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Neuronal Systems
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Z. Wang, L. Cruz,
Trainable Reference Spikes Improve Temporal Information
Processing of SNNs With Supervised Learning,
Neural Computation, 36, 2136–2169 (2024).
DOI
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Z. Wang, L. Cruz,
Spiking Neural Network with Plasticity in the Time Domain Recovers Temporal Information
from a Noisy Pattern using Reference Spikes,
Neurocomputing, 565, 126988 (2024).
DOI
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V. Baker, L. Cruz, Traveling Waves in Quasi One-Dimensional Neuronal Minicolumns,
Neural Computation, 34 (1), 78–103 (2021).
DOI
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J. S. Tumulty, M. Royster, and L. Cruz,
Columnar Grouping Preserves Synchronization in Neuronal Networks with Distance-Dependent Time Delays,
Physical Review E, 101, 022408 (2020).
DOI
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M. Henderson, B. Urbanc, L. Cruz, A Computational Model for the Loss of Neuronal Organization
in Microcolumns, Biophysical Journal, 106, 2233-2242 (2014).
DOI
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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 the ventral but not dorsal region part of area 46 of the
rhesus monkey, Neuroscience, 158, 1509-1520 (2009).
DOI
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S. H. Freeman, R. Kandel, L. Cruz, A. Rozkalne, K. Newell,
M. P. Frosch, E. T. Hedley-Whyte, J. J. Locascio, L. Lipsitz, B. T. Hyman,
Preservation of Neuronal Number Despite Age-Related Cortical Brain Atrophy in
Elderly Subjects Without Alzheimer Disease, Journal of Neuropathology &
Experimental Neurology, 67, 1205-1212 (2008).
DOI
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A. Inglis, L. Cruz, D. L. Roe, H. E. Stanley, D. L. Rosene,
and B. Urbanc, Automated identification of neurons and their locations,
J. Microscopy, 230 (3), 339-352 (2008).
DOI
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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 (3), 1105-1115 (2008).
DOI
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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. Neuroscience Methods,
141/2, 321-332 (2005).
DOI
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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. 101, 15846-15851 (2004).
DOI
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S. Peng, B. Urbanc, L. Cruz, B. T. Hyman, and
H. E. Stanley, Neuron Recognition by Parallel Potts
Segmentation, Proc. Natl. Acad. Sci.
100, 3847-3852 (2003).
DOI
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S. V. Buldyrev, L. Cruz, T. Gomez-Isla, E. Gomez-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. 97, 5039-5043 (2000).
DOI
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Peptide Dynamics
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C. Dias, S. Jalali, Y. Yang, and L. Cruz,
Role of Cholesterol on Binding of Amyloid Fibrils to Lipid Bilayers,
Journal of Physical Chemistry B, 124 (15), 3036-3042 (2020).
DOI
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M. D. Smith, J. Srinivasa Rao, E. Segelken, and L. Cruz,
Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS,
AMBER, CHARMM, and GROMOS Force-Fields,
Journal of Chemical Information and Modeling, 55 (12), 2587-2595 (2015).
DOI
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M. Smith, J. Rao, L. Cruz,
Spontaneous Dimer States of the Aβ21-30 Decapeptide,
Physical Chemistry Chemical Physics, 16 (26), 13069-13073 (2014).
DOI
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J. Srinivasa Rao, M. Smith, L. Cruz, The Stability of a β-hairpin in
Aβ(21-30) is altered by Surface-Water Interactions under Confinement, Journal
of Physical Chemistry B, 118 (13), 3517-3523 (2014).
DOI
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M. Smith, L. Cruz, Changes to the Structure and Dynamics in Mutations
of Aβ21-30 caused by Ions in Solution,
Journal of Physical Chemistry B, 117, 14907-14915 (2013).
