Amyloid Beta-Protein (1-40) assembly (click on the icon to play the movie)	Amyloid Beta-Protein (1-42) assembly (click on the icon to play the movie)

RESEARCH NEWS & INVITED TALKS:

• Elucidation of amyloid β-protein assembly and toxicity inhibition, Invited talk, Institute Jozef Stefan, Department of Biochemistry, Molecular and Structural Biology, Ljubljana, Slovenia (28 May 2012).
• Elucidation of amyloid β-protein oligomer formation in the absence and presence of toxicity inhibitors, Invited talk at CECAM Workshop entitled, Anchoring simulations to experiments: challenges for understanding and treating Alzheimer's disease, Paris, France (22 May 2012).
• Biophysics of amyloid β-protein folding and assembly: Relevance to Alzheimer's disease, Colloquium, Department of Physics, University of Missouri at St. Louis, St. Louis (13 April 2012).
• The on-line research news commentary entitled, Flexible N-Termini Key to Aβ Oligomer Toxicity? by Alzforum writer Esther Landhuis comments on computational results of my group that were presented at Neuroscience 2010, The 40th Annual Meeting of the Society for Neuroscience in San Diego (November 2010).
• Discrete molecular dynamics simulations of amyloid β-protein assembly, Invited talk at the conference Multiscale Modeling and Simulations of Hard and Soft Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India (19 December 2009).
• Computational studies of amyloid β-protein assembly relevant to Alzheimer's disease, Colloquium, University of Delaware, Physics Department, Newark (7 October 2009).
• Protein structure-toxicity relationship relevant to Alzheimer's disease: Discrete molecular dynamics study, Invited talk, Session Molecular Basis of Protein Aggregation and Amyloid Formation, 2009 Fall American Chemical Society Meeting, Washington DC (August 2009).
• Biological Physicist, The Newsletter of the Division of Biological Physics of the American Physical Society, Vol.9, No.3 (2009), Featured Article on Biophysics at Drexel University [PDF]
• Invited interview for The Scientist on the research news Alzheimer's drugs hurt brain?

PEER-REVIEWED PUBLICATIONS (reverse chronological order):

• D. Meral and B. Urbanc, Discrete Molecular Dynamics Study of Oligomer Formation by N-Terminally Truncated Amyloid β-Protein, J. Mol. Biol. (2013) [Epub ahead of print] [http://authors.elsevier.com/sd/article/S0022283613001575/] [http://dx.doi.org/10.1016/j.jmb.2013.03.010/]
• S. Toal, D. Meral, D. Verbaro, B. Urbanc, and R. Schweitzer-Stenner, The pH-Independence of Trialanine and the Effects of Termini Blocking in Short Peptides: A Combined Vibrational, NMR, UVCD, and Molecular Dynamics Study, J. Phys. Chem. B 117, 3689-3706 (2013). [http://pubs.acs.org/doi/abs/10.1021/jp310466b]
• M. Betnel, N.V. Dokholyan, and B. Urbanc, From disordered amyloid β-proteins to soluble oligomers and protofibrils using Discrete Molecular Dynamics, in Alzheimer's disease: Molecular basis of amyloid β-protein aggregation and cytotoxic aggregates from computer simulations, Molecular Medicine and Medicinal Chemistry 7, Part B, Ch. 12, 333-358, Ed. P. Derreumaux, Imperial College Press (2013). [http://www.worldscientific.com/doi/abs/10.1142/9781848167551_0012]
• J.-E. Shea and B. Urbanc, Insights into Aβ aggregation: A molecular dynamics perspective, in "Protein Misfolding in Conformational Disorders," Special Issue, Guest Ed. Claudio M. Gomes, Cur. Top. Med. Chem. 12, 2596-2610 (2012). [http://www.ncbi.nlm.nih.gov/pubmed/23339310/]
• B. Barz, B.S. Turner, R. Bansil, and B. Urbanc, Folding of Pig Gastric Mucin Non-glycosylated Domains: A Discrete Molecular Dynamics Study, J. Biol. Phys. 38, 681-703 (2012). [http://www.springerlink.com/content/c00455gj86274612/]
