MRSEC Publications

        Redner, G. S., Baskaran, A. and Hagan, M. F., "Reentrant phase behavior in active colloids with attraction," Physical Review E 88, 012305 (2013). 10.1103/PhysRevE.88.012305

        Zhang, Y., Zhou, N., Akella, S., Kuang Y., Kim, D. S., Schwartz, A., Bezpalko, M., Foxman, B. M., Fraden, S., Epstein, I. R., Xu, B., "Active Hyper Cross-linkers Confer Active Gels," Angew. Chem. Int. Ed. 52, 1-6 (2013). 10.1002/anie.201304437

        Redner, G. S., Hagan,  M.F. and Baskaran, A., "Structure and Dynamics of a Phase-Separating Active Colloidal Fluid,"  Physical Review Letters 110, 055701(2013).  10.1103/PhysRevLett.110.055701

       Zhang, Y., Zhang, B., Kuang, Y., Gao, Y., Shi, J., Zhang, X. X. and Xu, B., "A Redox Responsive, Fluorescent Supramolecular Metallohydrogel Consists of Nanofibers with Single-Molecule Width,"  J. Am. Chem. Soc.  135, 5008-5011 (2013). 10.1021/ja402490j 

      Sanders, H., Berends, M., Major, G., Goldman, M. and Lisman, J., "NMDA and GABAB (KIR) conductances: the "perfect couple" for bistability,"  The Journal of neuroscience  33, 424-429 (2013). 10.1523/JNEUROSCI.1854-12.2013

        Lu, X., Ren, L., Gao, Q., Zhao, Y., Wang, S., Yang, J. and Epstein, I. R., "Photophobic and phototropic movement of a self-oscillating gel,"  Chem. Commun. 49, 7690-7692 (2013). 10.1039/c3cc44480e

       Giver, M. C. and Chakraborty, B., "Effects of intrinsic fluctuations in a prototypical chemical oscillator: metastability and switching," http://arxiv.org/abs/1303.3048v1 (2013). arXiv:1303.3048 

      Chelakkot, R., Gopinath,  A.,  Mahadevan, L., and Hagan, M.F., "Flagellar dynamics of a connected chain of active, Brownian particles," (2013). arXiv:1211.5123

       Carbajal Gonzalez, B., Heuser, T., Fu, X., Lin, J., Smith, B., Mitchell, D. and Nicastro, D., "Conserved structural motifs in the central pair complex of eukaryotic flagella,"  Cytoskeleton  70, 101-120 (2013). 10.1002/cm.21094

      Zhang, Y., Li, N., Delgado, J., Zhou, N., Yoshida, R., Fraden, S., Epstein, I. R. and Xu, B., "Structural modulation of self-oscillating gels: Changing the proximity of the catalyst to the polymer backbone to tailor chemomechanical oscillation,"  Soft Matter  8, 7056-7061 (2012). 10.1039/c2sm25797a

     Zhang, Y., Li, N., Delgado, J., Gao, Y., Kuang, Y., Fraden, S., Epstein, I. R. and Xu, B., "Post-Self-Assembly Cross-Linking of Molecular Nanofibers for Oscillatory Hydrogels,"  Langmuir  28, 3063-3066 (2012). 10.1021/la203923d

     Yu, N. and Hagan, M., "Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association,"  Biophysical journal  103, 1363-1369 (2012). 10.1016/j.bpj.2012.08.016

     Yang, Y., Barry, E., Dogic, Z. and Hagan, M. F., "Self-assembly of 2D membranes from mixtures of hard rods and depleting polymers,"  Soft Matter  8, 707-714 (2012). 10.1039/c1sm06201h

      Sanchez, T. and Dogic, Z., "Engineering actively beating microtubule bundles,"  Methods in Enzymology  524, 205-223 (2012). 10.1016/B978-0-12-397945-2.00012-3

      Sanchez, T., Chen, D., DeCamp, S., Heymann, M. and Dogic, Z., "Spontaneous Motion in Hierarchically assembled active matter,"  Nature  491, 340-341 (2012). 10.1038/nature11591

       Ruiz Herrero, T., Velasco, E. and Hagan, M., "Mechanisms of budding of nanoscale particles through lipid bilayers,"  The Journal of Physical Chemistry B  116, 9595-9603 (2012). 10.1021/jp301601g       

      Ni, P., Wang, Z., Ma, X., Das, N., Sokol, P., Chiu, W., Dragnea, B., Hagan, M. and Kao, C. C., "An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs,"  Journal of Molecular Biology  419, 284-300 (2012). 10.1016/j.jmb.2012.03.023