DOI
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M. Smith, L. Cruz, Effect of Ionic Aqueous Environments on the
Structure and Dynamics of the Aβ21-30 Fragment: A Molecular-Dynamics
Study, Journal of Physical Chemistry B,
117, 6614-6624 (2013).
DOI
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J. Srinivasa Rao, L. Cruz, Effects of Confinement on the
Structure and Dynamics of an Intrinsically Disordered Peptide: A
Molecular-Dynamics Study, Journal of Physical Chemistry B,
117, 3707-3719 (2013).
DOI
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L. Cruz, J. Srinivasa Rao, D. B. Teplow, B.
Urbanc, Dynamics of Metastable β-Hairpin Structures in the Folding
Nucleus of Amyloid β-Protein, Journal of Physical Chemistry B,
116, 6311-6325 (2012).
DOI
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J. Srinivasa Rao, B. Urbanc, L. Cruz, Computational Studies of Folding
and Assembly of Amyloidogenic Proteins, in Folding, Misfolding and
Nonfolding of Peptides and Small Proteins, Reinhard Schweitzer-Stenner,
editor, John Wiley & Sons, Inc, pp. 479-527, April (2012).
DOI
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B. Urbanc, M. Betnel, L. Cruz, H. Li, E. A. Fradinger, B. H. Monien, and G. Bitan,
Structural basis for Aβ1-42 toxicity inhibition by
Aβ C-terminal fragments: Discrete molecular dynamics study,
J. Mol. Biol. 410, 316-328 (2011).
DOI
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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).
DOI
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E. A. 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. 105, 14175-14180 (2008).
DOI
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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).
DOI
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B. Urbanc, L. Cruz, D. B. Teplow, and H. E. Stanley,
Computer simulations of Alzheimer's amyloid
β-protein folding and assembly, invited review paper,
Current Alzheimer Research, 3, 493-504 (2006).
DOI
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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. Borreguero, H. E.
Stanley, Elucidating Amyloid β-Protein Folding and Assembly: A
Multidisciplinary Approach, Accounts of Chemical Research,
39, 635-645 (2006).
DOI
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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,
314-338 (2006).
DOI
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L. Cruz, B. Urbanc, J. M. Borreguero, N. D. Lazo, D. B. Teplow, and H. E.
Stanley, Solvent and Mutation Effects on the Nucleation of Amyloid
β-protein Folding, Proc. Natl. Acad. Sci., 102, 18258-18263 (2005).
DOI
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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. 101, 17345-17350 (2004).
DOI
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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 β
Dimer Formation, Biophys. J. 87, 2310-2321 (2004).
DOI
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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).
DOI
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Modeling of Plaques in AD
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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 in Transgenic Mice and Alzheimer's Disease,
Proc. Natl. Acad. Sci. 99, 13990-13995 (2002).
DOI
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R. Le, L. Cruz, B. Urbanc, R. B. Knowles, K. Hsiao-Ashe, K. Duff,
M. C. Irizarry, H. E. Stanley and B. T. Hyman,
Plaque-Induced Abnormalities in Neurite Geometry in Transgenic
Models of Alzheimer Disease: Implications for Neural System Disruption,
J. Neuropath. Exp. Neuro. 60, 753-758 (2001).
DOI
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B. Urbanc, L. Cruz}, S. V. Buldyrev, S. Havlin, B. T. Hyman, and
H. E. Stanley, Dynamic Feedback in an Aggregation-Disaggregation
Model, Physical Review E, 60, 2120-2126 (1999).
DOI
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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).
DOI
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R. B. Knowles, C. Wyart, S. V. Buldyrev, L. Cruz, B. Urbanc,
M. E. Hasselmo, H. E. Stanley, and B. T. Hyman, Plaque-Induced Neurite
Abnormalities: Implications for Disruption of Neural
Networks in Alzheimer's Disease, Proc. Natl. Acad. Sci.
96, 5274-5279 (1999).
