Klaus Schulten: Difference between revisions

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A 2009 review describes work in modeling and verifying simulations of proteins such as [[titin]], [[fibrinogen]], [[ankyrin]], and [[cadherin]] using the group's "computational microscope".<ref name="Lee">{{cite journal |last1=Lee |first1=Eric H. |last2=Hsin |first2=Jen |last3=Sotomayor |first3=Marcos |last4=Comellas |first4=Gemma |last5=Schulten |first5=Klaus |title=Discovery Through the Computational Microscope |journal=Structure |date=October 2009 |volume=17 |issue=10 |pages=1295–1306 |doi=10.1016/j.str.2009.09.001 |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927212/ |accessdate=8 January 2016}}</ref>
A 2009 review describes work in modeling and verifying simulations of proteins such as [[titin]], [[fibrinogen]], [[ankyrin]], and [[cadherin]] using the group's "computational microscope".<ref name="Lee">{{cite journal |last1=Lee |first1=Eric H. |last2=Hsin |first2=Jen |last3=Sotomayor |first3=Marcos |last4=Comellas |first4=Gemma |last5=Schulten |first5=Klaus |title=Discovery Through the Computational Microscope |journal=Structure |date=October 2009 |volume=17 |issue=10 |pages=1295–1306 |doi=10.1016/j.str.2009.09.001 |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927212/ |accessdate=8 January 2016}}</ref>

In 2010, Schulten's group at Illinois and researchers at the University of Utah published research examining the development of [[drug resistance]] to [[Tamiflu]] in [[H1N1|H1N1pdm]] [[swine influenza]] and [[Influenza A virus subtype H5N1|H5N1]] [[avian influenza]] [[virus]]. Their simulations suggested that drug resistance may arise from disruption of the binding process due to electrostatic attraction in charged neuraminidase pathways, in addition to disruption of Tamiflu's pentyl sidegroup.<ref name="Fashioning"/><ref name=Le>{{cite journal|last1=Le|first1=Ly|last2=Lee|first2=Eric H.|last3=Hardy|first3=David J.|last4=Truong|first4=Thanh N.|last5=Schulten|first5=Klaus|last6=Amaro|first6=Rommie E.|title=Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases|journal=PLoS Computational Biology|date=23 September 2010|volume=6|issue=9|pages=e1000939|doi=10.1371/journal.pcbi.1000939|url=http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000939|accessdate=11 January 2016}}</ref>


In 2013 Schulten's group published a simulated structure of the [[human immunodeficiency virus]] [[capsid]] containing 64 million atoms, among the largest simulations reported, produced using the supercomputer [[Blue Waters]].<ref>{{cite journal |last1=Zhao |first1=G |last2=Perilla |first2=JR |last3=Yufenyuy |first3=EL |last4=Meng |first4=X |last5=Chen |first5=B |last6=Ning |first6=J |last7=Ahn |first7=J |last8=Gronenborn |first8=AM |last9=Schulten |first9=K |last10=Aiken |first10=C |last11=Zhang |first11=P |title=Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. |journal=Nature |date=30 May 2013 |volume=497 |issue=7451 |pages=643–6 |pmid=23719463 |laysummary=http://news.illinois.edu/news/13/0529HIVcapsid_KlausSchulten.html |doi=10.1038/nature12162}}</ref>
In 2013 Schulten's group published a simulated structure of the [[human immunodeficiency virus]] [[capsid]] containing 64 million atoms, among the largest simulations reported, produced using the supercomputer [[Blue Waters]].<ref>{{cite journal |last1=Zhao |first1=G |last2=Perilla |first2=JR |last3=Yufenyuy |first3=EL |last4=Meng |first4=X |last5=Chen |first5=B |last6=Ning |first6=J |last7=Ahn |first7=J |last8=Gronenborn |first8=AM |last9=Schulten |first9=K |last10=Aiken |first10=C |last11=Zhang |first11=P |title=Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. |journal=Nature |date=30 May 2013 |volume=497 |issue=7451 |pages=643–6 |pmid=23719463 |laysummary=http://news.illinois.edu/news/13/0529HIVcapsid_KlausSchulten.html |doi=10.1038/nature12162}}</ref>

Revision as of 16:57, 11 January 2016

Klaus Schulten
Alma materHarvard University
Known forMolecular dynamics, Photosynthesis, High performance computing, Molecular graphics
SpouseZaida Luthey-Schulten
AwardsBiophysical Society National Lecturer, Sidney Fernbach Award
Scientific career
FieldsPhysics, Chemistry, Biophysics, Computational biology
InstitutionsUniversity of Illinois at Urbana Champaign
Doctoral advisorMartin Karplus
Doctoral studentsAxel Brunger[1]
Websitehttp://www.ks.uiuc.edu/~kschulte
External videos
video icon “Klaus Schulten, The Computational Microscope“, TEDxUIUC
video icon “Interview Klaus Schulten, 2015 National Lecturer, Biophysical Society

