Mohammed, Abdulmelik

Profile Picture

Abdulmelik Mohammed is an Assistant Professor at the Department of Biomedical Engineering whose research focuses on the computational modeling and analysis of natural and synthetic biomolecular systems. He obtained his Doctor of Science from Aalto University, Finland where his dissertation on the algorithmic design of biomolecular nanostructures won the School of Science dissertation award. Before joining SJSU, he was a postdoc in the Department of Mathematics and Statistics at the University of South Florida.

Research Interests

Computational modeling, design and analysis of biomolecular systems, biomolecular
nanotechnology, computational genomics.

Email

Preferred: abdulmelik.mohammed@sjsu.edu

Telephone

Preferred: 408-924-3833

Education

  • Doctor of Science (Technology), Aalto University, Finland
  • Master of Science (Technology), Aalto University, Finland
  • Bachelor of Engineering, Metropolia University of Applied Sciences, Finland

Bio

List of Publications

  • Elonen, A., Mohammed, A., & Orponen, P. (2024). A general design method for Scaffold-Free DNA wireframe nanostructures. In Lecture notes in computer science (pp. 178–189). https://doi.org/10.1007/978-3-031-63742-1_13  
  • Elonen, A., Wimbes, L., Mohammed, A., & Orponen, P. (2024). DNAforge: a design tool for nucleic acid wireframe nanostructures. Nucleic Acids Research, 52(W1), W13–W18. https://doi.org/10.1093/nar/gkae367  
  • Elonen, A., Natarajan, A. K., Kawamata, I., Oesinghaus, L., Mohammed, A., Seitsonen, J., Suzuki, Y., Simmel, F. C., Kuzyk, A., & Orponen, P. (2022). Algorithmic design of 3D wireframe RNA polyhedra. ACS Nano, 16(10), 16608–16616. https://doi.org/10.1021/acsnano.2c06035  
  • Mohammed, A., Jonoska, N., & Saito, M. (2020). The topology of scaffold routings on Non-Spherical Mesh wireframes. DNA. ‪26th International Conference on DNA Computing and Molecular Programming (DNA 26)‬.(n.d.) https://doi.org/10.4230/LIPIcs.DNA.2020.1 
  • Mohammed, A., Orponen, P., & Pai, S. (2018). Algorithmic design of cotranscriptionally folding 2D RNA origami structures. In Lecture notes in computer science (pp. 159–172). https://doi.org/10.1007/978-3-319-92435-9_12  
  • Benson, E., Mohammed, A., Rayneau-Kirkhope, D., Gadin, A., Orponen, P., & Högberg, B. (2018). Effects of design choices on the stiffness of wireframe DNA origami structures. ACS Nano, 12(9), 9291–9299. https://doi.org/10.1021/acsnano.8b04148  
  • Mohammed, A., & Hajij, M. (2017). Unknotted strand routings of triangulated meshes. In Lecture notes in computer science (pp. 46–63). International Conference on DNA-Based Computers, 46(63). https://doi.org/10.1007/978-3-319-66799-7_4  
  • Mohammed, A., Czeizler, E., & Czeizler, E. (2017). Computational modelling of the kinetic Tile Assembly Model using a rule-based approach. Theoretical Computer Science, 701, 203–215. https://doi.org/10.1016/j.tcs.2017.07.014  
  • Benson, E., Mohammed, A., Bosco, A., Teixeira, A. I., Orponen, P., & Högberg, B. (2016). Computer‐Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes. Angewandte Chemie International Edition, 55(31), 8869–8872. https://doi.org/10.1002/anie.201602446  
  • Benson, E., Mohammed, A., Gardell, J., Masich, S., Czeizler, E., Orponen, P., & Högberg, B. (2015). DNA rendering of polyhedral meshes at the nanoscale. Nature, 523(7561), 441–444. https://doi.org/10.1038/nature14586 

Honors and Awards

  • AMS-Simons Travel Grant (2020)
  • Aalto University Dissertation Award (2019)
  • Nokia Foundation Awards Scholarship (2017)
  • Nokia Foundation Awards Scholarship (2015)
  • Helsinki Doctoral Education Network in Information and Communications Technology (HICT) Doctoral Student (2014-2018)
  • Aalto School of Science Master’s Thesis Award (2014)

Classes Taught

  • BME 115 - Foundations of BME
  • BME 130 - Numerical Methods in Biomedical Engineering
  • BME 165 - Applied Engineering Biomechanics
  • BME 291 - Master's Thesis/Project Preparation Seminar

Links

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