     McCandlish, S. R., Baskaran, A. and Hagan, M. F., "Spontaneous segregation of self-propelled particles with different motilities,"  Soft Matter  8, 2527-2534 (2012). 10.1039/c2sm06960a 

       Lin, J., Heuser, T., Song, K., Fu, X., Nicastro, D. and Yang, Y., "One of the Nine Doublet Microtubules of Eukaryotic Flagella Exhibits Unique and Partially Conserved Structures,"  PLoS ONE  7, e46494 (2012). 10.1371/journal.pone.0046494

      Kale, S., Herzfeld, J., Dai, S. and Blank, M., "Lewis-inspired representation of dissociable water in clusters and Grotthuss chains,"  Journal of Biological Physics  38, 49-59 (2012). 10.1007/s10867-011-9229-5

        Kale, S. and Herzfeld, J., "Natural polarizability and flexibility via explicit valency: The case of water,"  Journal of Chemical Physics  136, 084109 (2012). 10.1063/1.3688228

     Horvath, V., Gentili, P., Vanag, V. and Epstein, I., "Pulse-coupled chemical oscillators with time delay,"  Angewandte Chemie (International ed.)  51, 6878-6881 (2012). 10.1002/anie.201201962

       Heuser, T., Dymek, E., Lin, J., Smith, E. and Nicastro, D., "The CSC connects three major axonemal complexes involved in dynein regulation,"  Molecular biology of the cell  23, 3143-3155 (2012). 10.1091/mbc.E12-05-0357 

        Heuser, T., Barber, C., Lin, J., Krell, J., Rebesco, M., Porter, M. and Nicastro, D., "Cryoelectron tomography reveals doublet-specific structures and unique interactions in the I1 dynein,"  PNAS USA 109, E2067-2076 (2012). 10.1073/pnas.1120690109 

      Gopinath, A., Hagan, M. F., Marchetti, M. C. and Baskaran, A., "Dynamical self-regulation in self-propelled particle flows,"  Physical Review E  85, 061903 (2012). 10.1103/PhysRevE.85.061903

       Giomi, L., Mahadevan, L., Chakraborty, B. and Hagan, M. F., "Banding, Excitability and Chaos in Active Nematic Suspensions,"  Nonlinearity  25, 2245–2269 (2012). 10.1088/0951-7715/25/8/2245

        Gibaud, T., Barry, E., Zakhary, M. J., Henglin, M., Ward, A., Yang, Y. S., Berciu, C., Oldenbourg, R., Hagan, M. F., Nicastro, D., Meyer, R. B. and Dogic, Z., "Reconfigurable self-assembly through chiral control of interfacial tension,"  Nature  481, 348-353 (2012). 10.1038/nature10769

        Gentili, P., Horvath, V., Vanag, V. and Epstein, I., "Belousov-Zhabotinsky "Chemical Neuron" as a Binary and Fuzzy Logic Processor,"  International Journal of Unconventional Computing  8, 177-192 (2012). ISSN: 1548-7199

      Garcia, Hernan G., Sanchez, A., Boedicker, James Q., Osborne, M., Gelles, J., Kondev, J. and Phillips, R., "Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria,"  Cell Reports  2, 150-161 (2012). 10.1016/j.celrep.2012.06.004

        Gao, Y., Shi, J. F., Yuan, D. and Xu, B., "Imaging enzyme-triggered self-assembly of small molecules inside live cells,"  Nat. Commun  3, 1033 (2012). 10.1038/ncomms2040

      Bourjaily, M. A. and Miller, P., "Dynamic afferent synapses to decision-making networks improve performance in tasks requiring stimulus associations and discriminations,"  Journal of Neurophysiology  108, 513-527 (2012). 10.1152/jn.00806.2011

        Baskaran, A. and Marchetti, M. C., "Self-regulation in Self-Propelled Nematic Fluids,"  European Physical Journal E  35, 1-8 (2012). 10.1140/epje/i2012-12095-8 

      Baskaran, A. and Dufty, J. W., "Kinetic theory of active and granular particles,"  Proceedings of RGD28, AIP Conference Proceedings 1501, 11 (2012). http://dx.doi.org/10.1063/1.4769462 

       Barber, C., Heuser, T., Carbajal-González, B., Botchkarev, V. J. and Nicastro, D., "Three-dimensional structure of the radial spokes reveals heterogeneity and interactions with dyneins in Chlamydomonas flagella,"  Mol. Biol. Cell  23, 111-120 (2012). 10.1091/mbc.E11-08-0692

