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Publications
Grant Period 5/1/1998 -
4/30/2004
Integrative Modeling of Subcellular Processes: Application
to Synaptic Activity and Pharmaceutical Discovery:
J. Andrew McCammon, Kim Baldridge, Michael Holst, Nathan Baker, Philip
Papadopoulos, Michel Sanner
Andrianantoandro, E., L. Blanchoin, D. Sept, J.A. McCammon,
T.D. Pollard. Kinetic Mechanism of End to End Annealing of
Actin Filaments. J. Mol. Biol. 312, 721-730 (2001).
Baker, N.A., D. Sept, M.J. Holst, J.A. McCammon. The Adaptive
Multilevel Finite Element Solution of the Poisson-Boltzmann
Equation on Massively Parallel Computers. IBM J. Res. Devel.
45, 427-438 (2001).
Baker, N.A., D. Sept, S. Joseph, M.J. Holst, J.A. McCammon.
Electrostatics of Nanosystems: Application to Microtubules
and the Ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041
(2001).*
Baldridge, K. K.; Bourne, P. The New Biology and the Grid,
In Grid Computing, Fran Berman, Ed., 2002, Chpt. 40.
Baldridge, K. K.; Greenberg, J .P.; Elbert, S.; Papadopoulos,
P.; Mock, S. "QMView and GAMESS: Integration into the
World Wide Computational Grid," SC2002 Conf. Proc., 2002.
Baldridge, K.K. and Siegel, J.S. Correlation of Empirical
d(TMS) and Absolute NMR Chemical Shifts Predicted by Ab Initio
Computations. Journal of Physical Chemistry A, 103:4038-4042,
1999.*
Baldridge, K.K., O'Connor, J.M., Chen, M-C, and Siegel, J.S.
Envelope-Flip Dynamics in CpCo(Diene) Complexes: an abInitio
Quatum Mechnaical Study. Journal of Physical Chemistry A,
103:10126-10131, 1999. *
Baldridge, K.K.; Brumer, Y.; Brumer, P.; Shapiro, M. Conformational
Dynamics of the Hydrogen Exchange Reaction between Formaldehyde
and Methanol. J. Phys. Chem., 2002, 106, 9512-9519.
Baldridge, K.K.; Jonas, V. Implementation and refinement of
the modified-conductor-like screening quantum mechanical solvation
model at the MP2 level. J. Chem. Phys., 113: 7511-7518, 2000.*
Baldridge, K.K.; Jonas, V.; Bain, A. Ground State Gas and
Solution Phase Conformational Dynamics of Polar Processes:
Furfural systems. J. Chem. Phys., 113:7519-24, 2000.*
Baldridge, K.K.; Siegel, J.S. Ab Initio Quantum Mechanical
Prediction of Planar Delocalized Cyclooctatetraene: A New
Target for Synthesis., J. Am. Chem. Soc., 2001, 123, 1755.*
Baldridge, K.K.; Siegel, J.S. Directing Power of Cyclobutenoid
Annelations on the Double Bonds of Cyclooctatetraene: Ring
Strain vs Resonance Effects, J. Am. Chem. Soc., 2002, 124,
5514-5517.
Baldridge, K.K.; Uzan, O.; Martin, J.M. Silabenzenes: Structure,
Properties, and Aromaticity. Organometallics., 1999.
Baldridge, K.K.and Siegel, J.S. Canastanes: Ab Initio Quantum
Mechanical Prediction of New Curved Polynuclear Aromatic Hydrocarbon
Motif. Journal of the American Chemical Society, 121:5332-5333,
1999.*
Barnett, L.; Douglas, M.-Ho.; Baldridge, K.K.; Pascal, R.
A., Jr. The Structure of Hexabenzotriphenylene and the Problem
of Overcrowded "D3h" Polycyclic Aromatic Compounds.
J. Am. Chem. Soc., 121, 727-733, 1999.
Bolding, B.; Baldridge, K.K. Multithreaded Shared Memory Parallel
Implementation of the Electronic Structure Theory Code: GAMESS,
Comp. Phys. Comm., 1999.
Canino LS, T Shen, and JA McCammon. Changes in flexibility
upon binding: Application of the self-consistent pair contact
probability method to protein-protein interaction. Journal
of Chemical Physics 117: 9927-33, 2002.
