Publications
MRSEC members, please acknowledge the MRSEC in all of your publications using one of the following example lines:- We acknowledge support from Brandeis NSF MRSEC, Bioinspired Soft Materials, DMR-2011846.
- We acknowledge support from the shared facilities of the Brandeis NSF MRSEC, Bioinspired Soft Materials, DMR-2011846.
- We acknowledge support from the NSF MRSEC DMR-2011846.
2024
Zhang, Qiuxin, Tan, Weiyi, Liu, Zhiyu, Zhang, Yichi, Wei, Wei-Shao, Fraden, Seth and Xu, Bing, "Unnatural Peptide Assemblies Rapidly Deplete Cholesterol and Potently Inhibit Cancer Cells," Journal of the American Chemical Society 146, 12901-12906 (2024).
Roback, Joseph C, Minnis, Montana B, Ghebreyessus, Kesete and Hayward, Ryan C, "Visible Light-Triggered Microactuators and Dynamic Surfaces from Hydrogels Containing Photoswitchable Host–Guest Complexes," ACS Applied Polymer Materials, (2024).
Hagan, Michael F., Zandi, Roya and Uetrecht, Charlotte, "Overview of the 2023 Physical Virology Gordon Research Conference—Viruses at Multiple Levels of Complexity," Viruses 16, 895 (2024).
Luo, W., Baskaran, A., Pelcovits, R. A. and Powers, T. R., "Flow states of two dimensional active gels driven by external shear," Soft Matter 20, 738-753 (2024).
Najma, B., Wei, W.-S., Baskaran, A., Foster, P. J. and Duclos, G., "Microscopic interactions control a structural transition in active mixtures of microtubules and molecular motors," Proceedings of the National Academy of Sciences 121, e2300174121 (2024).
Head, L. C., Doré, C., Keogh, R. R., Bonn, L., Negro, G., Marenduzzo, D., Doostmohammadi, A., Thijssen, K., López-León, T. and Shendruk, T. N., "Spontaneous self-constraint in active nematic flows," Nature Physics, 1-9 (2024).
Li, Y., Zarei, Z., Tran, P. N., Wang, Y., Baskaran, A., Fraden, S., Hagan, M. F. and Hong, P., "A machine learning approach to robustly determine director fields and analyze defects in active nematics," Soft matter 20, 1869-1883 (2024).
Shiff, C. E., Kondev, J. and Mohapatra, L., "Ultrasensitivity of microtubule severing due to damage repair," iScience 27, (2024).
Blanc, B., Agyapong, J. N., Hunter, I., Galas, J. C., Fernandez-Nieves, A. and Fraden, S., "Collective chemomechanical oscillations in active hydrogels," Proc Natl Acad Sci U S A 121, e2313258121 (2024).
Wei, W.-S., Trubiano, A., Sigl, C., Paquay, S., Dietz, H., Hagan, M. F. and Fraden, S., "Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids," Proceedings of the National Academy of Sciences 121, e2312775121 (2024).
Wang, M. and Grason, G., "Thermal stability and secondary aggregation of self-limiting, geometrically frustrated assemblies: Chain assembly of incommensurate polybricks," Physical Review E 109, 014608 (2024).
Memarian, Fereshteh L, Hammar, Derek, Sabbir, Md Mainul Hasan, Elias, Mark, Mitchell, Kevin A and Hirst, Linda S, "Controlling chaos: Periodic defect braiding in active nematics confined to a cardioid," Physical Review Letters 132, 228301 (2024).
Hayakawa, Daichi, Videbæk, Thomas E, Grason, Gregory M and Rogers, W Benjamin, "Symmetry-guided inverse design of self-assembling multiscale DNA origami tilings," ACS nano 18, 19169-19178 (2024).
Guo, Jiaqi, Zia, Ayisha, Qiu, Qianfeng, Norton, Michael, Qiu, Kangqiang, Usuba, Junichi, Liu, Zhiyu, Yi, Meihui, Rich-New, Shane T and Hagan, Michael, "Cell-Free Nonequilibrium Assembly for Hierarchical Protein/Peptide Nanopillars," Journal of the American Chemical Society 146, 26102-26112 (2024).
Guo, Jiaqi, Tan, Weiyi and Xu, Bing, "Enzymatic self-assembly of short peptides for cell spheroid formation," Journal of Materials Chemistry B, (2024).
Guo, Jiaqi, Chang, Annabelle and Xu, Bing, "Autocleaving Bonds for Better Drugs," ChemMedChem 19, e202400130 (2024).
Duque, Carlos M, Hall, Douglas M, Tyukodi, Botond, Hagan, Michael F, Santangelo, Christian D and Grason, Gregory M, "Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra," Proceedings of the National Academy of Sciences 121, e2315648121 (2024).
Curtis, Zachary, Escudeiro, Pedro, Mallon, John, Leland, Olivia, Rados, Theopi, Dodge, Ashley, Andre, Katherine, Kwak, Jasmin, Yun, Kun and Isaac, Berith, "Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators," Proceedings of the National Academy of Sciences 121, e2401583121 (2024).
Xu, Jing, Brown, Nathaniel JS, Seol, Yeonee and Neuman, Keir C, "Heterogeneous distribution of kinesin-streptavidin complexes revealed by Mass Photometry," Soft Matter, (2024).
Videbæk, Thomas E, Hayakawa, Daichi, Grason, Gregory M, Hagan, Michael F, Fraden, Seth and Rogers, W Benjamin, "Economical routes to size-specific assembly of self-closing structures," Science advances 10, eado5979 (2024).
Sullivan, Kyle T, Hayward, Ryan C and Grason, Gregory M, "Self-limiting stacks of curvature-frustrated colloidal plates: Roles of intraparticle versus interparticle deformations," Physical Review E 110, 024602 (2024).
Raju, Cijil, Sun, Zhenhuan, Koibuchi, Ryo, Choi, Ji Yong, Chakraborty, Subhayan, Park, Jihye, Houjou, Hirohiko, Schmidt-Rohr, Klaus and Han, Grace GD, "Elucidating the mechanism of solid-state energy release from dianthracenes via auto-catalyzed cycloreversion," Journal of Materials Chemistry A 12, 26678-26686 (2024).
Prabhune, Ameya G, García-Gordillo, Andy S, Aranson, Igor S, Powers, Thomas R and Figueroa-Morales, Nuris, "Bacteria Navigate Anisotropic Media using a Flagellar Tug-of-Oars," PRX Life 2, 033004 (2024).
Najma, Bibi, Wei, Wei-Shao, Baskaran, Aparna, Foster, Peter J and Duclos, Guillaume, "Microscopic interactions control a structural transition in active mixtures of microtubules and molecular motors," Proceedings of the National Academy of Sciences 121, e2300174121 (2024).
Caban-Penix, Suhaily, Ho, Kristin, Yang, Zhewen, Baral, Rishika and Bradshaw, Niels, "Docking interactions determine substrate specificity of members of a widespread family of protein phosphatases," Journal of Biological Chemistry 300, (2024).
Alam, Salman, Najma, Bibi, Singh, Abhinav, Laprade, Jeremy, Gajeshwar, Gauri, Yevick, Hannah G, Baskaran, Aparna, Foster, Peter J and Duclos, Guillaume, "Active Fréedericksz Transition in Active Nematic Droplets," Physical Review X 14, 041002 (2024).
2023
Memarian, F. L., Khaladj, D. A., Hammar, D. and Hirst, L. S., "Forming, Confining, and Observing Microtubule-Based Active Nematics," J Vis Exp, e64287 (2023).
Memarian, F. L. and Hirst, L. S., "Effect of internal energy depletion on active nematic texture and dynamics," Liquid Crystals 50, 1123-1128 (2023).
Guo, S., Hoeprich, G. J., Magliozzi, J. O., Gelles, J. and Goode, B. L., "Dynamic remodeling of actin networks by cyclase-associated protein and CAP-Abp1 complexes," Curr Biol 33, 4484-4495 e4485 (2023).
Qiu, Q., Qi, Q., Usuba, J., Lee, K., Aprahamian, I. and Han, G. G., "Visible light activated energy storage in solid-state Azo-BF 2 switches," Chemical Science 14, 11359-11364 (2023).
Zarei, Z., Berezney, J., Hensley, A., Lemma, L., Senbil, N., Dogic, Z. and Fraden, S., "Light-activated microtubule-based two-dimensional active nematic," Soft matter 19, 6691-6699 (2023).
Hagan, M. F. and Mohajerani, F., "Self-assembly coupled to liquid-liquid phase separation," PLoS Comput Biol 19, e1010652 (2023).
Guo, J., Rich-New, S. T., Liu, C., Huang, Y., Tan, W., He, H., Yi, M., Zhang, X., Egelman, E. H., Wang, F. and Xu, B., "Hierarchical Assembly of Intrinsically Disordered Short Peptides," Chem 9, 2530-2546 (2023).
Asor, R., Singaram, S. W., Levi-Kalisman, Y., Hagan, M. F. and Raviv, U., "Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate)," Eur Phys J E Soft Matter 46, 107 (2023).
Zheng, J., Mallon, J., Lammers, A., Rados, T., Litschel, T., Moody, E. R. R., Ramirez-Diaz, D. A., Schmid, A., Williams, T. A., Bisson-Filho, A. W. and Garner, E., "Salactin, a dynamically unstable actin homolog in Haloarchaea," mBio 14, e02272-02223 (2023).
Malakar, K., Rubenstein, R. I., Bi, D. and Chakraborty, B., "A mechanistic model of the organization of cell shapes in epithelial tissues," Frontiers in Soft Matter 3, (2023).
Rosario, A., McInally, S. G., Jelenkovic, P. R., Goode, B. L. and Kondev, J., "Universal length fluctuations of actin structures found in cells," eLife 12, (2023).
Elam, L., Quiñones-Frías, M. C., Zhang, Y., Rodal, A. A. and Fai, T. G., "Fast Solver for Diffusive Transport Times on Dynamic Intracellular Networks," SIAM Journal on Applied Mathematics 0, S476-S492 (2023).
Joshi, C., Zarei, Z., Norton, M. M., Fraden, S., Baskaran, A. and Hagan, M. F., "From disks to channels: dynamics of active nematics confined to an annulus," Soft Matter 19, 5630-5640 (2023).
Cho, S., Usuba, J., Chakraborty, S., Li, X. and Han, G. G., "Solid-state photon energy storage via reversible [2+ 2] cycloaddition of donor-acceptor styrylpyrylium system," Chem 9, 3159-3171 (2023).
Liu, Z., Guo, J., Qiao, Y. and Xu, B., "Enzyme-Instructed Intracellular Peptide Assemblies," Accounts of chemical research 56, 3076-3088 (2023).
Guo, J., Chang, A. and Xu, B., "Auto‐Cleaving Bond for Better Drugs," ChemMedChem, e202400130 (2024).
Duque, C. M., Hall, D. M., Tyukodi, B., Hagan, M. F., Santangelo, C. D. and Grason, G. M., "Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra," Proceedings of the National Academy of Sciences 121, e2315648121 (2024).Wang, D., Moreno, S., Gao, M., Guo, J., Xu, B., Voigt, D., Voit, B. and Appelhans, D., "Protocells Capable of Generating a Cytoskeleton‐Like Structure from Intracellular Membrane‐Active Artificial Organelles," Advanced Functional Materials, (2023).
Tyukodi, B., Barbot, A., Garciá-Garciá, R., Lerbinger, M., Patinet, S. and Vandembroucq, D., "Coarse-graining amorphous plasticity: impact of rejuvenation and disorder," Comptes Rendus. Physique 24, 1-19 (2023).
Li, X., Cho, S., Wan, J. and Han, G. G., "Photoswitches and photochemical reactions for optically controlled phase transition and energy storage," Chem 9, 2378-2389 (2023).
Hensley, A., Videbæk, T. E., Seyforth, H., Jacobs, W. M. and Rogers, W. B., "Macroscopic photonic single crystals via seeded growth of DNA-coated colloids," Nature communications 14, 4237 (2023).
