The attachement below is a map of the activities.

Yiwei Zhang will defend his dissertation “Graph based optimization for scientific computing” Monday 6/18/2012 @ 13:30 in SWGN 3A75. "This work investigates transforming scientific computing problems such as phylogenetic analysis, system simulation into abstract graph problems and developing algorithms for optimization. First, we investigate an efficient algorithm for unequal genome phylogeny reconstruction. Currently few method can solve the median problem for unequal genomes which is essential in evolution tree and ancestral genome reconstruction. We present a new distance measurement model for unequal genomes and develop a branch-and-bound algorithm based on multiple breakpoint graph to calculate the median for unequal genomes. We also present a mixture method to infer the ancestral gene order based on maximum likelihood approach and adequate graph median solver. The median solver is extremely time consuming under high rearrangement rate compared with maximum likelihood approach but it gives better accuracy. So our mixture method aims to increase both the speed and accuracy for ancestral genome reconstruction. We also investigate the method to improve the simulation problem for large systems. The Modified Nodal Analysis (MNA) simulation method is widely used to solve electrical system networks. It has the disadvantage that the simulation time increases disproportionally with system size. To accelerate the simulation, latency insertion method has been introduced to partition the original system into a number of smaller sub-systems so that computation will be reduced. But so far there is no automatic method to optimally exploit the existing latency in the system. Our work focuses on an algorithm based on graph search to optimally activate the optional latency decouplers in the network. With the optimal activation, the system is partitioned in the way that maximum simulation speed up will be achieved."

PhD defense will take place on Wednesday June 6, 2012 in room 3A75 Swearingen at 10 am. Matthew Fawcett Protein folding is the one of the most important topics of research in Biochemistry. The understanding of how a protein folds into its three dimensional shape from its amino acid sequence is of extreme importance in medicine today because proteins play important roles in diseases such as sickle cell anemia, Alzheimer’s disease, and Parkinson’s disease to name a few. Protein structures were traditionally determined by x-ray crystallography and more recently with nmr spectroscopy. However these methods are expensive and take a long time to perform. Recently, computational methods such as: ab initio, homology, and threading methods, have gained recogni- tion. The thermodynamics hypothesis of proteins states that a protein’s native structure is determined by its amino acid sequence, and resides in the lowest energy state. Ab initio methods provide the means to calculate the energy of proteins using an all atom forcefield. Traditional forcefields, like ones used in CHARMM and Xplor-NIH, use energy terms that are in two categories: bonded and non-bonded terms. However, there are problems with traditional forcefields in that, the energy landscapes are too complicated with too many variables. Also, the energy landscape does not exhibit a funneling effect to guide the protein down to the native conformation. Finally there is a notable lack of open source software to provide the community of Computer Scientists, Mathematicians, and Engineers with an opportunity to be engaged in this line of investigation and integrate their expertise. Here we propose addressing the above problems through the development of the software package Semi Classical Open-Source Protein Energy (SCOPE). SCOPE is an open-source C++ program that will reconstruct a protein within the rotamer space. Representation of a protein structure in the rotamer space reduces the degrees of freedom of the protein structure conformational space, allowing SCOPE forcefield to only have to calculate the non-bonded energy terms. The energy landscape will be simplified due to the reduction in the energy terms of the forcefield. Also, SCOPE will extend the traditional forcefield by calculating a hydrogen bond term along with the number of consecutive hydrogen bonds as they appear in a protein. The use of the extra hydrogen bond term is likely to create a funneling effect in the protein’s energy landscape to its native conformation. The program is also open-source which will allow the community of Computer Scientists, Mathematicians, and Engineers a chance to add to the solution without investing significant time and effort in becoming familiar with the field of biophysics. SCOPE’s energy profiles are incorporated into an artificial neural network(ANN) based approach to predict the backbone root mean square deviation(BB RMSD) of a given protein structure to that of the native structure based on its potential energy alone. This shows a remarkable correlation between the energy profiles and BB RMSD of a protein. The correlation was as high 0.99 in several experiments. The ANN can be used to help refine a protein from around 7.0 Å to approximately 2.0 Å.

Students in the CSE Capstone Project class (CSCE 492 & ENCP 492) will present posters of their work and demonstrate their projects in the Swearingen Lobby on Thursday April 19th 3:30 to 4:45. Come see what they have been doing!! John B. Bowles

Desperate Fishwives: A study in applied game design John Hodgson Date: April 19, 2012 Time: 1530-1700 (3:30pm-5:00pm) Place: Swearingen 3C02 Abstract This thesis is a presentation of the design and development of a novel computational artifact: the educational videogame Desperate Fishwives, which harnesses the idea of procedural rhetoric to instruct players on aspects of early modern (cc. 17th century) English life. Herein is detailed the validity of using games as rhetorical and educational devices and the process of designing a game to reflect a particular client’s pedagogical style and interpretation of history. This thesis, using the ideas of procedural rhetoric, procedural literacy, and expressive processing, seeks to bridge the gaps between humanities, rhetoric, and software development.

The UPE Induction Ceremony will be at 2:30 on Wednesday April 18th in the Faculty Lounge. This will be followed by the Keynote Lecture by Jeff Brewer at 4:00 (see attached flyer). The UPE Keynote Address by Jeff Brewer 4:00 PM Wednesday, April 18, 2012 Faculty Lounge Room 1A03, Swearingen Engineering Center What does it take to build a successful career in the field of engineering & computing? Where do you start? Who can you learn from and what do you need to know to achieve success and enjoy your career to the fullest? There are many options for engineering and computing graduates today. Demand for capable talent has remained a constant regardless of the economic climate, so how can today’s graduates maximize their opportunities? Jeff Brewer, a 1984 graduate of USC’s College of Engineering, was the founder of Business Vitals and is presently Vice President of Managed IT Services at Earthlink. He will share his insights, key success factors and lessons learned over the past 25 years working in industry and as a successful entrepreneur. Sponsored by: The University of South Carolina Department of Computer Science and Engineering