Chen, Y.-T.; Baldridge, K.K.; Ho, D.M.; Pascal, R.A., Jr.
Interconversion and Reactions of in and out- Isomers of Triarylphosphine-Containing
Cyclophane. Journal of the American Chemical Society, 121,
12082-12087, 1999.
Elcock, A.H., D. Sept, J.A. McCammon. Computer Simulation
of Protein-Protein Interactions. J. Phys. Chem. B 105, 1504-1518
(2001).
Elcock, A.H., J.A. McCammon. Calculation of Weak Protein-Protein
Interactions: The pH Dependence of the Second Virial Coefficient.
Biophys. J. 80, 613-625 (2001).
Elcock, A.H., J.A. McCammon. Identification of Protein Oligomerization
States by Analysis of Interface Conservation. Proc. Natl.
Acad. Sci. USA 98, 2990-2994 (2001).
Gregersen, L.; Siegel, J.S; Baldridge, K.K. Ab Initio Computational
Study of Environmentally Harmful Gasoline Additives: Methyl-Tert-Butyl-Ether
(MTBE) and Analogues, J. Phys. Chem., 104: 11106-11110, 2000.*
Gross, L.A.; Baird, G.S.; Hoffman, R.C.; Baldridge, K.K.;
Tsien, R.Y. The Structure of the Chromophore within DsRed,
a Red Fluorescent Protein from Coral, PNAS, 97:11990-11995,
2000.*
Henchman R.H., J.A. McCammon. Structural and dynamical properties
of water around acetylcholinesterase. Protein Science 11:
2080-90 (2002)*
Henchman R.H., K. Tai, T. Shen, J.A. McCammon. Properties
of water molecules in the active site gorge of acetylcholinesterase
from computer simulation. Biophysical Journal 82: 2671-82
(2002)*
Henchman R.H., K. Tai, T. Shen, J.A. McCammon. Influence of
water on the function of acetylcholinesterase. In Cholinergic
Mechanisms Symposium Proceedings, ed. A Fisher, H Soreq. in
press (2003)*
Jimenez, R.; Salazar, G.; Baldridge, K.K.; Romesberg, F. "Flexibility
and Molecular Recognition in the Immune System," PNAS,
(cover), 2002, 100, 92-97. *
Karplus M, McCammon JA. Molecular dynamics simulations of
macromolecules: A perspective. Nature structural biology 9:
646-52 (2002)*
Kua J, Zhang Y, McCammon JA. Studying enzyme binding specificity
in acetylcholinesterase using a combined molecular dynamics
and multiple docking approach. Journal of American Chemical
Society 124: 8260-7 (2002)*
Lin J.H., A. Perryman, J.R. Schames, J.A. McCammon. The relaxed
complex method: Accommodating receptor flexibility for drug
design with an improved scoring scheme. Biopolymers 68: 47-62,
(2002)*
Lin, J.H., A. Perryman, J. Schames, J.A. McCammon. Computational
Drug Design Accommodating Receptor Flexibility - The Relaxed
Complex Scheme. J. Amer. Chem. Soc. 124, 5632-5633 (2002)*
Lin, J.H., N.A. Baker, J.A. McCammon. Bridging the Implicit
and Explicit Solvent Approaches for Membrane Electrostatics.
Biophys. J. 83, 1374-1379 (2002).*
McCammon, J.A. Historical Overview and Future Challenges,
in "Free Energy Calculations in Rational Drug Design,"
M.R. Reddy and M.D. Erion, Eds. Kluwer Publishing, the Netherlands,
pp. 1-6 (2001).
Morikis, D., A.H. Elcock, P.A. Jennings, J.A. McCammon. Proton
Transfer Dynamics of GART: The pH-Dependent Catalytic Mechanism
Examined by Electrostatic Calculations. Protein Sci. 10, 2379-2392
(2001).
Ni, H., C.A. Sotriffer, J.A. McCammon. Ordered Water and Ligand
Mobility in the HIV-1 Integrase - 5CITEP Complex: A Molecular
Dynamics Study. J. Med. Chem. 44, 3043-3047 (2001).
Nielsen, J.E., J.A. McCammon. On the evaluation and optimization
of protein X-ray structures for pKa calculations. Protein
Science, 12(2), 313-326. (2002)*
Nolen, B., C.Y Yun, C.F. Wong, J.A. McCammon, X.D. Fu, G.