Klaus Schulten is a German American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign.[2] Schulten uses supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and model living systems.[3] His mathematical, theoretical, and technological innovations have led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks.[4]

Schulten identifies the goal of the life sciences as being to characterize biological systems from the atomic to the cellular level. He uses petascale computers, and plans to use exoscale computers, to model atomic-scale bio-chemical processes. His work makes possible the dynamic simulation of the activities of thousands of proteins working together at the macromolecular level. His research group developed and distributed software for computational structural biology, which Schulten has used to make a number of significant discoveries. The molecular dynamics package NAMD and the visualization software VMD are estimated to be used by at least 300,000 researchers worldwide.[3]

Education

Schulten received a Diplom degree from the University of Münster in 1969 and a PhD in chemical physics from Harvard University in 1974, advised by Martin Karplus. At Harvard Schulten studied vision, and the ways in which biomolecules respond to photoexcitation.[5] He was particularly interested in studying retinal, a polyene and a chromophore of visual pigment. Schulten was able to provide a theoretical explanation for experimental observations of an "optically forbidden" state which did not match predicted patterns of electronic excitation in polyenes. Schulten classified electrons into covalent and non-covalent states, and determined that electrons that acted in a coordinated (covalent) manner used less energy than those which were independent (non-covalent).[6][7]

Career and Research

Max Planck Institute for Biophysical Chemistry

After graduating, Schulten joined the Max Planck Institute for Biophysical Chemistry in Göttingen, where he remained till 1980. At the institute, he worked with Albert Weller on electron transfer reactions. One of his first projects was to explain a chemical reaction product called a "fast triplet", an excited molecule with a pair of electrons with parallel spins. What Schulten discovered was that a magnetic field could provably influence a chemical reaction, a physical effect that had not previously been demonstrated. It was possible to show the effect by causing the reaction to occur with and without a magnetic field. Schulten was particularly interested in implications of the magnetic field effect for biological systems such as electron transfer in photosynthesis.[7][8][9]

Technical University of Munich

In 1980, Schulten became a professor of theoretical physics at the Technical University of Munich. In 1988, Hartmut Michel, Johann Deisenhofer, and Robert Huber won the Nobel Prize in chemistry for determining the three-dimensional structure of the photosynthetic reaction center. Their elucidation of the reaction center's structure made it possible for Klaus Schulten to develop simulations models of photosynthesis. Schulten later worked with Michel and Deisenhofer on models of LH2.[10]

Schulten recognized that a successful attack on modeling the photosynthetic reaction center would require parallel computing power. He used his research grants to support Munich students Helmut Grubmüller and Helmut Heller in building a custom parallel computer optimized for molecular dynamics simulations. They developed a parallel computer, the T60, containing ten circuit boards with six Transputers each, for a total of 60 nodes. The T60 was small enough that Schulten was able to carry it through customs in a backpack, when he moved to the United States to join the University of Illinois at Urbana-Champaign. The T60's parallel computing software, which the students named EGO, was written in OCCAM II.[11]

University of Illinois at Urbana-Champaign

In 1988 Schulten moved to the University of Illinois at Urbana-Champaign (UIUC), where he founded the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology in 1989.[12][2]

The early development of NAMD at UIUC built on the work of Schulten's students in Munich to build a custom parallel computer optimized for molecular dynamics simulations. The first simulation on the T60 modeled 27,000 atoms of membrane structure, and took twenty months to run. The simulation results agreed with experimental results, and were eventually published in the Journal of Physical Chemistry.[11][13]

Work on the T60 and the Connection Machine convinced Schulten that more computing power and expertise were needed. Schulten partnered with computer scientists Robert Skeel, and Laxmikant V. Kale ("Sanjay" Kale) on a five-year grant from the NIH, and their students began writing molecular dynamics code in a new language, C++.[13][14] Since then, Schulten's research group has become well known for the development of software for computational structural biology, including the molecular dynamics package NAMD and the visualization software VMD. The packages are freely usable for non-commercial research, and are used by approximately 300,000 researchers world-wide.[3]

“If we want to understand health and disease, we need to understand life at the molecular level and to know how all the molecular components work together like clockwork."[5]

Over time, Schulten has targeted biological structures of increasing size and complexity, with larger and larger computers. By 2007 he was exploring molecular modeling using graphical processing units (GPUs).[15] Validation of models against experimental results is an integral part of development, for example, using molecular dynamics in combination with cryo-electron microscopy and X-ray crystallography. to study the structures of large macromolecular complexes.[16]

