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# Year Publication name
139 2016 Morphomechanical Innovation Drives Explosive Seed Dispersal
H. Hofhuis, D. Moulton, T. Lessinnes, A.-L. Routier-Kierzkowska, R. J. Bomphrey, G. Mosca, H. Reinhardt, P. Sarchet, X. Gan, M. Tsiantis, Y. Ventikos, S. Walker, A. Goriely, R. Smith, A. Hay
Cell 166 (2016), p. 1-12
DOI:10.1016/j.cell.2016.05.002
138 2015 Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics
M. Pasi, J.H. Maddocks, R. Lavery
Nucleic Acid Research (2015)
DOI:10.1093/nar/gkv080
137 2014 μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, P.D. Dans, B. Jayaram, F. Lankas, C. Laughton, J. Mitchell, R. Osman, M. Orozco, A. Pérez, D. Petkevičiūtė, N. Spackova, J. Sponer, K. Zakrzewska, R. Lavery
Nucleic Acids Research 42, no. 19 (2014), p. 12272–12283
DOI:10.1093/nar/gku855
136 2014 cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA
D. Petkevičiūtė, M. Pasi, O. Gonzalez, J.H. Maddocks
Nucleic Acids Research 42, no. 20 (2014), p. e153
DOI:10.1093/nar/gku825
135 2014 Analyzing ion distributions around DNA
R. Lavery, J.H. Maddocks, M. Pasi and K. Zakrzewska
Nucl. Acids Res. 42, no. 12 (2014), p. 8138–8149
DOI:10.1093/nar/gku504
134 2013 Twist and Stretch of Helices Explained via the Kirchhoff-Love Rod Model of Elastic Filaments
B. Ðurickovic, A. Goriely, J.H. Maddocks
Physical Review Letters 111 (2013), p. 108103 1-5
DOI:10.1103/PhysRevLett.111.108103
133 2011 Second-Order Inference for Functional Data with Application to DNA Minicircles
Victor M. Panaretos, David Kraus, John H. Maddocks
Recent Advances in Functional Data Analysis and Related Topics Chapter 38 (2011), p. 245-250
DOI:10.1007/978-3-7908-2736-1_38
132 2013 A sequence-dependent rigid-base model of DNA
Oscar Gonzalez, Daiva Petkevičiūtė, and John H. Maddocks
Journal of Chemical Physics 138, no. 5 (2013), p. 055122 1-28
DOI:10.1063/1.4789411
131 2011 Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems
J. Walter, C. Hartmann, J.H. Maddocks
Eur. Phys. J. Special Topics 200 (2011), p. 153 - 181
DOI:10.1140/epjst/e2011-01523-y
130 2012 Adaptive conformational sampling based on replicas
J. Curuksu
J. Math. Biol. 64, no. 6 (2012), p. 917-931
DOI:10.1007/s00285-011-0432-6
129 2011 A closed contact cycle on the ideal trefoil
Mathias Carlen, Henryk Gerlach
submitted (2011)
128 2010 Looping probabilities of elastic chains: A path integral approach
L. Cotta-Ramusino, J.H. Maddocks
Physical Review E 82 (2010), p. 051924 [15 pages]
DOI:10.1103/PhysRevE.82.051924
127 2012 Fourier approximation of symmetric ideal knots
Mathias Carlen, Henryk Gerlach
Journal of Knot Theory and Its Ramifications Vol. 21, no. 5 (2012), p. 1250057 1-14
126 2011 On sphere-filling ropes
Henryk Gerlach, Heiko von der Mosel
American Math Monthly 118, no. 10 (2011), p. 863 - 876