Guo, J., Tan, W., He, H. and Xu, B., "Autohydrolysis of Diglycine‐Activated Succinic Esters Boosts Cellular Uptake," Angewandte Chemie International Edition 62, e202308022 (2023).
Guo, J., Rich-New, S. T., Liu, C., Huang, Y., Tan, W., He, H., Yi, M., Zhang, X., Egelman, E. H. and Wang, F., "Hierarchical assembly of intrinsically disordered short peptides," Chem 9, 2378-2389 (2023).
Gonzalez, A., Qiu, Q., Usuba, J., Wan, J. and Han, G. G., "Photoinduced Solid–Liquid Phase Transition and Energy Storage Enabled by the Design of Linked Double Photoswitches," ACS Materials Au, (2023).
Tyukodi, B., Mohajerani, F., Hall, D. M., Grason, G. M. and Hagan, M. F., "Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries," ACS Nano 16, 9077-9085 (2022).
Foster, P. J., Bae, J., Lemma, B., Zheng, J., Ireland, W., Chandrakar, P., Boros, R., Dogic, Z., Needleman, D. J. and Vlassak, J. J., "Dissipation and energy propagation across scales in an active cytoskeletal material," Proc Natl Acad Sci U S A 120, e2207662120 (2023).
Del Signore, S. J., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell 34, ar51 (2023).
Spivack, I. R., Hall, D. M. and Grason, G. M., "Stress accumulation versus shape flattening in frustrated, warped-jigsaw particle assemblies," New Journal of Physics 24, 063023 (2022).
Guo, J., Wang, F., Huang, Y., He, H., Tan, W., Yi, M., Egelman, E. H. and Xu, B., "Cell spheroid creation by transcytotic intercellular gelation," Nature nanotechnology 18, 1-11 (2023).
Uplap, S., Hagan, M. F. and Baskaran, A., "Design principles for transporting vesicles with enclosed active particles (a)," Europhysics letters 143, 67001 (2023).
Hayakawa, D., Videbaek, T. E., Hall, D. M., Fang, H., Sigl, C., Feigl, E., Dietz, H., Fraden, S., Hagan, M. F., Grason, G. M. and 1Yardimci, S., Gibaud, T., Schwenger, W., Sartucci, M. R., Olmsted, P. D., Urbach, J. S. and Dogic, Z., "Bonded straight and helical flagellar filaments form ultra-low-density glasses," Proceedings of the National Academy of Sciences 120, e2215766120 (2023).
Starr, C. A., Nair, S., Huang, S.-Y., Hagan, M. F., Jacobson, S. C. and Zlotnick, A., "Engineering Metastability into a Virus-like Particle to Enable Triggered Dissociation," Journal of the American Chemical Society, (2023).
Signore, S. J. D., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell, mbc. E22-08-0372 (2023).
Sciortino, A., Neumann, L. J., Krüger, T., Maryshev, I., Teshima, T. F., Wolfrum, B., Frey, E. and Bausch, A. R., "Polarity and chirality control of an active fluid by passive nematic defects," Nature Materials 22, 260-268 (2023).
Starr, C. A., Nair, S., Huang, S.-Y., Hagan, M. F., Jacobson, S. C. and Zlotnick, A., "Engineering Metastability into a Virus-like Particle to Enable Triggered Dissociation," Journal of the American Chemical Society, (2023).
Signore, S. J. D., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell, mbc. E22-08-0372 (2023).
Sciortino, A., Neumann, L. J., Krüger, T., Maryshev, I., Teshima, T. F., Wolfrum, B., Frey, E. and Bausch, A. R., "Polarity and chirality control of an active fluid by passive nematic defects," Nature Materials 22, 260-268 (2023).
Yardimci, S., Gibaud, T., Schwenger, W., Sartucci, M. R., Olmsted, P. D., Urbach, J. S. and Dogic, Z., "Bonded straight and helical flagellar filaments form ultra-low-density glasses," Proceedings of the National Academy of Sciences 120, e2215766120 (2023).
Foster, P. J., Bae, J., Lemma, B., Zheng, J., Ireland, W., Chandrakar, P., Boros, R., Dogic, Z., Needleman, D. J. and Vlassak, J. J., "Dissipation and energy propagation across scales in an active cytoskeletal material," Proceedings of the National Academy of Sciences 120, e2207662120 (2023).
Starr, C. A., Nair, S., Huang, S.-Y., Hagan, M. F., Jacobson, S. C. and Zlotnick, A., "Engineering Metastability into a Virus-like Particle to Enable Triggered Dissociation," Journal of the American Chemical Society, (2023).
Signore, S. J. D., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell, mbc. E22-08-0372 (2023).
Qiu, Q., Sun, Z., Joubran, D., Li, X., Wan, J., Schmidt-Rohr, K. and Han, G. G. D., "Optically Controlled Recovery and Recycling of Homogeneous Organocatalysts Enabled by Photoswitches," Angew Chem Int Ed Engl 62, e202300723 (2023).
Li, X., Cho, S. and Han, G. G. D., "Light-Responsive Solid-Solid Phase Change Materials for Photon and Thermal Energy Storage," ACS Mater Au 3, 37-42 (2023).
Hall, D. M., Stevens, M. J. and Grason, G. M., "Building blocks of non-Euclidean ribbons: size-controlled self-assembly via discrete frustrated particles," Soft Matter 19, 858-881 (2023).
2022
Chung, J., Goode, B. L. and Gelles, J., "Single-molecule analysis of actin filament debranching by cofilin and GMF," Proc Natl Acad Sci U S A 119, e2115129119 (2022).
Chandrakar, P., Berezney, J., Lemma, B., Hishamunda, B., Berry, A., Wu, K. T., Subramanian, R., Chung, J., Needleman, D., Gelles, J. and Dogic, Z., "Engineering stability, longevity, and miscibility of microtubule-based active fluids," Soft Matter 18, 1825-1835 (2022).
Berezney, J. P. and Valentine, M. T., "A compact rotary magnetic tweezers device for dynamic material analysis," Rev Sci Instrum 93, 093701 (2022).
Berezney, J., Goode, B. L., Fraden, S. and Dogic, Z., "Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes," Proc Natl Acad Sci U S A 119, e2115895119 (2022).
Geometrically programmed self-limited assembly of tubules using DNA origami colloids," Proc Natl Acad Sci U S A 119, e2207902119 (2022).
Gonzalez, A., Odaybat, M., Le, M., Greenfield, J. L., White, A. J. P., Li, X., Fuchter, M. J. and Han, G. G. D., "Photocontrolled Energy Storage in Azobispyrazoles with Exceptionally Large Light Penetration Depths," Journal of the American Chemical Society 144, 19430-19436 (2022).
Fang, H., Tyukodi, B., Rogers, W. B. and Hagan, M. F., "Polymorphic self-assembly of helical tubules is kinetically controlled," Soft Matter 18, 6716-6728 (2022).
Chung, J., Goode, B. L. and Gelles, J., "Single-molecule analysis of actin filament debranching by cofilin and GMF," Proc Natl Acad Sci U S A 119, e2115129119 (2022).
Chandrakar, P., Berezney, J., Lemma, B., Hishamunda, B., Berry, A., Wu, K. T., Subramanian, R., Chung, J., Needleman, D., Gelles, J. and Dogic, Z., "Engineering stability, longevity, and miscibility of microtubule-based active fluids," Soft Matter 18, 1825-1835 (2022).
Berezney, J. P. and Valentine, M. T., "A compact rotary magnetic tweezers device for dynamic material analysis," Rev Sci Instrum 93, 093701 (2022).
Berezney, J., Goode, B. L., Fraden, S. and Dogic, Z., "Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes," Proc Natl Acad Sci U S A 119, e2115895119 (2022)
Hunter, I., Norton, M. M., Chen, B., Simonetti, C., Moustaka, M. E., Touboul, J. and Fraden, S., "Pattern formation in a four-ring reaction-diffusion network with heterogeneity," Phys Rev E 105, 024310 (2022).
Hoeprich, G. J., Sinclair, A. N., Shekhar, S. and Goode, B. L., "Single-molecule imaging of IQGAP1 regulating actin filament dynamics," Molecular biology of the cell 33, ar2 (2022).
Hayakawa, D., Videbaek, T. E., Hall, D. M., Fang, H., Sigl, C., Feigl, E., Dietz, H., Fraden, S., Hagan, M. F., Grason, G. M. and Rogers, W. B., "Geometrically programmed self-limited assembly of tubules using DNA origami colloids," Proc Natl Acad Sci U S A 119, e2207902119 (2022).
Gonzalez, A., Odaybat, M., Le, M., Greenfield, J. L., White, A. J. P., Li, X., Fuchter, M. J. and Han, G. G. D., "Photocontrolled Energy Storage in Azobispyrazoles with Exceptionally Large Light Penetration Depths," Journal of the American Chemical Society 144, 19430-19436 (2022).
Fang, H., Tyukodi, B., Rogers, W. B. and Hagan, M. F., "Polymorphic self-assembly of helical tubules is kinetically controlled," Soft Matter 18, 6716-6728 (2022).
Kalinin, S. V., Ophus, C., Voyles, P. M., Erni, R., Kepaptsoglou, D., Grillo, V., Lupini, A. R., Oxley, M. P., Schwenker, E., Chan, M. K. Y., Etheridge, J., Li, X., Han, G. G. D., Ziatdinov, M., Shibata, N. and Pennycook, S. J., "Machine learning in scanning transmission electron microscopy," Nature Reviews Methods Primers 2, 1-28 (2022).
Mohajerani, F., Tyukodi, B., Schlicksup, C. J., Hadden-Perilla, J. A., Zlotnick, A. and Hagan, M. F., "Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism," ACS nano 16, 13845-13859 (2022).
McInally, S. G., Kondev, J. and Goode, B. L., "Quantitative Analysis of Actin Cable Length in Yeast," Bio Protoc 12, e4402 (2022).
Liu, S., Zhang, Q., He, H., Yi, M., Tan, W., Guo, J. and Xu, B., "Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells," Angew Chem Int Ed Engl 61, e202210568 (2022).
Videbaek, T. E., Fang, H., Hayakawa, D., Tyukodi, B., Hagan, M. F. and Rogers, W. B., "Tiling a tubule: how increasing complexity improves the yield of self-limited assembly," Journal of physics. Condensed matter : an Institute of Physics journal 34, (2022).
Tyukodi, B., Mohajerani, F., Hall, D. M., Grason, G. M. and Hagan, M. F., "Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries," ACS Nano 16, 9077-9085 (2022).
Tsidilkovski, L., Mohajerani, F. and Hagan, M. F., "Microcompartment assembly around multicomponent fluid cargoes," The Journal of Chemical Physics 156, 245104 (2022).
Trubiano, A. and Hagan, M. F., "Optimization of non-equilibrium self-assembly protocols using Markov state models," The Journal of Chemical Physics 157, 244901 (2022).
Tanjeem, N., Hall, D. M., Minnis, M. B., Hayward, R. C. and Grason, G. M., "Focusing frustration for self-limiting assembly of flexible, curved particles," Physical Review Research 4, 033035 (2022).
Tan, W., Zhang, Q., Quinones-Frias, M. C., Hsu, A. Y., Zhang, Y., Rodal, A., Hong, P., Luo, H. R. and Xu, B., "Enzyme-Responsive Peptide Thioesters for Targeting Golgi Apparatus," Journal of the American Chemical Society 144, 6709-6713 (2022).
Tan, W., Zhang, Q., Hong, P. and Xu, B., "A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells," Bioconjug Chem 33, 1983-1988 (2022).
Spivack, I. R., Hall, D. M. and Grason, G. M., "Stress accumulation versus shape flattening in frustrated, warped-jigsaw particle assemblies," New Journal of Physics 24, 063023 (2022).