Ghosh. The Structure of Sky1p Reveals a Novel Mechanism for
Constitutive Activity, Nature Struct. Biol. 8, 176-183 (2001).
Noy, D.; Yerushalmi, R.; Brumfeld, V.; Ashur, I.; Scheer,
H.; Baldridge, K.K.; Scherz, A. Optical Absorption and Computational
Studies of [Ni]-Bacteriochlorophyll-a. New Insight into Charge
Distribution between Metal and Ligands, J. Am. Chem. Soc.,
122:3937-3944, 2000.
Noy, D.; Yerushalmi, R.; Brumfeld, V.; Ashur, I.; Scheer,
H.; Baldridge, K.K.; Scherz, A. Quantifying Electron Density
Migration Between Ligands and Metal Using Metal-Substituted
Bacteriochlorophyll-a., J. Am. Chem. Soc., 1999
Ondrechen, M.J., J.M. Briggs, J.A. McCammon. A Model for Enzyme-Substrate
Interactions in Alanine Racemase. J.Amer. Chem. Soc. 123,
2830-2834 (2001).
Perryman A, McCammon JA. Autodocking dinucleotides to the
HIV-1 integrase core domain: Exploring possible binding sites
for viral and genomic DNA. Journal of Medicinal Chemistry
45: 5624-27 (2002)*
Podtelezhnikov AA, Goa K, Bushman FD, McCammon JA. Modeling
HIV-1 integrase complexes based on their hydrodynamic properties.
Biopolymers 68: 110-20 (2002)*
Rowley DC, Hansen MST, Rhodes D, Sortriffer CA, Ni H, McCammon
JA. Thalassionlins A-C: New marine-derived inhibitors of HIV
cDNA integrase. Bioorganic and medicinal chemistry 10: 3619-25
(2002)*
Seiders, T.J., Baldridge, K.K., Elliot, E.L., Grube, G.H and
Siegel, J.S. Synthesis and quantum Mechanical Structure of
sym-Pentamethylcorannulene and Decamethylcorannulene. Journal
of the American Chemical Society, 121:7439-7440, 1999.*
Seiders, T.J.; Baldridge, K.K.; Gleiter, R.; Siegel, J.S.
Ionization of Corannulene and 1,6-Dimethylcorannulene: Photoelectron
Spectra, Electrochemistry, Charge Transfer Bands, and ab initio
Computations. Tetrahedron Lett., 41:4519-4522, 2000. *
Seiders, T.J.; Baldridge, K.K.; Grube, G.H.; Siegel, J.S.
Structure/Energy Correlation of Bowl Depth and Inversion Barrier
in Corannulene Derivatives: Combined Experimental, and Quantum
Mechanical Analysis. J. Am. Chem. Soc., 123:517-525, 2001.*
Seiders, T.J.; Baldridge, K.K.; Grube, G.H.; Siegel, J.S.
Structure/Energy Correlation of Bowl Depth and Inversion Barrier
in Corannulene Derivatives: Combined Experimental, and Quantum
Mechanical Analysis. J. Am. Chem. Soc., 2001, 123, 517-525.
Seiders, T.J.; Baldridge, K.K.; Siegel, J.S. "Baskets,
Covered Baskets, and Basket Balls: Corannulene Based Cylcophanes
as Fullerene Mimics," Tetrahedron, 2001, 3737-3742.
Sept, D., J.A. McCammon. Thermodynamics and Kinetics of Actin
Filament Nucleation. Biophys. J. 81, 667-674 (2001).
Shen, T., C.F. Wong, J.A. McCammon. Atomistic Brownian Dynamics
Simulation of Peptide Phosphorylation. J. Amer. Chem. Soc.
123, 9107-9111 (2001).
Shen, T.Y., K. Tai, J.A. McCammon. Statistical Analysis of
the Fractal Gating Motions of the Enzyme Acetylcholinesterase.
Phys. Rev. E 63, 041902 (2001).
