|
| 10262. Theoretical description of the primary proton-coupled electron
transfer reaction in the cytochrome bc1 complex.
Angela M. Barragan, Alexander V. Soudackov, Zaida Luthey-Schulten, Sharon
Hammes-Schiffer, Klaus Schulten, and Ilia A. Solov'yov.
Journal of the American Chemical Society, 143:715-723, 2021.
|
| 10261. Multiscale modeling and cinematic visualization of photosynthetic
energy conversion processes from electronic to cell scales.
Melih Sener, Stuart Levy, John E. Stone, AJ Christensen, Barry Isralewitz,
Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida
Luthey-Schulten, and Donna Cox.
Parallel Computing, 102:102698, 2021.
|
| 10237. In situ conformational changes of the Escherichia coli serine
chemoreceptor in different signaling states.
Wen Yang, Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten,
Zaida Luthey-Schulten, John S. Parkinson, and Ariane Briegel.
Molecular Biology and Physiology, 10:e00973-19, 2019.
|
| 10236. Structure and dynamics of the E. coli chemotaxis core
signaling complex by cryo-electron tomography and molecular simulations.
C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S.
Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten, and Peijun Zhang.
Communications Biology, 3:24, 2020.
|
| 10233. Mechanisms of nanonewton mechanostability in a protein complex
revealed by molecular dynamics simulations and single-molecule force
spectroscopy.
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.
Journal of the American Chemical Society, 141:14752-14763,
2019.
|
| 10230. Atoms to phenotypes: Molecular design principles of cellular energy
metabolism.
A. Singharoy, C. Maffeo, K. Delgardo, D. J. K. Swainsbury, M. Sener,
U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. Stone,
J. Phillips, T. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten,
P. Tieleman, C. N. Hunter, Emad Tajkhorshid, A. Aksimentiev, and K. Schulten.
Cell, 179:1098-1111, 2019.
|
| 10215. Direction matters: Monovalent streptavidin/biotin complex under load.
Steffen M. Sedlak, Leonard C. Schendel, Marcelo C. R. Melo, Diana A. Pippig,
Zaida Luthey-Schulten, Hermann E. Gaub, and Rafael C. Bernardi.
Nano Letters, 19:3415-3421, 2019.
|
| 10184. Simulating biological processes: Stochastic physics from whole cells
to colonies.
Tyler Earnest, John Cole, and Zaida Luthey-Schulten.
Reports on Progress in Physics, 81:052601, 2018.
|
| 10183. Population FBA predicts metabolic phenotypes in yeast.
Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, and Zaida Luthey-Schulten.
PLoS Computational Biology, 13:e1005728, 2017.
|
| 10177. Parametric studies of metabolic cooperativity in escherichia coli
colonies: Strain and geometric confinement effects.
Joseph R. Peterson, John A. Cole, and Zaida Luthey-Schulten.
PLoS One, 12:e0182570, 2017.
|
| 10176. Careful accounting of extrinsic noise in protein expression reveals
correlations among its sources.
John A. Cole and Zaida Luthey-Schulten.
Physical Review E, 95:062418, 2017.
|
| 10169. Ribosome biogenesis in replicating cells: integration of experiment
and theory.
Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock,
Thomas E. Kuhlman, and Zaida Luthey-Schulten.
Biopolymers, 105:735-751, 2016.
|
| 10166. CryoEM-based hybrid modeling approaches for structure
determination.
C Keith Cassidy, Benjamin A Himes, Zaida Luthey-Schulten, and Peijun Zhang.
Current Opinion in Microbiology, 43:14-23, 2018.
|
| 10161. Combining in Vitro and in Silico single molecule force
spectroscopy to characterize and tune cellulosomal scaffoldin mechanics.
Tobias Verdorfer, Rafael C. Bernardi, Aylin Meinhold, Wolfgang Ott, Zaida
Luthey-Schulten, Michael A. Nash, and Hermann E. Gaub.
Journal of the American Chemical Society, 139:17841-17852,
2017.
|
| 10155. Challenges of integrating stochastic dynamics and cryo-electron
tomograms in whole-cell simulations.
Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang
Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten.
Journal of Physical Chemistry B, 121:3871-3881, 2017.
|
| 10145. Genome-wide gene expression and RNA half-life measurements allow
predictions of regulation and metabolic behavior in Methanosarcina
acetivorans.