Signore, S. J. D., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell 0, mbcE22080372 (2022).
Sarfati, G., Maitra, A., Voituriez, R., Galas, J. C. and Estevez-Torres, A., "Crosslinking and depletion determine spatial instabilities in cytoskeletal active matter," Soft Matter 18, 3793-3800 (2022).
Qiu, Q., Yang, S., Gerkman, M. A., Fu, H., Aprahamian, I. and Han, G. G. D., "Photon Energy Storage in Strained Cyclic Hydrazones: Emerging Molecular Solar Thermal Energy Storage Compounds," Journal of the American Chemical Society 144, 12627-12631 (2022).
Yi, M., Wang, F., Tan, W., Hsieh, J. T., Egelman, E. H. and Xu, B., "Enzyme Responsive Rigid-Rod Aromatics Target "Undruggable" Phosphatases to Kill Cancer Cells in a Mimetic Bone Microenvironment," Journal of the American Chemical Society 144, 13055-13059 (2022).
Hunter, I., Norton, M. M., Chen, B., Simonetti, C., Moustaka, M. E., Touboul, J. and Fraden, S., "Pattern formation in a four-ring reaction-diffusion network with heterogeneity," Phys Rev E 105, 024310 (2022).
Hoeprich, G. J., Sinclair, A. N., Shekhar, S. and Goode, B. L., "Single-molecule imaging of IQGAP1 regulating actin filament dynamics," Molecular biology of the cell 33, ar2 (2022).
Kalinin, S. V., Ophus, C., Voyles, P. M., Erni, R., Kepaptsoglou, D., Grillo, V., Lupini, A. R., Oxley, M. P., Schwenker, E., Chan, M. K. Y., Etheridge, J., Li, X., Han, G. G. D., Ziatdinov, M., Shibata, N. and Pennycook, S. J., "Machine learning in scanning transmission electron microscopy," Nature Reviews Methods Primers 2, 1-28 (2022).
Mohajerani, F., Tyukodi, B., Schlicksup, C. J., Hadden-Perilla, J. A., Zlotnick, A. and Hagan, M. F., "Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism," ACS nano 16, 13845-13859 (2022).
McInally, S. G., Kondev, J. and Goode, B. L., "Quantitative Analysis of Actin Cable Length in Yeast," Bio Protoc 12, e4402 (2022).
Liu, S., Zhang, Q., He, H., Yi, M., Tan, W., Guo, J. and Xu, B., "Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells," Angew Chem Int Ed Engl 61, e202210568 (2022).
Tan, W., Zhang, Q., Quinones-Frias, M. C., Hsu, A. Y., Zhang, Y., Rodal, A., Hong, P., Luo, H. R. and Xu, B., "Enzyme-Responsive Peptide Thioesters for Targeting Golgi Apparatus," Journal of the American Chemical Society 144, 6709-6713 (2022).
Tan, W., Zhang, Q., Hong, P. and Xu, B., "A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells," Bioconjug Chem 33, 1983-1988 (2022).
Spivack, I. R., Hall, D. M. and Grason, G. M., "Stress accumulation versus shape flattening in frustrated, warped-jigsaw particle assemblies," New Journal of Physics 24, 063023 (2022).
Signore, S. J. D., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell 0, mbcE22080372 (2022).
Sarfati, G., Maitra, A., Voituriez, R., Galas, J. C. and Estevez-Torres, A., "Crosslinking and depletion determine spatial instabilities in cytoskeletal active matter," Soft Matter 18, 3793-3800 (2022).
Qiu, Q., Yang, S., Gerkman, M. A., Fu, H., Aprahamian, I. and Han, G. G. D., "Photon Energy Storage in Strained Cyclic Hydrazones: Emerging Molecular Solar Thermal Energy Storage Compounds," Journal of the American Chemical Society 144, 12627-12631 (2022).
Mohajerani, F., Tyukodi, B., Schlicksup, C. J., Hadden-Perilla, J. A., Zlotnick, A. and Hagan, M. F., "Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism," ACS nano 16, 13845-13859 (2022).
McInally, S. G., Kondev, J. and Goode, B. L., "Quantitative Analysis of Actin Cable Length in Yeast," Bio Protoc 12, e4402 (2022)
Liu, S., Zhang, Q., He, H., Yi, M., Tan, W., Guo, J. and Xu, B., "Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells," Angew Chem Int Ed Engl 61, e202210568 (2022).
Videbaek, T. E., Fang, H., Hayakawa, D., Tyukodi, B., Hagan, M. F. and Rogers, W. B., "Tiling a tubule: how increasing complexity improves the yield of self-limited assembly," Journal of physics. Condensed matter : an Institute of Physics journal 34, (2022).
Tyukodi, B., Mohajerani, F., Hall, D. M., Grason, G. M. and Hagan, M. F., "Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries," ACS Nano 16, 9077-9085 (2022).
Tsidilkovski, L., Mohajerani, F. and Hagan, M. F., "Microcompartment assembly around multicomponent fluid cargoes," The Journal of Chemical Physics 156, 245104 (2022).
Trubiano, A. and Hagan, M. F., "Optimization of non-equilibrium self-assembly protocols using Markov state models," The Journal of Chemical Physics 157, 244901 (2022).
Tanjeem, N., Hall, D. M., Minnis, M. B., Hayward, R. C. and Grason, G. M., "Focusing frustration for self-limiting assembly of flexible, curved particles," Physical Review Research 4, 033035 (2022).
Lemma, B., Mitchell, N. P., Subramanian, R., Needleman, D. J. and Dogic, Z., "Active microphase separation in mixtures of microtubules and tip-accumulating molecular motors," Physical Review X 12, 031006 (2022).
Khanra, A., Jia, L. L., Mitchell, N. P., Balchunas, A., Pelcovits, R. A., Powers, T. R., Dogic, Z. and Sharma, P., "Controlling the shape and topology of two-component colloidal membranes," Proceedings of the National Academy of Sciences 119, e2204453119 (2022).
Joshi, C., Ray, S., Lemma, L. M., Varghese, M., Sharp, G., Dogic, Z., Baskaran, A. and Hagan, M. F., "Data-driven discovery of active nematic hydrodynamics," Physical review letters 129, 258001 (2022).
Bate, T. E., Varney, M. E., Taylor, E. H., Dickie, J. H., Chueh, C.-C., Norton, M. M. and Wu, K.-T., "Self-mixing in microtubule-kinesin active fluid from nonuniform to uniform distribution of activity," Nature communications 13, 6573 (2022).
McInally, S. G., Kondev, J. and Goode, B. L., "Quantitative Analysis of Actin Cable Length in Yeast," Bio-protocol 12, e4402-e4402 (2022).
Chandrakar, P., Berezney, J., Lemma, B., Hishamunda, B., Berry, A., Wu, K.-T., Subramanian, R., Chung, J., Needleman, D. J. and Gelles, J., "Engineering stability, longevity, and miscibility of microtubule-based active fluids," Soft Matter, (2022).
Yi, M., Wang, F., Tan, W., Hsieh, J.-T., Egelman, E. H. and Xu, B., "Enzyme Responsive Rigid-Rod Aromatics Target “Undruggable” Phosphatases to Kill Cancer Cells in a Mimetic Bone Microenvironment," Journal of the American Chemical Society 144, 13055-13059 (2022).
Berezney, J. P. and Valentine, M. T., "A compact rotary magnetic tweezers device for dynamic material analysis," Review of Scientific Instruments 93, 093701 (2022).
Li, X., Cho, S. and Han, G. G., "Light-Responsive Solid–Solid Phase Change Materials for Photon and Thermal Energy Storage," ACS Materials Au, (2022).
Gonzalez, A., Odaybat, M., Le, M., Greenfield, J. L., White, A. J., Li, X., Fuchter, M. J. and Han, G. G., "Photocontrolled Energy Storage in Azobispyrazoles with Exceptionally Large Light Penetration Depths," Journal of the American Chemical Society, (2022).
Najma, B., Varghese, M., Tsidilkovski, L., Lemma, L., Baskaran, A. and Duclos, G., "Competing instabilities reveal how to rationally design and control active crosslinked gels," Nature communications 13, 1-10 (2022).
Adkins, R., Kolvin, I., You, Z., Witthaus, S., Marchetti, M. C. and Dogic, Z., "Dynamics of active liquid interfaces," Science 377, 768-772 (2022).
Ye, L., Huang, X., Zhang, L., Tong, L., Li, Z., Peng, Z., Lin, R., Xue, K.-H., Dai, H. and Cheng, H., "Manipulating Exchange Bias in 2D Magnetic Heterojunction for High-performance Robust Memory Applications," (2022).
Liu, S., Zhang, Q., He, H., Yi, M., Tan, W., Guo, J. and Xu, B., "Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells," Angewandte Chemie International Edition, (2022).
Chung, J., Goode, B. L. and Gelles, J., "Single-molecule analysis of actin filament debranching by cofilin and GMF," Proceedings of the National Academy of Sciences 119, e2115129119 (2022).
Qiu, Q., Yang, S., Gerkman, M. A., Fu, H., Aprahamian, I. and Han, G. G., "Photon Energy Storage in Strained Cyclic Hydrazones: Emerging Molecular Solar Thermal Energy Storage Compounds," Journal of the American Chemical Society, (2022).
Tan, W., Zhang, Q., Quiñones-Frías, M. C., Hsu, A. Y., Zhang, Y., Rodal, A., Hong, P., Luo, H. R. and Xu, B., "Enzyme-Responsive Peptide Thioesters for Targeting Golgi Apparatus," Journal of the American Chemical Society, (2022).
Kalinin, S. V., Ophus, C., Voyles, P. M., Erni, R., Kepaptsoglou, D., Grillo, V., Lupini, A. R., Oxley, M. P., Schwenker, E., Chan, M. K., Etheridge, J., Li, X., Han, G. G., Ziatdinov, M., Shibata, N., and Pennycook, S., "Machine learning in scanning transmission electron microscopy," Nature Reviews Methods Primers 2, 1-28 (2022).
Datta, A., Ghosh, S. and Kondev, J., "How to assemble a scale-invariant gradient," Elife 11, e71365 (2022).
Videbaek, T. E., Fang, H., Hayakawa, D., Tyukodi, B., Hagan, M. F. and Rogers, W. B., "Tiling a tubule: How increasing complexity improves the yield of self-limited assembly," Journal of Physics: Condensed Matter, (2022).
Wagner, C. G., Hagan, M. F. and Baskaran, A., "Steady states of active Brownian particles interacting with boundaries," Journal of Statistical Mechanics: Theory and Experiment 2022, 013208 (2022).
Tan, W., Zhang, Q., Hong, P. and Xu, B., "A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells," Bioconjugate chemistry, (2022).
Hunter, I., Norton, M. M., Chen, B., Simonetti, C., Moustaka, M. E., Touboul, J. and Fraden, S., "Pattern formation in a four-ring reaction-diffusion network with heterogeneity," Physical Review E 105, 024310 (2022).
Berezney, J., Goode, B. L., Fraden, S. and Dogic, Z., "Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes," Proceedings of the National Academy of Sciences 119, e2115895119 (2022).
2021
Chelakkot, R., Hagan, M. F. and Gopinath, A., "Synchronized oscillations, traveling waves, and jammed clusters induced by steric interactions in active filament arrays," Soft Matter 17, 1091-1104 (2021).
Chen, Y.-C., Jolicoeur, B., Chueh, C.-C. and Wu, K.-T., "Flow coupling between active and passive fluids across water–oil interfaces," Scientific reports 11, 1-16 (2021).
Del Signore, S. J., Kelley, C. F., Messelaar, E. M., Lemos, T., Marchan, M. F., Ermanoska, B., Mund, M., Fai, T. G., Kaksonen, M. and Rodal, A. A., "An autoinhibitory clamp of actin assembly constrains and directs synaptic endocytosis," Elife 10, (2021).
