Derek J. Cashman, Ph.D.

Curriculum Vitae

Computational Biophysical Chemist with over a decade of post-graduate experience specializing in structure-based drug design and molecular simulations of proteins and nucleic acids. The focus of my research is to connect virtual high-throughput screening and docking and scoring with the molecular modeling of protein fluctuations, utilizing molecular dynamics or Monte Carlo simulations, in order to better incorporate protein flexibility into structure-based drug design. Highly experienced in the use and parallel programming of High Performance Computing (HPC) systems, including supercomputing clusters such as ORNL’s TITAN and KRAKEN supercomputers. Author of over 15 peer-reviewed journal articles and presented research at over 35 regional and national scientific meetings. Teaching experience includes courses in chemistry and biochemistry with an emphasis on applications to the pharmaceutical biotechnology and energy industries, serving as a research mentor to undergraduate and graduate students, and the organization of peer-mentoring events and activities, such as a monthly seminar series and an annual poster symposium.

Professional Experience

Tennessee Technological University

  • Lecturer (2016 – present)
  • Instructor (2013 – 2016)

Teach biochemistry lecture and laboratory, physical chemistry and biophysics, introductory chemistry and organic chemistry.
Developing novel laboratory curriculum sessions in computational chemistry for undergraduate students.
Advising and mentoring of undergraduate and graduate students on original research projects related to computational chemistry and molecular biophysics.
Mentored high school students in computational chemistry methods as part of the Governor’s School for Emerging Technologies.

University of Tennessee at Knoxville / Oak Ridge National Laboratory

Performed homology modeling, molecular dynamics, and Monte Carlo simulations of bacterial chemotaxis proteins using bioinformatics, phylogenetic analysis, and experimental data as a guide, resulting in an improved understanding of their overall protein-protein interactions and dynamics.
Performed protein-protein docking calculations on bacterial chemotaxis proteins, as well as Ferredoxin and Photosystem I, guided by energy landscape theory, machine learning and experimental data, resulting in potential docked complexes and the characterization of key protein-protein interactions.
Advised and mentored graduate and undergraduate students on computational methodology and methods of homology modeling and protein-protein interactions.
Taught lectures on biophysical chemistry, computational chemistry, and facilitated discussion sessions on research topics for students in the department.

University of Pittsburgh

Simulation of protein systems using molecular dynamics & Monte Carlo methods, including those involved in bacterial chemotaxis and cancer, as part of the development and validation of Library-Based Monte Carlo (LBMC) software. LBMC enables faster sampling of protein configurational dynamics on desktop-capable workstations, providing a tremendous benefit for ensemble docking calculations.
Served as the Marketing & Communications Officers of the University of Pittsburgh Postdoctoral Association in 2009. Responsible for coordinating and advertising peer-mentoring events, including a monthly seminar series and an annual poster symposium for other postdoctoral researchers.

Northern Arizona University

Construction of homology models, virtual screening, biophysical characterization (ITC, DSC, spectroscopy), and molecular dynamics simulation of elements of telomeric DNA (G-quadruplex, i-Motif), resulting in an improved understanding of the pharmacophore and the identification of potential new lead compounds for cancer research.
Served as a mentor for undergraduate and graduate students in the laboratory, educating them on proper laboratory procedure and computational theory and methodology on a variety of research projects.

University of Louisville

  • Postdoctoral Research Fellow, Dr. Jonathan B. Chaires (2004 – 2005)

Developed a structural model for the binding of bis-anthracycline compounds to several sequences of double-stranded DNA, resulting in the identification of preferred binding sequences as well as the ability to visualize the pharmacophore of a new and potentially groundbreaking anticancer drug.
Assisted with the setup of a state-of-the-art biophysical core facility at the James Graham Brown Cancer Center.

Virginia Commonwealth University

  • Graduate Research & Teaching Assistant, Dr. Glen E. Kellogg (1998 – 2003)

Performed a virtual screening analysis of Doxorubicin analogs, including docking and free energy estimation of compounds to variable sequences of DNA, resulting in the identification of several modified compounds with increased affinity towards specific sequences.
Performed docking and free energy estimation of aminoglycoside analog binding to 16S ribosomal RNA, resulting in a better understanding of the mechanism by which the compounds interacted in their binding pocket.
Taught courses and laboratory sessions in chemistry and biochemistry, as well as computational tutorials and methodologies in QSAR and molecular modeling.
Assisted in the development of outreach activities to visiting high school, undergraduate, and graduate students visiting the Virginia Biotechnology Research Park.

