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Inbal Tuvi-Arad, Associate Professor

Inbal Tuvi-Arad
Contact Info

The Open University of Israel Department of Natural Sciences 1 University Road, P. O. Box 808, Raanana 43107
Office:972-9-778-1773 Fax:972-9-778-0661 Email:inbaltu@openu.ac.il

Areas of Interest
  • Computational chemistry
  • Symmetry and Chirality
  • Protein Structure
  • Cheminformatics
  • Chemistry Education
  • Educational Technology

 

Tuvi-Arad Research Group

Symmetry and Structure 

 

 

Symmetry, Chirality ​​​

 

 

   About me: I received my PhD in chemistry (summa cum laude) from Ben-Gurion University of the Negev (Israel) in 1999, under the supervision of Prof. Yehuda B. Band in the field of theoretical quantum chemistry. I then entered the field of chemical education working collaboratively with Prof. Rafi Nachmias ​from the School of Education at Tel-Aviv University on the topic of web-based learning. In 2002 I Joined the Department of Natural Sciences at the Open University of Israel. My research interests span both computational chemistry and chemistry education.

 

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Software and Websites

  1. Molecualr Symmetry Online - A virtual learning environment based on a set of tools that enable three-dimensional and interactive display of molecules and their symmetry elements​
  2. CoSyM - An online calculator for continuous symmetry measures of molecules and protein homomers
  3. CSM on GitHub - List of software and tools for download, including data from selected publications. 


