Scholarship

1. 1. Ananey-Obiri, D.*, Rhinehardt, K. (2023) NLPARG: Comparative Neural Word  Embedding Approaches for Antibiotic Resistance Prediction. J Proteomics Bioinform. 16:654

   2. Ananey-Obiri, D*., & Rhinehardt, K. (2022). Machine Learning for Annotating Sparsely Labeled Biocide and Metallotoxin Resistance Genes Using Natural Language Processing Techniques. Research Square

   3. Cathcart, A*., Wiggins, M.*, Kelly, W.*, Doss, C., Ford, Y., Hubal, R. and Rhinehardt, K., (2022) Recognition of Culturally Diverse Cuisine in Popular Nutrition Apps. Current Developments in Nutrition, 6(Supplement_1), pp.872-872.

   4. Boyd, SM., Rhinehardt, KL. et al. (2022) Experimental Evolution of Copper Resistance in Escherichia coli Produces Evolutionary Trade-Offs in the Antibiotics Chloramphenicol, Bacitracin, and Sulfonamide. Antibiotics 11.6: 711.

   5.  Rhinehardt, KL., Dong, M. Computational analysis of protein conformational heterogeneity. Journal of Biomolecular Structure and Dynamics. 1-6

   6. Uwiragiye, E.*, Rhinehardt, K.  (2021) TFIDF-Random Forest: Prediction of Aptamer-Protein Interacting Pairs. IEEE Transactions on Computational Biology and Bioinformatics. DOI:10.1109/TCBB.2021.3098709

   7. Rawal, A*., Rhinehardt, K., & Mohan, R. Pendse, M (2021) Influence Of Hydroxyproline On Mechanical Behavior of Collagen Mimetic Proteins Under Fraying Deformation - Molecular Dynamics Investigations. Journal of Biomechanical Engineering. https://doi.org/10.1115/1.4050648

   8.    Thomas M., Ewunkem, J. Rhinehardt, K., Van Beveren, E*. et al. (2020) Too much of a good thing: Gene expression associated with excess iron (II) resistance in Escherichia coli. Evolution, Medicine, and Public Health

   9. Graves, J., Ewunkem, J., Ward, J.*, Staley, C*., Thomas M., Rhinehardt, K., Jan, J., Harrison, S. (2020) Surviving the Greek Gift: Experimental Evolution of Gallium resistance in Escherichia coli. Evolution, Medicine, and Public Health

   10.  Rawal, A*., Rhinehardt, K., & Mohan, R. (2020). Molecular Dynamics Investigation of Self-Association of Synthetic Collagen and Spider Silk Composite System for Biomaterial Applications. MRS Advances, 1-8. doi:10.1557/adv.2019.490

   11. Rhinehardt, K.L., et al., Molecular modeling and SPRi investigations of interleukin 6 (IL6) protein and DNA aptamers (2018). Journal of Biomolecular Structure and Dynamics, 36(8): p. 1934-1947.

   12. Tajkarimi M, Rhinehardt K, Thomas M, Ewunkem JA, Campbell A, et al. (2017) Selection for Ionic- Confers Silver Nanoparticle Resistance in Escherichia coli. JSM Nanotechnol Nanomed 5(1): 1047

   13. Rhinehardt, K.; Srinivas, G.; Mohan, R. 2015. Molecular Dynamics Simulation Analysis of Anti-MUC1 Aptamer and Mucin 1 Peptide Binding. J Phys Chem B 119:6571-83

Book Chapters

1.  Uwiragiye, E*, Rhinehardt, KL. (2022) Identification of RNA Olignonucleotide and Protein interactions using Term Frequency Inverse Document Frequency and Random Forest. Sett, A. (Ed). Oligonucleotides - Overview and Applications,  (ISBN 978-1-80355-628-4) 

2.   Graves, JL Ewunkem, J., Thomas M.Han, J., Rhinehardt, K., Boyd, S., Edmonson, R., Jeffers-Francis, L., Harrison, S. (2019) Experimental Evolution of Metal Resistance in Bacteria. In Banzhaf et al. (Eds.)  Evolution in Action—Past, Present, and Future, Cham, Switzerland: Springer International Publishing, AG.

3.   Rhinehardt, K, Mohan, R, Srinivas, G. Computational Modeling of Peptide – Aptamer Binding. Walker, J. (Ed). Computational Peptidology. New York City, NY: Humana Press. 2014.

Conference Publications

1. Rawal, A.*, Rhinehardt, K., & Mohan, R. Mechanical Properties of Spider Silk For Use As A Biomaterial –Molecular Dynamics Investigation. Proceedings of the ASME 2020 International Mechanical Engineering Congress and Exposition (IMECE), 2020. November 15-19, Portland, OR.