Greenfield, J. L., Gerkman, M. A., Gibson, R. S., Han, G. G. and Fuchter, M. J., "Efficient electrocatalytic switching of azoheteroarenes in the condensed phases," Journal of the American Chemical Society 143, 15250-15257 (2021).
He, H., Guo, J. and Xu, B., "Enzymatic Delivery of Magnetic Nanoparticles into Mitochondria of Live Cells," Chemnanomat, (2021).
He, H., Guo, J., Xu, J., Wang, J., Liu, S. and Xu, B., "Dynamic Continuum of Nanoscale Peptide Assemblies Facilitates Endocytosis and Endosomal Escape," Nano Letters 21, 4078-4085 (2021).
Hoeprich, G. J., Sinclair, A. N., Shekhar, S. and Goode, B. L., "Single-molecule imaging of IQGAP1 regulating actin filament dynamics," Molecular biology of the cell, mbc. E21-04-0211 (2021).
Kim, H., Sundaram, S., Kang, J.-H., Tanjeem, N., Emrick, T. and Hayward, R. C., "Coupled oscillation and spinning of photothermal particles in Marangoni optical traps," Proceedings of the National Academy of Sciences 118, (2021).
Ksander, J., Katz, D. B. and Miller, P., "A model of naturalistic decision making in preference tests," PLoS computational biology 17, e1009012 (2021).
Lemma, L. M., Norton, M. M., Tayar, A. M., DeCamp, S. J., Aghvami, S. A., Fraden, S., Hagan, M. F. and Dogic, Z., "Multiscale Microtubule Dynamics in Active Nematics," Physical Review Letters 127, 148001 (2021).
Liu, S., Zhang, Q., Shy, A. N., Yi, M., He, H., Lu, S. and Xu, B., "Enzymatically Forming Intranuclear Peptide Assemblies for Selectively Killing Human Induced Pluripotent Stem Cells," Journal of the American Chemical Society 143, 15852-15862 (2021).
Memet, E., Hilitski, F., Dogic, Z. and Mahadevan, L., "Static adhesion hysteresis in elastic structures," Soft Matter 17, 2704-2710 (2021).
Merminod, S., Edison, J. R., Fang, H., Hagan, M. F. and Rogers, W. B., "Avidity and surface mobility in multivalent ligand-receptor binding," Nanoscale, (2021).
Mohajerani, F., Sayer, E., Neil, C., Inlow, K. and Hagan, M. F., "Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control," ACS nano 15, 4197-4212 (2021).
Moustaka, M. E., Norton, M. M., Blanc, B., Horvath, V., Aghvami, S. A. and Fraden, S., "Partition, Reaction, and Diffusion Coefficients of Bromine in Elastomeric Polydimethylsiloxane," The Journal of Physical Chemistry B, (2021).
Peterson, M. S. E., Baskaran, A. and Hagan, M. F., "Vesicle shape transformations driven by confined active filaments," Nature communications 12, 7247 (2021).
Qiu, Q., Gerkman, M. A., Shi, Y. and Han, G. G., "Design of phase-transition molecular solar thermal energy storage compounds: compact molecules with high energy densities," Chemical communications 57, 9458-9461 (2021).
Qiu, Q., Shi, Y. and Han, G. G., "Solar Energy Conversion and Storage by Photoswitchable Organic Materials in Solution, Liquid, Solid, and Changing Phases," Journal of Materials Chemistry C, (2021).
Shi, Y., Gerkman, M. A., Qiu, Q., Zhang, S. and Han, G. G., "Sunlight-activated phase change materials for controlled heat storage and triggered release," Journal of Materials Chemistry A 9, 9798-9808 (2021).
Sigl, C., Willner, E. M., Engelen, W., Kretzmann, J. A., Sachenbacher, K., Liedl, A., Kolbe, F., Wilsch, F., Aghvami, S. A., Protzer, U., Hagan, M. F., Fraden, S. and Dietz, H., "Programmable icosahedral shell system for virus trapping," Nature Materials 20, 1281-1289 (2021).
Tan, W., Zhang, Q., Wang, J., Yi, M., He, H. and Xu, B., "Enzymatic Assemblies of Thiophosphopeptides Instantly Target Golgi Apparatus and Selectively Kill Cancer Cells," Angewandte Chemie International Edition, (2021).
Tayar, A. M., Hagan, M. F. and Dogic, Z., "Active liquid crystals powered by force-sensing DNA-motor clusters," Proceedings of the National Academy of Sciences 118, (2021).
Walsh, R. B., Dresselhaus, E. C., Becalska, A. N., Zunitch, M. J., Blanchette, C. R., Scalera, A. L., Lemos, T., Lee, S. M., Apiki, J., Wang, S., Isaac, B., Yeh, A., Koles, K. and Rodal, A. A., "Opposing functions for retromer and Rab11 in extracellular vesicle traffic at presynaptic terminals," Journal of Cell Biology 220, (2021).
Yang, D., He, H., Kim, B. J. and Xu, B., "Peptide Assemblies Mimicking Chaperones for Protein Trafficking," Bioconjugate Chemistry 32, 502-506 (2021).
Yi, M., Guo, J., He, H., Tan, W., Harmon, N., Ghebreyessus, K. and Xu, B., "Phosphobisaromatic motifs enable rapid enzymatic self-assembly and hydrogelation of short peptides," Soft Matter 17, 8590-8594 (2021).
Yi, M., Tan, W., Guo, J. and Xu, B., "Enzymatic noncovalent synthesis of peptide assemblies generates multimolecular crowding in cells for biomedical applications," Chemical communications, (2021).
Zuraw-Weston, S. E., Siavashpouri, M., Moustaka, M. E., Gerling, T., Dietz, H., Fraden, S., Ribbe, A. E. and Dinsmore, A. D., "Membrane remodeling by DNA origami nanorods: Experiments exploring the parameter space for vesicle remodeling," Langmuir, (2021).
2020
Balchunas, A., Jia, L. L., Zakhary, M. J., Robaszewski, J., Gibaud, T., Dogic, Z., Pelcovits, R. A. and Powers, T. R., "Force-Induced Formation of Twisted Chiral Ribbons," Physical Review Letters 125, 018002 (2020).
Chandrakar, P., Varghese, M., Aghvami, S. A., Baskaran, A., Dogic, Z. and Duclos, G., "Confinement controls the bend instability of three-dimensional active liquid crystals," Physical Review Letters 125, 257801 (2020).
Ding, L., Pelcovits, R. A. and Powers, T. R., "Shapes of fluid membranes with chiral edges," Physical Review E 102, 032608 (2020).
Duclos, G., Adkins, R., Banerjee, D., Peterson, M. S. E., Varghese, M., Kolvin, I., Baskaran, A., Pelcovits, R. A., Powers, T. R., Baskaran, A., Toschi, F., Hagan, M. F., Streichan, S. J., Vitelli, V., Beller, D. A. and Dogic, Z., "Topological structure and dynamics of three-dimensional active nematics," Science 367, 1120-1124 (2020).
Fang, H., Hagan, M. F. and Rogers, W. B., "Two-step crystallization and solid–solid transitions in binary colloidal mixtures," Proceedings of the National Academy of Sciences 117, 27927-27933 (2020).
Farhadi, L., Ricketts, S. N., Rust, M. J., Das, M., Robertson-Anderson, R. M. and Ross, J. L., "Actin and microtubule crosslinkers tune mobility and control co-localization in a composite cytoskeletal network," Soft Matter, (2020).
Feng, Z., Wang, H., Wang, F., Oh, Y., Berciu, C., Cui, Q., Egelman, E. H. and Xu, B., "Artificial intracellular filaments," Cell Reports Physical Science 1, 100085 (2020).
Harden, T. T., Herlambang, K. S., Chamberlain, M., Lalanne, J.-B., Wells, C. D., Li, G.-W., Landick, R., Hochschild, A., Kondev, J. and Gelles, J., "Alternative transcription cycle for bacterial RNA polymerase," Nature communications 11, 663534 (2020).
He, H., Guo, J., Lin, X. and Xu, B., "Enzyme-Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells," Angewandte Chemie International Edition n/a, (2020).
He, H., Lin, X., Wu, D., Wang, J., Guo, J., Green, D. R., Zhang, H. and Xu, B., "Enzymatic Noncovalent Synthesis for Mitochondrial Genetic Engineering of Cancer Cells," Cell Reports Physical Science 1, 100270 (2020).
Ierushalmi, N., Malik-Garbi, M., Manhart, A., Abu Shah, E., Goode, B. L., Mogilner, A. and Keren, K., "Centering and symmetry breaking in confined contracting actomyosin networks," eLife 9, e55368 (2020).
Merrigan, C., Ramola, K., Chatterjee, R., Segall, N., Shokef, Y. and Chakraborty, B., "Arrested states in persistent active matter: Gelation without attraction," Physical Review Research 2, 013260 (2020).
Nguyen, D. N., Redman, R. L., Horiya, S., Bailey, J. K., Xu, B., Stanfield, R. L., Temme, J. S., LaBranche, C. C., Wang, S., Rodal, A. A., Montefiori, D. C., Wilson, I. A. and Krauss, I. J., "The Impact of Sustained Immunization Regimens on the Antibody Response to Oligomannose Glycans," ACS Chemical Biology 15, 789-798 (2020).
Norton, M. M., Grover, P., Hagan, M. F. and Fraden, S., "Optimal control of active nematics," Physical review letters 125, 178005 (2020).
Peterson, M. S., Hagan, M. F. and Baskaran, A., "Statistical properties of a tangentially driven active filament," J Stat Mech-Theory E 2020, (2020).
Rogers, W. B., "A mean-field model of linker-mediated colloidal interactions," The Journal of Chemical Physics 153, 124901 (2020).
Sheehy, J., Hunter, I., Moustaka, M. E., Aghvami, S. A., Fahmy, Y. and Fraden, S., "Impact of PDMS-Based Microfluidics on Belousov–Zhabotinsky Chemical Oscillators," The Journal of Physical Chemistry B 124, 11690-11698 (2020).
2019
Balchunas, A. J., Cabanas, R. A., Zakhary, M. J., Gibaud, T., Fraden, S., Sharma, P., Hagan, M. F. and Dogic, Z., "Equation of state of colloidal membranes," Soft Matter 15, 6791-6802 (2019).
Bate, T. E., Jarvis, E. J., Varney, M. E. and Wu, K. T., "Collective dynamics of microtubule-based 3D active fluids from single microtubules," Soft Matter 15, 5006-5016 (2019).
Bate, T. E., Jarvis, E. J., Varney, M. E. and Wu, K.-T., "Controlling Flow Speeds of Microtubule-Based 3D Active Fluids Using Temperature," JoVE, e60484 (2019).
Chatterjee, R., Segall, N., Merrigan, C., Ramola, K., Chakraborty, B. and Shokef, Y., "Motion of active tracer in a lattice gas with cross-shaped particles," J Chem Phys 150, 144508 (2019).
Choudhary, S. K., Baskaran, A. and Sharma, P., "Reentrant Efficiency of Phototaxis in Chlamydomonas reinhardtii Cells," Biophys J 117, 1508-1513 (2019).
Dharmavaram, S., She, S. B., Lazaro, G., Hagan, M. F. and Bruinsma, R., "Gaussian curvature and the budding kinetics of enveloped viruses," PLoS Comput Biol 15, e1006602 (2019).
Edozie, B., Sahu, S., Pitta, M., Englert, A., Do Rosario, C. F. and Ross, J. L., "Self-organization of spindle-like microtubule structures," Soft Matter 15, 4797-4807 (2019).
Fai, T. G., Mohapatra, L., Kar, P., Kondev, J. and Amir, A., "Length regulation of multiple flagella that self-assemble from a shared pool of components," eLife 8, e42599 (2019).
Feng, Z., Han, X., Wang, H., Tang, T. and Xu, B., "Enzyme-Instructed Peptide Assemblies Selectively Inhibit Bone Tumors," Chem 5, 2442-2449 (2019).
