A 2004, 1029, 223-227. 10.1016/j.chroma.2003.11.098

Lin, C.-H.M.; Pedersen, J.A.; Suffet, I.H. Influence of aeration on hydrophobic organic contaminant distribution and flux in estuarine sediments. Environ. Sci. Technol. 2003, 37, 3547-3554. 10.1021/es026048p

Pedersen, J.A.; Yeager, M.A.; Suffet, I.H. Xenobiotic organic compounds in runoff from fields irrigated with treated wastewater. J. Agric. Food Chem. 2003, 51, 1360-1372. 10.1021/jf025953q

Pedersen, J.A.; Schweitzer, L.E.; Lin, C.-H.; Suffet, I.H. Effect of oxic state on nonpolar organic contaminant distribution, mobility and bioavailability in estuarine sediments. Israel J. Chem. 2002, 42, 109-118. 10.1560/569Q-NH11-LXPM-KH1Q

Pedersen, J.A.; Yeager, M.A.; Suffet, I.H. Characterization and mass load estimates of organic compounds from agricultural irrigation runoff. Wat. Sci. Technol. 2002, 45, 103-110.

Jones, K.B.; Heggem, D.T.; Wade, T.G.; Neale, A.C.; Ebert, D.W.; Nash, M.S.; Mehaffey, M.H.; Hermann, K.A.; Selle, A.R.; Augustine, S.; Goodman, I.A.; Pedersen, J.A.; Bolgrien, D.; Viger, J.M.; Chiang, D.; Lin, C.J.; Zhong, Y.; Baker, J.; Van Remortel, R.D. Assessing landscape condition relative to water resources in the western United States: a strategic approach. Environ. Monitor. Assess. 2000, 64, 227-245. doi: 10.1023/A:1006448400047

Pedersen, J.A.; Gabelich, C.J.; Lin, C.-H.; Suffet, I.H. Aeration effects on the partitioning of a PCB to anoxic estuarine sediment pore water dissolved organic matter. Environ. Sci. Technol. 1999, 33, 1388-1397. 10.1021/es980717a



Fall 2016-2017

  • SOILSCI 699 - Special Problems
  • SOILSCI 990 - Research
  • SOILSCI 299 - Independent Study
  • CIVENGR 790 - Master\'s Research or Thesis
  • CIVENGR 890 - Pre-Dissertator\'s Research
  • CIVENGR 990 - Thesis
  • CIVENGR 699 - Independent Study
  • CHEM 699 - Directed Study
  • CHEM 993 - Research-Analytical
  • CHEM 299 - Directed Study
  • Profile Summary

    The Pedersen research group studies physicochemical and biophysical processes affecting the behavior of nanoparticles, biomolecules, and organic contaminants in terrestrial and aquatic environments. The group’s research emphasizes mechanistic studies of the interaction of these contaminants at environmental interfaces. Current research topics include molecular scale interactions of engineered nanoparticles with biomolecules and cell surfaces, transformation of nanomaterials in the environment, the processes governing the environmental transmission of prion diseases, and the uptake of polar and ionizable organic contaminants (particularly pharmaceuticals and personal care product ingredients) by plants.

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