125 2010 On the stochastic modeling of rigid body systems with application to polymer dynamics
J. Walter, O. Gonzalez, J.H. Maddocks
SIAM Multiscale Modeling and Simulation 8, no. 3 (2010), p. 1018 – 1053
124 2010 Second-Order Comparison of Gaussian Random Curves and the Geometry of DNA Minicircles
V.M. Panaretos, D. Kraus, J.H. Maddocks
Journal of the American Statistical Association 105, no. 490 (2010), p. 670 - 682
123 2009 A systematic molecular dynamics study of nearest neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
R. Lavery, K. Zakrzewska, D. Beveridge, T. C. Bishop, D. A. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, Ch. Laughton, J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, J. Sponer
Nucleic Acids Research 38, no. 1 (2009), p. 299-313
122 2009 On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations
F. Lankas, O. Gonzalez, L. M. Heffler, G. Stoll, M. Moakher, J. H. Maddocks
Phys. Chem. Chem. Phys. 11 (2009), p. 10565 - 10588
121 2009 Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
D. Demurtas, A. Amzallag, E.J. Rawdon, J.H. Maddocks, J. Dubochet, A. Stasiak
Nucleic Acids Research 37, no. 9 (2009), p. 2882 - 2893
120 2009 Conformational analysis of nucleic acids revisited: Curves+
R. Lavery, M. Moakher, J.H. Maddocks, D. Petkeviciute, K. Zakrzewska
Nucleic Acids Res. 37 (2009), p. 5917 - 5929
119 2011 What are the longest ropes on the unit sphere?
Henryk Gerlach, Heiko von der Mosel
Arch. Rat. Mech. Anal. 201 (2011), p. 303 - 342
118 2009 A 1D model for a closed rigid filament in Stokes flow
Ph. Caussignac
Mathematical Models and Methods in Applied Sciences 19 (2009), p. 911 - 937
117 2006 Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
K. Reblova, F. Lankas, F. Razga, M.V. Krasovska, J. Koca, J. Sponer
Biopolymers 82 (2006), p. 504 - 520
116 2007 Structural motifs of biomolecules
J.R. Banavar, T.X. Hoang, J.H. Maddocks, A. Maritan, C. Poletto, A. Stasiak, A. Trovato
PNAS 104, no. 44 (2007), p. 17283 – 1728
115 2007 Around the Möbius band
John H. Maddocks
Nature Materials 6 (2007), p. 547 - 548
114 2008 A gauge finite element method for the 2D Navier-Stokes problem
Ph. Caussignac
Applied Numerical Mathematics 58 (2008), p. 1413 - 1433
113 2007 Low-energy effective theory for a Randall-Sundrum scenario with a moving bulk brane
Ludovica Cotta-Ramusino and David Wands
Phys. Rev. D 75, no. 10 (2007), p. 104001 [9 pages]
112 2006 Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder
C. Vaillant, B. Audit, C. Thermes, A. Arneodo
Eur. Phys. J. E 19 (2006), p. 263 - 277
111 2007 Sequence-dependent twist-stretch coupling in DNA
T Lionnet, F Lankas
Biophysical Journal 92 (2007), p. L30 - L32
110 2006 3-D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy
Arnaud Amzallag, Cédric Vaillant, Mathews Jacob, Michael Unser, Jan Bednar, Jason Kahn, Andrzej Stasiak, Jacques Dubochet, John H. Maddocks.