Feng, Z., Wang, H., Yi, M., Lo, C. Y., Sallee, A., Hsieh, J. T. and Xu, B., "Instructed‐assembly of small peptides inhibits drug‐resistant prostate cancer cells," Peptide Science n/a, e24123 (2019).
Fürthauer, S., Lemma, B., Foster, P. J., Ems-McClung, S. C., Yu, C.-H., Walczak, C. E., Dogic, Z., Needleman, D. J. and Shelley, M. J., "Self-straining of actively crosslinked microtubule networks," Nature Physics, (2019).
Goldstein, D., Ramaswamy, S. and Chakraborty, B., "Stress fluctuations in transient active networks," Soft Matter 15, 3520-3526 (2019).
Hardoüin, J., Hughes, R., Doostmohammadi, A., Laurent, J., Lopez-Leon, T., Yeomans, J. M., Ignés-Mullol, J. and Sagués, F., "Reconfigurable flows and defect landscape of confined active nematics," Communications Physics 2, 121 (2019).
Kim, H., Kang, J. H., Zhou, Y., Kuenstler, A. S., Kim, Y., Chen, C., Emrick, T. and Hayward, R. C., "Light-Driven Shape Morphing, Assembly, and Motion of Nanocomposite Gel Surfers," Adv Mater 31, e1900932 (2019).
Lemma, L. M., DeCamp, S. J., You, Z., Giomi, L. and Dogic, Z., "Statistical properties of autonomous flows in 2D active nematics," Soft Matter 15, 3264-3272 (2019).
Levitus, R. P., Hoeprich, G. and Goode, B., "Closing the GAP Between IQGAP1 and its Yeast Homologue," The FASEB Journal 33, 631.624-631.624 (2019).
Lowensohn, J., Oyarzún, B., Narváez Paliza, G., Mognetti, B. M. and Rogers, W. B., "Linker-Mediated Phase Behavior of DNA-Coated Colloids," Physical Review X 9, 041054 (2019).
Malik-Garbi, M., Ierushalmi, N., Jansen, S., Abu-Shah, E., Goode, B. L., Mogilner, A. and Keren, K., "Scaling behaviour in steady-state contracting actomyosin networks," Nature Physics 15, 509-516 (2019).
Martinez-Prat, B., Ignes-Mullol, J., Casademunt, J. and Sagues, F., "Selection mechanism at the onset of active turbulence," Nature Physics 15, 362-+ (2019).
McInally, S. G., Kondev, J. and Dawson, S. C., "Length-dependent disassembly maintains four different flagellar lengths in Giardia," eLife 8, e48694 (2019).
Miller, J. M., Hall, D., Robaszewski, J., Sharma, P., Hagan, M. F., Grason, G. M. and Dogic, Z., "All twist and no bend makes raft edges splay: Spontaneous curvature of domain edges in colloidal membranes," Science advances 6, eaba2331 (2020).
Miller, J. M., Joshi, C., Sharma, P., Baskaran, A., Baskaran, A., Grason, G. M., Hagan, M. F. and Dogic, Z., "Conformational switching of chiral colloidal rafts regulates raft-raft attractions and repulsions," Proc Natl Acad Sci U S A 116, 15792-15801 (2019).
Norton, M. M., Tompkins, N., Blanc, B., Cambria, M. C., Held, J. and Fraden, S., "Dynamics of Reaction-Diffusion Oscillators in Star and other Networks with Cyclic Symmetries Exhibiting Multiple Clusters," Physical Review Letters 123, (2019).
Opathalage, A., Norton, M. M., Juniper, M. P. N., Langeslay, B., Aghvami, S. A., Fraden, S. and Dogic, Z., "Self-organized dynamics and the transition to turbulence of confined active nematics," Proc Natl Acad Sci U S A 116, 4788-4797 (2019).
Pearce, D. J. G., Ellis, P. W., Fernandez-Nieves, A. and Giomi, L., "Geometrical Control of Active Turbulence in Curved Topographies," Phys Rev Lett 122, 168002 168002 (2019).
Poitras, A. M., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "Cooperative activation of O-H and S-H bonds across the Co-P bond of an N-hetercyclic phosphido complex," Dalton Transactions 48, 5 (2019).
Rivas, D. P., Shendruk, T. N., Henry, R. R., Reich, D. H. and Leheny, R. L., "Driven topological transitions in active nematic films," Soft Matter 16, 9331-9338 (2020).
Ross, J. L., "Autonomous materials from biomimicry," Mrs Bull 44, 119-123 (2019).
Sanchez, T., Venturas, M., Aghvami, S. A., Yang, X., Fraden, S., Sakkas, D. and Needleman, D. J., "Combined noninvasive metabolic and spindle imaging as potential tools for embryo and oocyte assessment," Human Reproduction 34, 2349-2361 (2019).
Shekhar, S., Chung, J., Kondev, J., Gelles, J. and Goode, B. L., "Synergy between Cyclase-associated protein and Cofilin accelerates actin filament depolymerization by two orders of magnitude," Nature communications 10, 5319 (2019).
Siavashpouri, M., Sharma, P., Fung, J., Hagan, M. F. and Dogic, Z., "Structure, dynamics and phase behavior of short rod inclusions dissolved in a colloidal membrane," Soft Matter 15, 7033-7042 (2019).
Soni, H., Luo, W., Pelcovits, R. A. and Powers, T. R., "Stability of the interface of an isotropic active fluid," Soft Matter 15, 6318-6330 (2019).
Stiller, J. B., Jordan Kerns, S., Hoemberger, M., Cho, Y.-J., Otten, R., Hagan, M. F. and Kern, D., "Probing the transition state in enzyme catalysis by high-pressure NMR dynamics," Nat Catal 2, 726-734 (2019).
Summers, S., Olivier-Mason, A. J., Dang, M. and Chien, D. M., "Experiments in the Communication Lab: Adaptations of the Comm Lab Model in Three Institutions," 2019 ASEE Annual Conference & Exposition, (2019).
Tan, A. J., Roberts, E., Smith, S. A., Olvera, U. A., Arteaga, J., Fortini, S., Mitchell, K. A. and Hirst, L. S., "Topological chaos in active nematics," Nature Physics 15, 1033-1039 (2019).
Wagner, C. G. and Beals, R., "Constructing solutions to two-way diffusion problems," Journal of Physics A: Mathematical and Theoretical 52, 21 (2019).
Wagner, C. G., Hagan, M. F. and Baskaran, A., "Response of active Brownian particles to boundary driving," Physical Review E 100, 042610 (2019).
Walsh, R. B., Dresselhaus, E. C., Becalska, A. N., Zunitch, M. J., Blanchette, C. R., Scalera, A. L., Lemos, T., Lee, S. M., Apiki, J., Wang, S., Isaac, B., Yeh, A. and Rodal, A. A. "Opposing functions for retromer and Rab11 in extracellular vesicle traffic at presynaptic terminals," Journal of Cell Biology 220, e202012034 (2021).
Wang, H., Feng, Z. and Xu, B., "Dynamic Continuum of Molecular Assemblies for Controlling Cell Fates," Chembiochem, (2019).
Wang, H., Feng, Z. and Xu, B., "Instructed Assembly as Context-Dependent Signaling for the Death and Morphogenesis of Cells," Angew Chem Int Ed Engl 58, 5567-5571 (2019).
Wang, H., Feng, Z. and Xu, B., "Intercellular Instructed-Assembly Mimics Protein Dynamics To Induce Cell Spheroids," Journal of the American Chemical Society 141, 7271-7274 (2019).
Wang, H., Feng, Z. and Xu, B., "Supramolecular Assemblies of Peptides or Nucleopeptides for Gene Delivery," Theranostics 9, 3213-3222 (2019).
Wang, H., Feng, Z., Tan, W. and Xu, B., "Assemblies of d-Peptides for Targeting Cell Nucleolus," Bioconjug Chem 30, 2528-2532 (2019).
Wang, H., Feng, Z., Yang, C., Liu, J., Medina, J. E., Aghvami, S. A., Dinulescu, D. M., Liu, J., Fraden, S. and Xu, B., "Unraveling the Cellular Mechanism of Assembling Cholesterols for Selective Cancer Cell Death," Mol Cancer Res 17, 907-917 (2019).
Wang, J., Cooper, D. L., Zhan, W., Wu, D., He, H., Sun, S., Lovett, S. T. and Xu, B., "Diglycine Enables Rapid Intrabacterial Hydrolysis for Activating Anbiotics against Gram-negative Bacteria," Angew Chem Int Ed Engl 58, 10631-10634 (2019).
Wang, J., Shy, A., Wu, D., Cooper, D. L., Xu, J., He, H., Zhan, W., Sun, S., Lovett, S. T. and Xu, B., "Structure–Activity Relationship of Peptide-Conjugated Chloramphenicol for Inhibiting Escherichia coli," Journal of Medicinal Chemistry, (2019).
Wang, S., Zhao, Z. and Rodal, A. A., "Higher-order assembly of Sorting Nexin 16 controls tubulation and distribution of neuronal endosomes," J Cell Biol 218, 2600-2618 (2019).
Xu, B., Wang, H. and Feng, Z., "Assemblies of Peptides in Complex Environment and Their Applications," Angew Chem Int Ed Engl, (2019).
Xu, M., Ross, J. L., Valdez, L. and Sen, A., "Direct Single Molecule Imaging of Enhanced Enzyme Diffusion," Phys Rev Lett 123, 128101 128101 (2019).
Zuraw-Weston, S., Wood, D. A., Torres, I. K., Lee, Y., Wang, L. S., Jiang, Z., Lazaro, G. R., Wang, S., Rodal, A. A., Hagan, M. F., Rotello, V. M. and Dinsmore, A. D., "Nanoparticles binding to lipid membranes: from vesicle-based gels to vesicle tubulation and destruction," Nanoscale 11, 18464-18474 (2019).
2018
Farhadi, L., Do Rosario, C. F., Debold, E. P., Baskaran, A. and Ross, J. L., "Active Self-Organization of Actin-Microtubule Composite Self-Propelled Rods," Front Phys 6, (2018).
Feng, Z., Wang, H. and Xu, B., "Instructed Assembly of Peptides for Intracellular Enzyme Sequestration," Journal of the American Chemical Society 140, 16433-16437 (2018).
Feng, Z., Wang, H., Wang, S., Zhang, Q., Zhang, X., Rodal, A. A. and Xu, B., "Enzymatic Assemblies Disrupt the Membrane and Target Endoplasmic Reticulum for Selective Cancer Cell Death," Journal of the American Chemical Society 140, 9566-9573 (2018).
Fily, Y., Kafri, Y., Solon, A. P., Tailleur, J. and Turner, A., "Mechanical pressure and momentum conservation in dry active matter," J Phys a-Math Theor 51, 044003 (2018).
Garabedian, M. V., Stanishneva-Konovalova, T., Lou, C., Rands, T. J., Pollard, L. W., Sokolova, O. S. and Goode, B. L., "Integrated control of formin-mediated actin assembly by a stationary inhibitor and a mobile activator," J Cell Biol 217, 3512-3530 (2018).
Gaskins, D. K., Soohoo, J. S., Dolnik, M. and Epstein, I. R., "Birth and Death of Invading Standing Waves in the BZ-AOT Reaction-diffusion System," Isr J Chem 58, 776-780 (2018).
Gaskins, D. K., Soohoo, J. S., Epstein, I. R. and Dolnik, M., "Turing-Hopf front invasion: Rings and shells," Physical Review E 98, (2018).
Goode, B. L., Sweeney, M. O. and Eskin, J. A., "GMF as an Actin Network Remodeling Factor," Trends Cell Biol 28, 749-760 (2018).
Guillamat, P., Kos, Z., Hardouin, J., Ignes-Mullol, J., Ravnik, M. and Sagues, F., "Active nematic emulsions," Sci Adv 4, eaao1470 (2018).
