S.J. Hagen / Selected Publications

Microfluidic study of competence regulation in Streptococcus mutans: environmental inputs modulate bimodal and unimodal expression of comX
M. Son, S.-J. Ahn, Q. Guo, R.A. Burne, S.J. Hagen, Molecular Microbiology (2012) DOI: 10.1111/j.1365-2958.2012.08187.x; Cited in NIDCR Science News

Quorum activation at a distance: spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal
G. Dilanji, J. Langebrake, P. De Leenheer, S.J. Hagen, J. Am. Chem. Soc. 134 5618-5626. (2012).

Analysis of gene expression levels in individual bacterial cells without image segmentation
In Hae Kwak, Minjun Son, Stephen J. Hagen, Bioch. Biophys. Res. Comm. 421 425-430 (2012).

Noise and crosstalk in two quorum-sensing inputs of Vibrio fischeri
Pablo Delfino Perez, Joel T. Weiss, & Stephen J. Hagen, BMC Systems Biology 5 153 (2011). doi:10.1186/1752-0509-5-153

Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme
Jin Wang, Yong Wang, Xiakun Chu, Stephen J. Hagen, Wei Han, Erkang Wang, PLoS Comput Biol (2011) 7(4): e1001118. doi:10.1371/journal.pcbi.1001118
Heterogeneous Response to a Quorum-Sensing Signal in the Luminescence of Individual Vibrio fischeri,
Pablo Delfino Perez, Stephen J. Hagen, PLoS ONE (2010). 10.1371/journal.pone.0015473

Exponential growth of bacteria: Constant multiplication through division,
Stephen J. Hagen, Am. J. Phys. 78 1290-1296 (2010).

Bacterium in a box: Sensing of quorum and environment by the LuxI/LuxR gene regulatory circuit,
Stephen J. Hagen, Minjun Son, Joel Weiss, Jonathan H. Young, J. Biol. Phys 36 317-327 (2010).
DOI: 10.1007/s10867-010-9186-4, NIHMSID # 196131
Solvent viscosity and friction in protein folding dynamics,
Stephen J. Hagen, Curr. Prot. Peptide Sci. 11(5) 385-395 (2010).
Solvent friction changes the folding pathway of the tryptophan zipper TZ2,
Ranjani Narayanan, Leslie Pelakh, Stephen J. Hagen, Journal of Molecular Biology 390 538-546 (2009).
doi:10.1016/ j.jmb.2009.05.021.
Kinetics of folding and binding of an intrinsically disordered protein: the inhibitor of yeast aspartic proteinase YPrA,
Ranjani Narayanan, Omjoy K. Ganesh, Arthur S. Edison, Stephen J. Hagen, J. Am. Chem. Soc. 130 11477-11485 (2008).
doi 10.1021/ja803221c .
Kinetics of internal-loop formation in polypeptide chains: A simulation study,
Dana Doucet, Adrian Roitberg, Stephen J. Hagen, Biophysical Journal 92 2281-2289 (2007).
Probe-dependent and non-exponential relaxation kinetics: Unreliable signatures of downhill protein folding,
Stephen J. Hagen, Proteins 68 205-217 (2007).
Fast Folding Dynamics of Small Proteins: Placing Limits on Diffusional Limits
S. Hagen, in Wright, C. (ed.), Protein Folding, Aggregation and Design: Concepts, Experiments, Theories and Mechanisms,
The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London (2007).
(online at http://www.hstalks.com/?t=BL0031106-Hagen).

