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Computational Biochemistry and Proteomics

Abstract: 

Computational Biochemistry and Proteomics

This research group is involved in two major projects and uses MSI software resources for routine applications.

  • One project focuses on anti-cancer and antimicrobial drug design that target enzymes like the proteasome or integral membrane proteins like cell surface growth receptors and transporters. For example, inhibition of the proteasome leads to cancer cell apoptosis or programmed cell death. This project requires access to the molecular modeling and simulation resources to perform molecular docking (e.g., with AUTODOCK and DOCK) and QSAR studies (e.g., with Tripos Sybyl , GAUSSIAN, and the Cambridge Structural Database) to guide the synthesis of novel hybrid inhibitors with some similarity to known scaffolds. Similar methods will be applied to other anti-microbial compounds.
  • The second project is to identify the structure and function of a novel family of membrane-bound aspartyl proteases. This uses molecular modeling and simulation resources (e.g., Discovery Studio (Accelrys, Inc.) and PyMOL software packages) and will use structural biology resources (e.g., molecular dynamics software (Gromacs and NAMD) designed for biomolecular systems, biological force fields (CHARMm and AMBER), and docking software (AUTODOCK and DOCK)) in the future to perform docking studies in order to elucidate the preferred protein substrates for these proteases. In addition, this lab collaborates with the Center for Mass Spectrometry and their data are being stored on shared MSI/Mass Spec resources. They use a variety of the proteomics software packages (e.g., MAXQUANT, TINT, X! TANDEM, MASCOT, Scaffold Q+,and ProteinPilot ) for analyzing mass spectrometry data to identify proteins cleaved by their proteases.

In routine applications, the lab uses the Vector NTI software package for molecular biology and genetic engineering applications, the software for data analysis, curve fitting, and graphing (e.g., Origin Lab software and GraphPad Prism), and MATLAB and Mathematica for numerical computation.

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Group name: 
johnsonj

MSI Research Exhibition 2017 – Physical Sciences and Engineering Posters

The titles for the posters submitted in the Physical Sciences and Engineering category for the 2017 MSI Research Exhibition are listed are shown below. See posters in the Biological and Medical Sciences category . Return to the Research Exhibition main page . Physical Sciences and Engineering A...

Computer Simulations of Protein Kinase A

Protein kinase A (PKA) is involved in many cellular events and its activity can be tweaked and compartmentalized through mirystoylation of its N-terminus. (Mirystoylation is a type of protein modification that plays a role in directing and anchoring proteins to membranes and, thus, is involved with...

Modeling and Simulation of Turbulent, Reacting, Multiphase Flows

Abstract: 

Modeling and Simulation of Turbulent, Reacting, Multiphase Flows

The Garrick group is interested in the modeling and simulation of multiphase reacting flows. These include particle formation and growth dynamics in laminar and turbulent flow systems, combustion problems, and spray dynamics. This research draws on fluid dynamics, computational fluid dynamics, aerosol dynamics, chemistry, and physics to develop computational tools to simulate atomization, particle formation, coagulation, coalescence, aggregation, break-up, and other physico-chemical processes. The underlying processes and dynamics are modeled in a fashion that render them amenable to simulation via high-performance computing. The group utilizes a variety of simulation techniques including DNS and LES to perform both scientific and engineering simulation and analysis.

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Group name: 
garricks

Computational Design of Novel Multiferroics

Abstract: 

Computational Design of Novel Multiferroics

In the past decade, first principles computational tools, in particular the implementations of density functional theory (DFT), have achieved the power to not only support and explain experimental results but also to make predictions and design new materials. This so-called materials by design approach has been intensively used, especially in the field of oxides, to either come up with new compounds or optimize superlattice structures that give rise to new functionalities.

This research project focuses on magnetoelectric multiferroics, compounds that exhibit both magnetism and a macroscopic, switchable dipole moment. By using well-established evolutionary structure prediction algorithms (implemented, for example, in the USPEX package) interfaced with standard DFT (implemented, for example, in the Vienna Ab Initio Simulation Package), these researchers are determining new candidate compounds/structures and studying their properties, such as the magnetic order, magnetoelectric coupling coefficient, etc. Later stages of the project might possibly involve approaching these compounds with more state-of-the-art computational methods for strongly correlated systems, such as the Dynamical Mean Field Theory (implemented, for example, in the DMFT-Wien2K package). While this group's DFT calculations are not highly parallelizable, especially above couple of dozen cores, and have comparatively low memory needs, the evolutionary structure prediction is a length process, which requires considering thousands of different possible crystal structures to find the lowest energy one. As a result, the computation power required for this project can easily be very large.

