Kelly M. Thayer has extensive experience in teaching and research related to biochemistry and molecular biology. She received her Ph.D. in Molecular Biophysics from Wesleyan University and has held teaching positions at Skidmore College, Vassar College, and Assumption College where she taught courses including biochemistry, principles of chemistry, organic evolution, and physical chemistry. Her research focuses on computational studies of tumor suppressor protein p53 using molecular dynamics simulations and molecular modeling.

1. KELLY M. THAYER, Ph.D.
Skidmore College, Department of Chemistry, 815 N Broadway, Saratoga Springs, NY 12866 USA
kthayer@skidmore.edu kthayer@wesleyan.edu work 518-580-5461 cell 860-834-3011
EDUCATION
- Ph.D Molecular Biophysics Program, Molecular Biology and Biochemistry Dept.,Wesleyan University,
Middletown, CT, May 2004. GPA 3.86
- B.A. Biochemistry, Regis College, Weston, MA, 1995, summa cum laude. Minors in mathematics and English.
GPA 3.96
TEACHING EXPERIENCE
Visiting Asst. Prof. of Chemistry, Skidmore College, Saratoga Springs, NY 08/2015 to 05/2016:
- Biochemistry: Macromolecular Structure and Function, CH 341 – biological chemistry of proteins,
carbohydrates, lipids, nucleic acids, and enzymes with a focus on molecular level structure-function
relationships.
- Biochemistry: Macromolecular Structure and Function Lab, CH 341L – Laboratory component of
biochemistry course. Topics include protein purification, characterization, and identification by electrophoresis,
spectroscopy and Western blot assay, molecular cloning using plasmids in E. coli, PCR, DNA quantitation and
purification with polyacrylamide gels.
- Principles of Chemistry, CH 125 – introduction to fundamental principles of chemistry. Topics covered
include atomic and molecular structure, periodic table, gas laws, kinetics, equilibria, acids and bases,
electrochemistry, and thermodynamics.
- Principles of Chemistry Lab, CH 125L – Experimental component to complement the lecture portion of the
course. Topics include use of volumetric glassware, acid base titration, equilibria.
Visiting Asst. Prof. of Chemistry, Vassar College, Poughkeepsie, NY. 08/2013 to 07/2015:
- Physical Chemistry: Molecular Structure, Chem 352 (2 years) – quantum mechanics, covering the
emergence of the field, particle in a box, 1D and 2D harmonic oscillator, rigid rotator, hydrogen atom,
polyelectron systems, basis sets, solving Slater’s determinants, and applications to spectroscopy. I developed a
laboratory component teaching students to implement the Guassian QM software to compute electronic
configurations, geometry optimization, IR spectrum prediction, and partial atomic charges. Based on these
exercises, students carried out original research addressing three questions and wrote a final journal-style article
and gave an oral presentation and some traveled to present at national meetings.
- Physical Chemistry: Thermodynamics and Chemical Kinetics, Chem 350 (2 years) – This course covers an
in depth discussion of the properties and models of gases, partition functions, the three laws of thermodynamics,
free energies, phase equilibria, equilibrium dynamics, kinetic theory of gases, and rate laws and mechanisms. I
developed a lab component in which we carried out protein and RNA folding, molecular modeling with PyMol,
and short molecular dynamics using the Amber suite. Students investigated three original questions based on
these computer exercises and wrote a final journal-style article and gave an oral presentation.
- General Chemistry, Chem 108 – This is a two part course in introductory chemistry intended for science
majors and premedical students. Topics include atoms and molecules, bonding, molecular orbital theory, states
of matter, stoichiometry, and reactions. The course included lectures, problem solving, and regular assignments.
