Patricia Soto Becerra, BA, PhD
Patricia Soto Becerra, BA, PhD

Patricia Soto Becerra, BA, PhD

Associate Professor
College of Arts and Sciences

Academic Appointments

Department

  • Physics

Position

  • Associate Professor

Teaching Activity

  • Developer of general physics lecture and lab courses for life sciences students
  • Developer of upper level and master's level courses that integrate active learning techniques, including computational modeling
  • Teaching style: hybrid classroom, research-based active learning techniques, cognitive wrappers, Ignatian pedagogical paradigm

Biography

Patricia grew up in Bogotá, Colombia where she received her BS and MS in Physics from Los Andes University.  She then attended the University of Groningen, Groningen, The Netherlands where she earned her Doctorate in Mathematics and Natural Sciences. In 2004 she moved to the University of California in Santa Barbara to pursue postdoctoral training, partially funded by an international fellowship from the American Association of University Women. Patricia joined the Department of Physics at Creighton University in August 2007. Her scientific expertise falls in the broadly defined field of computational molecular biophysics and aims at deciphering the biophysical principles of the pathological folding process of proteins and peptides hallmark of neurodegenerative diseases, such as Alzheimer's and prion diseases.  Patricia’s scholarly purpose is to bridge physical and life sciences in an integrated research and educational program with undergraduates.
 

Education

  • University of California in Santa Barbara. Postdoctoral fellow
  • University of Groningen, Groningen, The Netherlands. Doctorate in Mathematics and Natural Sciences
  • Los Andes University, Bogota, Colombia. MS in physics
  • Los Andes University, Bogota, Colombia. BS in physics

Publications and Presentations

Articles

  • Glanzer, J. G., Carnes, K. A., Soto, Patricia, Liu, S., Parkhurst, L. J., Oakley, G. G. A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A, Nucleic Acids Research, 41, 2047-2059, 2013
  • Grabenauer, Megan, Wu, Chun, Soto, Patricia, Shea, Joan-Emma, Bowers, Michael T. Oligomers of the Prion Protein Fragment 106-126 Are Likely Assembled from ?-Hairpins in Solution, and Methionine Oxidation Inhibits Assembly without Altering the Peptide's Monomeric Conformation, Journal of the American Chemical Society, 132, 532-539, 2010
  • Armstrong, Brandon D., Soto, Patricia, Shea, Joan-Emma, Han, Songi Overhauser dynamic nuclear polarization and molecular dynamics simulations using pyrroline and piperidine ring nitroxide radicals, Journal of Magnetic Resonance, 200, 137-141, 2009
  • Soto, Patricia, Jewett, A., Zhuang, Z., Shea, J. E. Effect of surface tethering on the folding of the src-SH3 protein domain, Physical Biology, 6, 17 pages, 2009
  • Krone, M. G., Hua, L., Soto, P., Zhou, R., Berne, B. J., Shea, J. -. Role of Water in Mediating the Assembly of Alzheimer Amyloid-Beta ABeta16-22 Protofilaments, J. Am. Chem. Soc., 130, 11066-11072, 2008
  • Soto, P., Griffin, M. A., Shea, J. -. New insights into the mechanism of Alzheimer amylodi- Beta fibrillogenesis inhibition by N-methylated peptides, Biophysical Journal, 93, 3015-3025, 2007
  • Soto, Patricia, Barumketner, A., Joan-Emma, Shea Aggregation of polyalanine in a hydrophobic environment, Journal of Chemical Physics, 124, 134904, 2006