Articles in Refereed Journals

  1. I. Tuvi and Y. B. Band, Invariant Imbedding and Full Collision Matrix Methods: Incorporation of Closed Channels, Complex Potentials, and Determination of Bound State Energies, Journal of Chemical Physics 99, 9697-9703 (1993).
  2. Y. B. Band and I. Tuvi, Invariant Imbedding Method for Multichannel Schrödinger Equations with Derivative Coupling, Journal of Chemical Physics99, 9704-9708 (1993).
  3. Y.B. Band and I. Tuvi, Quantum Rearrangement Scattering Calculations Using the Invariant Imbedding Method, Journal of Chemical Physics100, 8869-8876 (1994).
  4. Y. B. Band, I. Tuvi, K-A. Suominen, K. Burnett, and P. S. Julienne, Loss from magneto-optical traps in strong laser fields, Physical ReviewA50 (Rapid Communication), R2826-R2829 (1994).
  5. Y. B. Band and I. Tuvi, Convergence of Diabatic to Adiabatic Scattering Calculations,Physical ReviewA51 (Rapid Communication), R3403-R3406 (1995).
  6. Y. B. Band and I. Tuvi, Reduced Optical Shielding of Collisional Loss for Laser Cooled Atoms, Physical ReviewA51 (Rapid Communication), R4329-R4332 (1995).
  7. I. Tuvi, Y. Avishai and Y. B. Band, Electronic Conductance in Mesoscopic Systems: Multichannel Quantum Scattering Calculations, Journal of Physics - Condensed Matter7, 6045-6063 (1995).
  8. I. Tuvi and Y. B. Band, Hermiticity of the Hamiltonian Matrix in a Discrete Variable Representation, Journal of Chemical Physics107, 9079-9084 (1997).
  9. K-A. Suominen, Y. B. Band, I. Tuvi, K. Burnett and P. S. Julienne, Quantum and Semiclassical Calculations of Cold Atom Collisions in Light Fields, Physical ReviewA57, 3724-3738 (1998).
  10. I. Tuvi and Y. B. Band, Nonadiabatic Coupling using a Corrected Born-Oppenheimer Basis: The Vibronic Spectrum of HD+, Physical ReviewA59, 2680-2683 (1999).
  11. I. Tuvi and Y. B. Band, Modified Born-Oppenheimer Basis for Nonadiabatic Coupling: Application to the Vibronic Spectrum of HD+, Journal of Chemical Physics111, 5808-5823 (1999).
  12. R. Nachmias and I. Tuvi, Taxonomy of Scientifically Oriented Educational Websites, Journal of Science Education and Technology10(1), 93-104 (2001).
  13. I. Tuvi and R. Nachmias, Current State of Websites in Science Education - Focus on Atomic Structure, Journal of Science Education and Technology10(4), 293-303 (2001).
  14. I. Tuvi and R. Nachmias, A Study of Web-Based Learning Environments Focusing on Atomic Structure, Journal of Computers in Mathematics and Science Teaching22(3), 225-240 (2003).
  15. P. Gorsky, A. Caspi and I. Tuvi-Arad, Use of Instructional Dialogue by University Students in a Distance Education Chemistry Course, Journal of Distance Education19(1), 1-19 (2004).
  16. I. Tuvi-Arad and P. Gorsky, New Visualization tools for learning molecular symmetry: A preliminary evaluation, Chemistry Education Research and Practice8(1), 61-72 (2007).
  17. I. Tuvi-Arad and R. Blonder , Continuous symmetry and chemistry teachers: learning advanced chemistry content through novel visualization tools, Chemistry Education Research and Practice11(1), 48-58 (2010).
  18. I. Tuvi-Arad and D. Avnir, Determining symmetry changes during a chemical reaction: the case of diazene isomerization, Journal of Mathematical Journal of Mathematical Chemistry47,1274-1286 (2010).
  19. I. Tuvi-Arad and D. Avnir,  Quantifying asymmetry in concerted reactions: Solvents effect on a Diels-Alder cycloaddition, Journal of Organic Chemistry  76, 4973-4979 (2011).
  20. I. Tuvi-Arad and D. Avnir, Symmetry-enthalpy correlations in Diels–Alder reactions, Chemistry - A European Journal18, 10014-10020 (2012).
  21. I. Tuvi-Arad, T. Rozgonyi and A. Stirling, Effect of Temperature and Substitution on Cope Rearrangement: A Symmetry Perspective, The Journal of Physical Chemistry A, 117(48), 12726-12733 (2013).
  22. Y. Feldman-Maggor, A. Rom and I. Tuvi-Arad, Open Educational Resources in Undergraduate Chemistry – Mapping Tool and Lecturers' Considerations for their Integration in Teaching, Chemistry Education Research and Practice, 17, 283-295 (2016).
  23. I. Tuvi-Arad and A. Stirling, Invited paper:The distortive nature of temperature – A symmetry analysis, Israel Journal of chemistry,56​,1067-2075 (2016).
  24. R. Iovita, I. Tuvi-Arad, M-H Moncel, J. Despriée, P. Voinchet, J-J. Bahain,High handaxe symmetry at the beginning of the European Acheulian: the data from la Noira (France) in context, PLOS ONE,12(5), e0177063 (2017).
  25. Y. Baruch-Shpigler, H. Wang, I. Tuvi-Arad and D. Avnir, Chiral Ramachandran plots I: Glycine, Biochemistry, 56, 5635-5643 (2017).
  26. G. Alon and I. Tuvi-Arad, Improved algorithms for symmetry analysis: structure preserving permutations, Journal of Mathematical Chemistry, 56, 193-212 (2018).
  27. A.W. Kaspi-Kaneti and I. Tuvi-Arad, Twisted and Bent Out of Shape: Symmetry and Chirality Analysis of Substituted Ferrocenes, Organometallics, 37(19), 3314–3321 (2018).
  28. H. Wang, D. Avnir and I. Tuvi-Arad, Chiral Ramachandran Plots II: General trends and proteins chirality spectra, Biochemistry, 57(45), 6395–6403 (2018). 
  29. I. Tuvi-Arad and R. Blonder, Invited review: Technology in the Service of Pedagogy: Teaching with Chemistry Databases, Israel Journal of Chemistry, 59, 572 – 582 (2019).
  30. I. Tuvi-Arad and G. Alon, Improved Algorithms for Quantifying the Near Symmetry of Proteins: Complete Side Chains Analysis, Journal of Cheminformatics, 11(1):39 (2019).
  31. Y. Shalit and I. Tuvi-Arad Side chain flexibility and the symmetry of protein homodimers, PLOS ONE 15(7): e0235863 (2020).
  32. M. Fossépré, I. Tuvi-Arad, D. Beljonne, S. Richeter, S. Clément and M. Surin, Binding mode multiplicity and multiscale chirality in the supramolecular assembly of DNA and a π-conjugated polymer, ChemPhysChem, 21, 2543 (2020).
  33. A.W. Kaspi-Kaneti, J. Barroso, G. Merino, D. Avnir, I.L. Garzón and I. Tuvi-Arad, Head to tail distortion wave characterizes the enantiomerization of helicenes​, J. Org. Chem.,  85(23), 15415–15421 (2020). 
  34. Y. Feldman-Maggor, S. Barhoom, R. Blonder and I. Tuvi-Arad, Behind the Scenes of Educational Data Mining, Education and Information Technologies, Educ. Inf. Technol., 26, 1455–1470 (2021).
  35. Y. Shalit and I. Tuvi-Arad, Symmetry–Binding Correlations of Crown Ether Complexes with Li and Na​, ACS Omega, 6, 19233–19237  (2021).
  36. I. Tuvi-Arad, Invited review: Computational chemistry in the undergraduate classroom - Pedagogical considerations and teaching challenges, Israel Journal of Chemistry, 6​2, e202100042 (2022).
  37. Y. Feldman-Maggor,  R. Blonder and I. Tuvi-Arad, Let them choose: Optional assignments and online learning patterns as predictors of success in online general chemistry courses, The Internet and Higher Education 55,100867,2022).
  38. Y. Feldman-Maggor, I. Tuvi-Arad and R. Blonder, Development and evaluation of an online course on nanotechnology for the professional development of chemistry teachers, International Journal of Science Education, 
    DOI: 10.1080/09500693.2022.2128930 (2022).