In 2006, Schulten's group modeled the satellite tobacco mosaic virus, emulating femtosecond interactions of approximately one million atoms in the virus and a surrounding drop of salt water for 50 billionths of a second. It was the first time that such a complete model had been generated, requiring the resources of the National Center for Supercomputing Applications at Urbana. The simulation provided new insights about activities of the virus. One discovery was that the virus, which looks symmetrical in still images, actually pulses in and out asymmetrically. Another was that the virus coat, the protein capsid, is dependent upon the genetic material in the RNA core of the particle and will collapse without it. This suggests that the genetic material must already be present before the virus can build its coat when reproducing.[17][18][19] Such research points to possible interventions that may help to control the virus, and also offers the possibility of exploring possible interventions in silico to predict effectiveness.[20]

A 2009 review describes work in modeling and verifying simulations of proteins such as titin, fibrinogen, ankyrin, and cadherin using the group's "computational microscope".[21]

In 2010, Schulten's group at Illinois and researchers at the University of Utah published research examining the development of drug resistance to Tamiflu in H1N1pdm swine influenza and H5N1 avian influenza virus. Their simulations suggested that drug resistance may arise from disruption of the binding process due to electrostatic attraction in charged neuraminidase pathways, in addition to disruption of Tamiflu's pentyl sidegroup.[11][22]

In 2013 Schulten's group published a simulated structure of the human immunodeficiency virus capsid containing 64 million atoms, among the largest simulations reported, produced using the supercomputer Blue Waters.[23]

As of 2015, the largest reported simulations involved a hundred million atoms. Schulten's team modeled the structure and function of a Purple bacteria’s chromatophore, one of the simplest living examples of photosynthesis. Modeling the processes involved in converting sunlight into chemical energy meant representing 100 million atoms, 16,000 lipids, and 101 proteins, the contents of a tiny sphere-shaped organelle one percent of the cell’s total volume. The team used the Titan supercomputer at the Oak Ridge National Laboratory in Tennessee. Schulten was already planning simulations for the exoscale Summit computer, expected to be built by 2018.[5]

Awards and memberships

Schulten is a Fellow of the Biophysical Society (2012)[24] and of the American Physical Society (1992).[25] He received the Sidney Fernbach Award (with Laxmikant V. Kale) from the IEEE Computer Society in 2012.[4] He received the Biophysical Society Distinguished Service Award for 2013, for "laying the groundwork for the realistic molecular dynamic simulations of biological macromolecules on time scales that match the physiological realm, and for making the methods and software openly available."[26][2] He was the Biophysical Society National Lecturer in 2015, the highest form of recognition given by the society.[27]