• L. Cruz, J. Srinivasa-Rao, D.B. Teplow, and B. Urbanc, Dynamics of Metastable β-Hairpin Structures in the Folding Nucleus of Amyloid β-Protein, J. Phys. Chem. B 116, 6311-6325 (2012). [http://pubs.acs.org/doi/abs/10.1021/jp301619v]
• B. Barz and B. Urbanc, Dimer Formation Enhances Structural Differences between Amyloid β-Protein (1-40) and (1-42): An Explicit-Solvent Molecular Dynamics Study, PLoS ONE 7, e34345 (2012). [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034345]
• J. S. Rao, B. Urbanc, and L. Cruz, Ch.16: Computational studies of folding and assembly of amyloidogenic proteins, in Folding, Misfolding and Nonfolding of Peptides and Small Proteins, Ed. R. Schweitzer-Stenner, John Wiley & Sons, Inc., Hoboken, NJ, USA; (2012). [http://onlinelibrary.wiley.com/doi/10.1002/9781118183373.ch16/summary/]
• T.L. Williams, B.R.G. Johnson, B. Urbanc, A.T.A. Jenkins, S.D.A. Connell and L.C. Serpell, Alzheimer's Aβ42 oligomers simultaneously bind to and damage ganglioside containing lipid membranes, Biochem. J. 439, 67-77 (2011). [http://www.biochemj.org/bj/439/0067/bj4390067.htm]
• B. Urbanc, M. Betnel, L. Cruz, H. Li, E. Fradinger, B.H. Monien, and G. Bitan, Structural basis of Aβ_1-42 toxicity inhibition by Aβ C-terminal fragments: Discrete molecular dynamics study, J. Mol. Biol. 410, 316-328 (2011). [http://www.sciencedirect.com/science/article/pii/S0022283611005717]
• H. Li, B.H. Monien, A. Lomakin, R. Zemel, E.A. Fradinger, M. Tan, S.M. Spring, B. Urbanc, C.W. Xie, G.B. Benedek, and G. Bitan, Mechanistic Investigation of the Inhibition of Aβ42 Assembly and Neurotoxicity by Aβ42 C-terminal Fragments, Biochemistry, 49, 6358-6364 (2010). [PDF] [Supporting Information]
• B. Urbanc, M. Betnel, L. Cruz, G. Bitan, and D.B. Teplow, Elucidation of amyloid β-protein oligomerization mechanisms: Discrete molecular dynamics study, J. Am. Chem. Soc. 132, 4266-4280 (2010). [PDF] [Supporting Information]
• H. Li, B.H. Monien, E.A. Fradinger, B. Urbanc, and G. Bitan, Biophysical Characterization of Aβ42 C-terminal Fragments--Inhibitors of Aβ Assembly and Neurotoxicity, Biochemistry 49, 1259-1267 (2010). [PDF]
• L. Cruz, D.L. Roe, B. Urbanc, A. Inglis, H.E. Stanley, and D.L. Rosene, Age-related reduction in microcolumnar structure correlates with cognitive decline in ventral but not dorsal area 46 of the rhesus monkey. Neuroscience 158, 1509-1520 (2009). [PDF]
• A. Lam, D.B. Teplow, H.E. Stanley, and B. Urbanc, Effects of the Arctic mutation on the full length amyloid β-protein folding: A discrete molecular dynamics study J. Am. Chem. Soc. 130, 17413-17422 (2008). [PDF]
• E. Fradinger, B.H. Monien, B. Urbanc, A. Lomakin, M. Tan, H. Li, S.M. Spring, M.M. Condron, L. Cruz, C.-W. Xie, G.B. Benedek and G. Bitan, C-terminal peptides coassemble into Aβ42 oligomers and protect neurons against Aβ42-induced neurotoxicity. Proc. Natl. Acad. Sci. USA 105, 14175-14180 (2008). [PDF] [Supporting Information]
• L. Cruz, B. Urbanc, A. Inglis, D.L. Rosene and H.E. Stanley, Generating a model of the three-dimensional spatial distribution of neurons using density maps. NeuroImage 40, 1105-1115 (2008). [PDF]
• A. Inglis, L. Cruz, D.L. Roe, H.E. Stanley, D.L. Rosene, and B. Urbanc, Automated identification of neurons and their locations. Journal of Microscopy 230, 339-347 (2008). [PDF]
• S. Yun, B. Urbanc, L. Cruz, G. Bitan, D.B. Teplow, and H.E. Stanley, Role of electrostatic interactions in amyloid β-protein oligomer formation: A discrete molecular dynamics study. Biophys. J. 92, 4064-4077 (2007). [PDF]