Teaching Experience

Tennessee Technological University

  • Nutritional Biochemistry (CHEM 4500)
  • General Biochemistry (CHEM 4610/5610/4620/5620)
  • Biochemistry Laboratory (CHEM 4650/5650)
  • Physical Chemistry (CHEM 3510/3520)
  • Physical Chemistry for the Life Sciences (CHEM 3500)
  • Quantum Chemistry (CHEM 5970)
  • Advanced Biochemistry (CHEM 6610)
  • Advanced Molecular Modeling (CHEM 6970)
  • Introductory Chemistry (CHEM 1010/1020)
  • Organic Chemistry (CHEM 3010)
  • Chemistry of Beer (CHEM 4970)

University of Tennessee at Knoxville

  • Introduction to Molecular Biophysics (BCMB 420/520/610)
  • Topics in Biochemistry, Biophysics and Molecular Biology (BCMB 601)

Virginia Commonwealth University

  • Pharmaceutical Analysis Laboratory (MEDC 602)
  • Biochemistry/Molecular Biology: (BIOC/MICR 503/504)
  • Advanced Molecular Modeling: (MEDC 630/670)

Grant Funding

Cashman, D.J.; Baudry, J.B. Elucidation of the Protein-Protein Binding/Dynamics of Electron Transport Proteins with Cyanobacterial Photosystem I. TN-SCORE (Tennessee EPSCoR, NSF EPS-1004083). December 2014. $23,719 (TTU – Cashman) + $8,000 (UTK – Baudry) = $31,719. Funded.

Zhan, X. (PI); Cashman, D.J. (co-PI). Assembly, Dynamics and Allosteric Regulation of Arrestin-Mediated MAPK Cascades. National Science Foundation. Submitted: November 15, 2015. $395,637. Not Funded.

Renfro, M. (PI); Leckie, B. (co-PI); Hurt, C. (co-PI); Krosnick, S. (co-PI);Walker, D. (co-PI); Biernacki, J. (co-PI); Pascal, J. (co-PI); Zhang, L. (co-PI); Cashman, D.J. (co-PI); Datta, T. (co-PI); Kalyanapu, A. (co-PI); Ghafoor, S. (co-PI); Scott, S. (co-PI); Wolak, J. (co-PI); Cui, J. (co-PI); Languri, E. (co-PI); Shirvanian, A. (co-PI); Wilson, C. (co-PI); Holley, A. (co-PI); Kidd, M. (co-PI); Rajabali, M. (co-PI). HPC Computing Grant, Silicon Mechanics. Submitted: February 29, 2016. $100,000. Not funded.

Zhan, X. (PI); Cashman, D.J. (co-PI). Assembly, Regulation and Catalysis of ASK1-initiated MAPK Cascades, National Science Foundation. Submitted November 15, 2016. $361,814. Not funded.

Cashman, D.J.; Callendar, A. The Science and Chemistry of Beer. EDGE Course Development Grant,

Quality Enhancement Program (QEP), Tennessee Technological University. May 2018. $8,000. Funded.

Jiang, X.; Cashman, D.I.; Zhan, X. Redesign and Incorporation of 3D Modeling into Undergraduate Biochemistry Laboratory. EDGE Course Development Grant, Quality Enhancement Program (QEP), Tennessee Technological University, November 2019. $9100. Funded.

Renfro, M.; Hurt, C.; Cashman, D.J.; Vaselbehagh, A.; Eberle, W. Acquisition of a Next Generation High Performance Computing Cluster at Tennessee Tech. Major Research Infrastructure, National Science Foundation. Submitted January 2021. $988,702. Pending.

Computer Experience

  • Highly skilled with several molecular modeling software packages, including MOE 2020, Hyperchem, Gaussian 09, Tripos Sybyl, Accelrys Discovery Studio, VMD, InsightII, Cerius2, PC SPARTAN, MacroModel, HINT (www.edusoft-lc.com), Unity, GRID, GAMESS, DOCK, Curves, and MDL QSAR.
  • Experienced with molecular dynamics software packages: AMBER, Gromacs, NAMD.
  • Experienced with High Performance Computing (HPC clusters, MPI, and multi-processor applications and simulations.
  • Experienced with programming in C/C++, Java, JavaScript, Fortran, Perl, PHP, MySQL, HTML, CSS.
  • Experienced with Mac OS X, Linux (Opensuse, Ubuntu, Red Hat), and Microsoft Windows. Experienced with Microsoft Office, ChemDraw, LibreOffice, Adobe Photoshop.

Education

Ph.D., Pharmaceutical Sciences (Concentration in Medicinal Chemistry)
Virginia Commonwealth University, Richmond, Virginia
December 2003

Dissertation: A Computational Model for Targeting Nucleic Acids: Estimating Changes in Free Energy of Drugs in Complex with RNA and Variable Sequences of DNA. (Advisor: Glen E. Kellogg, Ph.D.)


