Publications

In all of your publications, please acknowledge MRSEC:

  • We acknowledge support from Brandeis NSF MRSEC, Bioinspired Soft Materials, DMR-1420382
  • We acknowledge support from the NSF MRSEC DMR-1420382


Center Investigator Publications  

Aghvami, SA, Opathalage, A, Zhang, ZK, Ludwig, M, Heymann, M, Norton, M, Wilkins, N, & Fraden, S. "Rapid Prototyping of Cyclic Olefin Copolymer (COC) Microfluidic Devices", Sensors and Actuators B: Chemical, 10.1016/j.snb.2017.03.023 (2017). doi: 10.1016/j.snb.2017.03.023

Zhou, J, Li, J, Du, X, & Xu, B. "Supramolecular biofunctional materials", Biomaterials, 129, 1-27 (2017). doi: 10.1016/j.biomaterials.2017.03.014

Louzon D, Ginsburg A, Schwenger W, Dvir T, Dogic Z, Raviv U. "Structure and Intermolecular Interactions between L -Type Straight Flagellar Filaments", Biophysical Journal. 2017;112(10):2184-95. doi: 10.1016/j.bpj.2017.02.038

Wang, H, Feng, Z, Lu, A, Jiang, Y, Wu, H, & Xu, B. "Instant Hydrogelation Inspired by Inflammasomes", Angew Chem Int Ed Engl, 10.1002/anie.201702783 (2017). doi: 10.1002/anie.201702783

Siavashpouri, M, Wachauf, CH, Zakhary, MJ, Praetorius, F, Dietz, H, & Dogic, Z. "Molecular engineering of chiral colloidal liquid crystals using DNA origami",Nature Materials, 10.1038/nmat4909 (2017). doi: 10.1038/nmat4909

Gibaud, T, Kaplan, CN, Sharma, P, Zakhary, MJ, Ward, A, Oldenbourg, R, Meyer, RB, Kamien, RD, Powers, TR, & Dogic, Z. "Achiral symmetry breaking and positive Gaussian modulus lead to scalloped colloidal membranes", Proc Natl Acad Sci U S A, 114(17), E3376-E3384 (2017). doi: 10.1073/pnas.1617043114

Wagner, CG, Hagan, MF, & Baskaran, A. "Steady-state distributions of ideal active Brownian particles under confinement and forcing", Journal of Statistical Mechanics: Theory and Experiment, 2017(4), 043203 (2017). doi: 10.1088/1742-5468/aa60a8

Wu, KT, Hishamunda, JB, Chen, DT, DeCamp, SJ, Chang, YW, Fernandez-Nieves, A, Fraden, S, & Dogic, Z. "Transition from turbulent to coherent flows in confined three-dimensional active fluids", Science, 355(6331) (2017). doi: 10.1126/science.aal1979

Du, X, Zhou, J, Wang, H, Shi, J, Kuang, Y, Zeng, W, Yang, Z, & Xu, B. "In situ generated D-peptidic nanofibrils as multifaceted apoptotic inducers to target cancer cells", Cell Death Dis, 8(2), e2614 (2017). doi: 10.1038/cddis.2016.466

Zhou, N, Cao, X, Du, X, Wang, H, Wang, M, Liu, S, Nguyen, K, Schmidt-Rohr, K, Xu, Q, Liang, G, & Xu, B. "Hyper-Crosslinkers Lead to Temperature- and pH-Responsive Polymeric Nanogels with Unusual Volume Change", Angew Chem Int Ed Engl, 56(10), 2623-2627 (2017). doi: 10.1002/anie.201611479

Liu, KK, Hagan, MF, & Lisman, JE. "Gradation (approx. 10 size states) of synaptic strength by quantal addition of structural modules", Philos Trans R Soc Lond B Biol Sci, 372(1715) (2017). doi: 10.1098/rstb.2016.0328

Li, J, Du, X, Hashim, S, Shy, A, & Xu, B. "Aromatic-Aromatic Interactions Enable alpha-Helix to beta-Sheet Transition of Peptides to Form Supramolecular Hydrogels", J Am Chem Soc, 139(1), 71-74 (2017). doi: 10.1021/jacs.6b11512

Girabawe, C, & Fraden, S. "An image-driven drop-on-demand system", Sensors and Actuators B-Chemical, 238, 532-539 (2017). doi: 10.1016/j.snb.2016.07.065 

Wang, H, Feng, Z, Wang, Y, Zhou, R, Yang, Z, & Xu, B. "Integrating Enzymatic Self-Assembly and Mitochondria Targeting for Selectively Killing Cancer Cells without Acquired Drug Resistance", J Am Chem Soc, 138(49), 16046-16055 (2016). doi: 10.1021/jacs.6b09783