- General Chemistry Lab, Chem 108 - Weekly laboratory sessions paralleled the lecture portion. Experiments
included an introduction to volumetric glassware, UV-Vis spectroscopy, acid-base titrations, volumetric
measurement of gas given off by metal-acid reaction, studies of equilibrium via equilibrium perturbation, and
classification and identification of unknowns. I graded prelab exercises, gave weekly prelab lectures, taught the
lab, supervised data collection and graded lab notebooks, and graded weekly journal article style lab reports
based on writing content, accuracy and precision of results and calculations, and contextualization of results in
scientific literature.
- General Chemistry, Chem 109 Laboratory – Paralleling the lecture content, the laboratory component of the
second half of the course features titrations, more advanced applications of UV Vis, redox reactions,
crystallization for purification, acid-base reactions, and identification of unknowns utilizing solubility properties

2. KELLY M. THAYER, Ph.D.
Skidmore College, Department of Chemistry, 815 N Broadway, Saratoga Springs, NY 12866 USA
kthayer@skidmore.edu kthayer@wesleyan.edu work 518-580-5461 cell 860-834-3011
and equilibria. My duties were the same as 108 Lab.
- Chemical Principles, Chem 125 Lecture (taught twice) – This is an advanced chemistry course condensing the
content of the 108-109 sequence into a single semester. This course encouraged students to develop strong
problem solving techniques to enhance independent learning beyond the basics for students already having a
chemistry background.
- Chemical Principles Lab, Chem 125 Lab - The laboratory component parallels the course with a selection of
experiments from the 108-109 series modified to an advanced level. My duties were the same as for above labs.
Adjunct Professor of Natural Sciences, Assumption College, Worcester, MA. 01/2013 to 05/2013:
- Organic Evolution, BIO 320 - upper level majors course serving as in introduction to genetic changes in
populations over time, and the models and evidence to identify and explain those changes. Topics include:
environmental effects, genotype-phenotype connections, Hardy-Weinberg equilibrium, natural selection, gene
flow, phylogeny, macroevolutionary trends, and fossil record analysis. Introduced computer exercises and data
analysis to enhance classroom learning, and course culminated in research presentations for original student
research based on the computer exercises.
Teaching at Wesleyan University, Middletown, CT. 09/1999 to 05/2004:
- Physical Chemistry for Life Scientists, Chem/MB&B 381/581 (2 years) some lecturing, grading, writing
problem sets, running problem solving sessions for non-major undergraduate students and graduate students.
- Molecular Dynamics and Molecular Modeling, Chem 388. (2 years plus taught summer session) Included
some lecturing, writing weekly computer exercises, developing course materials, running the weekly computer
exercise portion of the class, and grading.
- Bioinformatics: Genomics and Proteomics, Chem/MB&B 389 (1 year) Following the Cold Spring Harbor
text, this course surveyed the field of bioinformatics from the perspective of theory and practice, covering topics
such as multiple sequence alignment, clustering algorithms, blast searches, Hidden Markov Models, machine
learning and grammars. I participated in developing this course as the pilot course for the newly established
Bioinformatics Program. Included substantial lecturing, developing course materials, grading, writing problem
sets and exams, and mentoring all course related original student research projects.
- Principles of Molecular Biology I&II/Lab, Biol/MB&B 205&206/215&216 (1 year) Instructing laboratory
sections for introductory molecular biology and developmental biology including lecturing, writing and
administering quizzes, advising final projects, grading; Holding office hours, grading exams.
RESEARCH APPOINTMENTS
Principle Investigator, Department of Chemistry, Skidmore College, Saratoga Springs, NY 08/2015 to
05/2016
- Computational Studies of p53 Tumor Suppressor Protein. Work with undergraduate researchers to
investigate the structure and dynamics of p53.
Visiting Scholar of Biophysics, Molecular Biophysics Program, Wesleyan University, Middletown, CT
06/2015 to 08/2015.
- Markov State Models from Systems of MD Simulations to Capture Allostery of p53 Tumor Suppressor
Protein. Developed novel methodology in the PDZ model system exhibiting allostery and applied the
technique to study post-translational modification effects on the structure and dynamics of p53. MS in
preparation.