Joseph R Peterson, ShengShee Thor, Lars Kohler, Petra RA Kohler, William W
Metcalf, and Zaida Luthey-Schulten.
BMC Genomics, 17:924, 2016.
|
| 10139. Noise contributions in an inducible genetic switch: a whole-cell
simulation study.
Elijah Roberts, Andrew Magis, Julio O Ortiz, Wolfgang Baumeister, and Zaida
Luthey-Schulten.
PLoS Computational Biology, 7:e1002010, 2011.
|
| 10138. Dna looping increases the range of bistability in a stochastic model
of the lac genetic switch.
Tyler M Earnest, Elijah Roberts, Michael Assaf, Karin Dahmen, and Zaida
Luthey-Schulten.
Physical Biology, 10:026002, 2013.
|
| 10137. Heterogeneity in protein expression induces metabolic variability in
a modeled Escherichia coli population.
Piyush Labhsetwar, John Andrew Cole, Elijah Roberts, Nathan D Price, and
Zaida A Luthey-Schulten.
Proceedings of the National Academy of Sciences, USA,
110:14006-14011, 2013.
|
| 10136. Towards a whole-cell model of ribosome biogenesis: Kinetic modeling
of SSU assembly.
Tyler M Earnest, Jonathan Lai, Ke Chen, Michael J Hallock, James R Williamson,
and Zaida Luthey-Schulten.
Biophysical Journal, 109:1117-1135, 2015.
|
| 10135. Spatially-resolved metabolic cooperativity within dense bacterial
colonies.
John A Cole, Lars Kohler, Jamila Hedhli, and Zaida Luthey-Schulten.
BMC Systems Biology, 9:15, 2015.
|
| 10133. Improving reaction kernel performance in Lattice Microbes:
particle-wise propensities and run-time generated code.
Michael J. Hallock and Zaida Luthey-Schulten.
pp. 428-434. IEEE, 2016.
|
| 10124. Towards a computational model of a methane producing archaeum.
Joseph R Peterson, Piyush Labhsetwar, Jeremy R Ellermeier, Petra R A Kohler,
Ankur Jain, Taekjip Ha, William W Metcalf, and Zaida Luthey-Schulten.
Archaea, 2014, 2014.
(18 pages).
|
| 10123. Effects of dna replication on mrna noise.
Joseph R. Peterson, John A. Cole, Jingyi Fei, Taekjip Ha, and Zaida A.
Luthey-Schulten.
Proceedings of the National Academy of Sciences, USA,
112:15886-15891, 2015.
|
| 10082. Simulation of reaction diffusion processes over biologically relevant
size and time scales using multi-GPU workstations.
Michael J. Hallock, John E. Stone, Elijah Roberts, Corey Fry, and Zaida
Luthey-Schulten.
Parallel Computing, 40:86-99, 2014.
|
| 10078. Lattice microbes: High-performance stochastic simulation method for
the reaction-diffusion master equation.
Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten.
Journal of Computational Chemistry, 34:245-255, 2013.
|
| 10039. Long time-scale simulations of in vivo diffusion using GPU
hardware.
Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida
Luthey-Schulten.
In Proceedings of the IEEE International Parallel &
Distributed Processing Symposium, pp. 1-8, 2009.
|
| 10004. Classical force field parameters for the heme prosthetic group of
cytochrome c.
F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten.
Journal of Computational Chemistry, 25:1613-1622, 2004.
|
| |
| 720. NAMD goes quantum: An integrative suite for hybrid simulations.
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 Nesse, Klaus Schulten, and Zaida
Luthey-Schulten.
Nature Methods, 15:351-354, 2018.
|
| 680. Evaluation of emerging energy-efficient heterogeneous computing
platforms for biomolecular and cellular simulation workloads.
John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida
Luthey-Schulten, and Klaus Schulten.
2016 IEEE International Parallel and Distributed Processing
Symposium Workshop (IPDPSW), pp. 89-100, 2016.
|
| 536. The role of L1 stalk-tRNA interaction in the ribosome elongation
cycle.
Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha,
Zaida Luthey-Schulten, and Klaus Schulten.
Journal of Molecular Biology, 402:741-760, 2010.
|
| 375. Role of water in transient cytochrome c2 docking.
Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten.
Journal of Physical Chemistry B, 108:20376-20387, 2004.
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