Referred Book Chapters

  1. Y. Feldman-Maggor, I. Tuvi-Arad and R. Blonder, book chapter: The potential of MOOCs for professional development of teachers, Learning Technologies in Higher Education in Israel, Eds: Anat Cohen, Gilad Ravid, et al., MEITAL (Inter University Center for Learning Technologies) (in Hebrew) (in press).


Articles in Refereed Conference Proceedings

  1. I. Tuvi and R. Nachmias, Educational Websites in Chemistry: Expectations versus Reality, Computer Based Learning in Science - Conference Proceedings, C. P. Constantinou and Z. C. Zacharia (eds.), Vol. 1, 955-963 (2003).
  2. I. Tuvi-Arad and R. Blonder, Continuous Symmetry & Chemistry Teachers: Learning Advanced Chemistry Content through Novel Visualization Tools, Proceedings of the Chais Conference on Instructional Technologies Research 2010: Learning in the technological era, Y. Eshet-Alkalai, A. Caspi, S. Eden and Y. Yair (eds.), Raanana: The Open University of Israel, 87-93 (2010). 
  3. Y. Feldman-Maggor, A. Rom and I. Tuvi-Arad, "Chemistry Lecturer's considerations for Integrating Educational Websites in the Classroom", Proceedings of the 12th annual Meital National Conference, Y. Yair and E. Shmueli (eds.), Vol. 1, 107-114 (2014). In Hebrew.
  4. Y. Feldman-Maggor, S. Barhoom, R. Blonder and I. Tuvi-Arad, "Behind the Scenes of Educational Data Mining", Proceedings of the Chais Conference on Instructional Technologies Research 2020, I. Blau et al. (editors), Raanana: The Open University of Israel, 177-1892 (2020). ​In Hebrew.​ 


Popular Science Posts (in Hebrew)

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​Computational Chemistry​​​​

S​ymmetry is a fascinating structural property of matter. Many molecular systems tend to create symmetric structures. While the common view of symmetry is dichotomous – a molecule is considered either symmetric or not - numerous experimental and theoretical measurements show that approximate symmetry is much more common. One may ask then how far from symmetry is a given molecular structure or "what is the symmetry content of a molecule". The continuous symmetry measure (CSM) methodology quantifies the level of symmetry of a given structure and provides a new terminology for symmetry analysis. 


Our group develop algorithms to calculate continuous symmetry and chirality measures and study various phenomenon related to near symmetry and the emergence of chirality using these tools in combination with other computational chemistry tools.


 

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Helicene with 43 phenyl rings.

Symmetry of protein homomers and chirality of their building blocks

Symmetry offers several advantages for the evolution, oligomerization and function of proteins. It has been shown that symmetry leads to a reduction of errors in the process of protein synthesis, it tends to increase the effectiveness of allosteric regulation, synthesizing a symmetric structure requires less information for coding the protein and may lead to faster processes. Usually closed symmetric systems tend to have lower energy than asymmetric ones as the interactions between the subunits are maximized due to the symmetry. Consequently symmetry could make proteins more stable and minimize unwanted excessive aggregation. Nevertheless, research shows repeatedly that protein symmetry is far from being perfect. Such imperfections have been related to several factors, including protein function, thermodynamic considerations, experimental conditions and frustration.

Our group focus on quantification of these imperfections asking questions regarding the abundance of symmetry and its level in homomeric proteins, and protein domains under various conditions in an attempt to explore the conditions that help preserve the symmetry and understand the driving forces for distortion.

 
The homodimer cyanovirin-N domain B mutant (PDB ID: 3CZZ).
 
 
 

​​​Educational Technology and Chemistry Education

The Internet offers unprecedented opportunities for chemical education.  The availability of huge chemical databases, of three-dimensional and dynamic graphics together with the computational power and the communicational features of the web, provide foundations for exciting new ways to teach learn and visualize complicated chemical phenomena.  
 
 
Our group focus on several main aspects related to educational technology as applied to undergraduate chemistry education:

1. Explore new pedagogies that emerge with the new technology and evaluate their effectiveness

2. Understand how students learn in technologically enhanced environment

3. Develop three-dimensional and interactive molecular visualization tools that increase our understanding of molecular structure.



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Group Members

Research Associates:
  • Yaffa Shalit

Software Developers:
  • Sagiv Barhoom,  The Open University of Israel
  • Itay Zandbank, The Research Software Company
 
Former Group Members:
  • Yael Baruch Shpigler
  • Dr. Chaim Dryzun
  • Dror Brachia
  • Bnaya Shtainmetz
  • Zhanna Tatus Portnoy
  • Dr. Huan Wang
  • Dr. Ariela Kaspi-Kaneti​
  • Dr. Israel Zadok
  • Dr. Yael Feldman-Maggor

 
Current Collaborators:
  • Dr. Gil Alon, Department of Mathematics and Computer Science, The Open University of Israel
  • Prof. David Avnir, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
  • Prof. Ron Blonder, Department of Science Education, The Weizmann Institute of Science, Rehovot, Israel