References

  1. ^ Mossman, K. (30 July 2008). "Profile of Axel Brunger". Proceedings of the National Academy of Sciences. 105 (31): 10643–10645. doi:10.1073/pnas.0806286105.
  2. ^ a b c "Klaus Schulten". Theoretical and Computational Biophysics Group. University of Illinois at Urbana-Champaign. Retrieved 16 March 2015.
  3. ^ a b c "Klaus Schulten Talks about the Evolution of Computational Biophysics". Scientific Computing. March 14, 2014. Retrieved 4 January 2016.
  4. ^ a b "Laxmikant V. Kale & Klaus Schulten". IEEE Computer Society. Retrieved 9 January 2016.
  5. ^ a b c Dougherty, Elizabeth (October 23, 2015). "Computing Cellular Clockworks: Klaus Schulten". SBGrid Consortium. President and Fellows of Harvard College.
  6. ^ Schulten, Klaus; Ohmine, I.; Karplus, Martin (1976). "Correlation effects in the spectra of polyenes" (PDF). J. Chem. Phys. 64: 4422–4441. Retrieved 8 January 2016.
  7. ^ a b Pollack, Lisa. "Unraveling Photosynthesis Step by Step: Four Decades of Research in Theoretical and Computational Biophysics". Theoretical and Computational Biophysics Group. University of Illinois at Urbana-Champaign. Retrieved 8 January 2016.
  8. ^ Schulten, Klaus; Staerk, H.; Weller, Albert; Werner, Hans-Joachim; Nickel, B. (1976). "Magnetic field dependence of the geminate recombination of radical ion pairs in polar solvents". Zeitschrift für Physikalische Chemie. NF101: 371–390.
  9. ^ Werner, Hans-Joachim; Schulten, Klaus; Weller, Albert (1978). "Electron transfer and spin exchange contributing to the magnetic field dependence of the primary photochemical reaction of bacterial photosynthesis" (PDF). Biochimica et Biophysica Acta. 502: 255–268. Retrieved 8 January 2016.
  10. ^ Govindjee, J. Thomas Beatty; Gest, H.; Allen, J.F. (2005). Discoveries in Photosynthesis. Netherlands: Springer. p. 417. ISBN 978-1-4020-3323-0. Retrieved 8 January 2016.
  11. ^ a b c Pollack, Lisa (2012). "Chapter 2: Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminisces". In Schlick, Tamar (ed.). Innovations in biomolecular modeling and simulations. Cambridge: Royal Soc Of Chemistry. pp. 8–22. ISBN 1-84973-410-0. {{cite book}}: Cite has empty unknown parameter: |1= (help)
  12. ^ "Overview - TCB Group". Theoretical and Computational Biophysics Group. University of Illinois at Urbana-Champaign. Retrieved 6 January 2016.
  13. ^ a b Heller, Helmut; Schaefer, Michael; Schulten, Klaus (August 1993). "Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase". The Journal of Physical Chemistry. 97 (31): 8343–8360. doi:10.1021/j100133a034. Retrieved 8 January 2016.
  14. ^ Kale, Laxmikant V.; Bhatele, Abhinav (2013). Parallel science and engineering applications : the Charm++ approach. Boca Raton: CRC Press. p. 62. ISBN 9781466504127. Retrieved 9 January 2016.
  15. ^ Stone, JE; Phillips, JC; Freddolino, PL; Hardy, DJ; Trabuco, LG; Schulten, K (December 2007). "Accelerating molecular modeling applications with graphics processors". Journal of computational chemistry. 28 (16): 2618–40. PMID 17894371. Retrieved 9 January 2016.
  16. ^ Trabuco, Leonardo G.; Villa, Elizabeth; Schreiner, Eduard; Harrison, Christopher B.; Schulten, Klaus (October 2009). "Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography". Methods. 49 (2): 174–180. doi:10.1016/j.ymeth.2009.04.005. Retrieved 9 January 2016.
  17. ^ Pearson, Helen (14 March 2006). "Supercomputer builds a virus: Vast simulation captures molecules in motion". Nature. doi:10.1038/news060313-4. Retrieved 8 January 2016.
  18. ^ Freddolino, PL; Arkhipov, AS; Larson, SB; McPherson, A; Schulten, K (March 2006). "Molecular dynamics simulations of the complete satellite tobacco mosaic virus". Structure (London, England : 1993). 14 (3): 437–49. PMID 16531228.
  19. ^ Bader, David A., ed. (2008). Petascale computing : algorithms and applications. Boca Raton: Chapman & Hall/CRC. pp. 214–215. ISBN 978-1-58488-909-0. Retrieved 8 January 2016.
  20. ^ Falkenburg, Brigitte; Morrison, Margaret, eds. (2015). Why More Is Different Philosophical Issues in Condensed Matter Physics and Complex Systems. Berlin Heidelberg: Springer-Verlag. ISBN 978-3-662-43911-1. Retrieved 8 January 2016.
  21. ^ Lee, Eric H.; Hsin, Jen; Sotomayor, Marcos; Comellas, Gemma; Schulten, Klaus (October 2009). "Discovery Through the Computational Microscope". Structure. 17 (10): 1295–1306. doi:10.1016/j.str.2009.09.001. Retrieved 8 January 2016.
  22. ^ Le, Ly; Lee, Eric H.; Hardy, David J.; Truong, Thanh N.; Schulten, Klaus; Amaro, Rommie E. (23 September 2010). "Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases". PLoS Computational Biology. 6 (9): e1000939. doi:10.1371/journal.pcbi.1000939. Retrieved 11 January 2016.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  23. ^ Zhao, G; Perilla, JR; Yufenyuy, EL; Meng, X; Chen, B; Ning, J; Ahn, J; Gronenborn, AM; Schulten, K; Aiken, C; Zhang, P (30 May 2013). "Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics". Nature. 497 (7451): 643–6. doi:10.1038/nature12162. PMID 23719463. {{cite journal}}: Unknown parameter |laysummary= ignored (help)
  24. ^ "Fellow of the Biophysical Society Award". Biophysical Society. Retrieved 9 January 2016.
  25. ^ "APS Fellowship". APS Physics. Division of Biological Physics. Retrieved 9 January 2016.
  26. ^ "Schulten Honored with Distinguished Service Award". Beckman Institute. December 3, 2012. Retrieved 9 January 2016.
  27. ^ "Klaus Schulten 2015 BPS National Lecturer". Center for the Physics of Living Cells. Retrieved 9 January 2016.
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