• D.B. Teplow, N.D. Lazo, G. Bitan, S. Bernstein, T. Wyttenbach, M.T. Bowers, A. Baumketner, J.-E. Shea, B. Urbanc, L. Cruz, J.M. Borreguero, and H.E. Stanley, Elucidating Amyloid β-protein Folding and Assembly: A Multidisciplinary Approach. Account of Chemical Research 39, 635-645 (2006). [PDF]
• A. Lam, B. Urbanc, J. M. Borreguero, N. D. Lazo, D. B. Teplow, and H. E. Stanley, Discrete Molecular Dynamics Study of Alzheimer Amyloid β-Protein (Aβ) Folding, Proceedings of The 2006 International Conference on Bioinformatics & Computational Biology, 322-328 (2006). [PDF]
• B. Urbanc, L. Cruz, D. B. Teplow, and H. E. Stanley, Computer simulations of Alzheimer's amyloid β-protein folding and assembly , invited review, Current Alzheimer Research, 3, 493-504 (2006). [PDF]
• B. Urbanc, J. M. Borreguero, L. Cruz, and H. E. Stanley, Ab initio discrete molecular dynamics approach to protein folding and aggregation, Methods in Enzymology 412, Ch.19, 314-338 (2006). [PDF]
• B. Urbanc and M. Cepic, Possible Isostructural Transitions in the Ferroelectric Liquid Crystals in High External Electric Fields , presented at the 20th International Liquid Crystal Conference, 4-9 July, 2004, Ljubljana (Slovenia), Mol. Cryst. Liq. Cryst. 438 , 41(1605)-46(1610) (2005). [PDF]
• L. Cruz, B. Urbanc, J. M. Borreguero, N. D. Lazo, D. B. Teplow, and H. E. Stanley, Molecular dynamics study of Aβ21-30: Solvent-Dependent Effects and Dutch Mutation Dynamics, Proc. Natl. Acad. Sci. USA 102, 18258-18263 (2005). [PDF] [Supporting Information]
• J. M. Borreguero, B. Urbanc, N. D. Lazo, S. V. Buldyrev, D. B. Teplow, and H. E. Stanley, Folding events in the 21-30 region of amyloid β-protein studied in silico, Proc. Natl. Acad. Sci. USA 102, 6015-6020 (2005). [PDF]
• L. Cruz, S. V. Buldyrev, S. Peng, D. L. Roe, B. Urbanc, H. E. Stanley, and D. L. Rosene, A Statistically Based Density Map Method for Identification and Quantification of Regional Differences in Microcolumnarity in the Monkey Brain, J. Neurosci. Methods 141, 321-332 (2005). [PDF]
• B. Urbanc, L. Cruz, S. Yun, S. V. Buldyrev, G. Bitan, D. B. Teplow, and H. E. Stanley, In silico study of amyloid β-protein folding and oligomerization, Proc. Natl. Acad. Sci. USA 101, 17345-17350 (2004). [PDF] [Supporting Information]
• L. Cruz, D. L. Roe, B. Urbanc, H. Cabral, H. E. Stanley, and D. L. Rosene, Age-related reduction in microcolumnar structure in area 46 of the rhesus monkey correlates with behavioral decline, Proc. Natl. Acad. Sci. USA 101, 15846-15851 (2004). [PDF]
• B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, Molecular Dynamics Simulation of Amyloid-Beta Dimer Formation, Biophys. J. 87, 2310-2321 (2004). [PDF]
• S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz, H. E. Stanley, and N. V. Dokholyan, Discrete molecular dynamics simulations of peptide aggregation, Phys. Rev. E 69, 041908 (2004). [PDF]
• S. Peng, B. Urbanc, L. Cruz, B. T. Hyman, and H. E. Stanley, Neuron Recognition by Parallel Potts Segmentation, Proc. Natl. Acad. Sci. USA 100, 3847-3852 (2003). [PDF]
• B. Urbanc, L. Cruz, R. Le, J. Sanders, K. Hsiao-Ashe, K. Duff, H. E. Stanley, M. C. Irrizarry and B. T. Hyman, Neurotoxic Effects of Thioflavin S Positive Amyloid Deposits, Proc. Natl. Acad. Sci. USA 99, 13990-13995 (2002). [PDF]
• R. Le, L. Cruz, B. Urbanc, R. B. Knowles, K. Hsiao-Ashe, K. Duff, M. Irizarry H. E. Stanley,and B. T. Hyman, Plaque-induced abnormailities in neurite geometry in transgenic models of Alzheiemr's diseasae: implications for neural system disruption, J. Neuropath. Exp. Neurol. 60, 763-758 (2001). [PDF]
