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Inbal Tuvi-Arad, Associate Professor

Inbal Tuvi-Arad
Contact Info

The Open University of Israel Head of the 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

News

Open Positions:

A postdoc position is open in the field of protein symmetry. To apply please submit curriculum vitae, list of publications and names of two people willing to provide letters of reference via email.

 

 

Tuvi-Arad Research Group

Computational Chemistry and More

 

 

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 chemical education.

 

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Software:

  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 - A list of software for download 

 


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 Physics 99, 9704-9708 (1993).
  3. Y.B. Band and I. Tuvi, Quantum Rearrangement Scattering Calculations Using the Invariant Imbedding Method, Journal of Chemical Physics 100, 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 Review A50 (Rapid Communication), R2826-R2829 (1994).
  5. Y. B. Band and I. Tuvi, Convergence of Diabatic to Adiabatic Scattering Calculations, Physical Review A51 (Rapid Communication), R3403-R3406 (1995).
  6. Y. B. Band and I. Tuvi, Reduced Optical Shielding of Collisional Loss for Laser Cooled Atoms, Physical Review A51 (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 Matter 7, 6045-6063 (1995).
  8. I. Tuvi and Y. B. Band, Hermiticity of the Hamiltonian Matrix in a Discrete Variable Representation, Journal of Chemical Physics 107, 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 Review A57, 3724-3738 (1998).
  10. I. Tuvi and Y. B. Band, Nonadiabatic Coupling using a Corrected Born-Oppenheimer Basis: The Vibronic Spectrum of HD+, Physical Review A59, 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 Physics 111, 5808-5823 (1999).
  12. R. Nachmias and I. Tuvi, Taxonomy of Scientifically Oriented Educational Websites, Journal of Science Education and Technology 10(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 Technology 10(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 Teaching 22(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 Education 19(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 Practice 8(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 Practice 11(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 Chemistry 47,1274-1286 (2010).
  19. I. Tuvi-Arad and D. Avnir,  Quantifying asymmetry in concerted reactions: Solvents effect on a Diels-Alder cycloadditionJournal of Organic Chemistry  76, 4973-4979 (2011).
  20. I. Tuvi-Arad and D. Avnir, Symmetry-enthalpy correlations in Diels–Alder reactions, Chemistry - A European Journal 18, 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 permutationsJournal of Mathematical Chemistry56, 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. I. Tuvi-Arad and R. Blonder, Invited review: Technology in the Service of Pedagogy: Teaching with Chemistry Databases, Israel Journal of Chemistry (in press, DOI: 10.1002/ijch.2).
  29. H. Wang, D. Avnir and I. Tuvi-Arad, Chiral Ramachandran Plots II: General trends and proteins chirality spectra, Biochemistry, 57(45), 6395–6403 (2018)
  30. I. Tuvi-Arad and G. Alon, Improved Algorithms for Quantifying the Near Symmetry of Proteins: Complete Side Chains AnalysisJournal of Cheminformatics, 11(1):39 (2019).

 

  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-Magor, 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.
 

 

Computational Chemistry

Symmetry 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.
 

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).
 

Developing Improved Algorithms for Symmetry Analysis

Our group focuses on improving the continous symmetry measure algorithms in terms of accuracy and efficiency, making them useful to study the symmetry of macromolecules and proteins, bulk systems and much more. In addition we are developing a host of supporting tools to calculate the CSM for huge databases of molecular coordinates taken from a variety of experimental molecular databases and computational results.
 
 
Helicene with 43 phenyl rings.
 


 
 
 

​​Chemical 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.  
 
 
 

Learning with Video

The technology of live video streaming (LVS) enables audio and video broadcasting through the internet directly into users' personal computers. When applied to education, students can view and interact, in real time, with their instructors and classmates during a live session. Following the session students can access the archive of recorded lessons. By allowing students to attend class remotely, LVS expands classroom walls and time frame. These features make it particularly attractive for distance education. The ability of students to access the class sessions archive provide them with full control over their learning pace with the confidence that they did not miss anything regardless of their participation in the live sessions. Our study focuses on LVS viewing strategies of undergraduate chemistry students. Our goal is to identify key aspects in the courses' materials that require special attention, assess the effectiveness of the video sessions, and learn how to improve them for future use. 
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PhD Students:
Yael Feldmann Maggor (Science Education), jointly supervised with Prof. Ron Blonder,The Weizmann Institute of Science​
 
Research Associates:
Dr. Ariela Kaspi-Kaneti
Yaffa Shalit

 Software Developers:
Sagiv Barhoom,  The Open University of Israel
Itay ZandbankThe Research Software Company
Devora WittyThe Research Software Company​
 
Former Group Members:
Yael Baruch Shpigler
Dr. Chaim Dryzun
Dror Brachia
Bnaya Shtainmetz
Zhanna Tatus Portnoy
Dr. Huan Wang

 
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
Dr. Radu Iovita,Center for the Study of Human Origins (CSHO),New-York University​, New-York, USA
Dr. András Stirling, Institute of Organic Chemistry, Research Center for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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