Haburcak, R, Shi, J, Du, X, Yuan, D, & Xu, B. "Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules", J Am Chem Soc, 138(47), 15397-15404 (2016). doi: 10.1021/jacs.6b07677

Yu, N, Ghosh, A, & Hagan, MF. "Faceted particles formed by the frustrated packing of anisotropic colloids on curved surfaces", Soft Matter, 12(44), 8990-8998 (2016). doi: 10.1039/c6sm01498d

Redner, GS, Wagner, CG, Baskaran, A, & Hagan, MF. "Classical Nucleation Theory Description of Active Colloid Assembly", Phys Rev Lett, 117(14), 148002 (2016). doi: 10.1103/PhysRevLett.117.148002

Zhou, J, Du, X, Berciu, C, He, H, Shi, J, Nicastro, D, & Xu, B. "Enzyme-Instructed Self-Assembly for Spatiotemporal Profiling of the Activities of Alkaline Phosphatases on Live Cells", Chem, 1(2), 246-263 (2016). doi: 10.1016/j.chempr.2016.07.003

Stanishneva-Konovalova, TB, Kelley, CF, Eskin, TL, Messelaar, EM, Wasserman, SA, Sokolova, OS, & Rodal, AA. "Coordinated autoinhibition of F-BAR domain membrane binding and WASp activation by Nervous Wreck", Proc Natl Acad Sci U S A, 113(38), E5552-5561 (2016). doi: 10.1073/pnas.1524412113

Mohapatra, L, Goode, BL, Jelenkovic, P, Phillips, R, & Kondev, J. "Design Principles of Length Control of Cytoskeletal Structures",  Annual Review of Biophysics, Vol 42, 45, 85-116 (2016). doi: 10.1146/annurev-biophys-070915-094206

Soni, H, Pelcovits, RA, & Powers, TR. "Wrinkling of a thin film on a nematic liquid-crystal elastomer", Physical Review E, 94(1-1), 012701 (2016). doi: 10.1103/PhysRevE.94.012701

Perkett, MR, Mirijanian, DT, & Hagan, MF. "The allosteric switching mechanism in bacteriophage MS2", Journal of Chemical Physics, 145(3), 035101 (2016). doi: 10.1063/1.4955187

Dogic, Z. "Filamentous Phages As a Model System in Soft Matter Physics", Front Microbiol, 7, 1013 (2016). doi: 10.3389/fmicb.2016.01013

Perlmutter, JD, Mohajerani, F, & Hagan, MF. "Many-molecule encapsulation by an icosahedral shell", elife, 5 (2016). doi: 10.7554/eLife.14078

Harbage, D, & Kondev, J. "Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits", Journal of Physical Chemistry B, 120(26), 6225-6230 (2016). doi: 10.1021/acs.jpcb.6b02242

Lazaro, GR, & Hagan, MF. "Allosteric Control of Icosahedral Capsid Assembly", Journal of Physical Chemistry B, 120(26), 6306-6318 (2016). doi: 10.1021/acs.jpcb.6b02768

Zhou, R, Kuang, Y, Zhou, J, Du, X, Li, J, Shi, J, Haburcak, R, & Xu, B. "Nanonets Collect Cancer Secretome from Pericellular Space", PLoS ONE, 11(4), e0154126 (2016). doi: 10.1371/journal.pone.0154126

Harbage, D, & Kondev, J. "Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits", Journal of Physical Chemistry B, 120(26), 6225-6230 (2016). doi: 10.1021/acs.jpcb.6b02242

Lazaro, GR, & Hagan, MF. "Allosteric Control of Icosahedral Capsid Assembly&", Journal of Physical Chemistry B, 120(26), 6306-6318 (2016). doi: 10.1021/acs.jpcb.6b02768

Zhou, R, Kuang, Y, Zhou, J, Du, X, Li, J, Shi, J, Haburcak, R, & Xu, B. "Nanonets Collect Cancer Secretome from Pericellular Space", PLoS ONE, 11(4), e0154126 (2016). doi: 10.1371/journal.pone.0154126

Hagan MF; Zandi, R, "Recent advances in coarse-grained modeling of virus assembly", Curr Opin Virol, 18, 36-43 (2016). DOI:10.1016/j.coviro.2016.02.012

Kang L, Gibaud T, Dogic Z, Lubensky TC, "Entropic forces stabilize diverse emergent structures in colloidal membranes", Soft Matter, 12, 386-401 (2016). DOI: 10.1039/C5SM02038G