Characterizing the Residue Level Folding of the Intrinsically Unstructured IA₃,
Omjoy Ganesh, Terry Green, Arthur S. Edison, and Stephen J. Hagen, Biochemistry 45, 13585-13596 (2006).
Do protein molecules unfold in a simple shear flow?,
Juan Jaspe and Stephen J. Hagen, Biophysical Journal 91, 3415-3424 (2006).
doi:10.1529/biophysj.106.089367.
Diffusional limits to the speed of protein folding: fact or friction?
Stephen J. Hagen, Linlin Qiu, & Suzette A. Pabit, J. Phys. Cond. Matt., 17, S1503-S1514 (2005).
DOI
Protein folding: defining a standard set of experimental conditions and a preliminary kinetic data set of two-state proteins,
Maxwell, K.L., Wildes, D., Zarrine-Afsar, A., de los Rios, M.A., Brown, A.G., Friel, C.T, Hedberg, L., Horng, J-C., Bona, D., Miller, E.J., Valle-Blisle, A., Main, E.R.G., Bemporad, F., Qiu, L., Teilum, K., Vu, N.-D., Edwards, A.M., Ruczinski, I., Poulsen, F.M., Kragelund, B.B., Michnick, S.W., Chiti, F., Bai, Y., Hagen, S.J., Serrano, L., Oliveberg, M., Raleigh, D.P., Wittung-Stafshede, P., Radford, S.E., Jackson, S.E., Sosnick, T.R., Marqusee, S., Davidson, A.R., Plaxco, K.W. Prot. Sci., 14 602-616 (2005).
Internal friction controls the speed of protein folding from a compact configuration,
S.A. Pabit, H. Roder, and S.J. Hagen, Biochemistry, 43, 12532-12538 (2004).
Internal friction in the ultrafast folding of the Tryptophan Cage,
Linlin Qiu and S.J. Hagen, Chem. Phys. (Special issue: The Physics of Protein Folding and Function), 307 243-249 (2004). doi:10.1016/j.chemphys.2004.12.002
(Book Review) Biological Physics: Energy Information, Life, by P. Nelson,
S.J. Hagen, American Journal of Physics, 72 1359-1360 (2004).
A limiting speed for protein folding at low solvent viscosity ,
Linlin Qiu and S.J. Hagen, J. Am Chem. Soc., 126 3398-3399 (2004).
IA₃, an aspartic proteinase inhibitor from Saccharomyces cerevisiae, is intrinsically unstructured in solution,
T. Green, O. Ganesh, K. Perry, L. Smith, L.H. Phylip, T.M. Logan, S.J. Hagen, B.M. Dunn, and A.S. Edison, Biochemistry, DOI: 10.1021/bi034823n (2004).
Tryptophan Zipper Folding Kinetics via Molecular Dynamics and Temperature-Jump Spectroscopy,
Christopher D. Snow, Linlin Qiu, Deguo Du, Feng Gai, Stephen J. Hagen, and Vijay S. Pande, Proc. Natl. Acad. Sci. USA, DOI 10.1073/pnas.0305260101 (2004).
Fast chain contraction during protein folding: "Foldability" and collapse dynamics,
L. Qiu, C. Zachariah, and S.J. Hagen, Phys. Rev. Lett., 90 (16) (2003). [DOI 10.1103/PhysRevLett.90.168103] . Also indexed in Virtual Journal of Biological Physics Research, 5 (9) May 1, 2003.
Exponential kinetics in 'downhill' protein folding,
S.J. Hagen, Proteins: Structure, Function, Genetics, 50, 1-4 (2003).
Smaller and faster: The 20-residue Trp-cage folds in 4 microseconds,
L.L. Qiu, S.A. Pabit, A.E. Roitberg, & S.J. Hagen, J. Am. Chem. Soc. Communications, 124, 12952-12953 (2002) [DOI 10.1021/ja0279141].
A laminar-flow fluid mixer for fast fluorescence kinetics studies,
S.A. Pabit & S.J. Hagen, Biophysical Journal, 83, 2872-2878 (2002).
Rapid intrachain binding of His-26 and His-33 to heme in unfolded ferrocytochrome c,
S.J. Hagen, R.F. Latypov, D.A. Dolgikh, & H. Roder, Biochemistry, 41, 1372-1380 (2002).
Rate of intrachain contact formation in an unfolded protein: temperature and denaturant effects,
S.J. Hagen, C.W. Carswell, & E.M. Sjolander, J. Mol. Biol., 305, 1161-1171 (2001).
Two-state expansion and collapse of a polypeptide,
