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a National Science Foundation Center of Research Excellence in Science and Technology

Publications

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Publications, April 2016 - March 2021
Publications, 2021

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de Alba E. (2022) "NMR Analysis of Protein Folding Interaction Networks." In: Muñoz V. (eds) Protein Folding. Methods in Molecular Biology, vol 2376. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1716-8_10

Chu X., Nagpal S., Muñoz V. (2022) "Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms." In: Muñoz V. (eds) Protein Folding. Methods in Molecular Biology, vol 2376. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1716-8_19 

Kristian Thijssen, Dimitrius A. Khaladj, S. Ali Aghvami, Mohamed Amine Gharbi, Seth Fraden, Julia M. Yeomans, Linda S. Hirst, Tyler N. Shendruk. "Submersed micropatterned structures control active nematic flow, topology, and concentration." Proceedings of the National Academy of Sciences. Sep 2021, 118 (38) e2106038118; DOI: 10.1073/pnas.2106038118

Veeramuthu Natarajan S., D’Amelio N., Muñoz V. (2022) "NMR Relaxation Dispersion Methods for the Structural and Dynamic Analysis of Quickly Interconverting, Low-Populated Conformational Substates." In: Muñoz V. (eds) Protein Folding. Methods in Molecular Biology, vol 2376. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1716-8_11

Bose, S.; Dasbiswas, K.; Gopinath, A. Matrix Stiffness Modulates Mechanical Interactions and Promotes Contact between Motile Cells. Biomedicines 2021, 9, 428. https://doi.org/10.3390/biomedicines9040428

Niranjan Sarpangala, Ajay Gopinathan. "Cargo surface fluidity reduces inter-motor interference, promotes load-sharing and enhances run-lengths in an ATP dependent manner." bioRxiv 2021.06.10.447989; doi: https://doi.org/10.1101/2021.06.10.447989

Nivin Mothi and Victor Muñoz. "Protein Folding Dynamics as Diffusion on a Free Energy Surface: Rate Equation Terms, Transition Paths, and Analysis of Single-Molecule Photon Trajectories." The Journal of Physical Chemistry B 2021 125 (45), 12413-12425. DOI: 10.1021/acs.jpcb.1c05401

Archana G. Chavan, Jeffrey A. Swan, Joel Heisler, Cigdem Sancar, Dustin C. Ernst, Mingxu Fang, Joseph G. Palacios, Rebecca K. Spangler, Clive R. Bagshaw, Sarvind Tripathi, Priya Crosby, Susan S. Golden, Carrie L. Partch, and Andy LiWang. "Reconstitution of an intact clock reveals mechanisms of circadian timekeeping." Science, 374 (6564), 2021. DOI: 10.1126/science.abd4453

Golden S.S., LiWang A. (2021) "Mechanistic Aspects of the Cyanobacterial Circadian Clock." In: Johnson C.H., Rust M.J. (eds) Circadian Rhythms in Bacteria and Microbiomes. Springer, Cham. https://doi.org/10.1007/978-3-030-72158-9_4

LaBelle, J., Ramos-Martinez, A., Shen, K., Motta-Mena L.B., Gardner, K.H., Materna, S.C., and Woo, S. Zebrafish. 18(1) Feb 2021.20-28. http://doi.org/10.1089/zeb.2020.1951

Shi, H., Quint, D., Grason, G., Gopinathan, A., Huang, K.C. "Chiral twisting in cytoskeletal polymers regulates filament size and orientation," Nature Communications, 2020

Holehouse and Sukenik, "Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning," J. Chem. Theor. Comput., 2020
 
Castellanos, M., Mothi, N., Muñoz, V. "Eukaryotic transcription factors can track and control their target genes using DNA antennas," Nat. Commun., 2020
 
Mothi, N., Sadqi, M., Muñoz, V. "Catching Fast Protein Folding in the Act: Resolving (Un)Folding Transition Paths using Advanced Single-molecule Spectroscopy." Biophys. J. , 2020
 
Duclos, G., et al. "Topological structure and dynamics of three dimensional active nematics," Science, 2020 (Beller)
 
Lopes, J., Quint, David A., Chapman, D. E., Xu, M., Gopinathan, A., & Hirst, L. S. (2019). Membrane mediated motor kinetics in microtubule gliding assays. Scientific Reports,9(1). doi:10.1038/s41598-019-45847-z
 
G. Boniello, Y. Luo, D.A. Beller, F. Serra, and K.J. Stebe. “Colloids in confined liquid crystals: a plot twist in the lock-and-key mechanism”, Soft Matter, DOI: 10.1039/C9SM00788A (2019). [link]
 
A. Suh, M.-J. Gim, D. Beller, and D.K. Yoon. “Topological defects and geometric memory across the nematicsmectic A liquid crystal phase transition”, Soft Matter, DOI: 10.1039/C9SM00781D (2019). [link]
S. Chu, M. Kardar, D.R. Nelson, and D.A. Beller. "Evolution in range expansions with competition at rough boundaries", Journal of Theoretical Biology, DOI: 10.1016/j.jtbi.2019.06.018 (2019). [link]
 
Y. Luo, T. Yao, D.A. Beller, F. Serra, and K.J. Stebe. "Deck the walls with anisotropic colloids in nematic liquid crystals", Langmuir, DOI: 10.1021/acs.langmuir.9b01811 (2019) [link]
 