Xu B, Zhou J, Du X, Yamagata N, "Enzyme-Instructed Self-Assembly of Small d-Peptides as a Multiple-Step Process for Selectively Killing Cancer Cells", J. Am. Chem. Soc., 138, 3813–3823 (2016). DOI: 10.1021/jacs.5b13541

Xie S, Hagan MF, Pelcovits RA, "Interaction of chiral rafts in self-assembled colloidal membranes", Physical Review E, 93, 032706 (2016). DOI: 10.1103/PhysRevE.93.032706

Hagan MF, Baskaran A, "Emergent self-organization in active materials", Current opinion in cell biology, 38, 74-80 (2016). DOI: 10.1016/j.ceb.2016.02.020

Putzig E, Redner GS, Baskaran A, Baskaran A, "Instabilities, defects, and defect ordering in an overdamped active nematic", Soft Matter,12, 3854-3859 (2016). DOI: 10.1039/c6sm00268d

Wang AL, Gold JM, Tompkins N, Heymann M, Harrington KI, Fraden S, "Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets", The European Physical Journal Special Topics, 225, 211-227 (2016). DOI: 10.1140/epjst/e2016-02622-y

Fraden S, Tompkins N, "An inexpensive programmable illumination microscope with active feedback", American Journal of Physics, 84, 150 (2016). DOI: 10.1119/1.4935806

Henty-Ridilla JL, Rankova A, Eskin JA, Kenny K, Goode BL, "Accelerated actin filament polymerization from microtubule plus ends", Science, 352, 1004-1009 (2016). DOI: 10.1126/science.aaf1709 

DeCamp SJ, Redner GS, Baskaran A, Hagan MF, Dogic Z, "Orientational order of motile defects in active nematics", Nature Materials 14, 1110-1115 (2015). DOI: 10.1038/NMAT4387

Hancock B, Baskaran A, "Effect of reorientation statistics on torque response of self-propelled particles", Physical Review E, 92, 052143 (2015). DOI: 10.1103/PhysRevE.92.052143

Bertin E, Baskaran A, Chaté H, Marchetti MC, "Comparison between Smoluchowski and Boltzmann approaches for self-propelled rods", Physical Review E, 92, 042141 (2015). DOI: 10.1103/PhysRevE.92.042141 

Solon AP, Fily Y, Baskaran A, Cates ME, Kafri Y, Kardar M, Tailleur J, "Pressure is not a state function for generic active fluids", Nature Physics, 11, 673-678 (2015). DOI: 10.1038/nphys3377

Chen DTN, Heymann M, Fraden S, Nicastro D, Dogic Z, "ATP consumption of eukaryotic flagella measured at a single-cell level", Biophysical Journal 109, 2562-2573 (2015).
DOI: 10.1016/j.bpj.2015.11.003

Goldstein, D and Giver, M and Chakraborty, B, "Synchronization patterns in geometrically frustrated rings of relaxation oscillators", Chaos25, 123109 (2015). DOI: 10.1063/1.4936246

Johnston AB, Collins A, Goode BL, "High-speed depolymerization at actin filament ends jointly catalysed by Twinfilin and Srv2/CAP", Nature Cell Biology, 17, 1504-1511 (2015). DOI: 10.1038/ncb3252. 

Ward A, Hilitski F, Schwenger W, Welch D, Lau AWC, Vitelli V, Mahadevan L, Dogic Z, "Solid friction between soft filaments", Nature Materials 14, 583-588 (2015). DOI: 10.1038/nmat4222 

Welch D, Lettinga MP, Ripoll M, Dogic Z, Vliegenthart GA, "Trains, tails and loops of partially adsorbed semi-flexible filaments", Soft Matter 11, 7507-7514 (2015). DOI: 10.1039/C5SM01457C  

Perlmutter JD, Hagan MF, "Mechanisms of Virus Assembly", Annu. Rev. Phys. Chem.66, 217–39 (2015). DOI: 10.1146/annurev-physchem-040214-121637

Feld GK, Heymann M, Benner WH, Pardini T, Tsai CJ, Boutet S, Coleman MA, Hunter MS, Li X, Messerschmidt M, Opathalage A, Pedrini B, Williams GJ, Krantz BA, Fraden S, Hau-Riege S, Evans JE, Segelke BW, Frank M, "Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography", Journal of Applied Crystallography 48, 1072-1079 (2015). DOI: 10.1107/S1600576715010493 

