Simulation-based engineering and science

Csanyi, G., T. Albaret, M.C. Payne, and A. De Vita. 2004. "Learn on the fly": A hybrid classical and quantum-mechanical molecular dynamics simulation. Physical Review Letters 93:4.

Csanyi, G., T. Albaret, G. Moras, M.C. Payne, and A. De Vita. 2005. Multiscale hybrid simulation methods for material systems. Journal of Physics-Condensed Matter 17:R691-R703.

Foulkes, W., L. Mitas, R. Needs, and G. Rajagopal. 2001. Quantum Monte Carlo simulations of solids. Reviews of Modern Physics 73:33-83.

Haynes, P.D., C. Skylaris, A.A. Mostofi, and M.C. Payne. 2006. ONETEP: linear-scaling density-functional theory with local orbitals and plane waves. Phys Status Solidi B 243:2489-2499.

Pickard, C.J., and R.J. Needs. 2006. High-pressure phases of silane. Physical Review Letters 97 Art. No. 045504.

———. 2007. Structure of phase III of solid hydrogen. Nature Physics 3:473-476.

Skylaris, C., P.D. Haynes, A.A. Mostofi, and M.C. Payne. 2008. Recent progress in linear-scaling density functional calculations with plane waves and pseudopotentials: the ONETEP code. Journal of Physics-Condensed Matter 20:064209.

Site: University of Karlsruhe and
Forschungszentrum Karlsruhe (Karlsruhe Research Center)
Karlsruhe Institute of Technology (KIT) and other affiliated institutes

Kaiserstrasse 12

D-76131 Karlsruhe, Germany

http://www.fzk.de/fzk/idcplg?IdcService=FZK&lang=en

http://www.ipc.uni-karlsruhe.de/english/

http://www.mathematik.uni-karlsruhe.de/ianm/de

http://www.rz.uni-karlsruhe.de/rz/scc/
Date Visited: February 25, 2008
WTEC Attendees: M. Head-Gordon (report author), C. Sagui, P. Westmoreland
Hosts: Prof. Dr. Wim Klopper, KIT, and Institute of Physical Chemistry, University of Karlsruhe; Email: willem.klopper@kit.edu

Prof. Dr. Reinhart Ahlrichs, Institute of Physical Chemistry

Prof. Dr. Matthias Olzmann, Institute of Physical Chemistry

Prof. Dr. Henning Bockhorn, Institute of Physical Chemistry and Polymer Chemistry and Engler Bunte Institute

Priv.-Doz. Dr. Wolfgang Wenzel, Institute of Nanotechnology, Forschungszentrum Karlsruhe

Prof. Dr. Christian Wieners, Institute for Applied and Numerical Mathematics, University of Karlsruhe

Prof. Dr. Willy Dorfler, Institute for Applied and Numerical Mathematics

Prof. Dr. Vincent Heuveline, Institute for Applied and Numerical Mathematics and Computing Center, University of Karlsruhe

The University of Karlsruhe is one of Germany’s leading technical universities, a position recognized by its being awarded one of the first three “Excellence Initiative” awards in 2006. These prestigious awards are designed to permit a small number of leading German universities to more effectively compete against leading international rivals. A key part of reorganizing for the Excellence Initiative is the merging of the University of Karlsruhe with the nearby national research laboratory, Forschungszentrum Karlsruhe, to create the Karlsruhe Institute of Technology (KIT). The combination of their large computer centers has created the largest high-performance computing center in Europe, the Steinbuch Center for Computing with over 200 staff. New research opportunities are being explored in areas of science and engineering that are of industrial and societal importance, including nanoscience, energy research, and biology, including positions that are jointly funded by private industry. This is a time of significant change at Karlsruhe.

During a 5-hour minisymposium on simulation-based science and engineering, the visiting WTEC panel heard seven technical presentations on relevant research at Karlsruhe, as well as a short overview of the new organization of KIT from Prof. Klopper. Short summaries of these presentations are given below.