Presentations

  • Robyn Scott, Carla Barrera, William Graft, Ronald Shikiya and Patricia Soto. Dynamics of residue contacts in prion proteins influences transmission barrier across species. INBRE meeting, Nebraska City, NE, 2016
  • Cognitive wrappers: Learning how to learn physics, presented at Physics education research conference and American Association of Physics Teachers, summer meeting, Sacramento, CA., 2016
  • Chad Nieri, Jesse Woo and Patricia Soto. Interactions between cellular prion protein PrPc and cholesterol molecules at the cell membrane environment. St. Albert’s day, Creighton University., 2016
  • Hamada, Robyn; Woo, Jesse; Shikiya, Ronald; Soto, Patricia. Comparative conformational dynamics of cellular prion proteins towards elucidating the species barrier. 60th Biophysical Society conference, Los Angeles, CA, 2016
  • Woo, Jesse; Nieri, Chad; Gonzales, Roger; Bartz, Jason; Soto, Patricia. Conformational dynamics of prion proteins at the membrane interface. 60th Biophysical Society conference, Los Angeles, CA, 2016
  • “Course transformation as a science experiment”. 60th Biophysical society meeting., 2016
  • Does gender influence bibliometrics of undergraduate research at PUIs? NSF ADAVANCE ASAP meeting, Seattle, WA. Collaborators: Birgit Mellis, Chrystal Bruce, Graciela Lacueva, and Anne M. Wilson, 2015
  • Patricia Soto, Cognitive wrappers: Metacognition and reflection tools to learn how to learn. Campus-wide day on assessment., 2015
  • Hamada, Robyn; Lax, Angela; Woo, Jesse; Shikiya, Ron and Soto, Patricia. Do the structures of prion proteins explain the transmission barrier among mammal species? INBRE meeting, Lincoln, NE, 2015
  • Patricia Soto, Michael Cherney, Gintaras Duda, David L. Sidebottom. Transforming the Introductory Physics for the Life Sciences (IPLS) course at a liberal arts primarily undergraduate institution (PUI). American Association of Physics Teachers Summer meeting, College Park, MD, 2015
  • Patricia Soto, Natalie Bui, Margaret Carter, Roger Gonzalez, William Graft, Angela Lax, Chad Nieri, Bo Zhao and Jason C. Bartz. Conformational dynamics of the cellular prion protein. NeuroPrion 2015, Colorado State University, Fort Collins, CO., 2015
  • Patricia Soto, Matt Armbruster, William Graft, Roger Gonzalez, Chad Nieri, Bo Zhao and Jason C. Bartz. Prion proteins and mechanisms of interaction with model membranes. Biophysical Society meeting,, 2015
  • Co presenter with research student Bo Zhao on the insight into the contribution to the species barrier effect of the conformational dynamics of the cellular from of the prion protein of two mustelids. Research Fair Day, 2014
  • Co presenter with research student Brendy Aoki about Molecular modeling of synthetic Ab protofilaments, Nebraska Academy of Science, Nebraska wesleyan University, Lincoln, NE, 2014
  • Co presenter with research student Charlie Nguyen about Molecular Modeling of the conformational dynamics of the cellular prion protein, Nebraska Wesleyan University, Lincoln, NE, 2014
  • Co presenter with research student Brendy Aoki about Molecular modeling of synthetic Ab protofilaments. St. Albert's day, Creighton University, 2014
  • Co presenter with research students Charlie Nguyen, Ian Colling and Jason Bartz about Molecular modeling of the conformational dynamics of the cellular prion protein. St. Albert's day, Creighton University., 2014
  • Co presenter with research students William Graft, Ian Colling, Charles Nguyen, Shannon L. Bartely-Hunt and Jason Bartz about Molecular modeling of the conformational dynamics of the cellular prion protein. St. Albert's day, Creighton University, 2014
  • Co presenter with research students Matt Armbruster, Nathan Horst, Brendy Aoki and Saad Malik about Conformational dynamics of amyloid proteins at the aqueous interface. St. Albert's Day, Creighton University, 2014
  • Co presenter with research student Brendy Aoki about molecular modeling of synthetic Ab protofilaments. ACS meeting, Dallas, TX, 2014
  • Co presenter with research students Charlie Nguyen, Ian Colling and Jason Bartz about Molecular modeling of the conformational dynamics of the cellular prion protein. APS meeting, Denver CO, 2014
  • The Nobel Prize in "Computational Molecular Biophysics 2013", Physics department, Creighton University, 2014
  • Co presenter with research students William Graft, Ian Colling, Charles Nguyen, and collaborators Shannon L. Bartely-Hunt and Jason Bartz about Molecular modeling of the conformational dynamics of the cellular prion protein. Prion Horizons conference, Fort Collins, CO, 2013
  • Hierarchial modeling of protein folding and aggregation, Physics department at University of Nebraska Omaha, 2013
  • Molecular Modeling of protein-surface interactions, BMS seminar at CU, Omaha, 2013
  • Co presenter with research students Matt Armbruster, Nathan Horst, Brendy Aoki and Saad Malik about Conformational dynamics of amyloid proteins at the aqueous interface. Structural Biology Workshop at UNMC., 2013
  • Co presenter with research students Nathan Horst, Matt Armbruster, Brendy Aoki, William Marquardt about Conformational dynamics of amyloid proteins at the aqueous interface. Honors day, 2013