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Group name: 
birolt

Computational Polymer Physics

Abstract: 

Computational Polymer Physics

Work in this group focuses on the use of analytic theory and computer simulations to elucidate molecular origins of the behavior of complex polymer fluids. The researchers focus primarily on self-assembling systems of block copolymers, and emphasize the study of highly simplified models to study generic aspects of behavior, rather than on accurate atomistic simulations of specific chemical systems. Work completed over the last several years used extensive simulations to demonstrate that phase boundaries and a variety of physical properties of block copolymer melts exhibit a universal dependence on a small set of dimensionless parameters, and provided a characterization of these universal functions in a form suitable for analysis of experimental data. Ongoing computational work is increasingly focused on the study of the study of dynamical and viscoelastic phenomena in block copolymer melts near the order disorder transition, equilibrium behavior and slow dynamical processes in systems in which either polymeric or small molecule surfactants form micelles, the study of liquid-liquid interfaces and the kinetics of surfactant adsorption to interfaces, and initial work on the bicontinuous microemulsion phase of systems containing two immiscible liquids and a surfactant.

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Group name: 
morsedc

July 2011

For 21 years, MSI has hosted an Undergraduate Internship Program (UIP) that provides opportunities for students to learn about supercomputing and scientific research. The 2011 MSI UIP began in June and will continue until mid-August. Nine undergraduates from around the country are working with MSI...

Data Storage Acceptable Use

Data storage is a finite and valuable resource. Storage services provided to MSI users are solely intended to support data and computationally intensive research. Storing personal files that are not related to data-intensive or high-performance computing workflows should not be stored on MSI...

Computational Surface Chemistry

Abstract: 

Computational Surface Chemistry

The structure and dynamics of interfaces control many processes in chemistry and chemical engineering. These researchers use classical molecular dynamics and quantum mechanical/molecular mechanics (QM/MM) methods to investigate the atomic nature of chemical interfaces in multiple contexts. Self-assembled monolayers provide a controllable semi-crystalline surface that they can tailor to exhibit a variety of functionalities spanning the range from completely hydrophobic to mixed surfaces to protic, hydrophilic surfaces that can hydrogen bond with the solvent. The group will exploit the tunable nature of these molecular surfaces to use them as models for such diverse applications as protein-water interfaces and hydrophobic interfaces used in froth flotation for industrial mining. By incorporating functional groups along the surface that are sensitive to the dynamic environment at the interface, they will monitor conditions such as surface field effects and alignment, solvent accessibility in rough molecular surfaces, and surface motion and clustering. This work is performed in close collaboration with experimental researchers to validate the calculations and guide future investigations.

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Group name: 
layfield

Development and Application of Computational Models for Purposes of Investigating Phenomena of Chemical, Biological, and Environmental Interest

Abstract: 

Development and Application of Computational Models for Purposes of Investigating Phenomena of Chemical, Biological, and Environmental Interest

These researchers develop, code, and apply novel and/or established classical and quantum mechanical methodologies to model chemical structures, properties, and reactivities. Current areas of focus include:

  • Modeling the factors that lead to improved performance of water-splitting catalysts in dye-sensitized solar cells
  • Rationalizing structure, reactivity, and experimental isotope effects in metalloenzyme systems and small-molecule models that activate molecular oxygen
  • Elucidating the factors controlling the thermochemistry of renewable polymer polymerization catalysts
  • Characterizing the dynamics of charge transfer in molecular wires and at complex interfaces
  • Modeling the use of metal-organic frameworks to serve as supports for catalysis of chemical transformations
  • Modeling detoxification mechanisms for chemical weapons agents and simulants
  • Designing catalysts for the capture and transformation of the greenhouse gas carbon dioxide
  • Including condensed-phase effects in quantum chemical calculations, particularly as it influences solvatochromism and redox properties

Research Spotlights about this group's work appeared on the MSI website in December 2015 and May 2014.

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Group name: 
cramercj

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