Scroll down to read the following articles:
- Research: Toward understanding biological functions in a cell: Multi-scale modeling of electrostatic potential in biological systems
- Frederick M. Cartwright named executive director of CU-ICAR
- Time to register for summer camp: Fike day camp discount for employees
- Obituaries
1. Research: Toward understanding biological functions in a cell: Multi-scale modeling of electrostatic potential in biological systems
Currently, computational biophysical science addresses biological questions on various scales and details. Some researchers aim at modeling and understanding how individual molecules, proteins, DNA and RNA, perform their biological function. Such an investigation typically models biological macromolecules as objects made of many atoms connected with chemical bonds. Other researchers focus on revealing the molecular mechanism of large biological assemblies as photosynthetic machinery, respiratory complex and viruses, applying different level of details from atomistic to coarse-grained models. Furthermore, other biophysicists are interested to understand the interactions between different types of cells and tissues, and in such a case the atomistic models are not feasible.
Increasing the scale, one wants to apply biophysical methods to study the function of organs as the heart, lung, kidney and many others, which obviously cannot be done with atomistic models. The question is: how to bridge such diverse scales, since the average size of a protein is about 30 Angstroms (3 nano-meters), while the size of an organ is about 10cm and more (about 10,000,000 larger than an average molecule)?
The most promising approach to the above question is called “multi-scale” method such that the large object and its building blocks (molecules) are investigated with different levels of details. Our efforts in this direction are to provide more robust and efficient computer algorithms and software to allow the computational biophysics community to study biological entities of different sizes, from relatively small macromolecules to viruses.
Our current research utilizes a well-known computer package, the DelPhi package, which was originally developed in Dr. Honig’s lab at Columbia University in New York. The efforts in the lab are directed to modernize Delphi and to make it capable of calculating electrostatic potential and energies of large systems as viruses and mitochondrial complex. This is done by developing parallelized schemes that dramatically reduce the computational time and computer memory requirements.
The uniqueness of our approach is that it employs different techniques depending on the physical nature of the problem, which needs to be parallelized. Thus, we have developed new multi-level (parallelization is achieved at different levels of the algorithm) and interleaved (parallelization is implemented by interleaving the computational tasks) method, the MLIPB method, to parallelize standard methods for computing electrostatics potential and energies in the framework of the Poisson-Boltzmann equation.
The leading scientist in this project, Dr. Chuan Li, a postdoctoral researcher at the Computational Biophysics Laboratory in the Department of Physics and Astronomy, revisited the existing DelPhi algorithm to group the algorithmic tasks into several distinctive classes depending on the physical process being modeled. This was a very important development because he managed to increase the computational speed of calculations without losing accuracy.
In other words, the parallelized DelPhi is almost 100 times faster than the serial one, while retaining the same accuracy. From point of view of biological applications, this translates into a tool that can mole small and large objects with the same accuracy, allowing viruses and large macromolecular assemblages to be investigated at the atomic level of detail.
The ability of precise modeling of electrostatic potential, energy and forces is crucial for understanding biological processes taking place on various scales. The reason for that is that each atom within a protein, a DNA or a RNA carries electrostatic charge and at the same time the atoms are positioned within very short distances among themselves.
Applying high-school physics formulas, the Coulomb Law of Electrostatics, reveals that the strength of interactions at such distances is greater than any other force. Because of that, our development provides the Biophysics Community with a tool that enables revealing the role of electrostatics in very large systems bridging the gap between understanding the function of individual biological macromolecules and the function of much larger entities made of many proteins, DNAs and RNAs.
Our research is highly relevant to any study involving biological macromolecules, their assemblages and even larger entities. It paves the way of understanding the molecular mechanism associated with various biological functions in the cell and in a long run the role of electrostatics in process occurring in various organs. This is also relevant to revealing the effects of genetic disorders and the corresponding mechanism of the diseases, providing the opportunity the disease effect to be modeled at various scales and details.
Our goal in a long run is to further increase our capability to model even larger objects as components of the cell and the entire cell on level of details which will allow for meaningful biological conclusions to be made. This will be done by “gluing” individual atoms into larger objects, called groups of atoms, which then will make the structure of the large object (for example cellular compartments or the entire cell).
Currently the lab is progressing very well in this direction, the leading researcher being Mr. Nicholas Smith, a graduate student in the lab, who developed a tool called Protein-Nano Object Integrator. This tool allows for generating 3D-objects as multitude of pseudo-atoms and manipulating the objects in real time.