Shen, T., L.S. Canino, J.A. McCammon. Unfolding Proteins under
External Forces: A Solvable Model under the Self-consistent
Pair Contact Probability Approximation. Phys. Rev. Lett. 89,
article number 068103 (2002).*
Shen T, Wong CF, McCammon JA. Brownian dynamics simulation
of helix-capping MOTIFs. Biopolymers in press (2003)*
Steffens, R.J.; Baldridge, K.K.; Siegel, J.S. Synthesis and
Properties of 2,3-Dihydro-1H-corannuleneo[2,3-cd]pyridine(=2,3-Dihydro-1H-dibenzo[1,10:6,7]fluorantheno[3,4-cd]pyridine)
Derivatives: Heterocyclic peri-Annelated Corannulenes, Helv.
Chim. Acta, 83:2644-2654, 2000.*
Straatsma, T.P., J.A. McCammon. Load Balancing of Molecular
Dynamics Simulation with NWChem. IBM Systems J. 40, 328-341
(2001).
Tai, K., T. Shen, U. Borjesson, M. Philippopoulos, J.A. McCammon.
Analysis of a Ten-nanosecond Molecular Dynamics Simulation
of Mouse Acetylcholinesterase. Biophys. J. 81, 715-724 (2001).*
Tai, K., T. Shen, R.H. Henchman, Y. Bourne, P. Marchot, J.A.
McCammon. Mechanism of Acetylcholinesterase Inhibition by
Fascinculin: A 5 ns Molecular Dynamics Simulation. In "Cholinergic
Mechanisms Symposium Proceedings", A. Fisher and H. Soreq,
Eds., in press (2003).*
Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon
JA. Finite element simulation sof acetylcholine diffusion
in neuromuscular junctions. Biophysical Journal to appear
(2003)*
Toendel K, Wong CF, McCammon JA. Computational analysis of
the interactions between the angiogenesis inhibitor PD173074
and fibroblast growth factor receptor 1. Journal of Theoretical
Computational Chemistry in press (2003)*
Vitalis A, Baker NA, McCammon JA. ISIM: A program for grand
canonical Monte Carlo simulations of the ionic environment
of biomolecules. Molecular simulations in press (2003)*
Wong, C.F., P.H. Hunenberger, P.Akamine, N. Narayana, T. Diller,
J.A. McCammon, S. Taylor, N.-H. Xuong. Computational Analysis
of PKA-Balanol Interactions. J. Med. Chem. 44, 1530-1539 (2001).
Wong, C.F., and J.A. McCammon. Protein Flexibility and Computer-aided
Drug Design. Annual Rev. Pharmacol. Toxicol. 43, 31-45 (2003).*
Wong CF, McCammon JA. Protein simulation and drug design.
Advances in Protein Chemistry in press (2003)*
Yerushalmil R.; Noy, D.; Baldridge, K. K.; Scherz, A. Molecular
Potentiometer - Following Charge Flow between Molecules. J.
Am. Chem. Soc., 2002, 124, 8406-8415.*
Zhang Y, Kua J, McCammon JA. Role of the catalytic triad and
oxyanion hole in acetylcholinesterase catalysis: An ab inito
QM/MM study. Journal of American Chemical Society 124: 10572-77
(2002)*
Zhang, Y. and J.A. McCammon. Studying the Affinity and Kinetics
of Molecular Association with Molecular Dynamics Simulation,
J. Chem. Phys. 118: 1821-27 (2003).*
Data Integration and Analytic Tools for Molecular Sequences:
Michael Gribskov, Chaitan Baru
Bailey, Timothy L.; Gribskov, Michael. Concerning the accuracy
of MAST E-values. Bioinformatics, 16(5):488-489, May 2000.
Bier, E.; Reiter, L.; Potocki, L.; Gribskov, M. Homophila:
A cross-genomic relational database of human disease genes
to the complete Drosophila melanogaster genome. (50th Annual
Meeting of the American Society of Human Genetics Philadelphia,
Pennsylvania, USA October 3-7, 2000) American Journal of Human
Genetics, 67(4 Supplement 2):255, October 2000.
Chien, S., Reiter, L.T., Bier, E., and Gribskov, M., "Homophila:
human disease genes in Drosophila", Nucleic Acids Research,
30, 149-151, 2002.
Fink JL; Drewes S; Masys DR; Welsh JB; Corbeil J; Gribskov
M. 2HAPI: a Microarray Data Analysis System. In press, Bioinformatics,
2003.