Guo, S., Sokolova, O. S., Chung, J., Padrick, S., Gelles, J. and Goode, B. L., "Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF," Nature communications 9, 2895 (2018).
He, H., Wang, J., Wang, H., Zhou, N., Yang, D., Green, D. R. and Xu, B., "Enzymatic Cleavage of Branched Peptides for Targeting Mitochondria," Journal of the American Chemical Society 140, 1215-1218 (2018).
Hilton, D. M., Aguilar, R. M., Johnston, A. B. and Goode, B. L., "Species-Specific Functions of Twinfilin in Actin Filament Depolymerization," J Mol Biol 430, 3323-3336 (2018).
Johnston, A. B., Hilton, D. M., McConnell, P., Johnson, B., Harris, M. T., Simone, A., Amarasinghe, G. K., Cooper, J. A. and Goode, B. L., "A novel mode of capping protein-regulation by twinfilin," Elife 7, (2018).
Joshi, A., Putzig, E., Baskaran, A. and Hagan, M. F., "The interplay between activity and filament flexibility determines the emergent properties of active nematics," Soft Matter 15, 94-101 (2018).
Kotila, T., Kogan, K., Enkavi, G., Guo, S., Vattulainen, I., Goode, B. L. and Lappalainen, P., "Structural basis of actin monomer re-charging by cyclase-associated protein," Nature communications 9, 1892 (2018).
Lazaro, G. R., Dragnea, B. and Hagan, M. F., "Self-assembly of convex particles on spherocylindrical surfaces," Soft Matter 14, 5728-5740 (2018).
Lazaro, G. R., Mukhopadhyay, S. and Hagan, M. F., "Why Enveloped Viruses Need Cores-The Contribution of a Nucleocapsid Core to Viral Budding," Biophys J 114, 619-630 (2018).
Li, J., Bullara, D., Du, X., He, H., Sofou, S., Kevrekidis, I. G., Epstein, I. R. and Xu, B., "Kinetic Analysis of Nanostructures Formed by Enzyme-Instructed Intracellular Assemblies against Cancer Cells," ACS Nano, (2018).
Li, J., Du, X., Powell, D. J., Zhou, R., Shi, J., He, H., Feng, Z. and Xu, B., "Down-regulating Proteolysis to Enhance Anticancer Activity of Peptide Nanofibers," Chem Asian J 13, 3464-3468 (2018).
Li, J., Zhan, Z., Du, X., Wang, J., Hong, B. and Xu, B., "Selection of Secondary Structures of Heterotypic Supramolecular Peptide Assemblies by an Enzymatic Reaction," Angew Chem Int Ed Engl 57, 11716-11721 (2018).
Litschel, T., Norton, M. M., Tserunyan, V. and Fraden, S., "Engineering reaction-diffusion networks with properties of neural tissue," Lab Chip 18, 714-722 (2018).
Liu, S., Zheng, C., Ye, Z., Blanc, B., Zhi, X., Shi, L. and Zhang, Z., "Filamentous Viruses Grafted with Thermoresponsive Block Polymers: Liquid Crystal Behaviors of a Rodlike Colloidal Model with “True” Attractive Interactions," Macromolecules 51, 8013-8026 (2018).
McMullen, A., de Haan, H. W., Tang, J. X. and Stein, D., "Buckling Causes Nonlinear Dynamics of Filamentous Viruses Driven through Nanopores," Phys Rev Lett 120, 078101 (2018).
Memet, E., Hilitski, F., Morris, M. A., Schwenger, W. J., Dogic, Z. and Mahadevan, L., "Microtubules soften due to cross-sectional flattening," Elife 7, (2018).
Mohajerani, F. and Hagan, M. F., "The role of the encapsulated cargo in microcompartment assembly," PLoS Comput Biol 14, e1006351 (2018).
Norton, M. M., Baskaran, A., Opathalage, A., Langeslay, B., Fraden, S., Baskaran, A. and Hagan, M. F., "Insensitivity of active nematic liquid crystal dynamics to topological constraints," Phys Rev E 97, 012702 (2018).
Poitras, A. M., Knight, S. E., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "Addition of H2 Across a Cobalt-Phosphorus Bond," Angew Chem Int Ed Engl 57, 1497-1500 (2018).
Soni, H., Pelcovits, R. A. and Powers, T. R., "Enhancement of Microorganism Swimming Speed in Active Matter," Phys Rev Lett 121, 178002 (2018).
Thomas, C. M., Hatzis, G. P. and Pepi, M. J., "Examining the effects of variations in ligand framework and pnictogen substitution on the geometry and electronic structure of metal complexes of N-heterocyclic phosphido ligands incorporated into a diphosphine pincer ligand framework," Polyhedron 143, 215-222 (2018).
Wang, H., Feng, Z., Del Signore, S. J., Rodal, A. A. and Xu, B., "Active Probes for Imaging Membrane Dynamics of Live Cells with High Spatial and Temporal Resolution over Extended Time Scales and Areas," Journal of the American Chemical Society 140, 3505-3509 (2018).
Wang, H., Feng, Z., Qin, Y., Wang, J. and Xu, B., "Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin," Angew Chem Int Ed Engl 57, 4931-4935 (2018).
Wang, J. Q., Xiong, T. T., Zhou, J., He, H. J., Wu, D. D., Du, X. W., Li, X. Y. and Xu, B., "Enzymatic formation of curcumin in vitro and in vivo," Nano Res 11, 3453-3461 (2018).
Zeng, C., Rodriguez Lazaro, G., Tsvetkova, I. B., Hagan, M. F. and Dragnea, B., "Defects and Chirality in the Nanoparticle-Directed Assembly of Spherocylindrical Shells of Virus Coat Proteins," ACS Nano 12, 5323-5332 (2018).
Zhou, J., Du, X., Berciu, C., Del Signore, S. J., Chen, X., Yamagata, N., Rodal, A. A., Nicastro, D. and Xu, B., "Cellular Uptake of A Taurine-Modified, Ester Bond-Decorated D-Peptide Derivative via Dynamin-Based Endocytosis and Macropinocytosis," Mol Ther 26, 648-658 (2018).
Zhou, J., Du, X., Chen, X. and Xu, B., "Adaptive Multifunctional Supramolecular Assemblies of Glycopeptides Rapidly Enable Morphogenesis," Biochemistry 57, 4867-4879 (2018).
Zhou, J., Du, X., Chen, X., Wang, J., Zhou, N., Wu, D. and Xu, B., "Enzymatic Self-Assembly Confers Exceptionally Strong Synergism with NF-kappaB Targeting for Selective Necroptosis of Cancer Cells," Journal of the American Chemical Society 140, 2301-2308 (2018).
2017
Aghvami, S. A., Opathalage, A., Zhang, Z. K., Ludwig, M., Heymann, M., Norton, M., Wilkins, N. and Fraden, S., "Rapid prototyping of cyclic olefin copolymer (COC) microfluidic devices," Sensor Actuat B-Chem 247, 940-949 (2017).
Bai, C. and Herzfeld, J., "Special Pairs Are Decisive in the Autoionization and Recombination of Water," J Phys Chem B 121, 4213-4219 (2017).
Bezpalko, M. W., Poitras, A. M., Foxman, B. M. and Thomas, C. M., "Cobalt N-Heterocyclic Phosphenium Complexes Stabilized by a Chelating Framework: Synthesis and Redox Properties," Inorg Chem 56, 503-510 (2017).
Christie, I. K., Miller, P. and Van Hooser, S. D., "Cortical amplification models of experience-dependent development of selective columns and response sparsification," J Neurophysiol 118, 874-893 (2017).
Culcu, G., Iovan, D. A., Krogman, J. P., Wilding, M. J. T., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "Heterobimetallic Complexes Comprised of Nb and Fe: Isolation of a Coordinatively Unsaturated Nb(III)/Fe(0) Bimetallic Complex Featuring a Nb identical withFe Triple Bond," Journal of the American Chemical Society 139, 9627-9636 (2017).
Du, X., Zhou, J., Li, X. and Xu, B., "Self-assembly of nucleopeptides to interact with DNAs," Interface Focus 7, 20160116 (2017).
Du, X., Zhou, J., Wang, H., Shi, J., Kuang, Y., Zeng, W., Yang, Z. and Xu, B., "In situ generated D-peptidic nanofibrils as multifaceted apoptotic inducers to target cancer cells," Cell Death Dis 8, e2614 (2017).
Du, X., Zhou, J., Wang, J., Zhou, R. and Xu, B., "Chirality Controls Reaction-Diffusion of Nanoparticles for Inhibiting Cancer Cells," Chemnanomat 3, 17-21 (2017).
Ellis, P. W., Pearce, D. J. G., Chang, Y.-W., Goldsztein, G., Giomi, L. and Fernandez-Nieves, A., "Curvature-induced defect unbinding and dynamics in active nematic toroids," Nature Physics 14, 85-90 (2017).
Feng, Z., Wang, H., Chen, X. and Xu, B., "Self-Assembling Ability Determines the Activity of Enzyme-Instructed Self-Assembly for Inhibiting Cancer Cells," Journal of the American Chemical Society 139, 15377-15384 (2017).
Feng, Z., Wang, H., Zhou, R., Li, J. and Xu, B., "Enzyme-Instructed Assembly and Disassembly Processes for Targeting Downregulation in Cancer Cells," Journal of the American Chemical Society 139, 3950-3953 (2017).
Feng, Z., Zhang, T., Wang, H. and Xu, B., "Supramolecular catalysis and dynamic assemblies for medicine," Chem Soc Rev 46, 6470-6479 (2017).
Fily, Y., Baskaran, A. and Hagan, M. F., "Equilibrium mappings in polar-isotropic confined active particles," Eur Phys J E Soft Matter 40, 61 (2017).
Gibaud, T., Kaplan, C. N., Sharma, P., Zakhary, M. J., Ward, A., Oldenbourg, R., Meyer, R. B., Kamien, R. D., Powers, T. R. and Dogic, Z., "Achiral symmetry breaking and positive Gaussian modulus lead to scalloped colloidal membranes," Proc Natl Acad Sci U S A 114, E3376-E3384 (2017).
Girabawe, C. and Fraden, S., "An image-driven drop-on-demand system," Sensor Actuat B-Chem 238, 532-539 (2017).
Guillamat, P., Hardouin, J., Prat, B. M., Ignes-Mullol, J. and Sagues, F., "Control of active turbulence through addressable soft interfaces," Journal of physics. Condensed matter : an Institute of Physics journal 29, 504003 (2017).
Guillamat, P., Ignes-Mullol, J. and Sagues, F., "Taming active turbulence with patterned soft interfaces," Nature communications 8, 564 (2017).
Hancock, B. and Baskaran, A., "Statistical mechanics and hydrodynamics of self-propelled hard spheres," J Stat Mech-Theory E, (2017).
Jia, L. L., Zakhary, M. J., Dogic, Z., Pelcovits, R. A. and Powers, T. R., "Chiral edge fluctuations of colloidal membranes," Phys Rev E 95, 060701 (2017).
Li, J., Du, X., Hashim, S., Shy, A. and Xu, B., "Aromatic-Aromatic Interactions Enable alpha-Helix to beta-Sheet Transition of Peptides to Form Supramolecular Hydrogels," Journal of the American Chemical Society 139, 71-74 (2017).
Liu, K. K., Hagan, M. F. and Lisman, J. E., "Gradation (approx. 10 size states) of synaptic strength by quantal addition of structural modules," Philos Trans R Soc Lond B Biol Sci 372, (2017).
Louzon, D., Ginsburg, A., Schwenger, W., Dvir, T., Dogic, Z. and Raviv, U., "Structure and Intermolecular Interactions between L-Type Straight Flagellar Filaments," Biophys J 112, 2184-2195 (2017).
McMullen, A. J., Tang, J. X. and Stein, D., "Nanopore Measurements of Filamentous Viruses Reveal a Sub-nanometer-Scale Stagnant Fluid Layer," ACS Nano 11, 11669-11677 (2017).
