Publications
Books
O. Gonzalez,
Topics in Applied Mathematics and Modeling:
Concise Theory with Case Studies,
Pure and Applied Undergraduate Texts, Volume 59,
American Mathematical Society (2023).
Print ISBN 978-1-4704-6991-7,
Electronic ISBN 978-1-4704-7217-7.
210 pages, 300+ exercises, 180+ illustrations.
O. Gonzalez & A. Stuart,
A First Course in Continuum Mechanics,
Cambridge Texts in Applied Mathematics, Cambridge University
Press (2008). ISBN 978-0-521-88680-2 hardback,
ISBN 978-0-521-71424-2 paperback.
416 pages, 170+ exercises.
O. Gonzalez & A. Stuart,
A First Course in Continuum Mechanics: Complete
Solutions Manual,
Cambridge University Press (2008).
119 pages.
Articles
O. Gonzalez,
Building a better bridge between
models and experimental data for DNA,
Biophysical Journal,
(2024) submitted.
O. Gonzalez,
Theorems on the stokesian hydrodynamics of a rigid filament
in the limit of vanishing radius,
SIAM Journal on Applied Mathematics,
81 (2021) 551-573.
Supplementary material:
PDF file.
A. Mauney, J. Tokuda, L. Gloss, O. Gonzalez & L. Pollack,
Local DNA sequence controls the cooperativity and asymmetry
of DNA unwrapping from nucleosome core particles,
Biophysical Journal,
115 (2018) 773-781.
[This work was recognized in a dedicated
commentary article.]
O. Gonzalez,
Bounds on the average velocity of a rigid body
in a Stokes fluid,
SIAM Journal on Applied Mathematics,
77 (2017) 1904-1920.
O. Gonzalez, M. Pasi, D. Petkeviciute, J. Glowacki & J.H. Maddocks,
Absolute versus relative entropy parameter estimation in
a coarse-grain model of DNA,
SIAM Multiscale Modeling and Simulation,
15 (2017) 1073-1107.
Supplementary website:
http://lcvmwww.epfl.ch/cgDNA.
cgDNAweb (a web-based viewer for the cgDNA model):
http://cgdnaweb.epfl.ch.
O. Gonzalez,
A theorem on the surface traction field
in potential representations of Stokes flow,
SIAM Journal on Applied Mathematics,
75 (2015) 1578-1598.
O. Gonzalez & J. Li,
A convergence theorem for a class of Nystrom methods for
weakly singular integral equations on surfaces in R^3,
Mathematics of Computation,
84 (2015) 675-714.
D. Petkeviciute, M. Pasi, O. Gonzalez & J.H. Maddocks,
cgDNA: a software package for the prediction
of sequence-dependent coarse-grain free energies of
B-form DNA,
Nucleic Acids Research,
42 (2014) e153: 1-9.
Supplementary material:
PDF file.
Supplementary website:
http://lcvmwww.epfl.ch/cgDNA.
cgDNAweb (a web-based viewer for the cgDNA model):
http://cgdnaweb.epfl.ch.
J. Li & O. Gonzalez,
Convergence and conditioning of a Nystrom method for
Stokes flow in exterior three-dimensional domains,
Advances in Computational Mathematics,
39 (2013) 143-174.
O. Gonzalez, D. Petkeviciute & J.H. Maddocks,
A sequence-dependent rigid-base model of DNA,
Journal of Chemical Physics,
138 (2013) 055102: 1-28.
Supplementary material:
PDF file.
Supplementary website:
http://lcvmwww.epfl.ch/cgDNA.
cgDNAweb (a web-based viewer for the cgDNA model):
http://cgdnaweb.epfl.ch.
[This article was selected for the 2013 JCP Editors'
Choice Collection.]
O. Gonzalez & J. Li,
On the hydrodynamic diffusion of rigid
particles of arbitrary shape with application to DNA,
SIAM Journal on Applied Mathematics,
70 (2010) 2627-2651.
J. Walter, O. Gonzalez & J.H. Maddocks,
On the stochastic modeling of rigid body systems with
application to polymer dynamics,
SIAM Multiscale Modeling and Simulation,
8 (2010) 1018-1053.