• 
  Accurate simulation of electronic structure. Prof. Klopper described new developments in highly accurate electronic structure methods, using bielectronic basis functions in addition to the usual 1 particle expansions. He also discussed how these accurate but computationally expensive approaches could be integrated with simpler and more approximate models to treat multiscale problems such as the interaction of methanol with carbon nanotubes, and solid C58 films.
  
• 
  Prediction of gas phase rate coefficients from first principles. Prof. Olzmann reviewed the present state of the art in unimolecular, bimolecular, and complex-forming bimolecular reaction rate theory. He also discussed future needs such as further improvements in statistical rate theories, advances in the treatment of nonadiabatic effects on kinetics, the treatment of very high temperatures, and the development of an integrated universal kinetics program suite with standard interfaces to electronic structure programs for potential energy surface information.
  
• 
  Numerical simulation on multiple scales in chemical engineering and combustion. Dr. Bockhorn discussed problems that involve interacting length scales ranging from 10^-10 m to 10² m, such as propagation of reaction zones involving the interaction of diffusive transport with radiation and chemistry, the functioning of a catalytic converter, and the modeling of a technical burner in gas turbines. These are all cases where true multiscale approaches are essential to obtaining physically realistic modeling.
  
• 
  Simulation of nanoscale pattern formation. Priv.-Doz Wenzel discussed problems in which long time scales are important, ranging from protein folding, in silico screening for promising drug leads, modeling of new light-emitting devices based on amorphous thin films, and the pursuit of a transistor that operates at the atomic level.
  
• 
  Mathematical modeling and scientific computing. Prof. Wieners discussed activities underway in both research and education at the Institute for Scientific Computing and Mathematical Modeling, which seeks to bring students with mathematical training towards applications in the biological and physical computational sciences. Examples included dynamics of the electrochemical double layer for colloidal particles, discrete methods for cellular reactions in systems biology, and porous media models for biological soft tissues, such as the human spine.
  
• 
  Analysis, simulation, and design of nanotechnological processes. Prof. Dörfler described research and training that bridges mathematics and nanoscience and technology, including issues such as optimization of the band gap in photonic crystals, and he gave an overview of the mathematical modeling used.
  
• 
  Research projects in high-performance computing (HPC). Prof. Heuveline briefly introduced a wide range of high-performance computing projects underway at the Steinbuch Center for Computing (SCC) (see below). These range from shape optimization (ship hull, keel, etc.), to weather forecasting, to respiratory tract simulation. Some of these projects have specific software packages as outcomes, which are generally open source codes.
  

High-performance computing at Karlsruhe is very strong, as the Steinbuch Center for Computing (SCC) is Europe’s largest with more than 200 personnel. The SCC was formed by the merger of the University of Karlsruhe and Forschungszentrum computer centers, as part of the overall merger to form the Karlsruhe Institute of Technology. The SCC aims to provide both research and development (under the direction of four professors representing numerical methods, networks, parallel and distributed computing, and computer systems and information processing), and information technology services under one roof. Their hardware resources are currently ranked third in Germany, with a 15.6 TFlop machine containing 3000 cpus and 12 TB memory. SCC is a Tier 1 center for repository of data generated by the high energy physics experiments performed at CERN.

During the talks, as well as at lunch where we were joined by the Rector of the University of Karlsruhe, Prof. Dr. Horst Hippler, there were some opportunities for discussion of both scientific issues directly related to the content of the talks, and also more general issues surrounding simulation-based engineering and science. There was also a small amount of time for some general discussion at the end of the minisymposium. Some of the additional issues that came up included:

• 
  Karlsruhe faculty members are enjoying very good resources and research opportunities due to the key achievement of achieving Centre of Excellence status.
  