Mohapatra, L., Lagny, T. J., Harbage, D., Jelenkovic, P. R. and Kondev, J., "The Limiting-Pool Mechanism Fails to Control the Size of Multiple Organelles," Cell Syst 4, 559-567 e514 (2017).
Needleman, D. and Dogic, Z., "Active matter at the interface between materials science and cell biology," Nat Rev Mater 2, 17048 (2017).
Pettenuzzo, D. and Timmermann, A., "Forecasting Macroeconomic Variables Under Model Instability," J Bus Econ Stat 35, 183-201 (2017).
Reiner, B. R., Foxman, B. M. and Wade, C. R., "Electrochemical and structural investigation of the interactions between naphthalene diimides and metal cations," Dalton Trans 46, 9472-9480 (2017).
Sakhardande, R., Stanojeviea, S., Baskaran, A., Baskaran, A., Hagan, M. F. and Chakraborty, B., "Theory of microphase separation in bidisperse chiral membranes," Phys Rev E 96, 012704 (2017).
Siavashpouri, M., Wachauf, C. H., Zakhary, M. J., Praetorius, F., Dietz, H. and Dogic, Z., "Molecular engineering of chiral colloidal liquid crystals using DNA origami," Nat Mater 16, 849-856 (2017).
Tietz, D. R., Podust, L. M., Sherman, D. H. and Pochapsky, T. C., "Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG," Biochemistry 56, 2701-2714 (2017).
Wagner, C. G., Hagan, M. F. and Baskaran, A., "Steady-state distributions of ideal active Brownian particles under confinement and forcing," J Stat Mech-Theory E 2017, 043203 (2017).
Walsh, L., Wagner, C. G., Schlossberg, S., Olson, C., Baskaran, A. and Menon, N., "Noise and diffusion of a vibrated self-propelled granular particle," Soft Matter 13, 8964-8968 (2017).
Wang, H., Feng, Z. and Xu, B., "Bioinspired assembly of small molecules in cell milieu," Chem Soc Rev 46, 2421-2436 (2017).
Wang, H., Feng, Z., Lu, A., Jiang, Y., Wu, H. and Xu, B., "Instant Hydrogelation Inspired by Inflammasomes," Angew Chem Int Ed Engl 56, 7579-7583 (2017).
Wang, H., Shi, J., Feng, Z., Zhou, R., Wang, S., Rodal, A. A. and Xu, B., "An in situ Dynamic Continuum of Supramolecular Phosphoglycopeptides Enables Formation of 3D Cell Spheroids," Angew Chem Int Ed Engl 56, 16297-16301 (2017).
Wu, G., Cho, H., Wood, D. A., Dinsmore, A. D. and Yang, S., "Confined Assemblies of Colloidal Particles with Soft Repulsive Interactions," Journal of the American Chemical Society 139, 5095-5101 (2017).
Wu, K. T., Hishamunda, J. B., Chen, D. T., DeCamp, S. J., Chang, Y. W., Fernandez-Nieves, A., Fraden, S. and Dogic, Z., "Transition from turbulent to coherent flows in confined three-dimensional active fluids," Science 355, (2017).
Yamagata, N., Chen, X., Zhou, J., Li, J., Du, X. and Xu, B., "Enzymatic self-assembly of an immunoreceptor tyrosine-based inhibitory motif (ITIM)," Org Biomol Chem 15, 5689-5692 (2017).
Zhang, H., Wu, B., Marquard, S. L., Litle, E. D., Dickie, D. A., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "Investigation of Ketone C═O Bond Activation Processes by Heterobimetallic Zr/Co and Ti/Co Tris(phosphinoamide) Complexes," Organometallics 36, 3498-3507 (2017).
Zhou, J., Du, X., Wang, J., Yamagata, N. and Xu, B., "Enzyme-Instructed Self-Assembly of Peptides Containing Phosphoserine to Form Supramolecular Hydrogels as Potential Soft Biomaterials," Front Chem Sci Eng 11, 509-515 (2017).
Zhou, J., Li, J., Du, X. and Xu, B., "Supramolecular biofunctional materials," Biomaterials 129, 1-27 (2017).
Zhou, N., Cao, X., Du, X., Wang, H., Wang, M., Liu, S., Nguyen, K., Schmidt-Rohr, K., Xu, Q., Liang, G. and Xu, B., "Hyper-Crosslinkers Lead to Temperature- and pH-Responsive Polymeric Nanogels with Unusual Volume Change," Angew Chem Int Ed Engl 56, 2623-2627 (2017).
Zhou, N., Cao, Z. and Xu, B., "Functional Hyper-Crosslinkers," Chemistry 23, 15844-15851 (2017).
2016
Bai, C. and Herzfeld, J., "Surface Propensities of the Self-Ions of Water," ACS Cent Sci 2, 225-231 (2016).
Bei, Y. and Hong, P., "Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes," BMC Bioinformatics 17, 541 (2016).
Cannon, J. and Miller, P., "Synaptic and intrinsic homeostasis cooperate to optimize single neuron response properties and tune integrator circuits," J Neurophysiol 116, 2004-2022 (2016).
Dogic, Z., "Filamentous Phages As a Model System in Soft Matter Physics," Front Microbiol 7, 1013 (2016).
Ekesan, S., Lin, D. Y. and Herzfeld, J., "Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons," J Phys Chem B 120, 6264-6269 (2016).
Evers-McGregor, D. A., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "N-heterocyclic phosphenium and phosphido nickel complexes supported by a pincer ligand framework," Dalton Trans 45, 1918-1929 (2016).
Gaskins, D. K., Pruc, E. E., Epstein, I. R. and Dolnik, M., "Multifold Increases in Turing Pattern Wavelength in the Chlorine Dioxide-Iodine-Malonic Acid Reaction-Diffusion System," Phys Rev Lett 117, 056001 (2016).
Guillamat, P., Ignes-Mullol, J., Shankar, S., Marchetti, M. C. and Sagues, F., "Probing the shear viscosity of an active nematic film," Phys Rev E 94, 060602 (2016).
Haburcak, R., Shi, J., Du, X., Yuan, D. and Xu, B., "Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules," Journal of the American Chemical Society 138, 15397-15404 (2016).
Hagan, M. F. and Baskaran, A., "Emergent self-organization in active materials," Curr Opin Cell Biol 38, 74-80 (2016).
Hagan, M. F. and Zandi, R., "Recent advances in coarse-grained modeling of virus assembly," Curr Opin Virol 18, 36-43 (2016).
Harbage, D. and Kondev, J., "Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits," J Phys Chem B 120, 6225-6230 (2016).
Henkes, S., Quint, D. A., Fily, Y. and Schwarz, J. M., "Rigid Cluster Decomposition Reveals Criticality in Frictional Jamming," Phys Rev Lett 116, 028301 (2016).
Henty-Ridilla, J. L., Rankova, A., Eskin, J. A., Kenny, K. and Goode, B. L., "Accelerated actin filament polymerization from microtubule plus ends," Science 352, 1004-1009 (2016).
Kang, L., Gibaud, T., Dogic, Z. and Lubensky, T. C., "Entropic forces stabilize diverse emergent structures in colloidal membranes," Soft Matter 12, 386-401 (2016).
Lazaro, G. R. and Hagan, M. F., "Allosteric Control of Icosahedral Capsid Assembly," J Phys Chem B 120, 6306-6318 (2016).
Marchetti, M. C., Fily, Y., Henkes, S., Patch, A. and Yllanes, D., "Minimal model of active colloids highlights the role of mechanical interactions in controlling the emergent behavior of active matter," Curr Opin Colloid In 21, 34-43 (2016).
Mohapatra, L., Goode, B. L., Jelenkovic, P., Phillips, R. and Kondev, J., "Design Principles of Length Control of Cytoskeletal Structures," Annu Rev Biophys 45, 85-116 (2016).
Perkett, M. R., Mirijanian, D. T. and Hagan, M. F., "The allosteric switching mechanism in bacteriophage MS2," J Chem Phys 145, 035101 (2016).
Perlmutter, J. D., Mohajerani, F. and Hagan, M. F., "Many-molecule encapsulation by an icosahedral shell," Elife 5, (2016).
Putzig, E., Redner, G. S., Baskaran, A. and Baskaran, A., "Instabilities, defects, and defect ordering in an overdamped active nematic," Soft Matter 12, 3854-3859 (2016).
Redner, G. S., Wagner, C. G., Baskaran, A. and Hagan, M. F., "Classical Nucleation Theory Description of Active Colloid Assembly," Phys Rev Lett 117, 148002 (2016).
Sadacca, B. F., Mukherjee, N., Vladusich, T., Li, J. X., Katz, D. B. and Miller, P., "The Behavioral Relevance of Cortical Neural Ensemble Responses Emerges Suddenly," J Neurosci 36, 655-669 (2016).
Soni, H., Pelcovits, R. A. and Powers, T. R., "Wrinkling of a thin film on a nematic liquid-crystal elastomer," Phys Rev E 94, 012701 (2016).
Stanishneva-Konovalova, T. B., Kelley, C. F., Eskin, T. L., Messelaar, E. M., Wasserman, S. A., Sokolova, O. S. and Rodal, A. A., "Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck," Proc Natl Acad Sci U S A 113, E5552-5561 (2016).
Tompkins, N. and Fraden, S., "An inexpensive programmable illumination microscope with active feedback," Am J Phys 84, 150-158 (2016).
Wang, A. L., Gold, J. M., Tompkins, N., Heymann, M., Harrington, K. I. and Fraden, S., "Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets," Eur Phys J-Spec Top 225, 211-227 (2016).
Wang, H., Feng, Z., Wang, Y., Zhou, R., Yang, Z. and Xu, B., "Integrating Enzymatic Self-Assembly and Mitochondria Targeting for Selectively Killing Cancer Cells without Acquired Drug Resistance," Journal of the American Chemical Society 138, 16046-16055 (2016).
Wu, B., Wilding, M. J., Kuppuswamy, S., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "Exploring Trends in Metal-Metal Bonding, Spectroscopic Properties, and Conformational Flexibility in a Series of Heterobimetallic Ti/M and V/M Complexes (M = Fe, Co, Ni, and Cu)," Inorg Chem 55, 12137-12148 (2016).
Xie, S., Hagan, M. F. and Pelcovits, R. A., "Interaction of chiral rafts in self-assembled colloidal membranes," Phys Rev E 93, 032706 (2016).
Xie, S., Pelcovits, R. A. and Hagan, M. F., "Probing a self-assembled fd virus membrane with a microtubule," Phys Rev E 93, 062608 (2016).
Yu, N., Ghosh, A. and Hagan, M. F., "Faceted particles formed by the frustrated packing of anisotropic colloids on curved surfaces," Soft Matter 12, 8990-8998 (2016).
Zhou, J., Du, X., Berciu, C., He, H., Shi, J., Nicastro, D. and Xu, B., "Enzyme-Instructed Self-Assembly for Spatiotemporal Profiling of the Activities of Alkaline Phosphatases on Live Cells," Chem 1, 246-263 (2016).
Zhou, J., Du, X., Yamagata, N. and Xu, B., "Enzyme-Instructed Self-Assembly of Small D-Peptides as a Multiple-Step Process for Selectively Killing Cancer Cells," Journal of the American Chemical Society 138, 3813-3823 (2016).
Zhou, R., Kuang, Y., Zhou, J., Du, X., Li, J., Shi, J., Haburcak, R. and Xu, B., "Nanonets Collect Cancer Secretome from Pericellular Space," PLoS One 11, e0154126 (2016).
2015
Bertin, E., Baskaran, A., Chate, H. and Marchetti, M. C., "Comparison between Smoluchowski and Boltzmann approaches for self-propelled rods," Physical review. E, Statistical, nonlinear, and soft matter physics 92, 042141 (2015).