        Asciutto, E., Young, M., Madura, J., Pochapsky, S. and Pochapsky, T., "Solution structural ensembles of substrate-free cytochrome P450(cam),"  Biochemistry  51, 3383-3393 (2012). 10.1021/bi300007r

        Zhou, W., Napoline, J. W. and Thomas, C. M., "A Catalytic Application of Co/Zr Heterobimetallic Complexes: Kumada Coupling of Unactivated Alkyl Halides with Alkyl Grignard Reagents,"  European Journal of Inorganic Chemistry  2011, 2029-2033 (2011). 10.1002/ejic.201100109 

       Zhang, Y., Kuang, Y., Gao, Y. A. and Xu, B., "Versatile Small-Molecule Motifs for Self-Assembly in Water and the Formation of Biofunctional Supramolecular Hydrogels,"  Langmuir  27, 529-537 (2011).  10.1021/la1020324

       Yang, Y. and Hagan, M. F., "Theoretical calculation of the phase behavior of colloidal membranes,"  Physical Review E  84, 051402 (2011). 10.1103/PhysRevE.84.051402

        Sumedha, S., Hagan, M. F. and Chakraborty, B., "Prolonging assembly through dissociation: A self-assembly paradigm in microtubules,"  Physical Review E  83, 051904 (2011). 10.1103/PhysRevE.83.051904 

        Setty, V. N., Zhou, W., Foxman, B. M. and Thomas, C. M., "Subtle Differences Between Zr and Hf in Early/Late Heterobimetallic Complexes with Cobalt,"  Inorganic Chemistry  50, 4647-4655 (2011). 10.1021/ic200445x 

        Sanchez, T., Welch, D., Nicastro, D. and Dogic, Z., "Cilia-Like Beating of Active Microtubule Bundles,"  Science  333, 456-459 (2011). 10.1126/science.1203963

       Rodal, A. A., Blunk, A. D., Akbergenova, Y., Jorquera, R. A., Buhl, L. K. and Littleton, J. T., "A presynaptic endosomal trafficking pathway controls synaptic growth signaling,"  Journal of Cell Biology  193, 201-217 (2011). 10.1083/jcb.201009052

        Reeves, D., Cheveralls, K. and Kondev, J., "Regulation of biochemical reaction rates by flexible tethers,"  Physical Review E  84, 021914 (2011).  10.1103/PhysRevE.84.021914

       Marder, E. and Taylor, A. L., "Multiple models to capture the variability in biological neurons and networks,"  Nature Neuroscience  14, 133-138 (2011). 10.1038/nn.2735  

       Kispersky, T. J., Economo, M. N., Randeria, P. and White, J. A., "GenNet: A Platform for Hybrid Network Experiments,"  Frontiers in neuroinformatics  5, 1-32 (2011). 10.3389/fninf.2011.00011

      Kispersky, T., Gutierrez, G. and Marder, E., "Functional connectivity in a rhythmic inhibitory circuit using Granger causality,"  Neural systems & circuits  1, 1-15 (2011). 10.1186/2042-1001-1-9

       Kale, S. and Herzfeld, J., "Pairwise Long-Range Compensation for Strongly Ionic Systems,"  Journal of Chemical Theory and Computation  7, 3620-3624 (2011). 10.1021/ct200392u

     Hagan, M. F., Elrad, O. M. and Jack, R. L., "Mechanisms of kinetic trapping in self-assembly and phase transformation,"  Journal of Chemical Physics  135, 104115 (2011). 10.1063/1.3635775

       Giver, M., Jabeen, Z. and Chakraborty, B., "Phase and frequency entrainment in locally coupled phase oscillators with repulsive interactions,"  Physical Review E  83, 046206 (2011). 10.1103/PhysRevE.83.046206

     Giomi, L., Mahadevan, L., Chakraborty, B. and Hagan, M. F., "Excitable Patterns in Active Nematics,"  Physical Review Letters  106, 218101 (2011). 10.1103/PhysRevLett.106.218101

     Di Michele, L., Yanagishima, T., Brewer, A. R., Kotar, J., Eiser, E. and Fraden, S., "Interactions between Colloids Induced by a Soft Cross-Linked Polymer Substrate,"  Physical Review Letters  107, 136101 (2011). 10.1103/PhysRevLett.107.136101