Nucleic Acids Research 34, no. 18 (2006), p. e125
DOI:DOI: 10.1093/nar/gkl675
109 2006 Kinking occurs during molecular dynamics simulations of small DNA minicircles
F. Lankas, R. Lavery, J.H. Maddocks
Structure 14 (2006), p. 1527 - 1534
108 2006 Helices
Nadia Chouaieb, Alain Goriely, and John H. Maddocks
Proceedings of the National Academy of Sciences USA 103 (2006), p. 9398 - 9403
107 2008 Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA
Illia Horenko, Evelyn Dittmer, Filip Lankas, John Maddocks, Phillip Metzner, Christof Schütte
SIAM J. Applied Dynamical Systems 7, no. 2 (2008), p. 532-560
106 2005 Thermodynamics of DNA Loops with Long-Range Correlated Structural Disorder
C. Vaillant, B. Audit and A. Arneodo
Physical Review Letters 95, no. 6 (2005), p. 68101
105 2005 Measuring limits of telomere movement on nuclear envelope
A. Rosa, J. H. Maddocks, F. R. Neumann, S. M. Gasser, A. Stasiak
Biophysical Journal: Biophysical Letters (2005), p. L24-L26
104 2006 Spatially confined polymer chains: implications of chromatin fibre flexibility and peripheral anchoring on telomere-telomere interaction
L. R. Gehlen, A. Rosa, K. Klenin, J. Langowski, S. M. Gasser, K. Bystricky
Journal of Physics: Condensed Matter 18 (2006), p. S245 - S252
103 2005 Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence
F. Barone, F. Lankas, N. Spackova, J. Sponer, P. Karran, M. Bignami, F. Mazzei
Biophysical Chemistry 118 (2005), p. 31 - 41
102 2005 Scaling exponents and probability distributions of DNA end-to-end distance
F. Valle, M. Favre, P. De Los Rios, A. Rosa, G. Dietler
Physical Review Letters 95 (2005), p. 158105 [4 pages]
101 2005 Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonuleotides. II. Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps
Surjit B. Dixit, David L. Beveridge, David A. Case, Thomas E. Cheatham III, Emmanuel Giudice, Filip Lankas, Richard Lavery, John H. Maddocks, Roman Osman, Heinz Sklenar, Kelly M. Thayer and Péter Varnai
Biophysical Journal 87 (2005), p. 3721 - 3740
100 2006 Long time behaviour of diffusing particles in constrained geometries; application to chromatin motion
A. Rosa, F. R. Neumann, S. Gasser, A. Stasiak
Journal of Physics: Condensed Matter 18 (2006), p. S235 - S243
99 2006 3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake
Mathews Jacob, Thierry Blu, Cedric Vaillant, John Maddocks, Michael Unser
IEEE Transactions on Image Processing 15, no. 1 (2006), p. 214 - 227
98 2005 A new interpolation formula for Semiflexible Polymers
A. Rosa, T.-X. Hoang, D. Marenduzzo, A. Maritan
Biophysical Chemistry 115 (2005), p. 251 - 254
97 2004 The relative flexibility of B-DNA and A-RNA duplexes: database analysis
A. Perez, A. Noy, F Lankas, F. Javier Luque, M. Orozco
Nucleic Acids Res. 32 (2004), p. 6144 - 6151
96 2004 Relative Flexibility of DNA and RNA: a Molecular Dynamics Study
A. Noy, A. Perez, F. Lankas, F. Javier Luque, M. Orozco
J. Mol. Biol 343 (2004), p. 627 - 638
95 2004 Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonuleotides. I. Research Design and Results on d(CpG) Steps
D.L. Beveridge, G. Barreiro, K.S. Byun, D.A. Case, T.E. Cheatham III, S.B. Dixit, E. Giudice, F. Lankas, R. Lavery, J.H. Maddocks, R. Osman, E. Seibert, H. Sklenar, G. Stoll, K.M. Thayer, P. Varnai, M.A. Young
Biophysical Journal 87 (2004), p. 3799 - 3813
94 2005 Correlation function and generalized master equation of arbitrary age
P. Allegrini, G. Aquino, P. Grigolini, L. Palatella, A. Rosa, B.J. West
Phys. Rev. E 71 (2005), p. 066109 [12 pages]
93 2004 Kirchhoff's Problem of Helical Equilibria of Uniform Rods
N. Chouaieb, J. H. Maddocks
Journal of Elasticity 77 (2004), p. 221-247
92 2004 Stepwise unfolding of collapsed polymers
D. Marenduzzo, A. Maritan, A. Rosa, F. Seno
The European Physical Journal E 15 (2004), p. 83 - 93
91 2005 Non-Poisson processes: regression to equilibrium versus equilibrium correlation functions
P. Allegrini, P. Grigolini, L. Palatella, A. Rosa, B.J. West
Physica A 347 (2005), p. 268 - 288
90 2004 DNA Deformability at the Base Pair Level
F. Lankas, J. Sponer, J. Langowski, T.E. Cheatham III
Journal of the American Chemical Society 126 (2004), p. 4124 - 4125
89 2004 DNA Sequence-dependent Deformability - Insights from Computer Simulations
F. Lankas
Biopolymers 73 (2004), p. 327 - 339
88 2003 DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
F. Lankas, J. Sponer, J. Langowski, T.E.Cheatham III
Biophysical Journal 85 (2003), p. 2872 - 2883
87 2004 Extracting DNA twist rigidity from experimental supercoiling data
Sébastien Neukirch
Physical Review Letters 93, no. 19 (2004), p. 198107 [4 pages]
86 2004 Wavelet analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences
B. Audit, C. Vaillant, A. Arnéodo, C. Thermes
Journal of Biological Physics 30 (2004), p. 33 - 81
85 2003 Extracting structural and dynamical informations from wavelet-based analysis of DNA sequences.