• S. V. Buldyrev, L. Cruz, T. Gómez-Isla, E. Gómez-Tortosa, S. Havlin, R. Le, H. E. Stanley, B. Urbanc and B. T. Hyman, Description of microcolumnar ensembles in association cortex and their disruption in Alzheimer and Lewy body dementias, Proc. Natl. Acad. Sci. USA 97, 5039-5043 (2000). [PDF]
• R. B. Knowles, C. Wyart, S. V. Buldyrev, L. Cruz, B. Urbanc, M. E. Hasselmo, H. E. Stanley, and B. T. Hyman, Plaque-Induced Neural Network Disruption in Alzheimer's Disease Proc. Natl. Acad. Sci. USA 96, 5274-5279 (1999). [PDF]
• B. Urbanc, L. Cruz, S. V. Buldyrev, S. Havlin, B. T. Hyman, and H. E. Stanley, Dynamic Feedback in an Aggregation-Disaggregation Model, Phys. Rev. E 60, 2120-2126 (1999). [PDF]
• B. Urbanc, L. Cruz, S. V. Buldyrev, S. Havlin, M. C. Irizarry, H. E. Stanley, and B. T. Hyman, Dynamics of Plaque Formation in Alzheimer Disease, Biophys. J. 76, 1330-1334, (1999). [PDF]
• H. E. Stanley, S. V. Buldyrev, L. Cruz, T. Gómez-Isla, S. Havlin, B. T. Hyman, R. Knowles, B. Urbanc and C. Wyart, Statistical Physics and Alzheimer's Disease [Proc. Bar-Ilan Conf], Physica A 249, 460-471 (1998). [PDF]
• B. Urbanc and L. Cruz, Order Parameter and Segregated Phases in a Sandpile Model with Two Particle Sizes, Phys. Rev. E 56, 1571-1579 (1997). [PDF]
• L. Cruz, B. Urbanc, S. V. Buldyrev, R. Christie, T. Gómez-Isla, S. Havlin, M. McNamara, H. E. Stanley, and B. T. Hyman, Aggregation and disaggregation of Senile Plaques in Alzheimer Disease, Proc. Natl. Acad. Sci. USA 94, 7612-7616 (1997). [PDF]
• B. Kutnjak-Urbanc, S. Havlin, H. E. Stanley, Temporal correlations in a one-dimensional sandpile model, Phys. Rev. E 54, 6109-6113 (1996). [PDF]
• B. Kutnjak-Urbanc, S. Zapperi, S. Miloševič, H. E. Stanley, Sandpile model on the Sierpinski gasket fractal, Phys. Rev. E 54, 272-277 (1996). [PDF]
• B. Kutnjak-Urbanc, B. Žekš, Phase excitation spectrum of ferroelectric liquid crystals in an external static electric field, Phys. Rev. E 52, 3892-3903 (1995). [PDF]
• B. Kutnjak-Urbanc, B. Žekš, Behavior of ferroelectric liquid crystals in external fields, Phys. Rev. E 51, 1569-1572 (1995). [PDF]
• B. Kutnjak-Urbanc, B. Žekš, Microscopic origin of spontaneous polarization in ferroelectric SmC* liquid crystals, Liq. Cryst. 18, 483-488 (1995).
• B. Žekš, T. Carlsson, I. Muševič, B. Kutnjak-Urbanc, Dielectric response of ferroelectric liquid crystals in bias electric field, Liq. Cryst. 15, 103-111 (1993).
• B. Kutnjak-Urbanc, B. Žekš, B. Rovšek, The influence of finite dimensions on the static ordering of the SmC* phase in an electric field, Liq. Cryst. 14, 999-1005 (1993).
• B. Kutnjak-Urbanc, B. Žekš, Theoretical investigation of the behavior of ferroelectric liquid crystals in a magnetic or in a high-frequency electric field, Phys. Rev. E 48, 455-464 (1993). [PDF]
• B. Kutnjak-Urbanc, B. Žekš, in Phase transitions in Liquid Crystals, edited by S. Martellucci and A. N. Chester, The phase transition from the SmC* to the SmC phase induced by an external magnetic field (Plenum, New York, 1992), Chap.23.
• B. Žekš, B. Urbanc, The microscopic model of polar and quadrupolar ordering in ferroelectric smectic C* liquid crystals, Ferroelectrics 113, 151-162 (1991).
• B. Urbanc, B. Žekš, T. Carlsson, Nonlinear effects in the dielectric response of ferroelectric liquid crystals, Ferroelectrics 113, 219-230 (1991).
• B. Urbanc, B. Žekš, Microscopic model of the spontaneous polarization in ferroelectric liquid crystals, Liq. Cryst. 5, 1075-1082 (1989).
• B. Žekš, T. Carlsson, C. Filipič, B. Urbanc, Thermodynamic model of ferroelectric liquid crystals and its microscopic basis, Ferroelectrics 84, 3-14 (1988).

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