Rajiv K. Kalia - US grants

0085344
Kalia
This award supports a Focused Research Group at Louisiana State University for research and education on computational materials. The grant is jointly supported by the Division of Materials Research and the Division for Advanced Computational Infrastructure and Research and is a blend of condensed matter physics, materials science and computer science. The objective of the research is to understand how the bonding between dissimilar materials at the atomic level determines structure and macroscopic properties such as adhesion, friction, stiffness, and fracture toughness. The research will focus on: (1) ceramic composites (SiC fibers coated with silica in a Si3N4 matrix and aluminum oxide matrix containing aluminum oxide fibers coated with LaPO4); (2) metal/ceramic interfaces (Al/SiC and Ti/TiO2) and nanostructured composites of passivated metallic nanoparticles; and (3) oxidation, fracture and nanoindentation in these materials.

These applications require a methodology that can describe physical and mechanical processes over several decades of length scales. Quantum mechanical (QM) simulations based on the density functional theory will be preformed in regions where atomic bonds are formed or broken; molecular dynamics (MD) simulations will be carried out in nonlinear regions surrounding the QM region; and the finite-element (FE) approach with constitutive input from QM or MD calculations will be used in regions far away from the process zones. The QM, MD, and FE schemes will be integrated with an approach based on control theory. Algorithms will be designed to carry out these hybrid QM/MD/FE simulations in a metacomputing environment with multiple parallel machines, mass storage devices, and immersive and interactive virtual environments on a Grid with high-speed networks.

The Concurrent Computing Laboratory for Materials Simulation, where the research will be performed, has a record of innovative educational activities including a joint MS/PhD program in computer science and physics. Efforts are underway for a joint masters degree in computer science and applied physics. In addition, a web-based computational physics course is being taught simultaneously at LSU and the Delft University of Technology in The Netherlands. As part of this grant, a workshop will be established to mentor and recruit minority students.
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This award supports a Focused Research Group at Louisiana State University for research and education on computational materials. The grant is jointly supported by the Division of Materials Research and the Division for Advanced Computational Infrastructure and Research and is a blend of condensed matter physics, materials science and computer science. The objective of the research is to understand how the bonding between dissimilar materials at the atomic level determines structure and macroscopic properties such as adhesion, friction, stiffness, and fracture toughness.

The Concurrent Computing Laboratory for Materials Simulation, where the research will be performed, has a record of innovative educational activities including a joint MS/PhD program in computer science and physics. Efforts are underway for a joint masters degree in computer science and applied physics. In addition, a web-based computational physics course is being taught simultaneously at LSU and the Delft University of Technology in The Netherlands. As part of this grant, a workshop will be established to mentor and recruit minority students.
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This award was made on a collaborative proposal submitted to the Division of Materials Research under the Information Technology Research solicitation NSF-04-012. The Division of Materials Research, the Chemistry Division, and the Division of Computing and Communications Foundations fund this award. The other proposals in this multidisciplinary collaborative are 0427177 and 0427540 and involve investigators at Caltech and Purdue. Research activities covered by this award fall under the National Priority Area, "Advances in Science and Engineering," and the Technical Focus Area, "Innovation in Computational Modeling or Simulation in Research." This award supports computational research and algorithm development with the aim of developing new modeling tools for materials failure and with the further aim of applying these tools to advance the understanding of stress corrosion cracking. This award also supports related educational activities some of which involve underrepresented groups.

The PIs aim to develop a scalable parallel and distributed computational framework consisting of methods, algorithms, and integrated data handling and visualization tools for: 1) an accurate quantum mechanical-level (QM) description; 2) reactive force fields (ReaxFF) to describe chemical reactions and polarization; 3) molecular dynamics (MD) simulations to extract atomistic mechanisms of SCC; 4) accelerated dynamics for long-time behavior to obtain parameters directly comparable to experiments; and 5) "atomistically informed" continuum models to reach macroscopic length and time scales. Automated model transitioning by novel techniques will be employed to embed higher fidelity simulations inside coarser simulations only when and where they are required, while controlled error propagation will ensure the overall accuracy of the results. The PIs plan to use this hierarchical multiscale computational framework to study stress corrosion cracking (SCC) of aluminum, iron, and nickel-aluminum superalloys in gaseous and aqueous environments. These materials are used widely in industrial applications and their performance and lifetime are often severely limited by stress corrosion in environments containing oxygen and water. Simulations will be used to extract an atomic-level understanding of the basic mechanisms underlying SCC. The PIs plan to investigate SCC inhibition by ceramic coatings (e.g., alumina and silicon carbide), self-assembled monolayers (e.g., oleic imidazolines), and by microorganisms (e.g., Shewanella oneidensis strain MR-1).