A. Arnéodo, B. Audit, C. Vaillant, Y. d'Aubenton-Carafa, C. Thermes
Inst. Phys. Conf. Ser. No. 173: Satellite colloquium (2003), p. 905 - 913
84 2003 Influence of the sequence on elastic properties of long DNA chains
C. Vaillant, B. Audit, A. Arnéodo, C. Thermes
Physical Review E 67 (2003), p. 032901
83 2003 A constructive approach to modelling the tight shapes of some linked structures
E. L. Starostin
Forma 18 (2003), p. 263 - 293
82 2005 Biarcs, Global Radius of Curvature, and the Computation of Ideal Knot Shapes
M. Carlen, B. Laurie, J.H. Maddocks, J. Smutny
Physical and Numerical Models in Knot Theory and Their Application to the Life Sciences Chapter 5 (2005), p. 75 - 108
81 2004 Bifurcation Theory, Symmetry Breaking and Homogenization in Continuum Mechanics Descriptions of DNA
John H. Maddocks
A Celebration of Mathematical Modeling: The Joseph B. Keller Anniversary Volume Chapter 7 (2004), p. 113 - 136
80 2005 A double-strand elastic rod theory
Maher Moakher, John H. Maddocks
Arch. Rational Mech. Anal. 177 (2005), p. 53 - 91
79 2002 Geometry and mechanics of uniform n-plies: from engineering ropes to biological filaments
Sébastien Neukirch, Gert van der Heijden
Journal of Elasticity 69 (2002), p. 41 - 72
78 2004 Dynamics of a rigid body in a Stokes fluid
O. Gonzalez, A. B. A. Graf, J. H. Maddocks
J. Fluid Mech. 519 (2004), p. 133-160
77 2004 Classification of the spatial equilibria of the clamped elastica: numerical continuation of the solution set
Michael E. Henderson, Sébastien Neukirch
International Journal of Bifurcation and Chaos 14 (2004), p. 1223 - 1239
76 2004 Symmetric equilibria of a thin elastic rod with self-contacts
E. L. Starostin
Philosophical Transactions of the Royal Society A 362, no. 1820 (2004), p. 1317 - 1334
DOI:10.1098/rsta.2004.1388
75 2002 Classification of the spatial equilibria of the clamped elastica: symmetries and zoology of solutions
Sébastien Neukirch, Michael E. Henderson
Journal of Elasticity 68 (2002), p. 95 - 121
74 2003 Link, Twist, Energy, and the Stability of DNA Minicircles
Kathleen A. Hoffman, Robert S. Manning, John H. Maddocks
Biopolymers 70, no. 2 (2003), p. 145 - 157
73 2005 A differential geometric approach to the geometric mean of symmetric positive-definite matrices
M. Moakher
SIAM Journal on Matrix Analysis and Applications 26, no. 3 (2005), p. 735 - 747
72 2005 On the writhing number of non-closed curves
E. L. Starostin
Physical and Numerical Models in Knot Theory and Their Application to the Life Sciences Chapter 26 (2005), p. 525 - 545
71 2003 Instability and self-contact phenomena in the writhing of clamped rods
G. van der Heijden, Sébastien Neukirch, V. G. A. Goss, J.M.T. Thompson
International Journal of Mechanical Science 45 (2003), p. 161 - 196
70 2003 A variational approach to loaded ply structures
G. van der Heijden, J.M.T. Thompson, Sébastien Neukirch
Journal of Vibration and Control 9 (2003), p. 175 - 185