Unwin RR, Cabanas RA, Yanagishima T, Blower TR, Takahashi H, Salmond GPC, Edwardson JM, Fraden S, Eiser E, "DNA driven self-assembly of micron-sized rods using DNA-grafted bacteriophage fd virions", Physical Chemistry Chemical Physics 17, 8194-8202 (2015). DOI: 10.1039/c4cp05405a 

Kelley CF, Messelaar EM, Eskin TL, Wang S, Song K, Vishnia K, Becalska AN, Shupliakov O, Hagan MF, Danino D, Sokolova OS, Nicastro DRodal AA, "Membrane Charge Directs the Outcome of F-BAR Domain Lipid Binding and Autoregulation", Cell Reports, 13, 2597-2609 (2015). DOI: 10.1016/j.celrep.2015.11.044

Fily Y, Baskaran A, Hagan MF, "Dynamics and density distribution of strongly confined noninteracting nonaligning self-propelled particles in a nonconvex boundary", Phys. Rev. E, 91, 012125 (2015). DOI: 10.1103/PhysRevE.91.012125

Tompkins N, Cambria MC, Wang AL, Heymann M, and Fraden S, "Creation and perturbation of planar networks of chemical oscillators", Chaos, 25, 064611 (2015). DOI: 10.1063/1.4922056

Du X, Zhou J, Shi J, Xu B, "Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials", Chemical Reviews 115, 13165-13307 (2015). DOI: 10.1021/acs.chemrev.5b00299

Yuan D, Shi J, Du X, Zhou N, Xu B, "Supramolecular Glycosylation Accelerates Proteolytic Degradation of Peptide Nanofibrils", Journal of the American Chemical Society 137, 10092–10095 (2015). DOI: 10.1021/jacs.5b05888

Zhou J, Du X, 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). DOI: 10.1080/19336896.2015.1022021

Zhang Y, Zhou N, Shi J, Pochapsky SS, Pochapsky TC, Zhang B, Zhang X, Xu B, "Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures", Nature Communications 6, 6165 (2015). DOI: 10.1038/ncomms7165 

Du X, Zhou J, 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). DOI: 10.1016/j.jcis.2014.12.023

Shi J, Du X, Yuan D, Haburcak R, Wu D, Zhou N, Xu B, "Enzyme transformation to modulate the ligand-receptor interactions between small molecules", Chemical Communications 51, 4899-4901 (2015). DOI: 10.1039/C4CC10374B

Shi J, Du X, Huang Y, Zhou J, Yuan D, Wu D, Zhang Y, Haburcak R, Epstein IR, 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). DOI: 10.1021/ja5100417 

Li N, Tompkins N, Gonzalez-Ochoa H, Fraden S, "Tunable diffusive lateral inhibition in chemical cells", Eur. Phys. J. E, 38, 18 (2015). DOI: 10.1140/epje/i2015-15018-3 

Mohapatra L, Goode BL, Kondev J, "Antenna mechanism of length control of actin cables", PLoS Comp. Biol., 11, e1004160 (2015). DOI: 10.1371/journal.pcbi.1004160

Fraden S, Tompkins N, "An inexpensive programmable illumination microscope with active feedback", American Journal of Physics, 84, 150 (2016). DOI: 10.1119/1.4935806

Chen DTN, Heymann M, Fraden SNicastro DDogic Z, "ATP consumption of eukaryotic flagella measured at a single-cell level", Biophysical Journal 109, 2562-2573 (2015). DOI: 10.1016/j.bpj.2015.11.003

Kang L, Gibaud T, Dogic Z, Lubensky TC, "Entropic forces stabilize diverse emergent structures in colloidal membranes", Soft Matter, 12, 386-401 (2016). DOI: 10.1039/C5SM02038G 

Ward A, Hilitski F, Schwenger W, Welch D, Lau AWC, Vitelli V, Mahadevan L, Dogic Z, "Solid friction between soft filaments", Nature Materials 14, 583-588 (2015). DOI: 10.1038/nmat4222

Welch D, Lettinga MP, Ripoll M, Dogic Z, Vliegenthart GA, "Trains, tails and loops of partially adsorbed semi-flexible filaments", Soft Matter 11, 7507-7514 (2015). DOI: 10.1039/C5SM01457C 

Hilitski F, Ward AR, Cajamarca L, Hagan MF, Grason GM, Dogic Z, "Measuring cohesion between macromolecular filaments, one pair at a time: Depletion-induced microtubule bundling", Phys. Rev. Lett., 114, 138102 (2015). DOI: 10.1103/PhysRevLett.114.138102