The PIs will deliver software tools having broad applicability across scientific disciplines and industry. This award supports annual computational science workshops for undergraduate students and faculty mentors from underrepresented groups. Workshops will be organized to foster close interactions between underrepresented minority graduate students at US institutions and postdoctoral level counterparts from Latin American institutions. Undergraduate students will be involved in the research through summer research experiences; at least half are expected to be from underrepresented groups. The PIs will also assist minority institutions in developing computational science curricula, and mentor early-career faculty from minority institutions and EPSCoR states.

This award also supports education. Elements of the PIs' education program include: 1) a unique graduate course jointly taught by USC and Caltech faculty emphasizing hands-on experience in hierarchical multiscale material simulations; 2) a dual-degree program at USC offering graduate students the opportunity to obtain a PhD in the physical sciences or engineering and an MS in computer science with specialization in high performance computing and simulations; and 3) summer research experiences for undergraduate students involving a total immersion course in computational science followed by research in simulation, parallel algorithms and visualization.
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This award was made on a collaborative proposal submitted to the Division of Materials Research under the Information Technology Research solicitation NSF-04-012. The Division of Materials Research, the Chemistry Division, and the Division of Computing and Communications Foundations fund this award. The other proposals in this multidisciplinary collaborative are 0427177 and 0427540 and involve investigators at Caltech and Purdue. Research activities covered by this award fall under the National Priority Area, "Advances in Science and Engineering," and the Technical Focus Area, "Innovation in Computational Modeling or Simulation in Research." This award supports computational research and algorithm development with the aim of developing new modeling tools for materials failure and with the further aim of applying these tools to advance the understanding of stress corrosion cracking. This award also supports related educational activities some of which involve underrepresented groups.

Stress corrosion cracking (SCC) is a complex technological and economic problem involving premature and catastrophic failure of materials due to an insidious combination of mechanical stresses and chemically aggressive environments. Safe and reliable operation of structural systems are endangered by uncertainties in SCC, the reduction of which could have enormous economic impact. The PIs plan to develop computational tools that contain essential physics across a wide range of length and time scales to achieve an atomic-level mechanistic understanding of SCC. Because of the large number of atoms and complex physical and chemical processes, these tools will be able to manage distributed computing resources and focus them on SCC simulation.

The PIs plan to use these tools to study SCC of aluminum, iron, and nickel-aluminum superalloys in gaseous and aqueous environments. These materials are used widely in industrial applications and their performance and lifetime are often severely limited by stress corrosion in environments containing oxygen and water. Simulations will be used to understand the basic mechanisms underlying SCC. The PIs plan to investigate how various coatings and microorganisms inhibit SSC.

This award also supports education. Elements of the PIs' education program include: 1) a graduate course jointly taught by USC and Caltech faculty emphasizing hands-on experience in hierarchical multiscale material simulations; 2) a dual-degree program at USC offering graduate students the opportunity to obtain a PhD in the physical sciences or engineering and an MS in computer science with specialization in high performance computing and simulations; and 3) summer research experiences for undergraduate students.

The PIs will deliver software tools having broad applicability across scientific disciplines and industry. This award supports annual computational science workshops for undergraduate students and faculty mentors from underrepresented groups. Workshops will be organized to foster close interactions between underrepresented minority graduate students at US institutions and postdoctoral level counterparts from Latin American institutions. Undergraduate students from underrepresented groups will be involved in the research. In addition, the PIs will assist minority institutions in developing computational science curricula and mentor early-career faculty from minority institutions and EPSCoR states.
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TECHNICAL SUMMARY:

This award is made on a proposal submitted to the PetaApps Solicitation. The Office of Cyberinfrastructure, the Division of Materials Research and Office of Multidisciplinary activities in the Mathematical and Physical Sciences Directorate, the Engineering Directorate, and the Computer and Information Science and Engineering Directorate contribute funds to this award.