B.S., Biology (Minor: Chemistry)
Old Dominion University, Norfolk, Virginia
May 1995

Publications

  1. Kellogg, G.E.; Scarsdale, J.N.; Cashman, D.J. (1999) Ligand Docking and Scoring in DNA Oligonucleotides. Binding of Doxorubicin and Modeled Analogs to Optimize Sequence Specificity. Medicinal Chemistry Research, Vol. 9, No. 7/8, 592 – 603.
  2. Cashman, D.J.; Rife, J.P.; Kellogg, G.E. (2001) Which Aminoglycoside Ring Is Most Important For Binding? A Hydropathic Analysis of Gentamicin, Paromomycin, and Analogues. Bioorganic & Medicinal Chemistry Letters, Vol. 11, 119 – 122.
  3. Cashman, D.J.; Scarsdale, J.N.; Kellogg, G.E. (2003) Hydropathic Analysis of the Free Energy Differences in Anthracycline Antibiotic Binding to DNA. Nucleic Acids Research, Vol. 31, No. 15, 4410 – 4416.
  4. Cashman, D.J. & Kellogg, G.E. (2004) A Computational Model for Anthracycline Antibiotic Binding to DNA: Tuning Groove-Binding Intercalators for Specific Sequences. Journal of Medicinal Chemistry, Vol. 47, 1360 – 1374.
  5. Cashman, D.J.; Rife, J.P.; Kellogg, G.E. (2004) Docking and Hydropathic Analysis of Hoechst 33258 with Double-Stranded RNA. Medicinal Chemistry Research, Vol. 12, No. 8, 445 – 455.
  6. Portugal, J.; Cashman, D.J.; Trent, J.O.; Ferrer-Miralles, N.; Przewloka, T.; Fokt, I.; Priebe, W.; Chaires, J.B. (2005) A New Bisintercalating Anthracycline with Picomolar DNA Binding Affinity. Journal of Medicinal Chemistry, Vol. 48, 8209 – 8219.
  7. Freyer, M.W.; Buscaglia, R.; Cashman, D.J.; Hyslop, S.; Wilson, W.D.; Chaires, J.B. Lewis, E.A. (2006) Binding of Netropsin to Several DNA Constructs: Evidence For at Least Two Different 1:1 Complexes Formed From an –AATT–containing ds–DNA Construct and a Single Minor Groove Binding Ligand. Biophysical Chemistry, Vol. 126, 186 – 196.
  8. Freyer, M.W.; Buscaglia, R.; Kaplan, K.; Cashman, D.J.; Hurley, L.H.; Lewis, E.A. (2007) Biophysical Studies of the c-MYC NHE-III1 Promoter: Model Quadruplex Interactions with a Cationic Porphyrin. Biophysical Journal, Vol. 92, 2007 – 2015.
  9. Cashman, D.J.; Freyer, M.W.; Dettler, J.M.; Hurley, L.H.; Lewis, E.A. (2008) Molecular Modeling and Biophysical Analysis of the c-MYC NHE-III1 Silencer Element. Journal of Molecular Modeling, Vol. 14, No. 2, 92 – 101.
  10. Mamonov, A.B.; Bhatt, D.; Cashman, D.J.; Ding, Y.; Zuckerman, D.M. (2009) General Library-Based Monte Carlo Technique Enables Rapid Equilibrium Sampling of a Protein Model with Atomistic Components. J. Phys. Chem. B, Vol. 113, No. 31, 10891 – 10904.