• 
  Computation and theory in chemistry are also an integral part of a Cluster of Excellence on Functional Nanostructures, which involves a total of 49 professors and group leaders and more than 70 projects, mostly funded by the DFG (German Research Foundation). This cluster takes pure science towards practical applications with a focus on optical, electronic, and biological properties at the nanoscale.
  
• 
  There are new mechanisms for interaction between industry and KIT. Karlsruhe has begun to appoint faculty members who are also employees of leading local industry. These appointments involve arrangements for periodic absences from the university to permit the management of dual responsibilities.
  
• 
  Multimethod/multiscale applications at the nanoscale inevitably involve hierarchies of methods operating at differing levels of accuracy. Inexpensive methods such as empirical potentials or tight-binding molecular dynamics can be used for preliminary exploration of potential surfaces followed by refinement with density functional theory, and in turn, still more accurate explicitly correlated methods. This demands a strong emphasis on validation of the low-level results, which in turn requires considerable experience and chemical knowledge in order to be accomplished effectively.
  
• 
  It was noted that within the Institute for Scientific Computing and Mathematical Modeling there are several issues involved in more effectively training students at the interface of mathematics and physical applications. It was felt that math students need more guidance in applications in the future, which might be provided by, for example, a competence center in modeling and simulation.
  
  
  

Pauline Chan Fellow and Tutor in Physics, St. Hilda's College

Email: j.yeomans1@physics.oxford.ac.uk

Website: http://www-thphys.physics.ox.ac.uk/user/JuliaYeomans/

Dr. Ard Louis, Royal Society Fellow

Email: ard.louis@physics.ox.ac.uk

Website: http://www-thphys.physics.ox.ac.uk/user/ArdLouis/
BACKGROUND

Julia Yeomans and Ard Louis are both faculty members in the Condensed Matter Theory Group, which is part of the Rudolf Peierls Centre for Theoretical Physics (http://www-thphys.physics.ox.ac.uk), a subdepartment of the Oxford University Physics Department (http://www.physics.ox.ac.uk). The other departments in theoretical physics are theoretical astrophysics, elementary particle theory, and nuclear structure theory.

Prof. Yeomans and Dr. Louis are both theorists and simulators working on soft condensed matter; the other members of the condensed matter theory group work on the statistical mechanics of lattice systems (Abrahams) and spin glasses (Sherrington), and on strongly correlated electron systems (Essler). The research that Yeomans and Louis perform is unusual. It involves coarse-grained modeling of biological, polymeric, and flowing systems, focusing on the fundamentals of self-assembly, rheology, and microfluidics.

In the WTEC visiting team’s discussions with our hosts, questions arose about the funding of the work described by Yeomans and Louis. The biological work, in particular, seemed too “physics”-based and fundamental to be funded by the Biotechnology and Biological Sciences Research Council (BBSRC) or the Medical Research Council (MRC). Louis expressed the opinion that in general the funding for biophysics in the UK is not sufficient. However, it turns out that the students that work for Yeomans and Louis are funded primarily through the Theoretical Physics Department’s Doctoral Training Account (DTA) (http://www.epsrc.ac.uk/PostgraduateTraining/DoctoralTrainingAccounts/default.htm). The DTA is a source of funding for graduate students allocated annually to each department by the Engineering and Physical Sciences Research Council (EPSRC) in proportion to the external funding received by that department from the EPSRC.

The faculty in the Theoretical Physics department prefer primarily to work with post-docs; as a result, there is a fairly large pool of DTA funding available for graduate students—enough, in the case of Yeomans and Louis, to be able to take up one new student per year on DTA funds. This contrasted with most departments the WTEC team visited, where generally the DTA funds were dismissed as being insufficient to have any real impact on the funding of research—that perhaps once every five years a researcher might receive DTA funding for a student. Hence, it is clear that the unusual situation in Theoretical Physics at Oxford is enabling Yeomans and Louis to pursue lines of research that they might otherwise not be able to follow.