- Casting Allostery in the Flux Balance Framework. Applying the flux balance framework to obtain the master
equation describing allostery as derived from molecular dynamics simulation.

3. KELLY M. THAYER, Ph.D.
Skidmore College, Department of Chemistry, 815 N Broadway, Saratoga Springs, NY 12866 USA
kthayer@skidmore.edu kthayer@wesleyan.edu work 518-580-5461 cell 860-834-3011
Principle Investigator, Department of Chemistry, Vassar College, Poughkeepsie, NY 09/2013 to 06/2015.
- Molecular Mechanisms of the Binding of p53 Tumor Suppressor Protein to Various Classes of Binding
Sites Investigated via Molecular Dynamics Simulations, Molecular Modelling, and Bioinformatics. Engaged 13
undergraduate researchers and mentored four thesis projects addressing structure and dynamics of p53 protein,
elucidating in molecular mechanism of macromolecular interactions, the effects of mutations, and providing
insight into rational development of novel therapeutics. Two manuscripts submitted and 4 additional
anticipated fall 2015.
Postdoctoral Research Scientist, Medical and National Defense Applications of Molecular Modelling, Univ.
of Mass. Med. School, MIT, and collaborators, Worcester/Boston, MA 01605 06/2007 to 12/2012.
- Structural Bioinformatics and Modelling of Circumsporozoite Protein, Jeffrey Bailey Lab, Program in
Bioinformatics and Integrative Biology. Studied molecular evolution between human immune system and the
rapidly evolving circumsporozoite protein used for development of vaccines.
- Structural Modelling of Effects of Comprehensive Mutagenesis of Ubiquitin, Konstantin Zeldovich and
Dan Bolon labs, Program in Bioinforamtics and Integrative Biology. Energetic study of exhaustively mutated
ubiquitin protein.
- Computational Engineering of Terpenoid Biosynthetic Enzyme, collaboration with Prather Lab, MIT.
Bioengineering with homology modelling of levopimaradiene synthaseenzyme to improve yield and specificity
of diterpenoid products used as precursors to antibiotics and industrial chemicals.
- Molecular Modelling and Molecular Dynamics of HIV-I Protease, Celia Schiffer Lab, Biochemistry and
Molecular Pharmacology, in collaboration with Bruce Tidor, MIT, Cambridge, MA. Carry out molecular
dynamics and energetic studies to characterize proprietary HIV-1 protease inhibitors and inform the engineering
of the next generation with increased potency and decreased susceptibility to mutational resistance.
- Molecular Dynamics and Molecular Modelling of Influenza Virus Neuraminidase. This project was part of
a multicampus collaboration operating under the auspices of DARPA of the US. Dept. of Defense.
Postdoctoral Researcher, Jonathan Widom Lab, Biology Molecular Biology and Biochemistry, and
Chemistry Departments, Northwestern University, Evanston, IL. 09/2004 to 12/2005.
- Experimental Mapping of Nucleosome Positioning. Using site directed hydroxyradial generation with
modified amino acids incorporated into nucleosomes, the sequence specificity of nucleosomal positioning of
genomic and engineered DNA was studied.
Graduate Thesis: Predicting Cyclic AMP Receptor Protein Binding Sites with Hidden Markov Models
from MD Simulations, Doctoral Thesis Studies in David L. Beveridge Lab, Wesleyan University, 1999-2004.
Using probabilistic mathematical modelling tools, a method for incorporation of DNA dynamic structure into
noisy search patterns was developed and utilized to advance prediction of low homology DNA binding sites of
cyclic AMP receptor protein, thereby capturing indirect readout in macromolecular recognition.
PUBLICATIONS
Scientific Research Journal Articles:
- “p53 R175H Hydrophobic Patch and H-Bond Reorganization Observed by MD Simulation.” Thayer, KM
and Quinn, TR. Biopolymers. 2015 Nov 13. doi: 10.1002/bip.22766. [Epub ahead of print].
