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Address:
Lash Miller Chemical Laboratories
Office: Lash Miller, Room 435 Phone: 946 7466
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PhD Project:
After finishing my master's degree in Physics at the University of Guelph, under Guelph-Waterloo Physics Institute, I joint the Chemistry department of University of Toronto in Sept. 2005 . Now I am working in the theoretical chemical physics group of the department under supervision of Prof. Jeremy Schofield. My PhD project is about Discontinuous Molecular Dynamics (DMD) simulation of Protein-Like Chain folding.
Understanding protein folding
pathways provides insight into diseases associated with misfolding, such as
Alzheimer's, Mad Cow, and Parkinson's. Despite decades of study, the
detailed nature of protein folding is still an unsolved problem. Numerical
investigation of protein folding is typically based on Molecular Dynamics
(MD) simulation methods. However MD is limited to relatively short time
scales compared to actual folding times and other common numerical methods,
such as lattice models and Monte Carlo, either fail to adequately describe
the geometrical properties of the proteins or generate biased folding
trajectories. Discontinuous Molecular Dynamics (DMD) is a relatively fast
simulation method based on using step potentials to allow simple but
efficient calculation of trajectories. Unlike the molecular dynamics method,
which requires integration of equations of motion over small time steps
using detailed potentials, in DMD method, program runs event by event using
simplified discontinuous potentials.
We modeled a protein as a chain consisting of periodic sequences of four
different kinds of beads, and their interactions including attraction,
repulsion, and bond vibrations are modeled by step, shoulder, and
square-well potentials, respectively. By using these kinds of potentials,
the secondary structure of Alpha helices and folded proteins have been
reproduced. This folding process has been studied in the absence of solvent
and at low temperatures. To find low energy conformations, we use parallel
tempering sampling to scan potential landscape carefully at higher
temperatures. Studies currently are underway to investigate the effects of
solvation on folding pathway. Using the relatively fast and cheap DMD method
will help us to understand more about the nature of protein folding and its
characteristics.
The above folding process has been studied in the absence of solvent and at low temperatures. The photos and the movies are made by VMD (Visual Molecular Dynamics) using videomach
Teaching Experiences:
2003-2005: I had been the teaching assistantship as a marker/tutor/demonstrator for the courses of 1070/1080/1110 (Text book: Physics For The Biological Sciences) for four semesters (4*140 hours) at the University of Guelph. To get more information regarding this course and the text book, please refer to http://www.physics.uoguelph.ca/biophysics/ .
2005-2008: I have been the lab demonstrator of First Year Laboratory at the physics department of University of Toronto during the Fall & Winter semesters of 2005-2006, 2006-2007, 2007-2008 and the summer of 2007. Beside being a TA at the physics department, I have been the lab demonstrator for the third year course of "Experimental Physical Chemistry" at the Chemistry department of University of Toronto during winter 2006 and winter 2007 and as a marker during winter 2008. I was the tutor of CHM220, a second-year course in introductory physical chemistry for the biosciences, during Fall 2007. To find more about CHM220 refer to this website.
Master Project: I
did my master thesis under
supervision of Prof.
Don Sullivan. The title of my master thesis
is "The
Phase Transitions of Semiflexible Hard Sphere Chain Liquids", which is
about the application of statistical physics in the complex liquids by
using the numerical methods.
We presented a
self-consistent theory for describing phase
transitions in liquid crystals by using the Onsager second-virial
approximation for the free energy. The key ingredients of this theory is the
calculation of excluded volume and excluded area using Monte Carlo methods. In
the first part, we solved the self consistent equation which resulted in the
probability density of the system. By using the probability density, we
observed the thermodynamics variables, and by using those variables
we observed the phase
transition point between isotropic-nematic phases in the hard sphere chain
system. Then in the second part, the theory was extended to account for a
smectic-A phase by assuming that a smectic-A solution for the probability
density is a small perturbation around the nematic solution obtained
previously. By this method we located where
the smectic-A solution bifurcation from the nematic solution. To find more about both
parts of my master thesis project please refer to my master defense
Presentation. To find all the details of my project please refer
to the my
M.Sc. Thesis.
Publication & Posters
Presenting a poster about my PhD project at the Chemical Biophysics Symposium (CBP 2008), UofT, Toronto, Canada, 2008.
Course paper (non-refereed) for "Thermodynamics" course, "Inequalities relating critical exponents", UofT, Toronto, Canada, 2007
Course paper (non-refereed) for "The current Interpretations of Quantum Mechanics" course, "The Role of Decoherence in the Copenhagen Interpretation of Quantum Mechanics", UofT, Toronto, Canada, 2007
"The phase transitions of semiflexible hard sphere chains liquid" by Hanif Bayat Movahed, Raul Cruz Hidalgo, and D. E. Sullivan, Phys. Rev. E 73, 032701, March 2006, Abstract & Full Text
Master thesis submitted to University of Guelph under GWPI program, August 2005
Presenting a poster regarding my master project results at the annual poster section of Guelph-Waterloo Physics Institute, Waterloo, Canada, July 2005.
Course paper (non-refereed) for Molecular biophysics course, "Simulation of Protein Folding", UofG, Guelph-Waterloo Physics Institute, Canada, 2004
Course paper (non-refereed) for Quantum Information Processing course, "Quantum key Distribution and Privacy Amplification, QKD&PA" , UofG, Guelph-Waterloo Physics Institute, Canada, 2003
Giving an algorithm and simulating the text to speech process for Persian language at “Institute for the theoretical physics and mathematics” (IPM), 2001-2002. Small part of the work has been presented in 5th Irano-Armenian workshop as a talk. Beside this the algorithm has been used in the special Persian editor program (Fmailer)
Below links are referred to my other website (more personal)
http://www.hanifworld.com
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Updated: April 17, 2008