  11. Dettler, J.; Buscaglia, R.; Cui, J.-J.; Cashman, D.J.; Blynn, M.; Lewis, E.A. (2010) Biophysical Characterization of an Ensemble of Intramolecular i-Motifs Formed by the Human c-MYC NHE-III1 P1 Promoter Mutant Sequence, Biophysical Journal, 99(2), 561 – 567.
  12. Cashman, D.J.; Mamonov, A.B.; Bhatt, D.; Zuckerman, D.M. (2011) Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Using Well-Sampled Semi-Atomistic Monte Carlo Simulations. Current Topics in Medicinal Chemistry, Vol. 11, Issue 2, 211-220.
  13. Cashman, D.J.; Ortega, D.R.; Zhulin, I.B.; Baudry, J.Y. (2013) Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex. PLOS ONE, Vol. 8, Issue 8, e70705.
  14. Cashman, D.J.; Zhu, T.; Scott, C.; Bruce, B.; Baudry, J. (2014) Molecular Interactions Between Photosystem I and Ferredoxin: An Integrated Energy Frustration and Experimental Model. Journal of Molecular Recognition, Vol. 27, 597-608.
  15. Ahmed, M.H.; Amadasi, A.; Bayden, A.S.; Cashman, D.J.; Cozzini, P.; Da, C.; Chen, D.L.; Fornabaio, M.; Koparde, V.N.; Mozzarelli, A.; Parikh, H.I.; Sarkar, A.; Scarsdale, J.N.; Spyrakis, F.; Zaidi, S.A.; Kellogg, G.E. Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery, in Methods in Pharmacology and Toxicology (2015).
  16. Kapoor, K.; Cashman, D.J.; Nientimp, L.; Bruce, B.D.; Baudry, J. (2018) Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model. J. Phys. Chem. B, Vol. 122 (3), 1026 – 1036. Co-First Author *.
  17. Swartling, D.J.; Coonce, J.G.; Cashman, D. J. (2018) Using Balloons to Model Pi-Conjugated Systems and to Teach Frontier Molecular Orbital Theory. World Journal of Chemical Education, Vol. 6 (2), 102-106.
  18. Morris, W.H.; Ngo, L.; Wilson, J.T.; Medawala, W.; Brown, A.; Conner, J.D.; Fabunmi, F.; Cashman, D.J.; Lisic, E.C.; Yu, T.; Deweese, J.E.; Jiang, X. (2019) Structural and Metal Ion Effects on Human Topoisomerase IIα Inhibition by α-(N)-Heterocyclic Thiosemicarbazones. Chemical Research in Toxicology, Vol. 32 (1), 90-99.
  19. Hill, A.R.; Cashman, D.J.; Boles, J.O. (2020) Computational Analysis of Wild-type and Selenium-Incorporated Down-regulated Proteins in E. coli. The FASEB Journal, Vol. 34, Issue S1, 1-1.
  20. Zaharias, S.; Scull, N.; Zhang, Zihan; Davis, K.; Fargason, T.; Cashman, D.J.; Yu, T.; Lucius, A.; Zhang, J. Intrinsically disordered electronegative clusters improve protein stability and binding specificity of RNA-binding proteins. Manuscript submitted to Journal of Chemical Biology; Manuscript under review.
  21. Davis, C.W.; Pleinis, J.M.; Howlader, S.I.; Carter, K.N.; Trybala, T.N.; Cashman, D.J.; Zhan, X. Structural Basis of Docking Interactions among the Kinase Domains with ASK1-MKK-JNK3 Cascades. Manuscript in preparation.