This PetaApps project focuses on hybrid quantum mechanical-atomistic-mesoscale simulations of ion transport and translocation of biopolymers such as DNA and RNA through nanometer scale pores and channels in silica and silicon nitride membranes. The PIs aim to develop a predictive hierarchical petascale simulation framework for: (1) Highly accurate quantum mechanical simulations to describe chemical processes in translocating biopolymers; (2) multibillion-atom molecular dynamics simulations for structural properties and dynamical processes of biopolymers in confined fluidic environments in solid state membranes, with interatomic interactions validated by quantum mechanical calculations and key experiments; (3) hybrid molecular dynamics and adaptive lattice Boltzmann simulations in which molecular dynamics is embedded close to the surfaces of nanopores/nanochannels and lattice Boltzmann in the rest of the fluid; (4) accelerated dynamics approaches to reach macroscopic time scales for direct comparison with experimental data; (5) meta-scalable, self-tuning multicore parallel simulation algorithms; and (6) automated model transitioning to embed higher fidelity simulations inside coarser simulations on demand with controlled error propagation to quantify uncertainty.

After validation, this hierarchical petascale simulation framework will be used to study: (1) Translocation kinetics and dynamics of DNA through silica and silicon nitride nanopores; (2) electronic properties of translocating DNAs for sequential identification of nucleotides; (3) ionic screening of surface charges in nanopores/nanochannels; (4) streaming electrical current generated by pressure-driven liquid flow in individual silica nanochannels as a function of channel height, pressure gradient, and salt concentration; (5) pressure-driven DNA transport in confined silica channels for novel diagnostic applications such as artificial gels and entropic trap arrays; and (6) surface functionalization, polarity switching, and transient response of silica nanotube, nanofluidic transistors.

This project supports training a new generation of graduate students to develop the tools needed to attack complex system level problems. They will learn to combine theory, modeling, and high performance computer simulation. Students will participate in a dual-degree program in which they will fulfill Ph.D. requirements within their own discipline and master?s degree requirements in computer science with specialization in high performance computing and simulations.
This award also supports the computational science workshops for underrepresented groups. Undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions participate in a special one-week intense hands-on experience in parallel computing and immersive and interactive visualization. African American, Hispanic and Native American students will be recruited through USC?s Center for Engineering Diversity and women through USC?s Women in Science and Engineering Program.

NON-TECHNICAL SUMMARY:

This award is made on a proposal submitted to the PetaApps Solicitation. The Office of Cyberinfrastructure, the Mathematical and Physical Sciences Directorate, the Engineering Directorate, and the Computer and Information Science and Engineering Directorate contribute funds to this award.

This award supports the development of software for the most advanced, ?petascale,? high performance supercomputers that will enable simulations that can capture phenomena that span across a range of length and time scales. The PIs will focus on a problem of particular importance, how biomolecules move through nanometer-sized pores in inorganic materials like silica and silicon nitride. The simulation can capture detailed physics of the problem and may illuminate possible applications to sequencing DNA and RNA molecules. The PIs will also focus on how charged atoms and molecules move through channels with dimensions on nanometer length scales more generally. There are potential applications to evolving ?lab-on-a-chip? technologies that seek to miniaturize laboratory analysis functions to the size of electronic device chips.

Developed software will be distributed and can be used by a broad community of researchers in a variety of disciplinary and multidiscplinary research involving materials research, chemistry, engineering, physics, and nanotechnology.

This project supports training a new generation of graduate students to develop the tools needed to attack complex system level problems. They will learn to combine theory, modeling, and high performance computer simulation to solve complex problems. Students will participate in a dual-degree program in which they will fulfill Ph.D. requirements within their own discipline and master?s degree requirements in computer science with specialization in high performance computing and simulations.

This award also supports the computational science workshops for underrepresented groups. Undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions participate in a special one-week intense hands-on experience in parallel computing and immersive and interactive visualization.

PETASCALE SIMULATIONS OF DNA DYNAMICS AND SELF-ASSEMBLY
Priya Vashishta?PI, Rajiv K. Kalia, Aiichiro Nakano (University of Southern California)
Ananth Grama (Purdue University)

DNA translocation through solid-state nanopores and nanofluidic channels underlie ?lab-on-a-chip? technology and solid-state nanopore ?microscopy? for molecular structure and high-speed sequencing. Highly efficient methods for directed self-assembly of DNA offer unprecedented opportunities for the synthesis of novel genes, chromosome mapping, biosensors, molecular machines, nanoelectronics and nanomechanical systems, and formulations of mesoscopic structural motifs as building blocks of emerging periodic and aperiodic nanostructures consisting of DNAs.
This project involves the study of DNA self-assembly and translocation through nanometer-scale pores in silica and silicon nitride membranes using a predictive hierarchical petascale simulation framework consisting of: (1) Highly accurate quantum mechanical (QM) simulations to describe chemical processes in DNA translocation and concatenation; (2) multibillion-atom molecular dynamics (MD) simulations for structural properties and dynamical processes of DNAs in confined fluidic environments, with interatomic interactions validated by QM calculations and key experiments; (3) hybrid MD and adaptive lattice Boltzmann (LB) simulations in which MD is embedded in translocation/concatenation regions, and LB in the rest of the fluid; (4) accelerated dynamics approaches to reach macroscopic time scales for direct comparison with experimental data; (5) metascalable, self-tuning, multicore parallel simulation algorithms; and (6) automated model transitioning to embed higher fidelity simulations inside coarser simulations on demand with controlled error propagation. A metascalable (or ?design once, scale on new architectures?) parallel application-development framework is also being developed for first-principles simulations of directed DNA self-assembly.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