Feld GK, Heymann M, Benner WH, Pardini T, Tsai CJ, Boutet S, Coleman MA, Hunter MS, Li X, Messerschmidt M, Opathalage A, Pedrini B, Williams GJ, Krantz BA, Fraden S, Hau-Riege S, Evans JE, Segelke BW, Frank M, "Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography", Journal of Applied Crystallography 48, 1072-1079 (2015). DOI: 10.1107/S1600576715010493

Unwin RR, Cabanas RA, Yanagishima T, Blower TR, Takahashi H, Salmond GPC, Edwardson JM, Fraden S, Eiser E, "DNA driven self-assembly of micron-sized rods using DNA-grafted bacteriophage fd virions", Physical Chemistry Chemical Physics 17, 8194-8202 (2015). DOI: 10.1039/c4cp05405a

Du X, Zhou J, Shi J, Xu B, "Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials", Chemical Reviews 115, 13165-13307 (2015). DOI: 10.1021/acs.chemrev.5b00299

Yuan D, Shi J, Du X, Zhou N, Xu B, "Supramolecular Glycosylation Accelerates Proteolytic Degradation of Peptide Nanofibrils", Journal of the American Chemical Society 137, 10092–10095 (2015). DOI: 10.1021/jacs.5b05888

Zhou J, Du X, 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). DOI: 10.1080/19336896.2015.1022021

Zhang Y, Zhou N, Shi J, Pochapsky SS, Pochapsky TC, Zhang B, Zhang X, Xu B, "Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures", Nature Communications 6, 6165 (2015). DOI: 10.1038/ncomms7165

Du X, Zhou J, 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). DOI: 10.1016/j.jcis.2014.12.023 

Shi J, Du X, Yuan D, Haburcak R, Wu D, Zhou N, Xu B, "Enzyme transformation to modulate the ligand-receptor interactions between small molecules", Chemical Communications 51, 4899-4901 (2015). DOI: 10.1039/C4CC10374B

Shi J, Du X, Huang Y, Zhou J, Yuan D, Wu D, Zhang Y, Haburcak R, Epstein IR, 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). DOI: 10.1021/ja5100417

DeCamp SJ, Redner GS, Baskaran AHagan MFDogic Z, "Orientational order of motile defects in active nematics", Nature Materials 14, 1110-1115 (2015). DOI: 10.1038/NMAT4387

Hancock B, Baskaran A, "Effect of reorientation statistics on torque response of self-propelled particles", Physical Review E, 92, 052143 (2015). DOI: 10.1103/PhysRevE.92.052143

Bertin E, Baskaran A, Chaté H, Marchetti MC, "Comparison between Smoluchowski and Boltzmann approaches for self-propelled rods", Physical Review E, 92, 042141 (2015). DOI: 10.1103/PhysRevE.92.042141

Solon AP, Fily Y, Baskaran A, Cates ME, Kafri Y, Kardar M, Tailleur J, "Pressure is not a state function for generic active fluids", Nature Physics, 11, 673-678 (2015). DOI: 10.1038/nphys3377

Jansen S, Collins, A, Golden L, Sokolova O, Goode BL, "Single-molecule imaging of a three component actin disassembly mechanism", Nat. Commun., 6, 7202 (2015). DOI: 10.1038/ncomms8202

Ruiz-Herrero T, Hagan MF, "Simulations show that virus assembly and budding are facilitated by membrane microdomains", Biophys. J., 108, 585-595 (2015). DOI: 10.1016/j.bpj.2014.12.017

Pontiggia F, Pachov D, Clarkson M, Villali J, Hagan MF, Pande V, Kern D, "Free energy landscape of activation in a signaling protein at atomic resolution", Nat. Comm., 6, 7284 (2015). DOI:10.1038/ncomms8284

Perlmutter JD, Hagan MF, "The role of packaging sites in efficient and specific virus assembly", J.Mol.Biol., 427, 2451-2467 (2015). DOI:10.1016/j.jmb.2015.05.008  

Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D, "The energy landscape of adenylate kinase during catalysis", Nat. Struct. Mol. Biol., 22, 124–131 (2015). DOI: 10.1038/nsmb.2941

N. Tompkins, N. Li, C. Girabawe, M. Heymann, G. B. Ermentrout, I. R. Epstein and S. Fraden, "Testing Turing's theory of morphogenesis in chemical cells", Proc. Nat. Acad. Sci. USA 111, 4397-4402 (2014). 10.1073/pnas.1322005111

N. Li, J. Delgado, H. O. González-Ochoa, I. R. Epstein and S. Fraden, "Combined excitatory and inhibitory coupling in a 1D array of Belousov- Zhabotinsky droplets", Phys. Chem. Chem. Phys. (2014). 10.1039/C4CP00957F