- Chemical Principles Additive Model Aligns Low Consensus DNA Targets of p53 Tumor Suppressor
Protein.” Thayer KM, Han IM. Computational Biology and Chemistry, submitted.
- “Exhaustive Computational Mutagenesis of the MDM2-p53Interaction: Energetic Landscape of MDM2-
p53 Interactions.” Thayer, KM and Beyer, GA. PLOS One, submitted.
- “DNA Dynamics Contribution of Induced Fit Binding of p53.” Thayer KM and Slaw BR. Journal of

4. KELLY M. THAYER, Ph.D.
Skidmore College, Department of Chemistry, 815 N Broadway, Saratoga Springs, NY 12866 USA
kthayer@skidmore.edu kthayer@wesleyan.edu work 518-580-5461 cell 860-834-3011
Chemical Information and Modeling, MS in prep.
- “Molecular Dynamics of A-tract Motif in Non-Consensus DNA–p53 Complexes Reveal Indirect Readout.”
Thayer, KM and Han, IM. Nucleic Acids Research, MS in prep.
- “Exhaustive Computational Mutagenesis of p53 Identifies Highly Mutable and Highly Constrained
Residues.” Thayer KM, Beyer GA, and Kugelmass L. MS in preparation.
- “A Molecular Dynamics Markov State Model of Protein Allosterism: The CRIP-PDZ Module of the Par-
6 Complex.” Lakhani B, Thayer KM, and Beveridge DL. MS in prep.
- “Markov State Model Captures Allosteric Switch Activating Apoptosis via p53-DNA Interactions.”
Thayer, KM. MS in preparation.
- “Derivation of the Flux Balance Master Equation for Allosteric Response of Protein System.” Thayer,
KM. MS in prep.
- “Diversity of T Cell Epitopes in Plasmodium falciparum Circumsporozoite Protein Likely Due to
Protein-Protein Interactions.” Aragam NA, Thayer KM, Nge N, Hoffman I, Martinson F, Kamwendo D, Lin
FC,Sutherland C, Bailey JA, Juliano JJ. PLOS One. 2013(8)e62427.
- “Analyses of the effects of all ubiquitin point mutants on yeast growth rate.” Roscoe BP, Thayer KM,
Zeldovich KB, Fushman D, Bolon DN. J Mol Biol. 2013(8)1363.
- “Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction
and selectivity control.” Leonard E, Ajikumar PK, Thayer K, Xiao Wh, Mo JD, Ditor B, Stephanopoulos G,
Prather KL. Proceedings of the National Academy of Sciences USA. 107(2010):13654-9.
- “Molecular Basis for Drug Resistance in HIV-1 Protease.” Ali A, Bandaranayake RM, Cai Y, King NM,
Kolli, M, Mittal S, Murzycki JF, Nalam MN, Nalivaika EA, Ozen A, Prabu-Jeyabalan MM, Thayer K, Schiffer
CA. Viruses. 2(2010):2509.
- “Hidden Markov models from molecular dynamics simulations on DNA.” Thayer KM and Beveridge DL.
Proceedings of the National Academy of Sciences USA. 99(2002):8642-8647.
- “Ion motions in molecular dynamics simulations on DNA.” Ponomarev SY, Thayer KM, Beveridge DL.
Proceedings of the National Academy of Sciences USA. 101(2004):14771-5.
- “Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting.”
Beveridge DL, Dixit SB, Barreiro G, Thayer KM. Biopolymers, 73(2004):380-403.
- “Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I:
Research design and results on d(CpG) steps.” Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham III
TE, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer
KM, Varnai P, Young MA. Biophysical Journal 87(2004):3799-813.
- “Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides.
II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.” Dixit SB,
Beveridge DL, Case DA, Cheatham III TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H,
Thayer KM, Varnai P. Biophysical Journal 89(2005):3721.