Chen, D. T., Heymann, M., Fraden, S., Nicastro, D. and Dogic, Z., "ATP Consumption of Eukaryotic Flagella Measured at a Single-Cell Level," Biophys J 109, 2562-2573 (2015).
DeCamp, S. J., Redner, G. S., Baskaran, A., Hagan, M. F. and Dogic, Z., "Orientational order of motile defects in active nematics," Nat Mater 14, 1110-1115 (2015).
Du, X., Zhou, J. and Xu, B., "Ectoenzyme switches the surface of magnetic nanoparticles for selective binding of cancer cells," Journal of colloid and interface science 447, 273-277 (2015).
Du, X., Zhou, J., Shi, J. and Xu, B., "Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials," Chem Rev 115, 13165-13307 (2015).
Feld, G. K., Heymann, M., Benner, W. H., Pardini, T., Tsai, C. J., Boutet, S., Coleman, M. A., Hunter, M. S., Li, X. D., Messerschmidt, M., Opathalage, A., Pedrini, B., Williams, G. J., Krantz, B. A., Fraden, S., Hau-Riege, S., Evans, J. E., Segelke, B. W. and Frank, M., "Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography," J Appl Crystallogr 48, 1072-1079 (2015).
Fily, Y., Baskaran, A. and Hagan, M. F., "Dynamics and density distribution of strongly confined noninteracting nonaligning self-propelled particles in a nonconvex boundary," Physical review. E, Statistical, nonlinear, and soft matter physics 91, 012125 (2015).
Goldstein, D., Giver, M. and Chakraborty, B., "Synchronization patterns in geometrically frustrated rings of relaxation oscillators," Chaos 25, 123109 (2015).
Hancock, B. and Baskaran, A., "Effect of reorientation statistics on torque response of self-propelled particles," Physical review. E, Statistical, nonlinear, and soft matter physics 92, 052143 (2015).
Hilitski, F., Ward, A. R., Cajamarca, L., Hagan, M. F., Grason, G. M. and Dogic, Z., "Measuring cohesion between macromolecular filaments one pair at a time: depletion-induced microtubule bundling," Phys Rev Lett 114, 138102 (2015).
Horvath, V., Kutner, D. J., Chavis, J. T., 3rd and Epstein, I. R., "Pulse-coupled BZ oscillators with unequal coupling strengths," Phys Chem Chem Phys 17, 4664-4676 (2015).
Jansen, S., Collins, A., Chin, S. M., Ydenberg, C. A., Gelles, J. and Goode, B. L., "Single-molecule imaging of a three-component ordered actin disassembly mechanism," Nature communications 6, 7202 (2015).
Johnston, A. B., Collins, A. and Goode, B. L., "High-speed depolymerization at actin filament ends jointly catalysed by Twinfilin and Srv2/CAP," Nat Cell Biol 17, 1504-1511 (2015).
Kelley, C. F., Messelaar, E. M., Eskin, T. L., Wang, S., Song, K., Vishnia, K., Becalska, A. N., Shupliakov, O., Hagan, M. F., Danino, D., Sokolova, O. S., Nicastro, D. and Rodal, A. A., "Membrane Charge Directs the Outcome of F-BAR Domain Lipid Binding and Autoregulation," Cell Rep 13, 2597-2609 (2015).
Kerns, S. J., Agafonov, R. V., Cho, Y. J., Pontiggia, F., Otten, R., Pachov, D. V., Kutter, S., Phung, L. A., Murphy, P. N., Thai, V., Alber, T., Hagan, M. F. and Kern, D., "The energy landscape of adenylate kinase during catalysis," Nature structural & molecular biology 22, 124-131 (2015).
Kuppuswamy, S., Cass, T. R., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "Synthesis and investigation of the metal-metal interactions in heterobimetallic Cr/Rh and Cr/Ir complexes," Inorg Chim Acta 424, 167-172 (2015).
Li, N., Tompkins, N., Gonzalez-Ochoa, H. and Fraden, S., "Tunable diffusive lateral inhibition in chemical cells," Eur Phys J E Soft Matter 38, 18 (2015).
Mohapatra, L., Goode, B. L. and Kondev, J., "Antenna Mechanism of Length Control of Actin Cables," PLoS Comput Biol 11, e1004160 (2015).
Perlmutter, J. D. and Hagan, M. F., "Mechanisms of virus assembly," Annual review of physical chemistry 66, 217-239 (2015).
Perlmutter, J. D. and Hagan, M. F., "The Role of Packaging Sites in Efficient and Specific Virus Assembly," J Mol Biol 427, 2451-2467 (2015).
Pontiggia, F., Pachov, D. V., Clarkson, M. W., Villali, J., Hagan, M. F., Pande, V. S. and Kern, D., "Free energy landscape of activation in a signalling protein at atomic resolution," Nature communications 6, 7284 (2015).
Ruiz-Herrero, T. and Hagan, M. F., "Simulations show that virus assembly and budding are facilitated by membrane microdomains," Biophys J 108, 585-595 (2015).
Shi, J., Du, X., Huang, Y., Zhou, J., Yuan, D., Wu, D., Zhang, Y., Haburcak, R., Epstein, I. R. and Xu, B., "Ligand-receptor interaction catalyzes the aggregation of small molecules to induce cell necroptosis," Journal of the American Chemical Society 137, 26-29 (2015).
Shi, J., Du, X., Yuan, D., Haburcak, R., Wu, D., Zhou, N. and Xu, B., "Enzyme transformation to modulate the ligand-receptor interactions between small molecules," Chemical communications 51, 4899-4901 (2015).
Solon, A. P., Fily, Y., Baskaran, A., Cates, M. E., Kafri, Y., Kardar, M. and Tailleur, J., "Pressure is not a state function for generic active fluids," Nature Physics 11, 673-678 (2015).
Sountsov, P. and Miller, P., "Spiking neuron network Helmholtz machine," Front Comput Neurosci 9, 46 (2015).
Tompkins, N., Cambria, M. C., Wang, A. L., Heymann, M. and Fraden, S., "Creation and perturbation of planar networks of chemical oscillators," Chaos 25, 064611 (2015).
Unwin, R. R., Cabanas, R. A., Yanagishima, T., Blower, T. R., Takahashi, H., Salmond, G. P., Edwardson, J. M., Fraden, S. and Eiser, E., "DNA driven self-assembly of micron-sized rods using DNA-grafted bacteriophage fd virions," Phys Chem Chem Phys 17, 8194-8202 (2015).
Ward, A., Hilitski, F., Schwenger, W., Welch, D., Lau, A. W., Vitelli, V., Mahadevan, L. and Dogic, Z., "Solid friction between soft filaments," Nat Mater 14, 583-588 (2015).
Welch, D., Lettinga, M. P., Ripoll, M., Dogic, Z. and Vliegenthart, G. A., "Trains, tails and loops of partially adsorbed semi-flexible filaments," Soft Matter 11, 7507-7514 (2015).
Wu, B., Bezpalko, M. W., Foxman, B. M. and Thomas, C. M., "A heterobimetallic complex featuring a Ti-Co multiple bond and its application to the reductive coupling of ketones to alkenes," Chem Sci 6, 2044-2049 (2015).
Yuan, D., Shi, J., Du, X., Zhou, N. and Xu, B., "Supramolecular Glycosylation Accelerates Proteolytic Degradation of Peptide Nanofibrils," Journal of the American Chemical Society 137, 10092-10095 (2015).
Zhang, Y., Zhou, N., Shi, J., Pochapsky, S. S., Pochapsky, T. C., Zhang, B., Zhang, X. and Xu, B., "Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures," Nature communications 6, 6165 (2015).
Zhou, J., Du, X. and Xu, B., "Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology," Prion 9, 110-118 (2015).
2014
Akella, S. V., Mowitz, A., Heymann, M. and Fraden, S., "Emulsion-Based Technique To Measure Protein Crystal Nucleation Rates of Lysozyme," Cryst Growth Des 14, 4487-4509 (2014).
Du, X., Zhou, J. and Xu, B., "Supramolecular hydrogels made of basic biological building blocks," Chem Asian J 9, 1446-1472 (2014).
Du, X., Zhou, J., Wu, L., Sun, S. and Xu, B., "Enzymatic transformation of phosphate decorated magnetic nanoparticles for selectively sorting and inhibiting cancer cells," Bioconjug Chem 25, 2129-2133 (2014).
Epstein, I. R., "Coupled chemical oscillators and emergent system properties," Chemical communications 50, 10758-10767 (2014).
Fily, Y., Baskaran, A. and Hagan, M. F., "Dynamics of self-propelled particles under strong confinement," Soft Matter 10, 5609-5617 (2014).
Graziano, B. R., Yu, H. Y., Alioto, S. L., Eskin, J. A., Ydenberg, C. A., Waterman, D. P., Garabedian, M. and Goode, B. L., "The F-BAR protein Hof1 tunes formin activity to sculpt actin cables during polarized growth," Molecular biology of the cell 25, 1730-1743 (2014).
Henkin, G., DeCamp, S. J., Chen, D. T., Sanchez, T. and Dogic, Z., "Tunable dynamics of microtubule-based active isotropic gels," Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 372, (2014).
Heymann, M., Fraden, S. and Kim, D., "Multi-Height Precision Alignment With Selectively Developed Alignment Marks," J Microelectromech S 23, 424-437 (2014).
Heymann, M., Opthalage, A., Wierman, J. L., Akella, S., Szebenyi, D. M., Gruner, S. M. and Fraden, S., "Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction," IUCrJ 1, 349-360 (2014).
Keber, F. C., Loiseau, E., Sanchez, T., DeCamp, S. J., Giomi, L., Bowick, M. J., Marchetti, M. C., Dogic, Z. and Bausch, A. R., "Topology and dynamics of active nematic vesicles," Science 345, 1135-1139 (2014).
Kornreich, M., Heymann, M., Fraden, S. and Beck, R., "Cross polarization compatible dialysis chip," Lab Chip 14, 3700-3704 (2014).
Kuang, Y., Du, X., Zhou, J. and Xu, B., "Supramolecular nanofibrils inhibit cancer progression in vitro and in vivo," Advanced healthcare materials 3, 1217-1221 (2014).
McMullen, A., de Haan, H. W., Tang, J. X. and Stein, D., "Stiff filamentous virus translocations through solid-state nanopores," Nature communications 5, 4171 (2014).
Paramanathan, T., Reeves, D., Friedman, L. J., Kondev, J. and Gelles, J., "A general mechanism for competitor-induced dissociation of molecular complexes," Nature communications 5, 5207 (2014).
Perkett, M. R. and Hagan, M. F., "Using Markov state models to study self-assembly," J Chem Phys 140, 214101 (2014).
Perlmutter, J. D., Perkett, M. R. and Hagan, M. F., "Pathways for virus assembly around nucleic acids," J Mol Biol 426, 3148-3165 (2014).
Putzig, E. and Baskaran, A., "Phase separation and emergent structures in an active nematic fluid," Physical review. E, Statistical, nonlinear, and soft matter physics 90, 042304 (2014).
Sharma, P., Ward, A., Gibaud, T., Hagan, M. F. and Dogic, Z., "Hierarchical organization of chiral rafts in colloidal membranes," Nature 513, 77-80 (2014).
Smith, B. A., Gelles, J. and Goode, B. L., "Single-molecule studies of actin assembly and disassembly factors," Methods in enzymology 540, 95-117 (2014).
Vanag, V. K. and Epstein, I. R., in Engineering of Chemical Complexity II, chap: Dissipative Bz Patterns in Systems of Coupled Nano- and Microdroplets, (WORLD SCIENTIFIC, 2014), pp. 169-183, https://www.worldscientific.com/doi/abs/10.1142/9789814616133_0010.
Zhang, Y., Zhou, N., Li, N., Sun, M., Kim, D., Fraden, S., Epstein, I. R. and Xu, B., "Giant volume change of active gels under continuous flow," Journal of the American Chemical Society 136, 7341-7347 (2014).
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