R&D ACTIVITIES

Yeomans and Louis both gave presentations about their research activities. Louis described research focused on biological self-assembly, biological networks, and dynamics of complex fluids. He is interested in minimal models that exhibit self-assembly similar to biological systems, specifically virus capsids and DNA tetrahedra. The models for virus capsid self-assembly is a minimal model, similar to those studied previously by Louis and co-workers (Wilber et al. 2007). Louis is additionally working on a minimal coarse-grained model for single strands of DNA that exhibits self-assembly into double-stranded DNA. Louis also indicated an interest in understanding biological networks and their evolution. Finally, he showed various simulations of complex fluid phenomena, including the impact of hydrodynamic forces on the sedimentation of Brownian particles, and modeling of peristaltic pumps created by colloidal spheres (Terray et al. 2002). Louis holds a Royal Society University Research Fellowship, which means that he has a prefaculty position funded by the Royal Society. Royal Society University Research Fellowships provide partial salary support and research support for five years (with a possible extension for another three years), with the expectation that the fellows will be strong candidates for permanent posts in the host universities at the end of their fellowships. Approximately 30 such fellowships are awarded per year.

Yeomans presented simulation-based research on four topics: (1) drops on patterned surfaces (e.g., see Kusumaatmaja and Yeomans 2007), (2) liquid crystal hydrodynamics (e.g., Marenduzzo et al. 2003), (3) low Reynolds number swimmers, and (4) polymer hydrodynamics (e.g., Ali and Yeomans 2005). In the first research area, for example, her interest is in the shape and motion of liquid water drops on patterned hydrophobic surfaces using a combination of Cahn-Hilliard-type free energy models and Navier-Stokes equations solved using the lattice Boltzmann method. Both analytic theory and simulations are used. In the third area of research, inspired by bacteria (which are the ultimate in low-Reynolds-numbers swimmers), she is investigating minimal models of swimmers that achieve motion by exploiting hydrodynamic forces. In all of the research presented, an elegant combination of minimal model(s), macroscopic/hydrodynamic theory, and mesoscale simulation methods are employed.

CONCLUSIONS

The two researchers Yeomans and Louis presented a wide range of simulation-based biophysics and soft materials research. On the issue of computing, their view was that the most important resource was to have local, powerful computers. All of the codes used in their respective groups are written within the groups; no community-based or commercial codes are used in either group.

Ali, I., and J.M. Yeomans. 2005. Polymer translocation: The effect of backflow. Journal of Chemical Physics 123, Art. No. 234903.

Kusumaatmaja, H., and J.M. Yeomans. 2007. Modeling contact angle hysteresis on chemically patterned and superhydrophobic surfaces. Langmuir 23:6019-6032.

Marenduzzo, D., E. Orlandini, and J.M. Yeomans. 2003. Rheology of distorted nematic liquid crystals. Europhysics Letters 64:406-412.

Terray, A., J. Oakey, and D.W.M. Marr. 2002. Microfluidic control using colloidal devices. Science 296:1841-1844.

Wilber, A.W., J.P.K. Doye, A.A. Louis, E.G. Noya, M.A. Miller, and P. Wong. 2007. Reversible self-assembly of patchy particles into monodisperse icosahedral clusters. Journal of Chemical Physics 127, Art. no. 085106.

Prof. Rodney Eatock Taylor, offshore engineering, structures, marine CFD

Janet Smart, manufacturing systems, major programmes, networks

Dr. Viannis Ventikos, micro-, nano-, bio- transport phenomena

Prof. Paul Taylor, offshore and coastal engineering, reliability/risk analysis

Lee He, computational turbomachinery

The background information is extracted from University of Oxford websites. The Department of Engineering Science at Oxford is the only unified department in the UK that offers accredited courses in all the major branches of engineering. Its students develop a broad view of the subject much appreciated by employers, but they can also choose from a very wide range of specialist options.