Book Chapters:
- “Molecular Dynamics Simulations on DNA and Protein-DNA Complexes: Progress on Sequence Effects,
Conformational Stability, Axis Curvature, and Structural Bioinformatics.” D. L. Beveridge, Surjit B. Dixit,
K. Suzie Byun, Gabriela Barreiro, Kelly M. Thayer, and Sergei Y. Ponomarev. In Nucleic Acids: Curvature and
Deformation. Recent Advances and New Paradigms. Nancy C. Stellwagen and Udayan Mohanty, eds. ACS
Symposium Series 884. American Chemical Society Press: New York, 2004.

5. KELLY M. THAYER, Ph.D.
Skidmore College, Department of Chemistry, 815 N Broadway, Saratoga Springs, NY 12866 USA
kthayer@skidmore.edu kthayer@wesleyan.edu work 518-580-5461 cell 860-834-3011
Scientific Education Journal Articles:
- “Neuraminidase Mutations: Structure Prediction and Analysis.” Kelly M. Thayer. Biology and Molecular
Biology Education, Accepted with minor revision.
- “Concretizing the Partition Function with Bead Model Interpretation of RNA Folding.” Kelly M. Thayer.
J Chem Ed, MS in prep.
US PATENTS
-“Methods for Microbial Production of Terpenoids,” U.S. Patent Application No. 13/509,032.
GRANTS AND FUNDING TO THAYER LAB
- Frances D. Ferguson Faculty Technology Exploration Fund - to fund equipment acquisition
- The Christian A. Johnson Endeavor Foundation – to fund an undergraduate researcher
- The Emily Abbey Fund – to fund another undergraduate researcher
- Elise Nichols and Margaret Sawyer Biochemistry Research Fellowship – fund a 3rd undergrad researcher
- The Undergraduate Research Summer Institute (URSI) – funding summer research program
- Diving Into Research Program – funding incoming freshman from underprivileged background
- The Asprey Center for Collaborative Approached to Science - computer time award
PROFESSIONAL ACTIVITIES
- Encore Series, 10/2015, Saratoga Springs, NY. Public outreach educational series. Invited speaker.
- American Chemical Society 250th
National Meeting, 08/2015, Boston, MA. Platform talk ANAL section:
“p53-DNA Interactions: Molecular Insights for Cancer Therapies.”
- Wesleyan University Chemistry Symposium Invited Speaker, 05/2015, Middletown, CT. “Molecular
Dynamics Simulations of p53 Tumor Suppressor Protein.”
- American Society of Biology and Molecular Biology, 04/2015, Boston, MA. 6 posters.
- Mid-Hudson American Chemical Society, 04/2015, SUNY New Paltz, NY. 10 posters.
- 13th
MERCURY Conference. 07/2014, Bucknell University. Molecular Education and Research Consortium
in Undergraduate Computational Chemistry Conference. 6 posters.
- Schrӧdinger Computational Chemistry. 05/2014, Princeton, NJ. Participant.
- Mid-Hudson American Chemical Society, 04/2014, SUNY New Paltz, NY. Poster.
- New Directions in Evolutionary and Population Genetics. 06/2010. The State University of New Jersey
Rutgers, Piscataway, NJ. Poster.
- HIV Program Project Convention. 05/2009. Beechwood, Worcester, MA. Oral presentation.
- NIH-Sponsored HIV Research Convention. 04/2009. University of Maryland, Bethesda, MD. Poster.
- NIH-Sponsored HIV Research Convention. 04/2008. University of Maryland, Bethesda, MD. Poster.
- Gordon Research Conference on Nucleic Acids. 06/2004. Salve Regina University, Newport, RI. Poster.
- Biophysical Society, 48th
Meeting, 02/2004. Baltimore, MD. Poster presentation.
- Thirteenth Conversation in Biomolecular Stereodynamics. 06/2003. SUNY Albany, Albany, NY. Poster.
- American Chemical Society 225th
National Meeting, 03/2003. New Orleans, LA. Platform presentation.