S. Park, D. Kim, S.Y. Ko, J.O. Park, S. Akella, B. Xu, Y. Zhang and S. Fraden, "Controlling uniformity of photopolymerized microscopic hydrogels", Lab on a Chip 14, 1551 – 1563 (2014). 10.1039/c4lc00158c

K.C. Anthony, C. Yo, J. Piehler, D.A. Pomeranz Krummel, "High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies", Structure 22, 628-635 (2014). 10.1016/j.str.2014.01.007

D.B. Doroquez, C. Berciu, J.R. Anderson, P. Sengupta, D. Nicastro, "A high-resolution morphological and ultrastructural map of anterior sensory cilia and glia in C. elegans", eLife 3, e01948 (2014). 10.7554/eLife.01948

M.J. Zakhary, T. Gibaud, C.N. Kaplan, E. Barry, R. Oldenbourg, R.B. Meyer, Z. Dogic, "Imprintable membranes from incomplete chiral coalescence", Nature Communications 5, 3063 (2014). 10.1038/ncomms4063

J.Villali, F. Pontiggia, M.W. Clarkson, M.F. Hagan, D. Kern, "Evidence against the ‘Y-T coupling’ mechanism of activation in the response regulator NtrC", J. Mol. Biol, 426, 1554–1567, (2014).10.1016/j.jmb.2013.12.027

M. Rosado, C.F. Barber, C. Berciu, S. Feldman, S. Birren, D. Nicastro, B.L. Goode, "Critical roles for multiple formins during cardiac myofibril development and repair", Mol Biol Cell. 25, 811-27 (2014). 10.1091/mbc.E13-08-0443

M.F. Hagan, "Modeling Viral Capsid Assembly", Adv. Chem. Phys. 155, 1-68 (2014). arXiv:1301.1657

J. Zhou, X.W. Du, Y. Gao, J.F. Shi, B. Xu, "Aromatic-Aromatic Interactions Enhance Interfiber Contacts for Enzymatic Formation of a Spontaneously Aligned Supramolecular Hydrogel", J. Am. Chem. Soc. 136, 2970-2973 (2014). 10.1021/ja4127399

J.D. Perlmutter, C. Qiao, M.F. Hagan, "Viral genome structures are optimal for capsid assembly", eLife 2, e00632 (2013).  10.7554/eLife.00632

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

T. Sanchez and Z. Dogic, "Engineering Oscillating Microtubule Bundles", Cilia, Pt A, Methods in Enzymology 524, W.F. Marshall, Editor, 205-224 (2013). 10.1016/B978-0-12-397945-2.00012-3

M.J. Zakhary, P. Sharma, A. Ward, S. Yardimici, Z. Dogic, "Geometrical edgeactants control interfacial bending rigidity of colloidal membranes", Soft Matter 9, 8306-8313 (2013).10.1039/c3sm50797a

Y. Zhang, N. Zhou, S. Akella, Y. Kuang, D. Kim, A. Schwartz, M. Bezpalko, B. M. Foxman, S. FradenI. R. Epstein and B. Xu, "Active Cross-Linkers that Lead to Active Gels", Angew. Chem. Int. Ed. 52, 11494-11498 (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 

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

A.N. Becalska, C.F. Kelley, C. Berciu, T.B. Stanishneva-Konovalova, X. Fu, S. Wang, O.S. Sokolova, D. NicastroA.A. Rodal, "Formation of membrane ridges and scallops by the F-BAR protein Nervous Wreck", Mol Biol Cell 24, 2406-2418 (2013).10.1091/mbc.E13-05-0271

Y. Gao, C. Berciu, Y. Kuang, J.F. Shi, D. Nicastro,  BXu, "Probing Nanoscale Self-Assembly of Nonfluorescent Small Molecules inside Live Mammalian Cells", ACS Nano 7, 9055-9063 (2013). 10.1021/nn403664n

Y. Gao, Y. Kuang, X.W. Du, J. Zhou, P. Chandran, F. Horkay, B. Xu, "Imaging Self-Assembly Dependent Spatial Distribution of Small Molecules in a Cellular Environment", Langmuir 29, 15191-15200 (2013). 10.1021/la403457c

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

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

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

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.83.05190

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

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

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

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

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

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

Facility Publications       

Guillamat, P, Ignes-Mullol, J, Shankar, S, Marchetti, MC, & Sagues, F. "Probing the shear viscosity of anactive nematic film", Physical Review E, 94(6-1), 060602 (2016). doi: 10.1103/PhysRevE.94.060602