Ghassemian, M; Waner, D; Tchieu, J; Gribskov, M; An integrated
Arabidopsis annotation database for Affymetrix Genechip (R)
data analysis, and tools for regulatory motif searches. Trends
in Plant Science, 2001, 6. 448-449.*
Gribskov, M, Bourne, P. and Smith, C.M. PKR - the Protein
Kinase Resource. In Genetic Databases (M.J. Bishop, ed.),
Academic Press, San Diego, CA, USA. pp 241-246, 1999.
Gribskov, M., Fana, F., Harper, J., Hope, D.A., Harmon, A.C.,
Smith, D.W., Tax, F.E., and Zhang, G.F., "PlantsP: a
functional genomics database for plant phosphorylation,"
Nucleic Acids Research, 29, 111-113, 2001.*
Harmon, A.C., Gribskov, M., Gubrium, E., and Harper, J.F..
"The CDPK superfamily of protein kinases," New Phytologist,
151, 175-183, 2001.*
Harmon, Alice C.; Gribskov, Michael; Harper, Jeffrey F. CDPKs:
A kinase for every Ca2+ signal?. Trends in Plant Science,
5(4):154-159, April 2000.
Maser, P., Thomine, S., Schroeder, J.I., Ward, J.M., Hirschi,
K., Sze, H., Talke, I.N., Amtmann, A., Maathuis, F.J.M., Sanders,
D., Harper, J.F., Tchieu, J., Gribskov, M., Persans, M.W.,
Salt, D.E., Kim, S.A., Guerinot, M.L., "Phylogenetic
relationships within cation transporter families of Arabidopsis,"
Plant Physiology, 126, 1,646-1,667, 2001.*
Masys, D.R., Welsh, J.B., Fink, J.L., Gribskov, M., Klacansky,
I., and Corbeil, J., "Use of keyword hierarchies to interpret
gene expression patterns," Bioinformatics, 17, 319-326,
2001.*
Reiter, L.T., Potocki, L., Chien, S., Gribskov, M., and Bier,
E., "A systematic analysis of human disease-associated
gene sequences in Drosophila melanogaster", Genome Research,
11, 1114-1125, 2001.*
Milik, E; Zhao, T;Wild, Laurence; Smith, CM. CMSMBR: Web
Portal for Data Analysis Tools and Databases, Molecular Biology
of the Cell, Supplement , Vol. 11, p. 132a, Abstract No. 692,
December 2000.*
Smith, C.M. The protein kinase resource and other bioinformation
resources. Progress in Biophysics and Molecular Biology ,
71:525-533, 1999.
Smith, C.M., Radio-Andzelm, E., Madhusudan, Akaamine, P. and
Taylor, S.S. The catalytic subunit of cAMP-dependent protein
kinase: prototype for an extended network of communication.
Progress in Biophysics and Molecular Biology, 71:313-341,
1999.
Smith, CM; Wild, L; Zhao, T; Milik, E. CMSMBR: Web Portal
for Data Analysis Tools and Databases, The FASEB Journal,
Vol. 15 (Experimental Biology 2001 Program), Abstract No.
690.18, March 7, 2001.
Smith, CM; Zhao, T; Milik, E; Wild, E. CMSMBR: Web Portal
for Data Analysis Tools and Databases. Abstracts of the AAAS
Annual Meeting & Science Innovation Exposition, p. A81,
February 15-20, 2001.*
Tchieu JH, Fana F, Fink JL, Harper J, Nair TM, Niedner RH,
Smith DW, Steube K, Tam TM, Veretnik S, Wang D, Gribskov M.,
"The PlantsP and PlantsT Functional Genomics Databases",
Nucleic Acids Res. 31, 342-344, 2003.
Veretnik, S. and Gribskov, M. RNA binding domain of HDV antigen
in homologous to the HMG Box of SRR. Archives of Virology,
144:1139-1158, 1999.
Structurally and Functionally Integrated Modeling of
Cell and Organ Biophysics:
Andrew McCulloch, Anushka Michailova,
Mark Ellisman, Philip Papadopoulos, Michel Sanner
Arts T, Costa KD, Covell JW , McCulloch AD (2001) Relating
myocardial laminar architecture to shear strain and muscle
fiber orientation. Am J Physiol Heart Circ Physiol 280(5):
H2222-9.
Baxter WW (1999). Mechanical Analysis of Intravascular Medical
Devices In Vivo. Bioengineering. La Jolla, University of California
San Diego: 230.