Presentations

  1. Cashman, D.J.; Kellogg, G.E. Docking and Scoring of Doxorubicin and 24 Analogs in DNA to Analyze Sequence Specificity. Sixteenth Annual Daniel T. Watts Symposium, Virginia Commonwealth University, Richmond, Virginia, November 1999. Poster
  2. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Docking and Scoring of Doxorubicin Analogs in DNA to Analyze Sequence Specificity. Virginia Meeting of the American Cancer Society, Norfolk, Virginia, March 2000. Oral
  3. Cashman, D.J.; Kellogg, G.E. Docking and Scoring of Doxorubicin and 40 Analogs in DNA to Analyze Sequence Specificity. School of Pharmacy Research Day, Virginia Commonwealth University, September 2000. Poster
  4. Cashman, D.J.; Kellogg, G.E.; Rife, J.P. Which Aminoglycoside Ring is Most Important to Binding? A Hydropathic Analysis of Gentamicin, Paromomycin, and Analogues. Seventeenth Annual Daniel T. Watts Symposium, Virginia Commonwealth University, Richmond, Virginia. October 2000. Poster
  5. Cashman, D.J.; Kellogg, G.E.; Rife, J.P. Determination of Hoechst 33258 Drug Binding Site in mRNA Using a Thermodynamic Molecular Probe. Eighteenth Annual Daniel T. Watts Symposium, Virginia Commonwealth University, Richmond, Virginia, October 2001. Poster
  6. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. The Hydropathic Analysis of DNA Intercalators to Design Highly Sequence-Specific Compounds. 80th Virginia Academy of Sciences Meeting, Hampton, Virginia, May 2002. Oral
  7. Cashman, D.J.; Kellogg, G.E. Scarsdale, J.N. Molecular Modeling of Doxorubicin Analogs with DNA Base Pair Quartet Sequences to Optimize Specificity. Bioinformatics & Pharmacogenomics 2002, Virginia Bioinformatics Consortium, Richmond, Virginia, June 12-14, 2002. Poster
  8. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Docking and Scoring of 60 Doxorubicin Analogs with 6 Unique DNA Base Pair Quartet Sequences to Optimize Sequence Specificity. Massey Cancer Center 2002 Research Retreat, Richmond, Virginia, June 14, 2002. Poster
  9. Cashman, D.J.; Kellogg, G.E. Scarsdale, J.N. Sequence Specificity Analysis of 60 Doxorubicin Analogs with 6 Unique DNA Sequences by Hydropathic Molecular Modeling Methods.” 224th ACS National Meeting, Boston, MA, August 18-22, 2002. Oral
  10. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Molecular Modeling Studies of 60 Doxorubicin Analogs in 6 Unique DNA Base Pair Quartet Sequences to Optimize Sequence Specificity. VCU Watts Day Symposium, October 2002. Poster
  11. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Molecular Modeling Studies of 60 Doxorubicin Analogs in 6 Unique DNA Base Pair Quartet Sequences to Optimize Sequence Specificity. VCU School of Pharmacy Research Day, November 2002. Poster
  12. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Determination of DNA Sequence Specificity of a Series of Doxorubicin Analogs Based on Hydropathic Molecular Modeling Studies.225th ACS National Meeting, New Orleans, LA, March 23-27, 2003. Oral
  13. Cashman, D.J.; Kellogg, G.E.; Scarsdale, J.N. Determination of the Free Energy Differences in Anthracycline Antibiotic Binding to DNA by Hydropathic Methods. Graduate Research Association of Students in Pharmacy (GRASP) Conference, Virginia Commonwealth University, Richmond, VA, May 30 – June 2, 2003. Oral
  14. Cashman, D.J.; Chaires, J.B. Quantitative Analysis of Experimental Binding Affinities of 126 DNA-Binding Compounds verses 13 Nucleic Acid Sequences to Investigate Specificity. UT-ORNL Bioinformatics Summit 2005, Lake Barkley State Park, Cadiz, KY, April 1 – 3, 2005. Oral & Poster
  15. Cashman, D.J.; Lewis, E.A. Docking & Scoring of Netropsin to a DNA Duplex Structure. Annual UA-NAU Hurley Research Retreat, Carefree Resort & Villas, Carefree, AZ, February 25, 2006. Oral
  16. Cashman, D.J.; Lewis, E.A. Computational Analysis of the c-MYC NHE-III1 Silencer Element. Annual UA-NAU Hurley Research Retreat, Carefree Resort & Villas, Carefree, AZ, November 17-19, 2006. Oral
  17. Cashman, D.J.; Zuckerman, D.M. An Analysis of the Thermal Motions of Surface a-Helices in the E. coli D-Galactose Chemosensory Receptor using Coarse-Grained Monte Carlo Simulations. Third Annual Data & Dine Symposium, University of Pittsburgh Postdoctoral Association, University of Pittsburgh, Pittsburgh, PA. May 8, 2008. Poster
  18. Cashman, D.J.; Zuckerman, D.M. Insights into the Thermal Motions of the Glucose-Galactose Binding Protein in E. Coli Using a Semi-Atomistic Monte Carlo Simulation Method. Monthly Post-Doctoral Lunchtime Seminar Series. University of Pittsburgh Postdoctoral Association, University of Pittsburgh, Pittsburgh, PA. November 9, 2008. Oral
