Zaida Luthey-Schulten

2020

C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S. Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten, and Peijun Zhang (2020): Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations, Communications Biology, Springer Nature Limited, Vol 3, Num 1
Alister Burt, C. Keith Cassidy, Peter Ames, Maria Bacia-Verloop, Megghane Baulard, Karine Huard, Zaida Luthey-Schulten, Ambroise Desfosses, Phillip J. Stansfeld, William Margolin, John S. Parkinson, and Irina Gutsche (2020): Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain, Nature Communications, Springer Nature Limited, Vol 11, Num 1, pp743

2019

Wen Yang, C. Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten, Zaida Luthey-Schulten, John S. Parkinson, and Ariane Briegel (2019): In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States, mBio, American Society for Microbiology, Vol 10, Num 4
Steffen M. Sedlak, Leonard C. Schendel, Marcelo C. R. Melo, Diana A. Pippig, Zaida Luthey-Schulten, Hermann E. Gaub, and Rafael C. Bernardi (2019): Direction Matters: Monovalent Streptavidin/Biotin Complex Under Load, Nano Letters, The American Chemical Society, Vol 19, Num 6, pp3415-3421
Rafael C. Bernardi, Ellis Durner, Constantin Schoeler, Klara H. Malinowska, Bruna G. Carvalho, Edward A. Bayer, Zaida Luthey-Schulten, Hermann E. Gaub, and Michael A. Nash (2019): Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy, Journal of the American Chemical Society, The American Chemical Society, Vol 141, Num 37, pp14752-14763
Abhishek Singharoy, Christopher Maffeo, Karelia H. Delgado-Magnero, David J.K. Swainsbury, Melih Sener, Ulrich Kleinekathöfer, John W. Vant, Jonathan Nguyen, Andrew Hitchcock, Barry Isralewitz, Ivan Teo, Danielle E. Chandler, John E. Stone, James C. Phillips, Taras V. Pogorelov, M. Ilaria Mallus, Christophe Chipot, Zaida Luthey-Schulten, D. Peter Tieleman, C. Neil Hunter, Emad Tajkhorshid, Aleksei Aksimentiev, and Klaus Schulten (2019): Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism, Cell, Elsevier B.V., Vol 179, Num 5, pp1098-1111.e23

2018

Marcelo C. R. Melo, Rafael C. Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C. Phillips, Julio D. C. Maia, Gerd B. Rocha, João V. Ribeiro, John E. Stone, Frank Neese, Klaus Schulten, and Zaida Luthey-Schulten (2018): NAMD Goes Quantum: An Integrative Suite for Hybrid Simulations, Nature Methods, Springer Nature, Vol 15, pp351-354
Wen Ma, Kevin D Whitley, Yann R Chemla, Zaida Luthey-Schulten, and Klaus Schulten (2018): Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase, eLife, eLife Sciences Publications, Ltd., Vol 7, ppe34186
David M. Bianchi, Joseph R. Peterson, Tyler M. Earnest, Michael J. Hallock, and Zaida Luthey-Schulten (2018): Hybrid CME-ODE Method for Efficient Simulation of the Galactose Switch in Yeast, IET Systems Biology, Institution of Engineering and Technology (IET), Vol 12, Num 4, pp170-176

2017

Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten (2017): Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations, Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 15, pp3871-3881
Jonathan Lai, Zhaleh Ghaemi, and Zaida Luthey-Schulten (2017): The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains, Biochemistry, American Chemical Society, Vol 56, Num 45, pp5972-5979
Tobias Verdorfer, Rafael C. Bernardi, Aylin Meinhold, Wolfgang Ott, Zaida Luthey-Schulten, Michael A. Nash, and Hermann E. Gaub (2017): Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics, Journal of the American Chemical Society, The American Chemical Society, Vol 139, Num 49, pp17841-17852

2016

Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock, Thomas E. Kuhlman, and Zaida Luthey-Schulten (2016): Ribosome Biogenesis in Replicating Cells: Integration of Experiment and Theory, Biopolymers, Wiley-Blackwell, Vol 105, Num 10, pp735

2015

Tyler M. Earnest, Jonathan Lai, Ke Chen, Michael J. Hallock, James R. Williamson, and Zaida Luthey-Schulten (2015): Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly, Biophysical Journal, Elsevier BV, Vol 109, Num 6, pp1117-1135

2018

Zaida Luthey-Schulten, David Bianchi, Tyler Earnest, Joseph Peterson, Michael Hallock (2018): An Efficient Hybrid Stochastic-Deterministic Simulation Technique for Living Cells, 2018 Blue Waters Annual Report, pp230-231

2017

2016

Zaida Luthey-Schulten (2016): Ribosome Biogenesis in Replicating Cells, 2016 Blue Waters Annual Report, pp221-223

2015

Zaida Luthey-Schulten (2015): Simulating Ribosome Biogenesis in Whole Cells, 2015 Blue Waters Annual Report, pp154-156
Zaida Ann Luthey-Schulten: Simulations of Biological Processes on the Whole Cell Level
Blue Waters Symposium 2014, May 15, 2014

Simulation reveals how bacterial organelle converts sunlight to chemical energy


Nov 14, 2019

Researchers used supercomputers to construct a 136 million-atom model of the chromatophore, a primitive light-harvesting structure in purple bacteria. The simulated organelle behaved just as it does in nature, the team reports.


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Computational models used to predict behavior of protein complexes


Oct 11, 2019

An international collaboration of researchers tested the strength of protein complexes and the results could provide insights that can help develop strategies to prevent bacteria resistance.


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University of Illinois Researchers Use Blue Waters to Make New DNA Discoveries


Oct 5, 2018

By running the Nanoscale Molecular Dynamics (NAMD) code on the Blue Waters supercomputer at Illinois’ National Center for Supercomputing Applications, researchers were able to create a simulation that included “hundreds of thousands of atoms” and study the helicase in further detail.


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17 campus teams to accelerate their research with Blue Waters


Jun 10, 2015

Seventeen U of I research teams from a wide range of disciplines have been awarded computational and data resources on the sustained-petascale Blue Waters supercomputer at NCSA. “These diverse projects highlight the breadth of computational research at the University of Illinois,” said Athol Kemball, associate professor of Astronomy and chair of the Illinois allocation review committee. “Illinois has a tremendous pool of talented researchers in fields from political science to chemistry to engineering who can harness the power of Blue Waters to discover and innovate.”


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U of I, Great Lakes Consortium award Blue Waters resources to 18 research teams


Apr 10, 2014

Eighteen research teams from a wide range of disciplines have been awarded computational and data resources on the sustained-petascale Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Blue Waters is one of the world’s most powerful supercomputers, capable of performing quadrillions of calculations every second and working with quadrillions of bytes of data. Its massive scale and balanced architecture enable scientists and engineers to tackle research challenges that could not be addressed with other computing systems.


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22 Illinois projects receive time on Blue Waters


Jun 11, 2013

The University of Illinois at Urbana-Champaign has awarded access to the Blue Waters supercomputer—which is capable of performing quadrillions of calculations every second and of working with quadrillions of bytes of data—to 22 campus research teams from a wide range of disciplines. The computing and data capabilities of Blue Waters, which is operated by the National Center for Supercomputing Applications (NCSA), will assist researchers in their work on understanding DNA, developing biofuels, simulating climate, and more.


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