Baxter WW , McCulloch AD (2001) In vivo finite element model-based
image analysis of pacemaker lead mechanics. Med Image Anal
5(4): 255-70.
Costa KD, Holmes JW , McCulloch AD (2001) Modeling cardiac
mechanical properties in three dimensions. Phil Trans R Soc
Lond A 359: 1233-1250.
Karlon WJ, Covell JW, McCulloch AD, Hunter JJ , Omens JH (1998)
Automated measurement of myofiber disarray in transgenic mice
with ventricular expression of ras. Anatomical Record 252(4):
612-625.
Karlon WJ, Hsu PP, Li S, Chien S, McCulloch AD , Omens JH
(1999) Measurement of orientation and distribution of cellular
alignment and cytoskeletal organization. Ann Biomed Eng 27(6):
712-20.
Mazhari R (1999) Regional Flow-Function Relations during Acute
Myocardial Ischemia and Reperfusion. Bioengineering. La Jolla,
University of California San Diego.
Mazhari R , McCulloch AD (2000) Integrative models for understanding
the structural basis of regional mechanical dysfunction in
ischemic myocardium. Ann Biomed Eng 28(8): 979-90.
Mazhari R, Omens JH, Covell JW , McCulloch AD (2000) Structural
basis of regional dysfunction in acutely ischemic myocardium.
Cardiovasc Res 47(2): 284-293.*
Mazhari R, Omens JH, Waldman LK , McCulloch AD (1998) Regional
myocardial perfusion and mechanics: a model based method of
analysis. Annals of Biomedical Engineering 26(5): 743-755.
McCulloch A, Sung D, Thomas ME , Michailova A (2001) Chapter
11: Computational and Experimental Modeling of Ventricular
Electromechanical Interactions. Computer Simulation and Experimental
Assessment of Cardiac Electrophysiology. Virag N, Blanc O
, Kappenberger L. Amonk, NY, Futura Publishing Company, Inc.:
89-96.*
McCulloch AD (2000) Modeling the human cardiome in silico
[editorial]. J Nucl Cardiol 7(5): 496-9.
McCulloch AD (2001). Regional stress and strain in healthy
and diseased ventricular myocardium. Measurement of Cardiac
Deformations from MRI: Physical and Mathematical Models. Amini
AA , Prinz JL. New York, NY, Kluwer Academic Publishers: 1-15.*
McCulloch AD , Huber G (2002) Integrative biological modelling
in silico. 'In Silico' Simulation of Biological Processes.
Bock G , Goode JA. Chichester, Wiley. 247: 4-25.*
McCulloch AD , Mazhari R (2001) Regional myocardial mechanics:
integrative computational models of flow-function relations.
J Nucl Cardiol 8(4): 506-19.
McCulloch AD, Sung D, Thomas ME , Michailova A (2001) Experimental
and computational modeling of cardiac electromechanical coupling.
Functional Imaging and Modeling of the Heart. Katila T, Magnin
IE, Clarysse P, Montagnet J , Nenonen J. Berlin, Springer-Verlag:
113-119.*
Michailova A, DelPrincipe F, Egger M , Niggli E (2002) Spatiotemporal
features of Ca(2+) buffering and diffusion in atrial cardiac
myocytes with inhibited sarcoplasmic reticulum. Biophys J
83(6): 3134-51.
Michailova A, DelPrincipe F, Egger M , Niggli E (in press)
Ca2+ signaling, buffering and diffusion in atrial myocytes:An
experimental and modeling study. International Journal of
Bifurcation and Chaos.*
Michailova A., McCulloch AD (2001) Model Study of ATP and
ADP Buffering, Transport of Ca2+ and Mg2+, and Regulation
of Ion Pumps in Ventricular Myocyte. Biophysical J 81(2):614-629.*
Omens JH, Usyk TP, Li Z , McCulloch AD (2002) Muscle LIM protein
deficiency leads to alterations in passive ventricular mechanics.
Am J Physiol Heart Circ Physiol 282: H680-H687.
Paternostro G, Vignola C, Bartsch D-U, Omens JH, McCulloch
AD , Reed JC (2001) Age-Associated Cardiac Dysfunction in
Drosophila melanogaster. Circ Res 88(10): 1053-1058.