69 2002 Equilibrium configurations of a thin elastic rod with self-contacts
E. L. Starostin
PAMM, Proc. Appl. Math. Mech. 1 (2002), p. 137 - 138
DOI:10.1002/1617-7061(200203)1:1<137::AID-PAMM137>3.0.CO;2-B
68 2002 Comment on 'Cyclic rotations, contractibility and Gauss-Bonnet'
E. L. Starostin
J. of Physics A: Math. & Gen. 35 (2002), p. 6183 - 6190
67 2002 Super-Coiling of DNA Plasmids: Mechanics of the Generalised Ply
J.M.T. Thompson, G. van der Heijden, Sébastien Neukirch
Proceedings of the Royal Society, London A 458 (2002), p. 959 - 985
66 2002 Writhing instabilities of twisted rods: from infinite to finite length
S. Neukirch, G.H.M. van der Heijden, J.M.T. Thompson
Journal of the Mechanics and Physics of Solids 50 (2002), p. 1175 - 1191
65 2002 Curves, Circles, and Spheres
O. Gonzalez, J. H. Maddocks, J. Smutny
Contemporary Mathematics (AMS) 304 (2002), p. 195 - 215
64 2002 La triple hélice : vers une mécanique du collagène
S. Neukirch & G.H.M. van der Heijden
Rencontre du Non-Linéaire (2002), p. 183 - 188
63 2002 Means and Averaging in the Group of Rotations
M. Moakher
SIAM Journal on Matrix Analysis and Application 24, no. 1 (2002), p. 1 - 16
62 2003 Self-interactions of strands and sheets
J.R. Banavar, O. Gonzalez, J.H. Maddocks, A. Maritan
Journal of Statistical Physics 110, no. 1/2 (2003), p. 35 - 50
61 2002 Global curvature and self-contact of nonlinearly elastic curves and rods
O. Gonzalez, J.H. Maddocks, F. Schuricht, H. von der Mosel
Calculus of Variation 14 (2002), p. 29 - 68
DOI:10.1007/s005260100089
60 2000 Closed loops of a thin elastic rod and its symmetric shapes with self-contacts
E. L. Starostin
Proceedings of the 16th IMACS World Congress 2000 , Lausanne, August 21-25 (2000)
59 2002 Simulation of some quantum models for semiconductors
Ph. Caussignac, J. Descloux, A. Yamnahakki
Mathematical Models and Methods in Applied Sciences 1 (2002), p. 1049 - 1074
58 2002 DataViewer: A Scene Graph Based Visualization Tool
R. Paffenroth, D. Vrajitoru, T. Stone, J. H. Maddocks
The 5th IASTED Conference on Computer Graphics and Imaging (CGIM 2002) (2002), p. 200 - 205
57 2000 Best packing in proteins and DNA
Andrzej Stasiak, John H. Maddocks
Nature 406 (2000), p. 251 - 252
56 2001 Extracting parameters for base-pair level models of DNA
Oscar Gonzalez, John H. Maddocks
Theoretical Chemistry Accounts 106 (2001), p. 76 - 82
55 2000 Buckling of an Elastic Rod with High Intrinsic Twist
S. Rey, J. H. Maddocks
Proceedings of the 16th IMACS World Congress 2000, Lausanne, August 21 - 25 (2000)
54 2000 Effective properties of elastic rods with high intrinsic twist
S. Kehrbaum, J. H. Maddocks
Proceedings of the 16th IMACS World Congress 2000, Lausanne, August 21 - 25 (2000)
53 2000 The Bordered Operator and the Index of a Constrained Critical Point
L. Greenberg, J.H. Maddocks, K.A. Rogers
Math. Nachr. 219 (2000), p. 109 - 124