DOI
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H. E. Stanley, S. V. Buldyrev, L. Cruz, T. Gomez-Isla,
S. Havlin, B. T. Hyman, R. Knowles, B. Urbanc and C. Wyart, Statistical
Physics and Alzheimer's Disease, Physica A - Statistical Mechanics and
its Applications 249 (1-4), 460-471 (1998).
DOI
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L. Cruz, B. Urbanc, S. V. Buldyrev, R. Christie, T. Gomez-Isla,
S. Havlin, M. McNamara, H. E. Stanley, B. T. Hyman, Aggregation and
disaggregation of Senile Plaques in Alzheimer Disease, Proc.
Natl. Acad. Sci. 94, 7612-7616 (1997).
DOI
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Conduction in 1D Polymers
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L. Cruz, P. Phillips, A. Castro-Neto,
Kondo Resonance and log-T Conductivity in Highly Conducting
trans-Polyacetylene, Europhysics Letters 29, 389-394 (1995).
DOI
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L. Cruz, P. Phillips,
Phase Diagram for Strongly-Correlated Doped trans Polyacetylene,
Physical Review B 49, 5149-5156 (1994).
DOI
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P. Phillips, L. Cruz,
Metallic Polyacetylene is a Soliton Lattice,
Synth. Met. 65, 225-232 (1994).
DOI
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Q. Li, L. Cruz, P. Phillips,
Granular-rod Model for Electronic Conduction in Polyaniline,
Physical Review B 47, 1840-1845 (1993).
DOI
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Q. Li, L. Cruz, P. Phillips,
Dimers and Rods in the Conducting States of Polyaniline,
Synth. Met. 55-57, 4697-4703 (1993).
DOI
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Scattering by Metallic Nanoparticles
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L. Fonseca, M. Gomez, L. Cruz,
Calculation of the Aggregation and Electrodynamic Effects in Granular Systems,
Physica A 207, 123-130 (1994).
DOI
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W. Vargas, L. Cruz, L. Fonseca, M. Gomez, T-Matrix Approach for
Calculating Local Fields around Clusters of Rotated Spheroids, App.
Opt. 32, 2164-2170 (1993).
DOI
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L. Fonseca, L. Cruz, M. Gomez, J. A. Gonzalo,
Determination of sizes of Potassium Colloids in KCl:O2 using Light
Scattering Techniques,
App. Phys. Comm. 12, 153-162 (1993).
DOI
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L. Fonseca, L. Cruz, W. Vargas, M. Gomez, Theoretical Calculation of
the Optical Absorption of Fractal Colloidal Aggregates Using a Multiple
Scattering Formalism, Condensed Matter Theories 8, 561-571, eds.
L.Blum, F. B. Malik, Plenum Press, N.Y. (1993).
DOI
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M. Gomez, L. Fonseca, L. Cruz}, W. Vargas, Calculation of Local Fields
for Clusters of Ellipsoids within the T-Matrix Approach, Mat. Res. Soc.
Symp. Proceedings 195, 109-114 (1990).
DOI
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L. Cruz, L. Fonseca, M. Gomez,
T-Matrix Approach for the Calculation of Local Fields in the Neighborhood
of Small Clusters in the Electrodynamic Regime,
Physical Review B 40, 7491-7500 (1989).
DOI
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M. Gomez, L. Fonseca, G. Rodriguez, A. Velazquez, L. Cruz,
Multiple Scattering theories including Correlation effects to obtain the
Effective Dielectric Constant of Non-Homogeneous Thin Films,
Physical Review B 32, 3429-3441 (1985).
DOI
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Dynamics of Granular Materials
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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).
DOI
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Liquid-liquid Phase Transition
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H. E. Stanley, L. Cruz, S. T. Harrington, P. H. Poole,
S. Sastry, F. Sciortino, F. W. Starr, and R. Zhang, Cooperative Molecular
Motions in Water: The Liquid-Liquid Critical Point Hypothesis, Physica A
236, 19-37 (1997).
DOI
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