S.J. Hagen & W.A. Eaton, J. Mol. Biol. 301, 1037-1045 (2000).
Fast kinetics and mechanisms in protein folding,
Eaton WA, Munoz V, Hagen SJ, Jas GS, Lapidus LJ, Henry ER, & Hofrichter J, Ann. Rev. Biophys. Biomolec. Struct., 29, 327-359 (2000).
Kinetics and mechanisms in protein folding W.A. Eaton, S.J. Hagen, E.R. Henry, J. Hofrichter, G. Jas, L. Lapidus, V. Munoz, J. Biosciences 24 5-31 (1999).
Rate of intrachain diffusion of unfolded cytochrome-c,
S.J. Hagen, J. Hofrichter, & W.A. Eaton, J. Phys. Chem. B 101, 2352 (1997).
Diffusion-limited contact formation in unfolded cytochrome-c: estimating the maximum rate of protein folding,
S.J. Hagen, J. Hofrichter, A. Szabo, & W.A. Eaton, Proc. Natl. Acad. Sci. USA 93, 11615 (1996). [See also Comment ary on this work by J.A. McCammon, Proc. Natl. Acad. Sci. USA 93, 11426 (1996).]
Geminate rebinding and conformational dynamics of myoglobin embedded in a glass at room temperature,
S.J. Hagen, J. Hofrichter, & W.A. Eaton, J. Phys. Chem. 100, 12008 (1996).
Fast Events in Protein Folding,
W.A. Eaton, P.A. Thompson, C.-K. Chan, S.J. Hagen, & J. Hofrichter, Structure 4, 1133 (1996).
Non-exponential structural relaxations in proteins,
S.J. Hagen & W.A. Eaton, J. Chem. Phys. 104, 3395 (1996).
Protein reaction kinetics in a room-temperature glass,
S.J. Hagen, J. Hofrichter, & W.A. Eaton, Science 269, 959 (1995).
Comments on the physics and chemistry of trehalose as a storage medium for hemoglobin-based blood substitutes: 'From Kramers Theory to the Battlefield',
S.J. Hagen, H.J. Hofrichter, H.F. Bunn, & W.A. Eaton, TCB 6, 423 (1995).
Handedness: basic physics,
S.J. Hagen, Science (letter) 265, 1792 (1994).
Asymmetric current-voltage characteristics in type-II superconductors,
X. Jiang, P.J. Connolly, S.J. Hagen, & C.J. Lobb, Phys. Rev. B 49, 9244 (1994).
Anomalous normal state magnetothermopower of electron-doped Nd_1.85Ce_0.15CuO_4+d crystal ,
W. Jiang, X.Q. Xu, S.J. Hagen, J.L Peng, Z.Y. Li, & R.L. Greene, J. Supercond. 7, 773 (1994).
Hall effect in the mixed state of Nd_1.85Ce_0.15CuO_4-d,
A.W. Smith, S.J. Hagen, M. Rajeswari, J.L. Peng, Z.Y. Li, R.L. Greene, S.N. Mao, X.X. Xi, S. Bhattacharya, Q. Li, & C.J. Lobb, Physica B, Part 2 194, 2257 (1994).
Effects of dimensional crossover on anisotropic pinning behavior in a model high T_c superconductor (YBCO/Y_1-xPr_xBCO superlattices) ,
Q. Li, C. Kwon, X.X. Xi, S. Bhattacharya, A. Walkenhorst, T. Venkatesan, S.J. Hagen, W. Jiang, & R.L. Greene, Physica B, Part 2 194, 2389 (1994).
Anomalous flux-flow Hall effect: Nd_1.85Ce_0.15CuO_4-y and evidence for vortex dynamics ,
S.J. Hagen, A.W. Smith, M. Rajeswari, J.L. Peng, Z.Y. Li, R.L. Greene, S.N. Mao, X.X. Xi, S. Bhattacharya, Q. Li & C.J. Lobb, Phys. Rev. B 47, 1064 (1993).
Anisotropic normal-state magnetothermopower of superconducting Nd_1.85Ce_0.15CuO_4-y crystals ,
Wu Jiang, X.Q. Xu, S.J. Hagen, J.L. Peng, Z.Y. Li, & R.L. Greene, Phys. Rev. B 48, 657 (1993).
Hall effect studies of Y_1-xPr_xBa₂Cu₃O₇ crystals , W. Jiang, J.L. Peng,
S.J. Hagen, & R.L. Greene, Phys. Rev. B 46, 8694 (1992).
Thermoelectric power of Nd_2-xCe_xCuO₄ crystals ,
X.Q. Xu, S.J. Hagen, W. Jiang, J.L. Peng, Z.Y. Li, & R.L. Greene, Phys. Rev. B 45, 7356 (1992).
Transport and localization in Nd_2-xCe_xCuO_4-y crystals at low doping ,
S.J. Hagen, X.Q. Xu, W. Jiang, J.L. Peng, Z.Y. Li, & R.L. Greene, Phys. Rev. B 45, 515 (1992).
Effects of dimensional crossover on flux pinning in a model high-T_c superconductor: YBa₂Cu₃O₇/(Pr_xY_1-x)Ba₂Cu₃O₇ superlattices ,