Alba, E. D. (2019). Structure, interactions and self-assembly of ASC-dependent inflammasomes. Archives of Biochemistry and Biophysics. doi:10.1016/j.abb.2019.05.023
 
Girish, V., Pazzi, J., Li, A., & Subramaniam, A. B. (2019). Fabrics of Diverse Chemistries Promote the Formation of Giant Vesicles from Phospholipids and Amphiphilic Block Copolymers. Langmuir,35(28), 9264-9273. doi:10.1021/acs.langmuir.9b01621
 
Wong, L., Kumar, A., Gabela-Zuniga, B., Chua, J., Singh, G., Happe, C. L., . . . McCloskey, K. E. (2019). Substrate Stiffness Directs Diverging Vascular Fates. Acta Biomaterialia. doi:10.1016/j.actbio.2019.07.030
 
Amanda J. Tan, Eric Roberts, Spencer Smith, Ulyses Alvarado, Jorge Arteaga, Sam Fortini, Kevin Mitchell, and Linda S. Hirst, Topological chaos in active nematics, Aug 5th, NATURE PHYSICS (2019) Link
 
Nambayan, R. J., Sandin, S. I., Quint, David A., Satyadi, D. M., & Alba, E. D. (2018). The inflammasome adapter ASC assembles into filaments with integral participation of its two Death Domains, PYD and CARD. Journal of Biological Chemistry,294(2), 439-452. doi:10.1074/jbc.ra118.004407
 
Wilson, J. O., Quint, David A., Gopinathan, A., & Xu, J. (2018). Cargo diffusion shortens single-kinesin runs at low viscous drag. doi:10.1101/391284
 
Li A, Pazzi J, Xu M, Subramaniam AB. Cellulose Abetted Assembly and Temporally Decoupled Loading of Cargo into Vesicles Synthesized from Functionally Diverse Lamellar Phase Forming Amphiphiles. 2018;19(3):849–859.
 
Hashmi A, Lucey FR, Sadqi M, Muñoz V. Coiled Coil Proteins as Scaffold for Broad Range, Ultrafast Biosensors. 2018;114(3).
 
Wong L, Pegan JD, Gabriela-Zuniga B, Khine M, McCloskey KE. Leaf-inspired microcontact printing vascular patterns. 2017;9(2):021001.
 
Li Q, King SJ, Xu J. Native Kinesin-1 does not Preferentially Bind to GTP-Rich Microtubules in vitro. 2018;114(3).
 
Li Q, Tseng K-F, King SJ, Qiu W, Xu J. A Fluid Membrane Enhances the Velocity of Cargo Transport by Small Teams of Kinesin-1. 2018;114(3).
 
Faysal KMR, Park JS, Nguyen J, Garcia L, Subramaniam AB. Lipid Bilayers Are Long-Lived on Solvent Cleaned Plasma-Oxidized poly(dimethyl)siloxane (ox-PDMS). 2017;12(1).
 
Chu X, Muñoz V. Roles of conformational disorder and downhill folding in modulating protein–DNA recognition. 2017;19(42):28527–28539.
 
Ando D, Gopinathan A. Cooperative Interactions between Different Classes of Disordered Proteins Play a Functional Role in the Nuclear Pore Complex of Baker’s Yeast. 2017;12(1).
 
Quint MT, Sarang S, Quint, David A., Keshavarz A, Stokes BJ, Subramaniam AB, Huang KC, Gopinathan A, Hirst LS, Ghosh S. Plasmon-actuated nano-assembled microshells. 2017;7(1).
 
V. Muñoz, L.A. Campos, M. Sadqi, (2016) Limited cooperativity in protein folding. Curr. Opin. Struct. Biol. 36: 58-66.
 
J. Schönfelder, R. Perez-Jimenez & V. Muñoz (2016) A Simple Two-State Protein Unfolds Mechanically via Multiple Heterogeneous Pathways at Single-Molecule Resolution.Nature Comms. 7: 11777.
 
M. Cerminara & V. Muñoz (2016) When Fast is Better: Protein Folding Fundamentals and Mechanisms from Ultrafast Approaches. Biochemical J. 473: 2545-2559.
 
V. Muñoz, Z. Wang & L.A. Campos (2016) Single molecule fluorescence of fast folding proteins. Meth Enzymol. 581: 417-459.
 
Kresse KM, Xu M, Pazzi J, García-Ojeda M, Subramaniam AB. Novel Application of Cellulose Paper As a Platform for the Macromolecular Self-Assembly of Biomimetic Giant Liposomes. 2016;8(47):32102–32107.
 
Rahimi M, Regan D, Arroyo M, Subramaniam AB, Stone HA, Staykova M. Shape Transformations of Lipid Bilayers Following Rapid Cholesterol Uptake. 2016;111(12):2651–2657.
 
Tan AJ, Chapman DE, Hirst LS, Xu J. Understanding the role of transport velocity in biomotor-powered microtubule spool assembly. 2016;6(82):79143–79146.
 
Quint, David A., Gopinathan A, Grason GM. Shape Selection of Surface-Bound Helical Filaments: Biopolymers on Curved Membranes. 2016;111(7):1575–1585.
 
Glaser DE, Turner WS, Madfis N, Wong L, Zamora J, White N, Reyes S, Burns AB, Gopinathan A, McCloskey KE. Multifactorial Optimizations for Directing Endothelial Fate from Stem Cells. 2016;11(12).