Every year the Department of Engineering Science, one of the largest departments in the university, produces around 160 new engineering graduates. They go off to a huge variety of occupations: designing cars, building roads and bridges, developing new electronic devices, manufacturing pharmaceuticals, healthcare and aerospace, into further study for higher degrees, and in many other directions. Some graduates also develop their managerial, financial, or entrepreneurial skills and go into commerce, financial services, or start their own companies.

Each year 60 to 70 students take higher degrees, either MSc or PhD by research, and since October 2006, a number take an MSc course in Biomedical Engineering.

Oxford’s Department of Engineering Science has a substantial research portfolio, including much that is directly supported by industry. In the department there are no barriers between the different branches of engineering, and they are involved in a great deal of multidisciplinary research, collaborating with groups in other departments from Archaeology to Zoology.

This broad view of engineering, based on a scientific approach to the fundamentals, is part of the tradition that started with the department’s foundation in 1908—one hundred years of educating great engineers and researching at the cutting edge.

There are opportunities in the Department of Engineering Science for postgraduate study and research over a wide range of engineering disciplines, including civil, electrical, mechanical, process, biomedical, and information engineering. This breadth of expertise makes it possible to apply a multidisciplinary approach to the solution of engineering problems, as appropriate.

At present there are approximately 220 postgraduate students, about 70 academic staff, and over 100 post-doctoral research workers, supported by 70 technicians. The department works in close collaboration with many government and industrial laboratories, and 40 percent of the Department's research funding comes from industry.

An indication of Department of Engineering Science research areas is provided in the list of its graduate degrees below; further details are available online at http://www.eng.ox.ac.uk and http://www.admin.ox.ac.uk/postgraduate/caz/engi.shtml.

• 
  Chemical and Process Engineering and Biotechnology
  

• 
  Bioprocessing and Tissue Engineering
  
• 
  Environmental Biotechnology
  
• 
  Sustainable Development
  
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  Liquid Surfaces and Foam
  
• 
  Multiphase Flow and Boiling
  
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  Combustion in Internal Combustion Engines
  
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  Cryogenic Engineering and Vacuum Technology
  

• 
  Civil Engineering
  

• 
  In situ Testing
  
• 
  Soft Soils and Environmental Applications
  
• 
  Unsaturated and Gassy Soils
  
• 
  Offshore Foundations and Sea-bed Soil Mechanics
  
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  Reinforced Soil
  
• 
  Dynamics of Civil Engineering Structures
  
• 
  Tunnelling and Settlement Damage
  
• 
  Theoretical Modelling of Soils
  
• 
  Structural Glass
  
• 
  Deployable Structures
  

• 
  Electrical Engineering
  

• 
  Communications and Sensors
  
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  Functional Materials
  
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  Imaging and Displays
  
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  Pulsed Power Technology, Plasmas and Machines
  
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  Neural Networks
  
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  Analogue Microelectronics
  

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  Information Engineering
  

• 
  Control and System Dynamics
  
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  Advanced Instrumentation
  
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  Robotics and Sensor Systems
  
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  Medical Image Understanding
  
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  Machine Vision, Inspection and Visualisation
  
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  Production Engineering; Complexity in Manufacturing
  

• 
  Mechanical Engineering
  

• 
  Turbomachinery
  
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  Hypersonics and Low Density Flows
  
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  Aerodynamics, Heat Transfer and Measurement
  
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  Ocean Engineering
  
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  Coastal Engineering
  
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  Water Resources Engineering
  
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  Vibrations and Condition Monitoring
  
• 
  Contact Stresses, Fatigue, Cracking and Plasticity
  
• 
  Structural Strength under Impact
  
• 
  Theory of Structures and Structural Integrity
  
• 
  Advanced Materials Engineering
  

• 
  Biomedical Engineering
  

• 
  Gene and Drug Delivery Research
  
• 
  Orthopaedic Engineering
  
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  Ophthalmic Engineering
  
• 
  Medical Signal Processing
  
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  Medical Image Understanding