David Toth

A large scale virtual screen of DprE1

Tuberculosis continues to plague the world with the World Health Organization estimating that about one third of the worlds population is infected. Due to the emergence of MDR and XDR strains of TB, the need for novel therapeutics has become increasing urgent. Herein we report the results of a virtual screen of 4.1 million compounds against a promising drug target, DrpE1. The virtual compounds were obtained from the Zinc docking site and screened using the molecular docking program, AutoDock Vina. The computational hits have led to the identification of several promising lead compounds.

A structural comparative approach to identifying novel antimalarial inhibitors

Malaria continues to affect millions of people annually. With the rise of drug resistant strains, the need for alternative treatments has become increasingly urgent. Recently, PfUCHL3 was identified as an essential deubiquitinating enzyme. The increasing number of drug target structures being solved has increased the feasibility of utilizing a structural comparative approach to identifying novel inhibitors. Using AutoDock Vina, we recently screened the NCI library of about 320,000 compounds against the crystal structure of PfUCHL3. The top hits were subsequently screened against its human ortholog UCHL3 as to identify compounds that could specifically target the PfUCHL3 over its human counterpart. This method was used to identify small molecule inhibitors that can preferentially inhibit the parasitic enzyme. Several compounds were identified that demonstrated significant binding affinity preference for the malaria target over the human enzyme. Two of these compounds demonstrated ng/mL activity.

A Portable Cluster for Each Student

Although some colleges and universities have access to parallel computing hardware, none that we are aware of can provide dedicated parallel computing hardware to each student. Instead, institutions often provide shared parallel computing equipment for the students, if they can afford to provide any. It is difficult for students to really get an understanding of the performance of their programs and how they scale when they are using shared equipment that is not dedicated to them and where other students or other users may interfere with their work. The current emphasis on network security at some institutions also prevents some shared resources that students could use from being easily accessible or sometimes accessible at all. We provide a parts list, information, and microSD card images to make a small, affordable compute cluster that each student in a parallel computing course can purchase in lieu of a textbook so each student has their own private compute cluster.

Development of undergraduate and graduate programs in computational science

There is a pressing need for a workforce with the modeling and simulation skills associated with computational science. A number of national studies have substantiated those needs with respect to the future competitiveness of USA in research and development, the innovation of new products, and the competitiveness of many industries. Creating computational science programs at academic institutions organized along disciplinary boundaries represents a challenge because aspects of computer science, mathematics, and a science or engineering domain are required parts of any program. Gaining agreement on the associated requirements, integrating the classes with those in the traditional curriculum, and obtaining the necessary support through academic and administrative reviews represent substantial challenges. Clark Atlanta University, the University of Mary Washington, and Southern University are all working on establishing undergraduate or graduate programs in computational science and have had a number of common experiences. Copyright

Attacking HIV, tuberculosis and histoplasmosis with XSEDE resources

HIV, tuberculosis and histoplasmosis are infectious diseases that affect millions of people world-wide. We describe our efforts to find cures for these diseases using the technique of virtual screening to identify possible inhibitors for essential proteins in these organisms using one of the XSEDE supercomputers. We have completed the virtual screens and have found promising compounds for each disease. Cell culture experiments have supported the likelihood of a number of the compounds being effective for treating both histoplasmosis and tuberculosis.

Development of undergraduate programs in computational science: panel

There is a pressing need for a workforce with the simulation and modeling skills associated with computational science. A number of national studies have substantiated those needs with respect to the future competitiveness of the US in research and development, the innovation of new products, and the competitiveness of our industry [1,2,3].

An Introductory Course on Modeling and Simulation

We describe our experiences teaching CPSC 109 - Introduction to Modeling and Simulation, an introductory course that we developed [1]. The course fills one of two quantitative reasoning requirements for the general education program at the University of Mary Washington (UMW) and serves as one of two possible prerequisites for UMWs Computer Science 1 course [2]. It is also intended to serve as a bridge between computer science and other disciplines at UMW, particularly those in the natural and physical sciences. The course is based on the National Computational Science Institute (NCSI) [3] Introduction to Computational Thinking Workshop, but adds in an explicit emphasis on introductory programming concepts for several weeks to ensure adequate preparation for Computer Science 1. We discuss the tools the students use in the course, some assignments, and the projects that students have created at the end of the semester. In addition, we discuss a special version of the course we have created for students in UMWs honors program [4].

Using NP-Complete Problems to Compare a CPU, GPU, and the Intel® Xeon Phi™ Coprocessor

As accelerators are integrated into many of the newest workstations and supercomputers to provide large amounts of additional processing power, selecting the appropriate one is critical for achieving the best performance. The new Intel® Xeon® PhiTM coprocessor provides more processing cores than a CPU but less than a graphics processing unit (GPU). However, the Phis cores do not have the limitations of a GPUs cores and can also run code written for traditional CPUs instead of requiring code written specifically for GPUs. We used the traveling salesman problem, the knapsack problem, and the party problem, three NP-complete problems, as benchmark applications to compare the relative performance of the Phi with a contemporary GPU and CPU. Programs were written to solve the problems on the CPU and on the coprocessor that could be easily ported to run on the GPU with only minor modifications. The length of time the programs took to complete on the coprocessor, the GPU, and the CPU was measured. While the GPU attained speedups of almost 14 to 80 over a single CPU core for the problems, the coprocessor only attained speedups between 4 and 7 for the problems.