Q. Li, C. Kwon, X.X. Xi, S. Bhattacharya, A. Walkenhorst, T. Venkatesan, S.J. Hagen, W. Jiang, & R.L. Greene, Phys. Rev. Lett. 69, 2713 (1992).
Hall and Nernst effect studies of vortex motion in Tl₂Ba₂CaCu₂O₈ ,
S.J. Hagen, C.J. Lobb, R.L. Greene, & M. Eddy, Physica C 185-189, 1769 (1991).
In-plane transport properties of single-crystal Nd_2-xCe_xCuO₄ ,
S.J. Hagen, X.Q. Xu, J.L. Peng, Z.Y. Li, W. Jiang, & R.L. Greene, Physica C 185-189, 1275 (1991).
Effect of stress along the ab plane on the J_c and T_c of YBa₂Cu₃O₇ thin films,
G.L. Belenky, S.M. Green, A. Roytburd, C.J. Lobb, S.J. Hagen, R.L. Greene, M.G. Forrester, & J. Talvacchio, Phys. Rev. B 44, 10117 (1991).
In-plane transport properties of single-crystal R_2-xCe_xCuO_4-y (R=Nd,Sm) ,
S.J. Hagen, J.L. Peng, Z.Y. Li, & R.L. Greene, Phys. Rev. B 43, 13606 (1991).
Flux-flow Hall effect in superconducting Tl₂Ba₂CaCu₂O₈ films ,
S.J. Hagen, C.J. Lobb, R.L. Greene, & M. Eddy, Phys. Rev. B 43, 6246 (1991).
Phonon density of states in Pr_2-xCe_xCuO₄ and Pr₂CuO₄ ,
I.W. Sumarlin, J.W. Lynn, D.A. Neumann, J.J. Rush, J.L. Peng, Z.Y. Li, & S.J. Hagen, Physica C, Part 4 184, 2571 (1991).
Flux-flow Nernst effect in epitaxial YBa₂Cu₃O₇ ,
S.J. Hagen, C.J. Lobb, R.L. Greene, M.G. Forrester, & J. Talvacchio, Phys. Rev. B 42, 6777 (1990).
Anomalous Hall effect in superconductors near their critical temperatures,
S.J. Hagen, C.J. Lobb, R.L. Greene, M.G. Forrester, & J.H. Kang, Phys. Rev. B 41, 11630 (1990).
Anisotropy of the thermal conductivity of YBa₂Cu₃O₇ ,
S.J. Hagen, Z.Z. Wang, & N.P. Ong, Phys. Rev. B 40, 9389 (1989).
Approaching the Mott-Hubbard insulator in the 85-K superconductor Bi₂(Sr,Ca)₃Cu₂O_8+d by doping with Tm ,
J. Clayhold, S.J. Hagen, N.P. Ong, J.M. Tarascon, & P. Barboux, Phys. Rev. B 39, 7320 (1989).
Chain-site versus plane-site Cu substitution in YBa₂Cu_3-xM_xO₇ (M=Co,Ni): Hall and thermopower studies ,
J. Clayhold, S. Hagen, Z.Z. Wang, N.P. Ong, J.M. Tarascon, & P. Barboux, Phys. Rev. B 39, 777 (1989).
Andreev reflection, thermal conductivity, torque magnetometry, and Hall effect studies on high-T_c systems ,
N.P. Ong, T.W. Jing, Z.Z. Wang, J. Clayhold, S.J. Hagen, & T.R. Chien, in Strong Correlation and Superconductivity: Proceedings of the IBM Japan International Symposium, Mt. Fuji, Japan, 1989. Springer Verlag (Berlin 1989), p. 204.
Anomalous in-plane paraconductivity in single-crystal YBa₂Cu₃O₇ ,
S.J. Hagen, Z.Z. Wang, & N.P. Ong, Phys. Rev. B 38, 7137 (1988).
Optical anisotropy of YBa₂Cu₃O₇ ,
I. Bozovic, K. Char, S.J.B. Yoo, A. Kapitulnik, M.R. Beasley, T.H. Geballe, Z.Z. Wang, S. Hagen, N.P. Ong, D.E. Aspnes, & M.K. Kelly, Phys. Rev. B 38, 5077 (1988).
Out-of-plane conductivity in single-crystal YBa₂Cu₃O₇ ,
S.J. Hagen, T.W. Jing, Z.Z. Wang, J. Horvath, & N.P. Ong, Phys. Rev. B 37, 7928 (1988).
Transport and tunneling studies on single crystals of YBa₂Cu₃O₇ ,
N.P. Ong, Z.Z. Wang, S. Hagen, T.W. Jing, J. Clayhold, & J. Horvath, Proceedings of the International Conference on High-Temperature Superconductors and Materials and Mechanisms of Superconductivity -Interlaken, Switzerland, 1988, ed. J. Muller and J.L. Olsen, Physica C 153-155, 1072 (1988).
Experimental search for a heavy neutrino in the beta spectrum of ³⁵S ,
T. Altzitzoglou, F. Calaprice, M. Dewey, M. Lowry, L. Piilonen, J. Brorsen, S. Hagen, & F. Loeser, Phys. Rev. Lett. 55, 799 (1985).

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