The Center for Simulation and Modeling (SaM) at the University of Pittsburgh is dedicated to supporting and facilitating computational-based research across campus. SaM serves as a catalyst for multidisciplinary collaborations among professors, sponsors modeling-focused seminars, teaches graduate-level modeling courses and provides individual consultation in modeling to all researchers at the University. Our areas of research include: energy and sustainability, nanoscience and materials engineering, medicine and biology, and economics and the social sciences.
SaM Researchers in the News
Density functional theory has evolved into the most widely used method for the computational characterization of the electronic structure of complex materials. However it is well known that standard DFT methods do not describe long-range dispersion interaction. Recently Ken Jordan, co-director of SaM, his student Ozan Karalti and Wissam Al-Saidi of Chemical Engineering at Pitt, introduced an extended method originally introduced by Rothlesberger and co-workers for connecting DFT for long-range dispersion interactions. As of March 10, this was the 4th most downloaded paper in Chemical Physics Letters over the past 90 days. [O. Karalti, W. A. Al-Saidi, and K. D. Jordan, Chemical Physics Letters 591, 133-137 (2014)
An accurate description of the interactions between gas molecules and SWNTs is important for designing better materials for adsorption and purification of fluids using these nanoporous materials. Towards this, Center for Simulation and Modeling (SaM)-affiliated researchers De-Li Chen, Wissam A. Saidi, and J. Karl Johnson recently published two papers, in conjunction with collaborators at Penn State and the University of Virginia where atomistic simulations were used to predict the outcome of experiments carried out by their colleagues at UVa. The papers were published in the Journal of the American Chemical Society, 135, 7768-7776 (2013) DOI: 10.1021/ja402928s
and Physical Review Letters, 110 135503 (2013) DOI: 10.1103/PhysRevLett.110.135503
. The calculations predicted that the interaction energies between gases and either metallic or semiconducting single walled carbon nanotubes (SWNTs) would be the same, as long as the diameters of the nanotubes were the same. Specific calculations were carried out for adsorption of noble gases and n heptane on a series of nanotubes that were either metallic or semiconducting, having similar diameters. The theoretical predictions were confirmed by temperature programmed desorption experiments carried out at UVa on samples of purified metallic or semiconducting SWNTs.
Excess electron states
Ken Jordan: Orbitals associated with excess electron states in water clusters. Results from a model Hamiltonian approached developed in the Jordan group.
Karl Johnson: Gases (CO, CO2, and H2) entering the mouth of a metal organic framework nanoporous sorbent. Oxygen atoms are red, carbons are gray, hydrogens are white.
Daniel Zuckerman: An ensemble of polypeptides configurations can be generated by a computer process of “combinatorial growth.” Such a growth process avoids the dynamical bottlenecks of conventional simulations, which can be severe.
Inter-Bone Spacing of Anatomical Joints
Liz Marai: Visualizing dynamic changes in the inter-bone spacing of anatomical joints. Such visualizations help orthopedists discover the mechanism through which badly-healed injuries can lead to a degenerative disease like arthritis.
Polythiophene Undergoing Electron Transfer
Geoff Hutchison: Schematic of a polythiophene undergoing electron transfer to a C60 molecule in a plastic solar cell. Computational studies of the electronic properties of this polythiophene suggest the potential for highly efficient devices.
Lillian Chong: The Chong Lab uses simulations to study protein dynamics. Shown are snapshots from a simulation exhibiting the mechanically-induced unfolding that results from the fusion of two proteins.
Peyman Givi: Modeling turbulence to build more efficient engines. Load balancing at an instance of time during the simulation. 3D turbulent scalar fields (rendered on top left) affect CPU load distribution over solution domain.
H2S, H2Se, and AsH3
Karl Johnson: H2S, H2Se, and AsH3 contaminants adsorbing on a metal oxide surface, Zn2TiO4(010). Sulfur atoms are yellow, selenium orange, arsenic purple, hydrogen white, oxygen red, titanium silver, and zinc atoms are blue.
Understanding genetic components of human disease
The Barmada lab uses data-intensive high-throughput technologies such as microarray-based SNP genotyping and whole exome/whole genome sequencing to investigate the relationship between genetic variation and inherited diseases or traits.