This project establishes a dedicated computing platform for microsecond simulations to study DNA self-assembly and translocation through solid-state nanopores. The project uses a predictive hierarchical petascale simulation framework to study: Translocation kinetics and dynamics of DNAs through solid state nanopores; electronic properties of translocating DNAs for sequencing nucleotides; ionic screening of surface charges in nanopores; pressure-driven DNA transport in confined silica channels; and shear-induced DNA self-assembly.

The computing platform will also support computer science research in techniques for the parallelization of such simulations, and for the integration of multi-scale, multi-phenomena simulation codes for molecular biology and biological materials science.

Petascale simulations of DNA translocation through solid-state nanopores and nanofluidic channels underlie "lab-on-a-chip" technology and solid-state nanopore "microscopy" for molecular structure and high-speed sequencing.

The infrastructure will help in training a new generation of graduate students. Students participate in a dual-degree program in which they do a PhD in physical sciences or engineering and a master's degree in computer science. The infrastructure also strengthens the annual computational science workshops for underrepresented groups, in which undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions acquire hands-on experience in parallel computing.

Further information on the project can be found at the project web page: http://cacs.usc.edu/cri/index.php

The research objective of this award is to combine experiment and computer simulation to investigate the relationships between cell membrane composition, organization, and mechanical behavior. The nanoscale response of cell membranes to mechanical stress is an essential aspect of important biophysical processes such as endo- and exocytosis, viral fusion and budding, and intracellular trafficking. The joint experimental-simulation studies conducted under this award will probe how molecular processes such as phase separation into liquid-ordered and liquid-disordered domains by membrane lipids and cholesterol flip-flop across the cell membrane bilayer modulate the nanomechanical response of membranes. Newly developed computational tools include a petascale computational framework to perform multimillion-atom MD simulations embedded in coarse-grained MD simulations.

These studies will add significantly to biophysical understanding of bending mechanics of cell membranes, which has profound implications for viral infection and neuron communication. The educational plan focuses on a dual-degree program in which students fulfill Ph.D. requirements within their own discipline while studying towards an M.S. in computer science. Dual-degree students will help organize computational science workshops for underrepresented groups, which are held regularly at the University of Southern California. The educational outreach plan also integrates high-school students into experimental research.

The discovery of RNA interference mediated gene silencing by double-stranded RNA is one of the most exciting recent developments in the biological and biomedical sciences. RNAi utilizes a pathway whereby a double-stranded small interfering RNA (siRNA) targets and destroys complementary mRNA in eukaryotic cells to regulate gene expression. Since its discovery just over a decade ago scientists have investigated the potential use of siRNA-based treatment of many diseases such as cancer, liver cirrhosis, hepatitis B, human papillomavirus, and hypercholesterolemia. In principle, siRNA has much broader therapeutic applications than other types of drugs because siRNA can be synthetically designed to silence any gene via the RNAi machinery. Therefore, the primary challenge for therapeutic applications is efficient and non-toxic delivery of siRNA to cells within tissues of interest. The research goal of this CDI project is to design efficient delivery systems for siRNA via supercomputer simulations. Multimillion-atom simulations are performed to study: (1) the effect of siRNAs on the molecular structure of lipid membranes and how structural changes affect the membrane permeability; (2) molecular mechanisms by which siRNA molecules attached to gold nanoparticles cross the membrane and go into a cell; and (3) delivery of siRNAs encapsulated in liposomes by ultrasound. Computational technologies will be used to enable automated design of efficient siRNA delivery systems. This project is promoting scholastic and professional excellence among students. A dual-degree program has been established which gives students the opportunity to obtain a Ph.D. in the physical sciences or an engineering discipline and an M.S. in computer science with specialization in high performance computing and simulations. This research team will also organize computational science workshops for undergraduate students and faculty mentors from Historically Black Colleges and Universities and Minority Serving Institutions.