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Principal Investigator: Prof. David Sherrill
Weak interactions, such as the noncovalent interactions governing drug binding and the structures of organic crystals, are very challenging to understand. Experimentally, these interactions are often seen in complex environments, where it can be difficult to pick out only the interaction of interest. Theoretically, they feature shallow potential energy surfaces and require very accurate quantum-mechanical modeling for reliable results. Definitive theoretical investigations of pi-pi, alkyl-pi, and sulfur-pi interactions which elucidate the strength, geometrical preferences, and fundamental nature of these prototype biomolecular interactions will be presented. In particular, it is shown that the current paradigm for understanding pi-pi interactions, which emphasizes electrostatic interactions, fails qualitatively. Better models developed on the basis of high-quality quantum mechanical benchmarks will aid in rational design of drugs and supramolecular architectures. Click here for more information.

Principal Investigator: Prof. Rigoberto Hernandez
A new approach to understanding nonstationary processes has recently been developed through the use of the so-called irreversible generalized Langevin equation (iGLE). The iGLE model can accommodate nonstationary changes in temperature and the friction strength of the environment. These changes may be coupled to macroscopic averages of the environment as induced by the collective motion of many equivalent tagged particles. As these environments may not be identical, the WiGLE model has also been developed, and it accounts for heterogeneous environments, each of which is coupled to a set of w neighbors. Possible applications of these models include the chemical reaction dynamics of thermosetting polymers and living polymers, and the folding dynamics of proteins. Click here for more information.

Principal Investigator: Prof. David Sherrill
New theoretical methods are being developed to treat systems featuring more than one important electron configuration, e.g., diradicals, transition metals, and bond-breaking reactions. In these cases, commonly used electronic structure techniques (e.g., Hartree-Fock molecular orbital theory, many-body perturbation theory, density functional theory) can sometimes fail dramatically. Applications of the new theoretical methods include the potential role of diradical intermediates in pericyclic reactions (including diradicals formed by the enediyne anti-cancer agents) and the general description of potential energy surfaces. Click here for more information.

Principal Investigator: Prof. Rigoberto Hernandez
Existing theories of polymers are often aimed at the characterization of the final product and often omit treatment of the reaction dynamics in which the viscosity self-consistently affects the reaction process. For example, the polymerizations may end not because the reactants have been depleted, but because of diffusional quenching due to the dramatic change in viscosity with the polymerization. To better understand this question, two different approaches are being developed: a generalization of the bond-percolation model to provide a system in which the growth may be observed within a Monte Carlo simulation, and a non-stationary dissipative model to provide real time information. Ultimately, these models will be used within interactive programs for the design and characterization of polymeric materials with specified time-dependent material properties. Click here for more information.

Principal Investigator: Prof. Rigoberto Hernandez
Minimalist lattice and off-lattice models provide rich insight characterizing the universal behavior of protein folding without suffering high computational costs. Monte Carlo simulations of designed minimalist proteins are being analyzed through novel projections to provide a better understanding of the connection between structure and protein dynamics. Click here for more information.

Principal Investigator: Prof. Karl Jacob
Segregation of a specific component from a binary mixture is examined using the Monte Carlo simulation techniques. This phase segregation phenomenon has been studied using the Potts model, and grain growth, agglomeration, and solvation can be characterized and quantified using the methodology. Click here for more information.

Principal Investigator: Prof. Kevin Brennan
In this work, we examine the transport properties of emerging semiconductor materials, particularly the wide band gap semiconductors as well as the antimonides. To date we have provided some of the first information on the breakdown properties and carrier dynamics in GaN, AlN and their related ternary compounds. Using this information we have made comprehensive studies of the operation of MESFET device structures made from GaN and its related compounds. All of our codes have been developed in-house. For the proposed work, we plan to perform device simulations that include quantum effects, multi-band transport and high field transport. Click here for more information.

Principal Investigator: Prof. Sotira Yiacoumi
The electrical double layer will be modeled by considering anions, molecular solvent, and an electrified surface. The TIP4P model (Jorgen 1983), which represents water as rigid molecules with four interaction sites wil to simulate the water behavior in the solution. For cross interactions involvin water/electrolytes and water/interfaces, an ab initio calculation with the 6-31G set and MP2 correction will be used to calculate the force field. A modified Gr Canonical Monte Carlo simulation will be used for the calculations. Click here for more information.

