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Trevor on the beach


DR. TREVOR M. CICKOVSKI
 RESEARCH ASSISTANT
INSTRUCTOR, C/C++ PROGRAMMING, FALL 2007
 UNIVERSITY OF NOTRE DAME (site)
 DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING (site)
You may contact me at:               
       LCLS
LABORATORY FOR COMPUTATIONAL LIFE SCIENCES (LCLS)
325 CUSHING HALL
NOTRE DAME, IN 46556
OFFICE PHONE: 631-3906
E-MAIL: tcickovs@nd.edu

Past Research Journals:  Summer 08
Spring 08     Fall 07     Summer 07
Spring 07     Fall 06     Summer 06
Spring 06     Fall 05     Summer 05
Spring 05     Fall 04     Summer 04
Spring 04    Fall 03    Summer 03
Spring 03    Fall 02    Summer 02
Spring 02    Fall 01    Summer 01   
Papers Published/Accepted
 1. From Genes To Organisms Via The Cell: A Problem Solving Environment For Multicellular Development  Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman and Jesus A. Izaguirre, Computing in Science and Engineering,  9(4):50-60, 2007.
2. MDL, A Domain-Specific Language For Molecular Dynamics  Trevor Cickovski, Chris Sweet and Jesus A. Izaguirre, Proceedings of IEEE 40th Annual Simulation Symposium, Norfolk, VA, March 2007.
3. A Framework for Three-Dimensional Simulation of Morphogenesis  Trevor Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, George Hentschel, Mark Alber, James A. Glazier, Stuart A. Newman, Jesus A. Izaguirre :  ACM Transactions on Computational Biology and Biocomplexity 2(4):273-288,  2005.
4. CompuCell, A Multi-Model Framework For Simulations Of Morphogenesis  Jesus A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor Cickovski, Joseph Coffland, Gilberto Thomas, Gabor Forgacs, Mark Alber, Stuart Newman, James A. Glazier :  Bioinformatics 20(7):1129-1137, 2004.
5. ProtoMol, An Object-Oriented Framework For Prototyping Novel Algorithms For Molecular Dynamics  Thierry Matthey, Trevor Cickovski, Scott Hampton, Alice Ko, Qun Ma, Matt Nyerges, Troy Raeder, Tom Slabach, Jesus A. Izaguirre :  ACM Transactions on Mathematical Software, 20(3):237-265, 2004.
6. Multi-Model Simulations of Chicken Limb Morphogenesis  Rajiv Chaturvedi, Jesus A. Izaguirre,
Chengbang Huang, Trevor Cickovski, Patrick Virtue, Gilberto Thomas, Gabor Forgacs, Mark Alber, Stuart A. Newman, and James A. Glazier : Springer Verlag LNCS 2659, Computational Science - ICCS 2003, International conference Melbourne, Australia and St. Petersburg, Russia, Part II, pp 39-49, June 2003.

Technical Reports
 1. Design Patterns For Generic Object-Oriented Scientific Software  Trevor Cickovski, Thierry Matthey and Jesus A. Izaguirre, Notre Dame Technical Report 2004-29, November 2004.
2. Empirical Analysis of Design Patterns in Scientific Application  Kedar Aras, Trevor Cickovski and Jesus A. Izaguirre, Notre Dame Technical Report 2005-08, May 2005.
3. Simulation of Chicken Limb Growth With Irregular Domain Shape  Kedar Aras, Trevor Cickovski, David Cieslak, Chengbang Huang and Jesus A. Izaguirre, Notre Dame Technical Report 2005-09, July 2005.
4. Interactive Molecular Dynamics  Dylan Brandtner, Trevor Cickovski and Jesus A. Izaguirre, Notre Dame Technical Report 2005-11, July 2005.
5. Molecular Dynamics Language (MDL)  Chun Bong Benjamin Yau, Trevor Cickovski and Jesus A. Izaguirre, Notre Dame Technical Report 2005-13, August 2005.
 		Awards and Honors
2001 - CAM summer research fellowship
2001 - Inducted into Tau Beta Pi
2002 - CAM summer research fellowship
2002 - Arthur J. Schmitt Graduate Student Fellowship
2004 - Inducted into Upsilon Pi Epsilon
2006 - Kaneb Award for Excellence in Teaching
2006 - CAM summer research fellowship

Highest Degree Earned
Ph.D. University of Notre Dame, Computer Science and Engineering - May 2008

Research Projects
MDL  A domain-specific language for molecular dynamics
BioLogo A domain-specific language for morphogenesis
CompuCell3D A three-dimensional multi-model software framework for morphogenesis
ProtoMol An extensible software package for simulations of molecular dynamics
Conference Presentations

 1. Midwest Numerical Analysis Day (presentation), May 2003  POWERPOINT
2. Biocomplexity IV (poster), May 2003
3. Biocomplexity VI (poster), May 2004
4. SIAM (presentation), February 2005, SESSION CHAIR   POWERPOINT
5. Biocomplexity VIII: Notre Dame Workshop on Applications of Methods of Stochastic Systems and Statistical Physics in Biology (poster), October 2005
6. Midwest Molecular Dynamics Workshop (discussion), November 2005
7. Midwest Society for Programming Languages and Systems Meeting (presentation), April 2006   POWERPOINT
8. ALife X, (poster and tutorial), June 2006
9. Helpful Hints for TAs in Computer Science and Engineering (panelist), August 2006
10. Society for Advancement of Native Americans and Chicanos in Science (recruiter), October 2006
11. IEEE 40th Annual Simulation Symposium, March 2007
12. IMA Classical and Quantum Approaches in Molecular Modeling (presentation), July 2007
13. CompuCell3D Workshop (instructor), August 2007
 Organizations I am/have been involved with at Notre Dame:
* Peer Mentoring, 2007-present
* Notre Dame Grad School Recruiter, 2006
* Cybervice, 2006
* Notre Dame Handbell Choir 2004-present (site)
* Notre Dame Celebration Choir 1998-present (site)
    President, 2003-2004
* Flipside, 1999-2004 (site)
* Intramural Softball
   GM, 2003, Coach 2006-2007
* Fischer Graduate Residences Choir 2002-2007
Papers Submitted/In Progress
 1. Parallelization of the Finite Temperature String Method   Trevor Cickovski, Chris Sweet and Jesus A. Izaguirre, to be submitted, 2007.
2. Extension of the Finite Temperature String Method to the WW Domain.  Trevor Cickovski, Chris Sweet and Jesus A. Izaguirre, to be submitted, 2007.
3. Catastrophes and Rescues in Detailed Kinetic Model of Microtubule Dynamics Instability.  Gennady Margolin, Ivan V. Gregoretti, Trevor M. Cickovski, Holly V. Goodson and Mark S. Alber, to be submitted to PNAS, 2007.
 Pictures
2004: Michigan Game
2005: Orlando  Sunrises  Graduation  Michael Essany
2006: St. Louis  Easter  Craig's Wedding  Heart  PSU
2007: Bell Tour
Other Interesting Stuff
* Ultimate '80s Songs
* Ubiquitin in Nobel Research!! 
* You Grew Up In the '80s If...
 Charity Organizations
* Todd M. Beamer Foundation
* Catholic Relief Services
* The ONE Campaign


Remo  In memory of Remo DiGirolamo, my high school classmate.  You will not be forgotten.