F. Lankas, O. Gonzalez, L.M. Heffler,
G. Stoll, M. Moakher & J.H. Maddocks,
On the parameterization of rigid base and basepair
models of DNA from molecular dynamics simulations,
Physical Chemistry Chemical Physics,
11 (2009) 10565-10588.
O. Gonzalez,
On stable, complete and singularity-free boundary
integral formulations of exterior Stokes flow,
SIAM Journal on Applied Mathematics
69 (2009) 933-958.
O. Gonzalez & J. Li,
Modeling the sequence-dependent diffusion
coefficients of short DNA sequences,
Journal of Chemical Physics
129 (2008) 165105: 1-12.
O. Gonzalez, A.B.A. Graf & J.H. Maddocks,
Dynamics of a rigid body in a Stokes fluid,
Journal of Fluid Mechanics
519 (2004) 133-160.
O. Gonzalez & R. de la Llave,
Existence of ideal knots,
Journal of Knot Theory and Its Ramifications
12 (2003) 123-133.
J.R. Banavar, O. Gonzalez, J.H. Maddocks & A. Maritan,
Self-interactions of strands and sheets,
Journal of Statistical Physics
110 (2003) 35-50.
O. Gonzalez, J.H. Maddocks & J. Smutny,
Curves, circles and spheres,
Contemporary Mathematics
304 (2002) 195-215.
O. Gonzalez, J.H. Maddocks, F. Schuricht & H. von der Mosel,
Global curvature and self-contact of nonlinearly
elastic curves and rods,
Calculus of Variations and Partial
Differential Equations 14 (2002) 29-68.
O. Gonzalez & J.H. Maddocks,
Extracting parameters for base-pair level models
of DNA from molecular dynamics simulations,
Theoretical Chemistry Accounts
106 (2001) 76-82.
O. Gonzalez, J.H. Maddocks & R.L. Pego,
Multi-multiplier ambient space formulations of constrained
dynamical systems, with an application to elastodynamics,
Archive for Rational Mechanics and Analysis
157 (2001) 285-323.
O. Gonzalez,
Exact energy-momentum conserving algorithms
for general models in nonlinear elasticity,
Computer Methods in Applied Mechanics and Engineering
190 (2000) 1763-1783.
O. Gonzalez & J.H. Maddocks,
Global curvature, thickness and the ideal shapes of knots,
The Proceedings of the National Academy of Sciences,
USA 96 (1999) 4769-4773.
O. Gonzalez,
Mechanical systems subject to holonomic constraints:
differential-algebraic formulations and conservative
integration,
Physica D 132 (1999) 165-174.
O. Gonzalez, D.J. Higham & A.M. Stuart,
Qualitative properties of modified equations,
IMA Journal of Numerical Analysis
19 (1999) 169-190.
A. Stasiak, J. Dubochet, P. Furrer,
O. Gonzalez & J. Maddocks,
DNA: uncooked, al dente, or scotti?,
Science 283 (1999) 1641.
O. Gonzalez & A.M. Stuart,
On the qualitative properties of modified equations,
in Foundations of Computational Mathematics,
edited by F. Cucker & M. Shub, Springer Verlag, Berlin
(1997) 169-179.
O. Gonzalez,
Time integration and discrete hamiltonian systems,
Journal of Nonlinear Science
6 (1996) 449-467.
O. Gonzalez & J.C. Simo,
On the stability of symplectic and energy-momentum
algorithms for nonlinear hamiltonian systems with symmetry,
Computer Methods in Applied Mechanics and Engineering
134 (1996) 197-222.
J.C. Simo & O. Gonzalez,
Recent results on the numerical integration
of infinite-dimensional hamiltonian systems,
in Recent Developments in Finite Element Analysis,
edited by T.J.R. Hughes, E. Onate, and O.C. Zienkiewicz,
International Center for Numerical Methods in Engineering,
Barcelona, Spain (1994) 255-271.
J.C. Simo & O. Gonzalez,
Assessment of energy-momentum and symplectic
schemes for stiff dynamical systems,
American Society of Mechanical Engineers,
proceedings of the ASME Winter Annual Meeting,
New Orleans, Louisiana (1993) 1-12.
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