52 2001 Multi-Multiplier Ambient Space Formulations of Constrained Dynamical Systems, with an Application to Elastodynamics
O. Gonzalez, J.H. Maddocks, R.L. Pego
Archive for Rational Mechanics and Analysis 157 (2001), p. 285 - 323
51 2000 DNA Rings with Multiple Energy Minima
Patrick B. Furrer, Robert S. Manning, John H. Maddocks
Biophysical Journal 79 (2000), p. 116 - 136
50 1996 Evaluation of Learning Schemes Used in Information Retrieval
J. Savoy, D. Vrajitoru
Journal of the American Society for Information Science (1996)
49 1999 Genetic Programming Operators Applied to Genetic Algorithms
D. Vrajitoru
GECCO-99 (1999), p. 686 - 693
48 1999 DNA: Uncooked, al Dente, or Scotti?
A. Stasiak, J. Dubochet, P. Furrer, O. Gonzalez, J.H.Maddocks
Science 283, no. 5408 (1999), p. 1641
47 1999 Mechanical Systems Subject to Holonomic Constraints: Differential-Algebraic Formulations and Conservative Integration
O. Gonzalez
Physica D 132 (1999), p. 165 - 174
46 1999 Qualitative Properties of Modified Equations
O. Gonzalez, D.J. Higham, A.M. Stuart
IMA Journal of Numerical Analysis 19 (1999), p. 169 - 190
45 1999 An Energy-Transport Model for Semiconductor Heterostructure Devices : Application to AlGaAs/GaAs Modfets
C. Lab, Ph. Caussignac
The International Journal for Computation and Mathematics in Electrical and Electronic 18, no. 1 (1999), p. 61 - 76
44 1999 Structural Effect of Complete [Rp]-Phosphorothioate and Phosphorodithioate Substitutions in the DNA Strand of a Model Antisense Inhibitor-Target RNA Complex
Patrick Furrer, Todd M. Billeci, Alessandro Donati, Chojiro Kojima, Boleslaw Karwowski, Agnieszka Sierzchala, Wojciech Stec, Thomas L. James
J. Mol. Biol. 285 (1999), p. 1609 - 1622
43 1999 Global curvature, thickness, and the ideal shapes of knots
O. Gonzalez & J.H. Maddocks
Proc. National Academy of Sciences USA 96 (1999), p. 4769 - 4773
42 1999 Symmetry breaking and the Twisted Elastic Ring
R.S. Manning, J.H. Maddocks
Computer Methods in Applied Mechanics and Engineering 370 (1999), p. 313
41 1998 Algorithmes génétiques en recherche d'informations
D. Vrajitoru
Apprentissage : des principes naturels aux méthodes artificielles (1998), p. 271 - 278
40 1997 Determination of Structural Ensembles from NMR Data: Conformational Sampling and Probability Assessment
Nikolai B. Ulyanov, Anwer Mujeeb, Alessandro Donati, Patrick Furrer, He Liu, Shauna Farr-Jones, David E. Konerding, Uli Schmitz, and Thomas L. James
ACS Meeting Proceedings, Section Computational Chemistry and Nucleic Acids, San Francisco Chapter 11 (1997), p. 181 – 194
DOI:10.1021/bk-1998-0682.ch011
39 1998 Crossover Improvement For The Genetic Algorithm In Information Retrieval
D. Vrajitoru
Information Processing and Management 34, no. 4 (1998), p. 405 - 415
38 1998 VBM and MCCC : Packages for Objected Oriented Visualization and Computation of Bifurcation Manifolds
Randy C. Paffenroth
