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.