Bei, Y, & Hong, P.  "Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes", BMC Bioinformatics, 17(1), 541 (2016). doi: 10.1186/s12859-016-1386-x

Wu, B, Wilding, MJ, Kuppuswamy, S, Bezpalko, MW, Foxman, BM, & Thomas, CM. "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(23), 12137-12148(2016). doi: 10.1021/acs.inorgchem.6b01543

Cannon, J, & Miller, P. "Synaptic and intrinsic homeostasis cooperate to optimize single neuron responseproperties and tune integrator circuits", J Neurophysiol, 116(5), 2004-2022 (2016). doi:10.1152/jn.00253.2016

Evers-McGregor, DA, Bezpalko, MW, Foxman, BM, & Thomas, CM. "N-heterocyclic phosphenium andphosphido nickel complexes supported by a pincer ligand framework", Dalton Trans, 45(5), 1918-1929(2016). doi: 10.1039/c5dt03549j

Ekesan, S, Lin, DY, & Herzfeld, J. "Magnetism and Bond Order in Diatomic Molecules Described bySemiclassical Electrons", Journal of Physical Chemistry B, 120(26), 6264-6269 (2016). doi:10.1021/acs.jpcb.6b02576

Bai, C, & Herzfeld, J. "Surface Propensities of the Self-Ions of Water", ACS Cent Sci, 2(4), 225-231(2016). doi: 10.1021/acscentsci.6b00013

Sadacca, BF, Mukherjee, N, Vladusich, T, Li, JX, Katz, DB, & Miller, P. "The Behavioral Relevance ofCortical Neural Ensemble Responses Emerges Suddenly", J Neurosci, 36(3), 655-669 (2016). doi:10.1523/JNEUROSCI.2265-15.2016

Guillamat P, Ignés-Mullol J, Sagués F, "Control of active liquid crystals with a magnetic field", Proceedings of the National Academy of Sciences, 113, 5498-502 (2016). DOI: 10.1073/pnas.1600339113 

Marchetti MC, Fily Y, Henkes S, Patch A, Yllanes D, "Minimal model of active colloids highlights the role of mechanical interactions in controlling the emergent behavior of active matter", Current Opinion in Colloid & Interface Science, 21, 34-43 (2016). DOI: 10.1016/j.cocis.2016.01.003  

Henkes S, Quint DA, Fily Y, Schwarz JM, "Rigid cluster decomposition reveals criticality in frictional jamming", Physical Review Letters, 116, 028301 (2016). DOI: 10.1103/PhysRevLett.116.028301

S.D. Van Hooser, G.M. Escobar, A. Maffei, P. Miller, "Emerging feed-forward inhibition allows the robust formation of direction selectivity in the developing ferret visual cortex", J Neurophysiol, (2014). 10.1152/jn.00891.2013

Wu B, Bezpalko MW, Foxman BM, Thomas, CM, "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). DOI: 10.1039/c4sc03772c

Sountsov P, Miller P, "Spiking neuron network Helmholtz machine", Front Comput Neurosci., 9, 46 (2015). DOI: 10.3389/fncom.2015.00046

Pettenuzzo D, Timmermann A, "Forecasting Macroeconomic Variables Under Model Instability", Journal of Business & Economic Statistics, 1-41 (2015). DOI: 10.1080/07350015.2015.1051183

A. Moran, D.B. Katz, "Sensory Cortical Population Dynamics Uniquely Track Behavior across Learning and Extinction", The Journal of Neuroscience, 34, 1248-1257 (2014). 10.1523/JNEUROSCI.3331-13.2014

J.S. Caplan, A.H. Williams, E. Marder, "Many parameter sets in a multicompartment model oscillator are robust to temperature perturbations", J Neurosci., 34, 4963-75 (2014).10.1523/JNEUROSCI.0280-14.2014

S. Ekesan, S. Kale, J. Herzfeld, "Transferable pseudo-classical electrons for aufbau of atomic ions", Journal of Computational Chemistry, 35, 1159–1164 (2014).10.1002/jcc.23612

H. White, D. Pettenuzzo, "Granger causality, exogeneity, cointegration, and economic policy analysis". Journal of Econometrics, 178, 316-30 (2014).10.1016/j.jeconom.2013.08.030

G.J. Gutierrez, E. Marder, "Rectifying electrical synapses can affect the influence of synaptic modulation on output pattern robustness", J Neurosci., 33, 13238-48 (2013). 10.1523/JNEUROSCI.0937-13.2013