Ramakrishna R, Edwards JS, McCulloch A , Palsson BO (2001)
Flux-balance analysis of mitochondrial energy metabolism:
consequences of systemic stoichiometric constraints. Am J
Physiol Regul Integr Comp Physiol 280(3): R695-704.
Sung D (2001) Effects of Mechanical Load on Ventricular action
Potential Propagation and Repolarization. Bioengineering.
La Jolla, University of California San Diego: 221.
Sung D, Mills RW, Schettler J, Narayan S, Omens JH , McCulloch
AD (submitted) Ventricular filling slows epicardial conduction
and increases action potential duration in an optical mapping
study of the isolated rabbit heart. J Cardiovasc Electrophysiol.
Sung D, Omens JH , McCulloch AD (2000) Model-Based analysis
of optically mapped epicardial activation patterns and conduction
velocity. Ann Biomed Eng 28(9): 1085-92.*
Sung D, Somayajula-Jagai J, Cosman P, Mills RW , McCulloch
AD (2001) Phase-shifting prior to spatial filtering enhances
optical recordings of cardiac action potential propagation.
Ann Biomed Eng 29: 854-861.*
Usyk TP, LeGrice IJ , McCulloch AD (2002) Computational model
of three-dimensional cardiac electromechanics. Comput Visual
Sci 4(4): 249-257.*
Usyk TP, Mazhari R , McCulloch AD (2000) Effect of laminar
orthotropic myofiber architecture on regional stress and strain
in the canine left ventricle. J Elasticity 61(1/3): 143-164.*
Usyk TP , McCulloch AD (in press). Computational methods for
soft tissue biomechanics. Mechanics of Soft Biological Tissues.
Holzapfel G OR: 1-84.
Usyk TP , McCulloch AD (submitted) Relationship between regional
shortening and asynchronous electrical activation in a three-dimensional
model of ventricular electromechanics. Journal of Cardiovascular
Electrophysiology.*
Usyk TP, Omens JH , McCulloch AD (2001) Regional septal dysfunction
in a three-dimensional computational model of focal myofiber
disarray. Am. J. Physiol. 281(2): H506-514.*
Vetter FJ (1999). Mechanoelectric Feedback in Ventricular
Myocardium. Bioengineering. La Jolla, University of California
San Diego.*
Vetter FJ , McCulloch AD (1998) Three-dimensional analysis
of regional cardiac function: a model of rabbit ventricular
anatomy. Progress in Biophysics and Molecular Biology 69(2-3):
157-183.*
Vetter FJ , McCulloch AD (2000) Three-dimensional stress and
strain in passive rabbit left ventricle: a model study. Ann
Biomed Eng 28(7): 781-92.*
Vetter FJ , McCulloch AD (2001) Mechanoelectric feedback in
a model of the passively inflated left ventricle. Ann Biomed
Eng 29: 414-426 (and cover).*
Young AA, Dokos S, Powell KA, Sturm B, McCulloch AD, Starling
RC, McCarthy PM , White RD (2001) Regional heterogeneity of
function in nonischemic dilated cardiomyopathy. Cardiovasc
Res 49(2): 308-318.
Visualization Environments for Multi-Scale Biomedical
Modeling:
Michel Sanner, Art Olson
Coon, Sophie I., Michel F. Sanner and Arthur J. Olson. Re-Usable
components for Structural Bioinformatics. In Proceedings of
thre 10th International Python conference. 103-115. February
4-7, 2002. ISBN 1-930792-05-0.
Coon, S.I.; Sanner, M.F.; Olson, A.J. Re-usable components
for structural bioinformatics. Proc. Ninth Annual Python Conference.,
Long Beach, CA, March 2001.
Lewis WG, Green LG, Grynszpan F, Radic Z, Carlier PR, Taylor
P, Finn MG, Sharpless KB. (2002). "Click chemistry in
situ: acetylcholinesterase as a reaction vessel for the selective
assembly of a femtomolar inhibitor from an array of building
blocks." Angew Chem Int Ed Engl, 41(6):1053-7.
Macke, T.J., Duncan, B.S., Goodsell, D.S. & Olson, A.J.
(1999) Interactive Modeling of Supramolecular Assemblies.
J. Mol. Graphics and Modelling 16:115-120
MGLTOOLS
http://www.scripps.edu/pub/olson-web/people/sanner/html/Python/index.html
Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart,
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