Proceedings of the 1998 SIAM Workshop: Object Oriented Methods for Interoperable Scientific and Engineering Computing (1998), p. 255 - 263
37 1998 Shortest Distance Paths for Wheeled Mobile Robots
James C. Alexander, John H. Maddocks, Brian A. Michalowski
IEEE Transactions on Robotics and Automation 14, no. 5 (1998), p. 657 - 662
36 1998 Isoperimetric Conjugate Points with Application to the Stability of DNA Minicircles
R.S. Manning, K.A. Rogers, J.H. Maddocks
Proc. R. Soc. Lond. A: Mathematical and Physical Sciences 454 (1998), p. 3047 - 3074
35 1997 On the Qualitative Properties of Modified Equatio
O. Gonzalez & A.M. Stuart
Foundations of Computational Mathematics (1997), p. 169 - 179
34 1997 Opposite Effect of Counterions on the Persistence Length of Nicked and Non-nicked DNA
Patrick Furrer, Jan Bednar, Alicja Z. Stasiak, Vsevolod Katritch, Didier Michoud, Andrzej Stasiak, Jacques Dubochet
J. Mol. Biol. 266 (1997), p. 711 - 721
33 1997 The Calogero - Sutherland - Moser (csm) model as a quantum billiard
Stéphane Rey, Philippe Choquard
Eur.J. Phys. 18 (1997), p. 94 - 98
32 1997 Incompletely parabolic systems from Friedrichs theory point of view
Ph. Caussignac
Mathematical Models and Methods in Applied Sciences 7, no. 8 (1997), p. 1141 - 1152
31 1997 Elastic rods, rigid bodies, quaternions and the last quadrature
Stefan Kehrbaum, John H. Maddocks
Philosophical Transactions Royal Society of London 355 (1997), p. 2117 - 2136
30 1997 Interactive computation, parameter continuation, and visualization
J.H. Maddocks, R.S. Manning, R.C. Paffenroth, K.A. Rogers, and J.A. Warner
Int. J. Bif. Chaos 7 (1997), p. 1699
29 1996 On the Computation of Equilibria of Elastic Rods - Part I: Integrals, Symmetry and a Hamiltonian Formulation
Y. Li, J.H. Maddocks
to appear J. Computational Physics (1996)
28 1996 Hamiltonian Formulations and Symmetries in Rod Mechanics
D.J. Dichmann, Y. Li, J.H. Maddocks
Mathematical Approaches to Biomolecular Structure and Dynamics, IMA Volumes in Mathematics and its Applications 82 (1996), p. 71 - 113
27 1996 A Continuum Rod Model of Sequence-Dependent DNA Structure
R.S. Manning, J.H. Maddocks, J.D. Kahn
J. Chem. Phys. 105 (1996), p. 5626 - 5646
26 1996 An Impetus-Striction Simulation of the Dynamics of an Elastica
D.J. Dichmann, J.H. Maddocks
J. Nonlinear Science 6 (1996), p. 271 - 292
25 1996 Hamiltonian dynamics of an elastica and the stability of solitary waves
D.J. Dichmann, J.H. Maddocks, R.L. Pego
Arch. Rational Mech. Anal. 135 (1996), p. 357 - 396
24 1988 Errata: Restricted quadratic forms and their application to bifurcation and stability in constrained variational principles
J.H. Maddocks
Siam J. Math. Anal. 19 (1988), p. 1256-1257
23 1995 Constrained Variational Principles and Stability in Hamiltonian Systems
J.H. Maddocks, R.L. Sachs
IMA Volumes in Mathematics and Its Applications 63 (1995), p. 231 - 264
22 1995 Stability Theory for Dissipatively Perturbed Hamiltonian Systems