  19. Cashman, D.J.; Mamonov, A.B.; Bhatt, D.; Zuckerman, D.M. Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled “Semi-Atomistic” Simulations. 2009 Biophysical Society Meeting, Boston, Massachusetts. March 4, 2009. Oral
  20. Cashman, D.J.; Mamonov, A.B.; Bhatt, D.; Zuckerman, D.M. An Analysis of the Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Using a “Semi-Atomistic” Library-Based Monte Carlo Simulation Method. 2009 Fourth Annual Postdoctoral Data & Dine Symposium, University of Pittsburgh, Pittsburgh, Pennsylvania. May 19, 2009. Poster
  21. Cashman, D.J. Computational Simulations of Proteins Using a Fast, “Semi-Atomistic” Library-Based Monte Carlo Simulation Method. Department of Chemistry, Mississippi State University. March 12, 2010. Oral
  22. Collaco, A; Putzier, I.; Hong, L.; Chanthaphavong, S.; Lee, P.; Thickman, K.R.; Cashman, D.J.; Rajkumar, R.; Cronican, A.A.; Chuang, P.-Y.; Dagda, R.K.; Dudgeon, D.D.; Maul, T.M.; Woodcock, S.R.; Dennis, T.L.; Zellers, D.F. Postdoc Lunch Live! Providing a Monthly Forum for Postdoctoral Fellows to Develop Scientific Presentation Skills and Network with Colleagues Across the University of Pittsburgh. National Postdoctoral Association 2010 Annual Meeting, Philadelphia, Pennsylvania. March 12-14, 2010. Poster
  23. Cashman, D.J.; Ortega, D.R.; Zhulin, I.B.; Baudry, J.B. A Molecular Jigsaw Puzzle: Putting the Pieces of the Bacterial Chemotaxis System Together. Receptor Fest XIV. August 2, 2011, University of Utah, Salt Lake City, Utah. Oral
  24. Cashman, D.J.; Baudry, J.B. Conformational Analysis and Refinement of Homology Models of CheW Protein Using Molecular Dynamics and Monte Carlo Simulations. BCMB Symposium, University of Tennessee, Knoxville. September 20, 2011. Poster
  25. Cashman, D.J. Modeling of Proteins Involved in Bacterial Chemotaxis. BCMB Colloquium, University of Tennessee, Knoxville. October 3, 2011. Oral
  26. Scott, C.; Cashman, D.J.; Bruce, B.; Baudry, J.B. Modeling Protein/Protein Interactions: Three-dimensional Modeling of Psa C, D and E Interactions with Ferredoxin & Flavodoxin. BCMB Graduate Symposium, University of Tennessee, Knoxville. March 6, 2012.
  27. Cashman, D.J.; Ortega, D.R.; Fleetwood, A.D.; Zhulin, I.B.; Baudry, J.B. Homology Modeling and Molecular Simulations of CheW. A Look into the Dynamic Nature of a Key Chemotaxis Protein. Computational Structural Biology 2012 Conference, UT/ORNL. June 3, 2012. Poster
  28. Cashman, D.J.; Ortega, D.R.; Fleetwood, A.D.; Zhulin, I.B.; Baudry, J.B. Studying the Structure and Dynamics of Bacterial Chemoreceptor Arrays Using Computational Methods. BCMB Day, University of Tennessee, Knoxville. September 4, 2012. Poster
  29. Cashman, D.J.; Ortega, D.R.; Zhulin, I.B.; Baudry, J.B. Studying the Protein-Protein Interactions of the Receptor Complex Involved in Bacterial Chemotaxis. UTK/ORNL Retreat 2013. March 1, 2013. Poster
  30. Williams, A.R.; Cashman, D.J. Applications of Computational Modeling Software for Use in the Instruction of General Chemistry. 9th Annual Student Research Day, Tennessee Technological University. April 10, 2014.
  31. Oladinni, O.; Cashman, D.J.; Ballal, S.K. Computational Binding Site Analysis and Comparative Study of A, B and C RAF Kinase in bovine and pigs using an Integrated Energy Frustration Method. 2015 Southern Association of Agricultural Scientists Convention, Atlanta, Georgia. January 31 – February 3, 2015. Oral
  32. Cashman, D.J.; Oladinni, O.; Ballal, S.K. The Effects of Energetically Frustrated Residues on the Structural Dynamics of A, B and C RAF Kinases. 2015 Southern Association of Agricultural Scientists Convention, Atlanta, Georgia. January 31 – February 3, 2015. Oral
  33. Nientimp, L.; Baudry, J.; Cashman, D.J. Bioinformatics Methods Used to Probe the 3D Structure of Photosystem I. 10th Annual Student Research Day, Tennessee Technological University, Cookeville, Tennessee. April 9, 2015. Poster
  34. Nientimp, L.; Baudry, J.; Cashman, D.J. Probing the Potential Binding Sites of Cytochrome c6 and Ferredoxin with Photosystem I Using State-of-the-Art Bioinformatics Methods. TN-SCORE Annual Meeting, Nashville, Tennessee. June 18-19, 2015. Poster
  35. Cashman, D.J. Exploring the Protein-Protein Interactions and Structural Dynamics Between Cyanobacterial Photosystem I and Ferredoxin. Chemistry Department Seminar, Tennessee Technological University, Cookeville, Tennessee. September 25, 2015. Oral