- American Chemical Society East Texas Meeting. 11/2002. Panola College, Carthage, Texas. Keynote
speaker and invited speaker to several area colleges.
- NSF Workshop: Molecular Genetics and Protein Structure/Function Techniques. 08/2002. Georgia
Institute of Technology and Georgia State University, Atlanta, Georgia. workshop attendee.
- NSF Workshop: Computational and Theoretical Chemistry. 06/2002. Georgia Institute of Technology,
Atlanta, Georgia. Workshop attendee.
- American Chemical Society 223rd National Meeting, 04/2002. Orlando, Florida. Platform presentation.
- CECAM workshop From DNA sequence to Function 09/2001 to 09/2001 Lyon, France. Oral presentation.

6. KELLY M. THAYER, Ph.D.
Skidmore College, Department of Chemistry, 815 N Broadway, Saratoga Springs, NY 12866 USA
kthayer@skidmore.edu kthayer@wesleyan.edu work 518-580-5461 cell 860-834-3011
- CECAM workshop Single molecule studies: From experiments to their analysis. Lyon, France. Attendee.
- Atomistic to Continuum Models for Long Molecules and Thin Films. 07/2001. Ascona, Switzerland. Poster.
- Twelfth Conversation in Biomolecular Stereodynamics. 06/2001. Albany, New York. Poster.
- Methods for Macromolecular Modeling. 10/2000. New York University, New York, NY. Attendee.
- New England Psychological Association (NEPA) 10/1998. Providence, RI. Platform presentation.
ACADEMIC AWARDS AND HONORS
- National Institute of Health (NIH) Graduate Traineeship in Molecular Biophysics Grant GM-08271
- Peterson Fellowship for excellence in graduate biochemistry research, Wesleyan University, May 2004.
- American Chemical Society (ACS) member beginning 2002.
- Biophysical Society member beginning 2003.
- Beta Beta Beta Biological Society – inducted in 1997 in Regis College chapter.
SERVICE TO COLLEGE/UNIVERSITY
Vassar College Service:
- Pre-Major Advisor to freshman science majors
- Fellowship Committee to recommend students for national scholarships and fellowships
- International Student Host Program – host incoming freshmen from abroad
- Chemistry Department Service - Chem dept representative at recruiting and accepted students events.
Wesleyan University Service:
- Graduate Council Representative - graduate student government body
- MB&B/Biophysics Program Service - interview perspective faculty and grad students and provide reports
- Housing Committee – negotiate and implement policies dealing with grad student housing
- Qualifier Study Group – organize comprehensive review of contents on qualifier exam in weekly meetings.
COMMUNITY SERVICE
- Board of Directors and Finance Committee at Abby's House, a non-profit organization serving homeless
women and children of central Massachusetts; staff emergency overnight shelter; volunteer at the thrift shop.
- Board of Advisors at Spirit of Hope, a non-profit sponsoring volunteers to perform service work in Haiti.
- Performing Arts -semiprofessional violinist in Chicago Businessmen’s Orchestra (Chicago, IL), Seven Hills
Symphony Orchestra (Worcester, MA).
- Music Ministry -volunteer as a choral member in my hometown church.
ADDITIONAL SKILLS
- Computer and Technology Skills include high performance computing, proficiency in Microsoft, Linux, and
Mac operating systems. System administration experience. Code development in Fortran, C and B shells, C
languages, Visual Basic, Perl, Python. Web master experience, FrontPage, HTML, database programming
MYSQL, MS Access. Molecular modelling software includes AMBER, AMBER Tools, CHARMM, Gaussian,
VMD, PyMol. Technology into the classroom. Blackboard, Moodle, Sapling Learning. Online instruction.
- Extracurricular hiking, camping, run 5K, travel, drawing and painting, digital arts, writing fiction and poetry.
- Language Proficiency read and write Spanish at an advanced level, speak conversantly.