Principal Investigator: Prof. Rina Tannenbaum
The aggregation process of metal nanoprticles in the presen chains is examined. The metallic precursors react both with each other (via two mechanisms whose onset is cluster-size dependent), and with the polymer. Therefo the final equilibrium particle size will be a function of the weighted contribut both processes. The simulations that are proposed will examine the influence of metal-polymer interactions on the aggregation process and the final metal partic The simulation method used here can be extended to include any aggregating syste with secondary surface interaction and can be applied to biological systems. Click here for more information.

Principal Investigator: Prof. Robert Dickson
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Principal Investigator: Prof. Robert Dickson
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Principal Investigator: Prof. Mark White
The research will model the properties of a family of solids known as hydrotalcite. We have made several members of this family by selectively replacing the trivalent and divalent ions that comprise the cationic sheet in the layers. These solids have been characterized by PXRD and IR to show systematic changes in the unit cell parameters and the appearance of new peaks in the IR pattern as Ga is replaced for Al. Moreover, the CO2 adsorption properties for the Ga-substituted samples are 3-5 times greater than the samples that contain only Al. We will model these solids so as to predict the affinity for CO2.Click here for more information.

Principal Investigator: Prof. Jim Mulholland
We are studying the formation of toxic combustion byproducts, in particular those produced by combinations of resonance-stabilized radicals. These reactions are interesting because the radicals are neutral (compared with non-stabilized radicals) and ambident (multiple reactive channels yield several product isomers, including interesting stereochemistry). We have looked at combinations of cyclopentadienyl radicals and indenyl radicals to form two to four ring aromatics. We are also studying the formation of polychlorinated dibenzo-p-dioxins and dibenzofurans from condensation of phenoxy radicals. We have performed laboratory experiments and semiempirical molecular modeling. We will extend our current efforts, particularly for PCDD formation from chlorinated phenols. Click here for more information.

Principal Investigator: Prof. Christoph Fahrni
Intramolecular protontransfer in the excited state can be disrupted by coordination of transition metals. We try to model the excited state reaction pathway of the coordinated metal, which might include ejection of the cation or strong distortion of the ground state coordination geometry. Click here for more information.

Principal Investigator: Prof. Pete Ludovice
The gauche effect in the ethylene oxide bond of poly(ethylene)terephtalate (PET) is well characterized. The conformational behavior of this bond can be determined by acoustic IR. This conformation along with the characteristic ratio of the polymer is being used to parameterize a Rotational Isomeric States (RIS) model. However, three parameters are required for this polymer so an additional conformational descriptor is required. We will use the torsional states of the CCOC bond in PET which is adjacent to the ethylene oxide COOC bond. Unfortunately this is not easily measured spectroscopically. Semiempirical and ab initio Hartree-Fock calculations give conflicting results. Preliminary results suggest that the gauche is becoming lower in energy as the basis set is increased (i.e. from STO-3G to 3-21G*). We will establish accurate measure of the energy difference between these states by using DFT methods. This in turn will be used to finish fitting the parameters for the RIS model. This RIS model will then be used to generate initial conformations of PET glasses which are being used to predict oxygen solubility in PET derivatives. Such a model can ultimately explain differences in gas barrier properties for various PET derivatives. Click here for more information.

Principal Investigator: Prof. Nicholas Hud
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Principal Investigator: Prof. Roman Grigoriev
The goal of this investigation is to test several theoretical predictions regarding the dynamics and control of the fingering instability in thermocapillarity driven liquid films. Click here for more information.

Principal Investigator: Prof. Stephen Harvey
Molecular dynamics (MD) simulations are planned on a solvated all-atom model of ribosome recycling factor, which is a protein whose structure strongly resembles that of transfer RNA (tRNA). Previous studies have suggested hinge-bending motions between the two arms of the molecule, each of which is a functional domain. These studies are intened to quantitatively examine the extent of this flexibility. Click here for more information.

Principal Investigator: Prof. Konstantin Mischaikow
This project involves the simulation of spiral/fibrillating wave patterns using a reaction-diffusion equation and then computing the homology groups of the resulting excited regions in space and time. This produces a time series of integers which measure the existence of holes and volumes in space and time. Standard nonlinear time series techniques are then used to compute quantities such as Lyapunov exponents. Preliminary results indicate chaotic behavior. Click here for more information.

Principal Investigator: Prof. Cheng Zhu
Use MD simulations to understand how externally applied force regulates the dissociation rate of macromolecular complexes and how conformational changes propagate long range to affect binding. The systems include selectins, integrins, and Ig superfamily members. Click here for more information.