      Delgado, J., Zhang, Y., Xu, B. and Epstein, I. R., "Terpyridine- and Bipyridine-Based Ruthenium Complexes as Catalysts for the Belousov-Zhabotinsky Reaction,"  Journal of Physical Chemistry A  115, 2208-2215 (2011). 10.1021/jp111724t

      Delgado, J., Li, N., Leda, M., Gonzalez-Ochoa, H. O., Fraden, S. and Epstein, I. R., "Coupled oscillations in a 1D emulsion of Belousov-Zhabotinsky droplets,"  Soft Matter  7, 3155-3167 (2011). 10.1039/c0sm01240h

      Coic, E., Martin, J., Ryu, T., Tay, S. Y., Kondev, J. and Haber, J. E., "Dynamics of Homology Searching During Gene Conversion in Saccharomyces cerevisiae Revealed by Donor Competition,"  Genetics  189, 1225-1233 (2011). 10.1534/genetics.111.132738

       Bourjaily, M. A. and Miller, P., "Synaptic Plasticity and Connectivity Requirements to Produce Stimulus-Pair Specific Responses in Recurrent Networks of Spiking Neurons,"  Plos Computational Biology  7, e1001091 (2011). 10.1371/journal.pcbi.1001091

       Bourjaily, M. A. and Miller, P., "Excitatory, inhibitory, and structural plasticity produce correlated connectivity in random networks trained to solve paired-stimulus tasks,"  Frontiers in Computational Neuroscience  5, 1-45 (2011). 10.3389/fncom.2011.00037

     Bansagi, T., Vanag, V. K. and Epstein, I. R., "Tomography of Reaction-Diffusion Microemulsions Reveals Three-Dimensional Turing Patterns,"  Science  331, 1309-1312 (2011). 10.1126/science.1200815 

       Yang, Y., Meyer, R. B. and Hagan, M. F., "Self-Limited Self-Assembly of Chiral Filaments,"  Physical Review Letters  104, 258102 (2010). 10.1103/PhysRevLett.104.258102

     Wiggins, P. A., Cheveralls, K. C., Martin, J. S., Lintner, R. and Kondev, J., "Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament,"  Proceedings of the National Academy of Sciences of the United States of America  107, 4991-4995 (2010). 10.1073/pnas.0912062107

      Toiya, M., Gonzalez-Ochoa, H. O., Vanag, V. K., Fraden, S. and Epstein, I. R., "Synchronization of Chemical Micro-oscillators,"  Journal of Physical Chemistry Letters  1, 1241-1246 (2010). 10.1021/jz100238u

    Tang, L. S., Goeritz, M. L., Caplan, J. S., Taylor, A. L., Fisek, M. and Marder, E., "Precise Temperature Compensation of Phase in a Rhythmic Motor Pattern,"  Plos Biology  8, e1000469 (2010). 10.1371/journal.pbio.1000469

    Selimovic, Š., Gobeaux, F. and Fraden, S., "Mapping and manipulating temperature-concentration phase diagrams using microfluidics,"  Lab Chip  10, 1696-1699 (2010). 10.1039/b925661j

      Sanchez, T., Kulic, I. and Dogic, Z., "Circularization, Photomechanical Switching, and a Supercoiling Transition of Actin Filaments,"  Physical Review Letters  104, 098103 (2010). 10.1103/PhysRevLett.104.098103

      Miller, P. and Wingfield, A., "Distinct effects of perceptual quality on auditory word recognition, memory formation and recall in a neural model of sequential memory,"  Front Syst Neurosci  4, 4-14 (2010). 10.3389/fnsys.2010.00014

       Ma, M. L., Kuang, Y., Gao, Y., Zhang, Y., Gao, P. and Xu, B., "Aromatic-Aromatic Interactions Induce the Self-Assembly of Pentapeptidic Derivatives in Water To Form Nanofibers and Supramolecular Hydrogels,"  Journal of the American Chemical Society  132, 2719-2728 (2010). 10.1021/ja9088764

       Li, X. M., Gao, Y., Kuang, Y. and Xu, B., "Enzymatic formation of a photoresponsive supramolecular hydrogel,"  Chemical Communications  46, 5364-5366 (2010). 10.1039/c0cc00163e

        Kivenson, A. and Hagan, M. F., "Mechanisms of Capsid Assembly around a Polymer,"  Biophysical Journal  99, 619-628 (2010). 10.1016/j.bpj.2010.04.035

      Kaplan, C. N., Tu, H., Pelcovits, R. A. and Meyer, R. B., "Theory of depletion-induced phase transition from chiral smectic-A twisted ribbons to semi-infinite flat membranes,"  Physical Review E  82, 021701 (2010). 10.1103/PhysRevE.82.021701