 2.  Rawal, A.*, Rhinehardt, K., & Mohan, R. Mechanical Behavior of Collagen Mimetic Peptides Under Fraying Deformation via Molecular Dynamics. Technical Paper Publication: ASME International Mechanical Engineering Conference & Exposition (IMECE), 2019. November 11 – 14, Salt Lake City, UT.

 3. Rhinehardt, K.; Mohan, R.; Srinivas, G.; Kelkar, A., Analysis and understanding of aptamer and peptide molecular interactions: Application to mucin 1 (Muc1) aptasensor. 2015 2nd International Symposium on Physics and Technology of Sensors (ISPTS), pp.297-302, 7-10 March 2015

 4. Rhinehardt, K, Mohan, R, Srinivas, G, Kelkar, A. 2013. Computational Modeling of Peptide – Aptamer Binding in Biosensor Applications. International Journal of Bioscience, Biochemistry and Bioinformatics 3:639-642.

1. Dutchatelier, M.*, Rhinehardt, K. A Molecular Dynamics Investigation of Synthetic Collagen Thermal Properties.  Presented at MRS 2024. 2023 November 26-December 1 Boston Massachusetts

2.  Davenport, J.*, Rhinehardt, K. AI Enabled Cultural and Molecular Analysis of Nutrition for Improved Health Equity.  Presented at MRS 2024. 2023 November 26-December 1 Boston Massachusetts

3. Ejeta, J.* Rhinehardt, K. A Machine Learning Approach to Predict the Corrosion Rate of CO2 Transport Pipeline. Presented at: U. S. National Congress on Computational Mechanics. 2023 July 23-27, Albuquerque, New Mexico

4. Bartley, S.* Rhinehardt, K. Dellinger, K. Molecular Dynamics Investigations of the Binding of S-protein to DNA Aptamers. Presented at: STEM Noire. 2023 June 22-25, San Juan, Puerto Rico

5. Perry, D.* Rhinehardt, K. Benchmarking Protein Folding Using Variational Quantum Eigensolver. Presented at: Adiabatic Quantum Computing 2023 June 19, Albuquerque, New Mexico

6. Rhinehardt, K. Scientific AI and Molecular Modeling of Bacterial Genomes and Synthetic Biological Systems. Presented at: Los Alamos National Lab T-CNLS. 2022 January 24, virtual.

7.  Ananey-Obiri, D.*, and Rhinehardt, K. Natural Language Processing Techniques for Antibiotic Resistance Prediction. Poster presented at: BEACON Congress; 2021 August 17-20; virtual.

8. Ananey-Obiri, D*., Rhinehardt, K.  Comparative Neural Word Embedding Approaches for Antibiotic Resistance Prediction. Poster Presented at: NCAT 10th Annual Graduate Research Poster Competition. 2021 April 20-21, Virtual

9. Rhinehardt. K Perspectives on Mentoring for Fortifying a Future in Academia.  Presented at: NC AGEP Winter Alliance Meeting. 2021 January 15, Virtual.

10.  Rhinehardt. K. Assessing policy effects on workforce deficits in STEM advanced degree candidates. Presented at: Centers of Excellence Research Symposium. 2020 December 11. Virtual

11.  Rhinehardt, K. Diversity in Computing. Presented at: Transforming Undergraduate Research. 2020 November 11. Virtual

12.   Rhinehardt, K. Computational Molecular Engineering: It’s a small world after all Presented at: North Carolina Career and Technical Education Conference, 2020 July 13-17. Virtual

13.  Uwiragiye, E.*, Rhinehardt, K.  Using Machine Learning/ Deep Learning to predict selection of Aptamer-Proteins Interaction Pairs. Poster Presented at: NCAT 9th Annual Graduate Research Poster Competition. 2020 April 27-28, Greensboro, NC

14. Rawal, A.*, Rhinehardt, K., & Mohan, R. Molecular Dynamics Investigation of Self-Association of Synthetic Collagen and Spider Silk Composite System for Biomaterial Applications. Presented at: MRS, 2019. December 1-6, 2019

15. Rawal, A.*, Rhinehardt, K., & Mohan, R. Mechanical Behavior of Collagen Mimetic

16.  Peptides Under Fraying Deformation via Molecular Dynamics. Poster Presented at: ASME International Mechanical Engineering Conference & Exhibition, 2019. November 11 – 14, Salt Lake City, UT.

17. Rawal, A.*, Rhinehardt, K., & Mohan, R . Mechanical Properties of Nanoscale Collagen Mimetic Peptides via Molecular Dynamics. Poster Presented at: Carolina Science Symposium, 2019. November 8, Raleigh. NC.

18. Rawal, A.*, Rhinehardt, K.L., Mohan, R.V. Mechanical and Electrostatic Properties of Synthetic Collagen Molecules via Molecular Dynamics Modeling. Poster presented at: International Mechanical Engineering Congress & Exposition; 2018 November 9-15; Pittsburgh, PA

19. Rawal, A.*, Rhinehardt, K.L., Mohan, R.V. A Molecular Dynamics Study of Self-Assembly and Stability Of Synthetic Collagen Molecules For Tissue Engineering Applications. Poster & Talk presented at: ASME's NanoEngineering for Medicine and Biology Conference (NEMB), 2018 August 23; Los Angeles, CA.