  • Co presenter with master research student Matt Armbruster, William Marquardt about Computational self-assembly of phospholipid bilayers, Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2013
  • Co presenter with undergraduate research students Nathan Horst and Brendy Aoki, and master research student Matt Armbruster about Coarse grain molecular dynamics analysis of the interaction between Ab Alzheimer's protofilaments and a lipid bilayer, Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2013
  • Co presenter with research student Saad Malik about Conformational dynamics of the Syrian hamster prion protein during interaction with a model lipid bilayer, Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, Ne, 2013
  • Co presenter with research students Charles Nguyen, Dalton Bourke, Will Graft and Jason Bartz about Molecular modeling of amyloid proteins. St. Albert's day, 2013
  • Co presenter with research students Matt Armbruster, Nathan Horst, Brendy Aoki and Saad Malik about Conformational dynamics of amyloid proteins at the aqueous interface. St. Albert's day., 2013
  • Co presenter with research students Matt Armbruster, Nathan Horst, Brendy Aoki and Saad Malik about Conformational dynamics of amyloid proteins at the aqueous interface. APS meeting in Baltimore, 2013
  • Co presenter with research student Nathan Horst at Ferlic Symposium about "Course-grain modeling of Ab protofilaments interacting with model bilayers". Creighton University, Omaha, NE, 2012
  • Co presenter with research students Matt Armbruster, Nathan Horst, Brendy Aoki and Saad Malik at Regional Midwest ACS meeting about "Conformational dynamics of amyloid proteins at the aqueous interface". ACS, Omaha, NE, 2012
  • Co presenter with research student Matt Armbruster about Polymorphic Ab protofibrils exhibit distinct conformational dynamics as calculated by normal mode analysis, Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2012
  • Co presenter with research student Ian Colling about Binding modes of AGAAAAGA to syriam hamster prion protein, Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2012
  • Invited speaker at the Oakley research group at the School of Dentistry, UNMC, Lincoln, NE, 2012
  • Co presenter with research students Brendy Aoki, Ian Colling, Nathan Horst, Daisy Liberato, Dhwani Shah, Samantha Swerdferger, Jason Bartz about "Conformational dynamics of amyloid proteins. St. Albert's day, 2012
  • Co presenter with research students Matt Armbruster about Polymorphic amyloid- b protofilaments exhibit distinct conformational dynamics as calculated by normal mode analysis. APS meeting in Boston, MA, 2012
  • Invited speaker at the GAA/INBRE meeting, Omaha, NE, 2011
  • Invited speaker at the AAPT Summer meeting, Omaha,NE, 2011
  • Co presenter with research students Matt Armbruster about Polymorphic amyloid-b protofilaments exhibit distinct conformational dynamics as calculated by normal mode analysis. 4th Structural Bilogy and Molecular Biophysics workshop at UNMC, Omaha, NE, 2011
  • Co presenter with research student Trang Doan about the elasticity of Alzheimer's AB protofibrils studied with fully atomistic normal mode analysis. Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2011
  • Co presenter with research student Tana Friesth about the Identification and characterization of prion inhibitor binding regions for the AGAAAAGA peptide. Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2011
  • Co presenter with research student Curtis Jordan about the use of coarse grained normal mode analysis in understanding AB protofibril dynamics. Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2011
  • Invited speaker at Northwestern College, Orange City, IA, 2010
  • Co presenter with research students Tana Friesth about Identification and Characterization of Prion Inhibitor Binding Regions for the AFAAAAGA peptide. Ferlic Symposium, Creighton University, Omaha, NE, 2010
  • Co presenter with research students Tana Freisth, Shannon L. Bartelt-Hunt, and Jason C. Bartz about Prion proteins and mechanisms of interaction with inhibitors and model surfaces. 45th Regional ACS meeting in Wichita, KS, 2010
  • Co presenter with research students Curtis Jordan about Dynamics of a spin label molecule in water and in a lipid environment, St. Albert's Day, Creighton University, Omaha, NE, 2010
  • Invited speaker at Augustana College, Sioux Falls, SD, 2010
  • Co presenter with research student Ben Soukup about Micromechanical properties of model Alzheimer's b-amyloid fribrils. 54th Biophysical meeting, San Francisco, CA., 2010
  • Speaker at IRG-1 meeting, Materials Research Lab at University of California at Santa Barbara, 2009
  • Keynote speaker at the 118th annual meeting Nebraska Academy of Sciences- Nebraska Wesleyan University, Lincoln, NE, 2008
  • Co presenter with research student Jenny Burns about "Protein nanofiibrils", Nebraska Academy of Science, Nebraska Wesleyan University, Lincoln, NE, 2008
  • Post doctoral research presentation on Therapeutic strategies for Alzheimer's disease: The rational design of amyloid inhibitors. Gordon Research Conference on Protein Dynamics, Ventura, CA, USA January 8th-12th, 2008