       Hagan, M. F. and Elrad, O., "Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics—the Origin of the Lag Time and Identifying the Critical Nucleus Size,"  Biophysical Journal  98, 1065–1074 (2010). 10.1016/j.bpj.2009.11.023

      Grashow, R., Brookings, T. and Marder, E., "Compensation for Variable Intrinsic Neuronal Excitability by Circuit-Synaptic Interactions,"  Journal of Neuroscience  30, 9145-9156 (2010). 10.1523/JNEUROSCI.0980-10.2010

      Gao, Y., Zhao, F., Wang, L. Z., Y. and Xu, B., "Small Peptide Nanofibers as the Matrices of Molecular Hydrogels for Mimicking Enzymes and Enhancing the Activity of Enzymes,"  Chem. Soc. Rev. 39, 3425-3433 (2010). 10.1039/b919450a

     Elrad, O. M. and Hagan, M. F., "Encapsulation of a polymer by an icosahedral virus,"  Physical Biology  7, 1-17 (2010). 10.1088/1478-3975/7/4/045003

       Barry, E. and Dogic, Z., "Entropy driven self-assembly of nonamphiphilic colloidal membranes,"  Proceedings of the National Academy of Sciences of the United States of America  107, 10348-10353 (2010). 10.1073/pnas.1000406107

      Yang, Z. M., Ma, M. L. and Xu, B., "Using matrix metalloprotease-9 (MMP-9) to trigger supramolecular hydrogelation,"  Soft Matter  5, 2546-2548 (2009). 10.1039/b908206a

       Pelcovits, R. A. and Meyer, R. B., "Twist penetration in single-layer smectic A discs of colloidal virus particles,"  Liquid Crystals  36, 1157-1160 (2009). 10.1080/02678290902921752

       Liu, Y. and Chakraborty, B., "Segregation of Polymers in Confined Spaces,"  Physical Biology  9, 1-4 (2009). 10.1088/1478-3975/9/6/066005

        Lau, A. W. C., Prasad, A. and Dogic, Z., "Condensation of isolated semi-flexible filaments driven by depletion interactions,"  EPL  87, 48006 (2009). 10.1209/0295-5075/87/48006

       Huang, F., Rotstein, R., Fraden, S., Kasza, K. E. and Flynn, N. T., "Phase Behavior and Rheology of Attractive Rod Like Particles,"  Soft Matter  5, 2766-2771 (2009). 10.1039/b823522h

        Huang, F., Addas, K., Ward, A., Flynn, N. T., Velasco, E., Hagan, M. F., Dogic, Z. and Fraden, S., "Pair Potential of Charged Colloidal Stars,"  Physical Review Letters  102, 108302 (2009). 10.1103/PhysRevLett.102.108302

        Heuser, T., Raytchev, M., Krell, J., Porter, M. E. and Nicastro, D., "The dynein regulatory complex is the nexin link and a major regulatory node in cilia and flagella,"  Journal of Cell Biology  187, 921-933 (2009). 10.1083/jcb.200908067

     Hagan, M. F., "A theory for viral capsid assembly around electrostatic cores,"  Journal of Chemical Physics  130, 114902 (2009). 10.1063/1.3086041

       Gao, Y., Yang, Z. M., Kuang, Y., Ma, M. L., Li, J. Y., Zhao, F. and Xu, B., "Enzyme-Instructed Self-Assembly of Peptide Derivatives to Form Nanofibers and Hydrogels,"  Biopolymers  94, 19-31 (2009). 10.1002/bip.21321

       Barry, E., Dogic, Z., Meyer, R. B., Pelcovits, R. A. and Oldenbourg, R., "Direct Measurement of the Twist Penetration Length in a Single Smectic A Layer of Colloidal Virus Particles,"  Journal of Physical Chemistry B  113, 3910-3913 (2009). 10.1021/jp8067377

        Barry, E., Beller, D. and Dogic, Z., "A model liquid crystalline system based on rodlike viruses with variable chirality and persistence length,"  Soft Matter  5, 2563-2570 (2009). 10.1039/b822478a

       Liu, Y. and Chakraborty, B., "Shapes of semiflexible polymers in confined spaces,"  Physical Biology  5, 026004 (2008). 10.1088/1478-3975/5/2/026004

        Elrad, O. M. and Hagan, M. F., "Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly,"  Nano Letters  8, 3850-3857 (2008). 10.1021/nl802269a