20. Rhinehardt KL, Boyd SM*, Edmonson R, Ewenkum AJ, Graves JL.  Bacterial Adaptations to Metallotoxins. Symposium presented at: BEACON Congress; 2018 August 9; East Lansing, MI.

21. Boyd SM*, Tapia AE*, Ewenkum AJ, Rhinehardt KL, Graves JL. Evolution of general metal resistance in Copper Resistant E. coli. Poster presented at: BEACON Congress; 2018 August 8; East Lansing, MI.

22.  Rawal, A.*, Rhinehardt, K.L., Mohan, R.V. Collagen Based Bio-Materials. Poster & Talk presented at: IEEE Albany Nanotechnology Symposium; 2017 November 16; Albany, NY.

23.  Rawal, A.*, Rhinehardt, K.L., Mohan, R.V. Collagen Based Bio-Materials for Bio-Medical Applications. Poster presented at: AVS MRS ASM Carolina Science Symposium; 2017 November 10; Raleigh, NC

24. Rawal, A.*,  Rhinehardt, K., Mohan, R. Structural Stability of Collagen Based Bio-Materials – Molecular Dynamics Modeling. Poster presented at: 2017 Nanomanufacturing Conference.  2017 September 27; Greensboro, NC

25. Rhinehardt, K. It’s a small world after all: 3D Simulations and Modeling of Biomolecules.  Talk presented at: 2017 Translational Collaborations at North Carolina Agricultural and Technical State University. 2017 April 1; Greensboro, NC.

26. Rhinehardt, K. Computational Modeling of Protein Biomarkers for Traumatic Brain Injury. Talk presented at: 47th Annual Council of Historically Black Graduate Schools Conference. 2017 March 1-2; Annapolis, MD.

27. Rhinehardt, K. Computational Modeling of Nucleic and Peptide Aptamer Interactions in Biosensor Applications: IL6 Traumatic Brain Injury Biomarkers. Mini Symposium presented at: 12th World Congress on Computational Mechanics.  2016 July 24-29; Seoul, Korea

28. Rhinehardt, K. Mohan, R. Srinivas, G. Sandros, M. Aptamer Based Biosensors for Diagnostics: A Computational Approach. Poster Session presented at: ASME 2014 3rd Global Congress on NanoEngineering for Medicine and Biology. 2014 Feb. 2-5; San Francisco, CA. 

29. Rhinehardt, K, Mohan, R, Srinivas, G. Computational Modeling of Mucin 1 (MUC1) Peptide and Anti – MUC1 Aptamer Binding. Poster Session presented at: ASME 2012 International Mechanical Engineering Congress and Exposition. 2012 November 9-15; Houston, TX.

Funded Projects

1. NIH U24: Genomic Research and Data Science Center for Computational Cloud-Computing (GRADS-4C) (PI) 

2. NIH-RTI: All of Us Researcher Academy Cardiovascular Disease and Social Determinants of Health  (co-PI)

3. AMGEN: Training Program for Implementing Biotechnology Research Based Experiences in Central North Carolina Schools. (co-PI) 

4. NSF ERC: Engineering Research Center for Precision Microbiome Engineering (PreMiEr) (Senior Personnel) 

5. DOE EFRC: Center of Electrochemical Dynamics and Reactions on Surfaces (CERDAS) (Co-PI)

Previously Funded Projects

1.  NSF PREM seed grant: Collaborative Research and Education in Energy  Materials  (CREEM) (Senior Personnel) 

2. IBM Quantum Computing: Metallotoxin Resistance Multi-Scale Modeling and Analysis. (PI)Sandia National Labs: Utilization of deep learning models for ab-initio molecular dynamics of heterogenous metallic-biological systems (PI)    

3. AMD COVID-19 HPC Fund – Donation of Server Hardware 

4. NC Policy Collabortory Grant Designing an Anti-Viral Nanoparticle Against SARS-CoV-2 (co-PI)

5. CREO Seed Grant: Assessing policy effects on workforce deficits in STEM advanced degree candidates (PI)  

6. NC A&T TraCS Interdisciplinary Team Science Award: Development of high-affinity SARS-CoV-2 nucleic aptamers for portable COVID-19 testing (PI) 

7. NC A&T TraCS Interdisciplinary Team Science Award: Isolation and Characterization of Protein Complexes Involved in Wound Healing (co-PI) 

8. NVIDIA: Hardware donation Hands on learning through Multi Scale Modeling (PI)

9. NSF HBCU-UP EIR: Deep learning based approaches for protein post-translational modifications site prediction (co-PI)

10. NSF NRT: Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) (Investigator)