  • Post doctoral research presentation on Inhibition mechanism of inhibitors to prevent amyloid fibril growth as monitored by molecular dynamics simulations. 229th ACS National Meeting, San Diego, CA, USA March 13-17th, 2005
  • Doctoral research presentation on Aggregation of the SIV peptide in different chemical environments. Gordon Research Conference on Protein Dynamics, Ventura, CA, USA January 11th-16th., 2004
  • Doctoral research presentation on Stability of SIV p32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations. The fourth Georgia Tech and University of Georgia International Conference on Bioinformatics. In Silico Biological Networks: From Genomics to Epidemiology, Atlanta, GA, USA, November 13th-16th., 2003
  • Doctoral research presentation on Characterization of the sterochemical selectivity of b-hairpin formation by molecular dynamics simulations. Nanoscience and Technology Conference, Groningen, The Netherlands, May 18th- 21st., 2003
  • Doctoral research presentation at the Annual Biomes meeting, Burg Arras, Alf-Mosel, Germany about Aggregation of the SIV peptide in different chemical environments., 2003
  • Doctoral research presentation on Aggregation of the SIV peptide in different chemical environments. Meeting of the study group on proteins, Lunteren, The Netherlands., 2003
  • Doctoral research presentation on Characterization of the sterochemical selectivity of b-hairpin formation by molecular dynamics simulations. Biophysics from First Principles EuroConference: From the Electronic to the Mesoscale, San Feliu de Guixols, Spain, September 7th- 12th., 2002
  • Doctoral research presentation on a systematic molecular dynamics study of the conformational behavior of Betanova and its mutants. ESS Workshop: Flexibility and Function of Proteins, Heidelberg, Germany, January 25th- 27th., 2002
  • Doctoral research presentation at the Annual Biomes meeting, Burg Arras, Alf-Mosel, Germany about a Characterization of the sterochemical selectivity of b-hairpin formation by molecular dynamics simulations, 2002
  • Doctoral research presentation on Characterization of the stereochemical selectivity of b-hairpin formation by molecular dynamics simulations. Meeting of the study group on proteins, Lunteren, The Netherlands., 2002
  • Doctoral research presentation on a molecular dynamics study of a three stranded antiparallel b-sheet forming peptide and some of its mutants. Conference of the SIMU Program "Bridging the Time-Scale Gap", Konstanz, Germany, September 10th-13th., 2001
  • Doctoral research presentation on a molecular dynamics study of a three stranded antiparallel b-sheet forming peptide and some of its mutants. 27th meeting on the Federation of European biochemical societies FEBS. Lisbon, Portugal, June 30th - July 5th., 2001
  • Doctoral research presentation on a molecular dynamics study of a three stranded antiparallel b-sheet forming peptide and some of its mutants. FEBS Forum of Young Scientists. Protein Structure-Function, Trafficking and Signaling. Instituto de Tecnologia Quimica e Biologica ITQB, Oeiras, Portugal, June 28th- 30th, 2001
  • Doctoral research presentation at the Annual Biomes meeting, Burg Arras, Alf-Mosel, Germany about a molecular dynamics study of Betanova and its mutants, 2001
  • Doctoral research presentation on A systematic molecular dynamics study of the conformational behavior of Betanova and its mutants. Meeting of the study group on proteins, Lunteren, The Netherlands., 2001
  • Doctoral research presentation at the Annual Biomes meeting, Burg Arras, Alf-Mosel, Germany about a molecular dynamics study of Betanova, 2000
  • Master studies presentation on molecular modeling of a synthetic malaria peptide. XIII International Congress IUPAB, New Delhi, India, September 19th- 24th., 1999
  • A molecular modeling of the melting ion channel. Congreso Nacional de Fisica ( National Congress of Physics), Medellin, Columbia, June 1997, 1997

Research and Scholarship

Research and Scholarship Interests

  • Science topics: protein conformational dynamics, pathological protein folding. Technique: computational statistical mechanics, structural bioinformatics, biomolecular modeling, molecular dynamics simulations, molecular docking, normal mode analysis, continuum electrostatics

Current Research Projects

  • Conformational dynamics of amyloid proteins at the cell membrane interface.

Grant Funding Received

  • NSF-TUES. "Conference on Introductory Physics for Life Sciences"
  • NE EPSCoR FIRST award
  • Teragrid: 30,000 hours of computer time.
  • Creighton University Magis Core Curriculum grant for the new course of General Physics Lab II PHY 206.
  • Creighton University - CURAS Faculty Fellowship 2014
  • Creighton University George Haddix President Fund 2012- 2013
  • Creighton University, Graduate school 2011
  • Creighton University George Haddix President Fund 2015- 2016
  • NIH INBRE DRPP

Awards and Honors

  • MAC travel award to attend 59th Biophysical Society meeting, Biophysical Society, 2014
  • Faculty Mission Fellowship, College of Arts and Sciences, Creighton University, 2013