  36. Cashman, D.J.; Kapoor, K.; Nientimp, L.; Baudry, J. Molecular Docking and Dynamics Studies of the Protein-Protein Interactions involved in Cyanobacterial Photosystem I and Ferredoxin, TN-SCORE Fall Research Meeting, Knoxville, Tennessee. October 12, 2015. Oral
  37. Cashman, D.J.; Kapoor, K.; Nientimp, L.; Baudry, J. Protein-Protein Docking and Molecular Dynamics Suggest Potential Mechanisms of Electron Transfer Between Ferredoxin and Cyanobacterial Photosystem I. Southeast Regional Meeting of the American Chemical Society, Memphis, Tennessee. November 4-7, 2015. Oral
  38. Andrews, Jen; Brookover, Zoe; Richard, Kaylie; Stark, Sophie; Subramanian, Deepak; Whitaker, Sydney; Nientimp, Luke C.; Cashman, D.J. 3D Models and Molecular Dynamics Used to Study Photosynthesis Proteins. 2015 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  39. Stout, R.; Cashman, D.J.; Zhan, X. Structural Basis of the Functional Differences Between Two Non-Visual Arrestin Isoforms. 11th Annual Student Research Day, Tennessee Technological University. April 6, 2016. Poster
  40. Jeskey, Alan; Kerns, Holli; Legaux, Nicholas; Seiber, Kristina; Vaughn, Vanessa; Yousef, Nassem; Williams, Adam; Cashman, D.J. Studying the MAPK Pathway and p38 Inhibitor Design Using Evolutionary Trace and Energetic Frustration Models. 2016 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  41. Mondal, J; Cashman, D.J.; Baudry, J.; Bruce, B.D. Engineering Enhanced Affinity Between Ferredoxin and Stromal Subunits of Photosystem I. 17th International Conference on Photosynthesis Research, Maastricht, The Netherlands. August 7-12, 2016. Poster
  42. Mohammad, A.S.; Biernacki, J.; Northrup, S.H.; Cashman, D.J. Molecular-Scale Modeling of Whole Biomass Pyrolysis – Morphological Changes. 2016 American Institute of Chemical Engineers Annual Meeting, San Francisco, California. November 13-18, 2016. Poster
  43. Mondal, J.; Cecil, J.; Cashman, D.J.; Baudry, J.; Bruce, B.D. Sticking it to PSI: Enhancing e- transfer thru T. elongates PSI by bioengineering the PSI:FD interface. The 26th Western Photosynthesis Conference, WPC/2017, San Francisco, California. January 5-8, 2017. Poster
  44. Suhagia, Tejaskumar; Cashman, D.J. QSAR Models of Organophosphate Pesticides. 12th Annual Student Research Day, Tennessee Technological University. April 6, 2017. Poster
  45. Fan, Rachel; Huynh, Brandon; Luthy, Claire; McNabb, Jackson; Pitts, Catherine; Zhou, Amy; Davis, Cameron; Cashman, D.J. Computational Drug Discovery of Novel Bacterial Dihydrofolate Reductase Inhibitors. 2017 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  46. Cashman, D.J.; Kapoor, K.; Nientimp, LC.; Baudry, J.; Bruce, B.D. Predictions of Protein-Protein Interactions and Conformational Dynamics of Cyanobacterial Ferredoxin and Cytochrome c6 with Photosystem I. The 27th Western Photosynthesis Conference, WPC/2019, Oracle, Arizona. January 5-8, 2018. Poster
  47. Mondal, J.; Cecil, J.; Cashman, D.J.; Baudry J.; Bruce, B.D. Sticking it to PSI: Enhancing e-transfer thru T. elongates PSI by Bioengineering the PSI:FD Interface. Predictions of Protein-Protein Interactions and Conformational Dynamics of Cyanobacterial Ferredoxin and Cytochrome c6 with Photosystem I. The 27th Western Photosynthesis Conference, WPC/2019, Oracle, Arizona. January 5-8, 2018. Poster
  48. Powell, S.T.; Cashman, D.J.; Ballal, S.K. Computational Predictions of the Binding Sites of RAF Kinases with hRAS. 13th Annual Research and Creative Inquiry Day. April 9-10, 2018. Selected as Best Biology Poster
  49. Brown, Anna; Calhoun, Claire; He, Stephanie; Krishnan, Reethu; Stewart, Leon; White, Abbie; Dixon, Benjamin; Cashman, D.J. Computational Drug Discovery of M. Tuberculosis Tryptophan Synthase Inhibitors. 2018 Governor’s School for Emerging Technologies, Tennessee Technological University, Cookeville, Tennessee. Poster/Oral
  50. Mondal, J.; Cecil, J.; Nguyen, T.; Kumar, R.; Cashman, D.J.; Bruce, B.D. Enhancing Electron Transfer Through Photosystem I (PSI) by Bioengineering the PSI-Ferredoxin Interface. The 28th Western Photosynthesis Conference, WPC/2019, Friday Harbor, Washington. January 4-7, 2019. Poster.
  51. Adams, A.; Cashman, D.J. Computational Design of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species. 16th Annual Student Research Day, Tennessee Technological University. April 13, 2021. Poster.
  52. Edmonds, M.; Carrick, Jesse D.; Cashman, D.J. Virtual Screening of Hamigomycin B Natural Product Derivativbes in 26 Kinase Proteins. 16th Annual Student Research Day, Tennessee Technological University. April 13, 2021. Poster.