2. Frederick M. Cartwright named executive director of CU-ICAR
A seasoned auto industry executive with more than three decades of experience will lead one of the world’s foremost automotive research campuses into an exciting new era of research and collaboration.
Frederick M. Cartwright, who spent 30 years in the automotive industry with General Motors, has been appointed executive director of the award-winning Clemson University International Center for Automotive Research. His appointment is effective April 1.
Cartwright’s extensive experience includes design and development of advanced powertrains for commercial and military vehicles, management of GM’s hybrid bus program and numerous new business-development initiatives involving other auto manufacturers.
Among other executive positions, he previously was vice president for alliances and new business development for General Motors Europe in Rüsselsheim, Germany. Most recently he was director of new business initiatives based in Detroit.
In this role, he was responsible for development of new technology and product-based initiatives, including establishment of multiple alliances. He has a bachelor’s degree in mechanical engineering from Rose-Hulman Institute of Technology and a Master of Business Administration degree from Butler University.
Cartwright’s industry-centric experience will help steer CU-ICAR to a new chapter of growth and excellence, said John Kelly, Clemson University vice president for economic development. He will prove an exciting and valuable member of the team, he said.
“Since opening five years ago, CU-ICAR as become an international model for economic development,” Kelly said. “The campus has an enviable list of transport-related industry partners. With Fred at the helm, those relationships will only strengthen and more are sure to join.
“Fred’s appointment will not only further CU-ICAR’s mission, but help enhance the reputation of Upstate South Carolina as the go-to place for business,” Kelly said.
The campus has garnered more than $250 million in public and private investments and created more than 700 jobs. CU-ICAR boasts 19 campus partners and every year hosts hundreds of guests from around the world.
Cartwright said his focus will be to maintain momentum.
“CU-ICAR has a talented and dedicated team that has positioned the campus as a world leader in transportation research,” Cartwright said. “Its reputation for economic development and automotive research is known far beyond South Carolina’s Upstate.
“Its list of partners, from BMW Manufacturing Co. and Michelin North America Inc. to Sage Automotive Interiors and, most recently, EcoDual Inc., speak to the high regard CU-ICAR’s students, faculty and staff are held. I am eager to start work and excited to become part of such an energetic business community.”
Interim CU-ICAR director John Boyette said Cartwright will make Greenville his home and he quickly will become an asset to the community. The region enjoys a vibrant business climate, which is vital to its success, he said.
“Fred can draw on a wealth of experience from working relationships around the world,” Boyette said. “What he brings to the table will benefit us all.”
3. Time to register for summer camp: Fike day camp discount for employees
http://www.clemson.edu/campus-life/campus-recreation/additional_services/camps/
4. Obituaries:
- Thomas Berry “Dick” Tillman, Jr., retiree
Thomas Berry “Dick” Tillman, Jr., 88, died March 15, 2013. He served as a county extension director for Sumter County for 32 years. Tillman is survived by his son, John D. Tillman, Sr., family and friends. Funeral services were held this morning in the Elmore Hill McCreight Funeral Home chapel with burial in Evergreen Memorial Park Cemetery.Memorials may be made to Pisgah Baptist Church, 8620 Black River Road, Rembert, S.C. 29128, or to the Sumter 4-H Foundation, 2400 Bart Davis Road, Alcolu, S.C. 29001. Online condolences may be sent to www.sumterfunerals.com.
- Cecil Cook Davis, retiree
Cecil Cook Davis, 87, died March 18, 2013. He served as a department head and professor of accounting and finance and retired in 1982 with 35 years of service.Davis is survived by his wife, two daughters, family and friends.A graveside service will be held 2 p.m. Thursday in Woodland Cemetery on the campus of Clemson University. The family will greet friends following the service at the cemetery. In lieu of flowers, memorials may be made to:
- First Baptist Church of Clemson, 397 College Ave., Clemson, S.C. 29631;
- Clemson Free Clinic, 1200 Clemson Blvd., Suite 1, Clemson, S.C. 29631;
- Anderson Free Clinic, 414 N. Fant St., Anderson, S.C. 29621;
- Or to the charity of one’s choice.
Condolences may be expressed online at www.robinsonfuneralhomes.com or at Duckett-Robinson Funeral Home.
Upcoming events
- Office of Research Compliance (ORC) Brown Bag Seminar: Biological Safety-How to Perform a Risk Assessment March 26
- Italian Summit Year VI March 27
- June Pilcher: The Mystery of Intention: Some Brain-Based Ideas March 27