F. Gerhard, T. Kispersky, G.J. Gutierrez, E. Marder, M. Kramer, U. Eden, "Successful reconstruction of a physiological circuit with known connectivity from spiking activity alone", Plos Comput Biol., 9, e1003138 (2013). 10.1371/journal.pcbi.1003138

A. Rinberg, A.L. Taylor, E. Marder, "The effects of temperature on the stability of a neuronal oscillator", Plos Comput Biol, 9, e1002857 (2013). 10.1371/journal.pcbi.1002857

G.J. Gutierrez, T. O'Leary, E. Marder, "Multiple mechanisms switch an electrically coupled, synaptically inhibited neuron between competing rhythmic oscillators", Neuron., 77, 845-58 (2013). 10.1016/j.neuron.2013.01.016

A.H. Williams, A. Calkins, T. O'Leary, R. Symonds, E. Marder, P.S. Dickinson, "The neuromuscular transform of the lobster cardiac system explains the opposing effects of a neuromodulator on muscle output", J Neurosci., 33, 16565-75 (2013).10.1523/JNEUROSCI.2903-13.2013

T. O'Leary, A.H. Williams, J.S. Caplan, E. Marder, "Correlations in ion channel expression emerge from homeostatic tuning rules", Proc Natl Acad Sci U S A, 110, E2645-54 (2013). 10.1073/pnas.1309966110

Y. Cheng, P. Anick, P. Hong, N. Xue, "Temporal relation discovery between events and temporal expressions identified in clinical narrative", Journal of biomedical informatics, 46, S48-53 (2013). 10.1016/j.jbi.2013.09.010

X.  Sun, P. Hong, M. Kulkarni, Y. Kwon, N. Perrimon, "PPIRank - an advanced method for ranking protein-protein interations in TAP/MS data", Proteome Sci., 11, S16 (2013.10.1186/1477-5956-11- S1-S16

Y. Kwon, A. Vinayagam, X. Sun, N. Dephoure, S.P. Gygi, P. Hong, N. Perrimon, "The Hippo signaling pathway interactome", Science, 342, 737-40 (2013). 10.1126/science.1243971

A.H. Williams, M.A. Kwiatkowski, A.L. Mortimer, E. Marder, M.L. Zeeman, P.S. Dickinson, "Animal-to- animal variability in the phasing of the crustacean cardiac motor pattern: an experimental and computational analysis", J Neurophysiol, 109, 2451-65 (2013). 10.1152/jn.01010.2012

P. Miller, D.B. Katz, "Accuracy and response-time distributions for decision-making: linear perfect integrators versus nonlinear attractor-based neural circuits", J Comput Neurosci., 35, 261-94 (2013).  10.1007/s10827-013-0452-x

P. Miller, "Stabilization of memory States by stochastic facilitating synapses", J Math Neurosci. 3, 19 (2013). 10.1186/2190-8567-3-19

Y.Z. Bei, P.Y. Hong, "A novel approach to minimize false discovery rate in genome-wide data analysis", Bmc Syst Biol 7, S1 (2013). 10.1186/1752-0509-7-S4-S1

P. Miller,"Stimulus number, duration and intensity encoding in randomly connected attractor networks with synaptic depression", Frontiers in computational neuroscience, 7 (2013). 10.3389/fncom.2013.00059

T.P. Vogels, R.C. Froemke, N. Doyon, M. Gilson, J.S. Haas, R. Liu, A. Maffei, P. Miller, C.J. Wierenga, M.A. Woodin, F. Zenke, H. Sprekeler, "Inhibitory synaptic plasticity: spike timing-dependence and putative network function", Front Neural Circuits, 7 (2013).  10.3389/fncir.2013.00119

M.J. Ranaghan, R.P. Kumar, K.S. Chakrabarti, V. Buosi, D. Kern, D.D. Oprian, "A highly conserved cysteine of neuronal calcium sensing proteins controls cooperative binding of Ca2+ to recoverin", J Biol Chem 288, 36160-36167 (2013). 10.1074/jbc.M113.524355

K. Harrington, E. Awa, S. Cussat-Blanc, and J. Pollack, "Robot Coverage Control by Evolved Neuromodulation", Proceedings of the International Joint Conference on Neural Networks, 543-550 (2013). 10.1109/IJCNN.2013.6706784

K.A.Q. Cousins, J.H. Dar, A. Wingfield, P. Miller, "Acoustic masking disrupts time-dependent mechanisms of memory encoding in word-list recall", Memory & Cognition (2013). 10.3758/s13421-013-0377-7

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

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

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