Students Mentored

A * indicates service as the student’s primary research advisor. A ** indicates service on the student’s graduate thesis committee.

  • Tyler McBride (UTK, undergraduate student); Fall 2012 – Spring 2013
  • Cathy Scott (UTK, MS graduate student); Spring 2012
  • Tuo Zhu (UTK, MS graduate student); Spring 2012 – Fall 2013
  • Adam Williams (TTU, undergraduate student); Fall 2013 – Spring 2014
  • Brita Anderson (TTU, MS graduate student); Fall 2013 – Summer 2015 **
  • Samar Aldhahry (TTU, MS graduate student); Fall 2013 – Spring 2016 **
  • Lasantha Rathnayake (TTU, Ph.D. graduate student); Fall 2013 – Summer 2017) **
  • Lola Oladinni (TTU, MS graduate student in Biology); Fall 2014 – Fall 2015 **
  • Luke Nientimp (TTU, undergraduate student); Fall 2014 – Fall 2015
  • Abdul S. Mohammad (TTU, MS graduate student); Spring 2016 – Fall 2016)
  • Qiao Chu (TTU, MS graduate student); Spring 2016 – Spring 2017 **
  • John Pleinis (TTU, MS graduate student, Spring 2016 – Fall 2016)
  • Nick Trybala (TTU, undergraduate student, Spring 2016 – Spring 2018)
  • Morgan Overstreet (TTU, undergraduate student, Summer 2017)
  • Cameron Davis (TTU, MS graduate student, Fall 2016 – Summer 2017)
  • Tejaskumar Suhagia (TTU, MS graduate student, Fall 2016 – Summer 2017 *
  • Adua Rahman (TTU, MS graduate student, Spring 2017 – Summer 2018) **
  • Rebecca Stout (TTU, MS graduate student, Spring 2017 – Summer 2018) **
  • Shanrya T. Powell (TTU, MS graduate student in Biology, Spring 2017 – Summer 2018) **
  • Amy Ridings (TTU, MS graduate student, Spring 2017 – Spring 2019) **
  • Florence Fabunmi (TTU, MS graduate student, Spring 2018 – Fall 2019) *
  • Sariful Howlader (TTU, MS graduate student, Fall 2017 – Summer 2019) **
  • Kristin Carter (TTU, MS graduate student, Fall 2018 – Spring 2020 **
  • Austin Hill (TTU, MS graduate student, Fall 2018 – Spring 2020) **
  • Allison Adams (TTU, undergraduate student, Fall 2020 – present)
  • Meagan Edmonds (TTU, undergraduate student, Fall 2020 – present)
  • Amanuel Gimikael (TTU, undergraduate student, Fall 2020)
  • Hajar Taheri Afarani (TTU, Ph.D. graduate student, Spring 2021 – present) **
  • Jacob Thorn (TTU, MS graduate student, Spring 2021 – present) **
  • Aaron Bain (TTU, Ph.D. graduate student, Spring 2021 – present) **

Awards and Recognition

  • Columbia-HCA Academic Scholarship; Old Dominion University (1992-1993)
  • Student Leader Scholarship; Old Dominion University (1993-1994)
  • Commonwealth Scholarship; VCU School of Pharmacy (1999-2000)
  • Outstanding Chemistry Presentation; 80th Virginia Academy of Sciences Meeting, Hampton, VA. (May, 2002)
  • VCU Graduate School Travel Grant Award; 224th ACS National Meeting, Boston, MA (August, 2002)
  • Outstanding Poster Presentation; VCU Watts Day Symposium (October, 2002)
  • Sectional Distinguished Service Award; Alpha Phi Omega (March 2004). Awarded for outstanding community service at the sectional (Virginia) level.
  • Volunteer of the Year Award; FIRST (For Inspiration in Robotics, Science and Technology) Robotics Competition (March 2004).
  • Alpha Delta Iota Chapter Distinguished Service Award; Alpha Phi Omega (November 2004). Awarded for outstanding community service at the local level.
  • Best Practices in Teaching Certificate; University of Tennessee, Knoxville (December 2012).
  • Region IV Distinguished Service Award, Alpha Phi Omega (December 2018). Awarded for outstanding community service at the regional (southeastern United States) level.

Academic and Community Activities

  • Alpha Phi Omega; Member of volunteer staff (since 1998). Advise and mentor students, present leadership workshops and seminars, and developed PHP/MySQL applications for the national website (www.apo.org). Currently serving as a Faculty/Staff Advisor to the Iota Alpha Chapter at the University of Tennessee – Knoxville (February 2012-present), as the Section 68 Chair for Eastern Tennessee (2012-2013), and as Section 70/I-2 Chair for Western Tennessee and Western Kentucky (2014-present).
  • American Society for Biochemistry and Molecular Biology; Serve as faculty advisor to the student affiliate chapter of the ASBMB at Tennessee Technological University. Fall 2013 -present.
  • Science Fair Judging; Served as a Judge for the Pittsburgh Regional Science and Engineering Fair (2009-2010), the Southern Appalachia Science and Engineering Fair (2012-2013), Tennessee Science Olympiad (2011 and 2012), and the Tennessee Chemistry Olympiad (2014-present).
  • University of Pittsburgh Postdoctoral Association; Marketing & Communications Officer (2008-2009). Responsible for organizing and promoting UPPDA events, including seminars, symposia, and other peer mentoring events. Maintained organization website, www.uppda.pitt.edu. Participation in events increased dramatically during my term of office.
  • Governor’s School for Emerging Technologies (2015 – present); Serve as research mentor for teams of 6 – 12 high school students engaging in computational modeling projects to train them in STEM education.

Affiliations