J.H. Maddocks, M.L. Overton
Commun. On Pure and Applied Math. XLVIII (1995), p. 583 - 610
DOI:10.1002/cpa.3160480602
21 1995 An unconstrained Hamiltonian formulation for incompressible fluid flow
J.H. Maddocks, R.L. Pego
Commun. Math. Phys. 170 (1995), p. 207 - 217
20 1994 On the forward kinematics of parallel manipulators
R. Nair, J.H. Maddocks
Int. J. Robotics Research 13, no. 2 (1994), p. 171 - 188
19 1994 Conservation laws in the dynamics of rods
J.H. Maddocks, D.J. Dichmann
J. of Elasticity 34 (1994), p. 83 - 96
18 1993 On the stability of KdV multi-solitons
J.H. Maddocks, R.L. Sachs
Comm. Pure and Applied Math. 46 (1993), p. 867 - 901
DOI:10.1002/cpa.3160460604
17 1993 Bounds on the friction-dominated motion of a pushed object
J.C. Alexander, J.H. Maddocks
Int. J. of Robotics Research 12, no. 3 (1993), p. 231 - 248
16 1992 On the dynamics of chains
D. Jacobson, J.H. Maddocks
SIAM J. Applied Math. 52 (1992), p. 1563 - 1583
15 1992 Steady rigid-body motions in a central gravitational field
L-S. Wang, J.H. Maddocks, P.K. Krishnaprasad
J. of the Astronautical Sciences 40, no. 4 (1992), p. 449 - 478
14 1992 Steady-State shear-bands in thermo plasticity, Part I: vanishing yield stress
J.H. Maddocks, R. Malek-Madani
Int. J. Solids Structures 29, no. 16 (1992), p. 2063 - 2076
13 1991 Hamiltonian dynamics of a rigid body in a central gravitational field
L-S. Wang, P.K. Krishnaprasad, J.H. Maddocks
Celestial Mechanics and Dynamical Astronomy 50 (1991), p. 59 - 96
12 1991 On the stability of relative equilibria
J.H. Maddocks
IMA J. Applied Math. 46 (1991), p. 71 - 99
11 1989 On the kinematics of wheeled mobile robots
J.C. Alexander, J.H. Maddocks
Int. J. Robotics Research 8 (1989), p. 15 - 27
10 1988 Restricted quadratic forms, inertia theorems, and the Schur complement
J.H. Maddocks
Linear Algebra and Appl. 108 (1988), p. 1 - 36
9 1988 On the maneuvering of vehicles
J.C. Alexander, J.H. Maddocks
SIAM J. Appl. Math. 48, no. 1 (1988), p. 38-52
8 1987 Ropes in equilibrium
J.H. Maddocks, J.B. Keller
SIAM J.Appl. Math. 47, no. 6 (1987), p. 1185 - 1200
7 1987 A model for disclinations in nematic liquid crystal
J.H. Maddocks
IMA Volumes in Mathematics and Its Applications 5 Theory and Applications of Liquid Crystals (1987), p. 255 - 269
6 1987 Stability and folds
J.H. Maddocks
Arch. Rat. Mech. Anal. 99 (1987), p. 301 - 328
5 1986 A model for twinning
J.H. Maddocks, G.P. Parry
J. Elasticity 16 (1986), p. 113 - 133
4 1985 Restricted quadratic forms and their application to bifurcation and stability in constrained variational principles
J.H. Maddocks
SIAM J. Math. Anal. 16 (1985), p. 47 - 68
3 1984 Nonlinear dynamical theory of the elastica
R.E. Caflisch, J.H. Maddocks
Proc. Roy. Soc. Edinburgh 99A (1984), p. 1 - 23
2 1984 Stability of nonlinearly elastic rods
J.H. Maddocks
Arch. Rat. Mech. Anal. 85 (1984), p. 311 - 354
1 1983 Stability of the elastica
J.H. Maddocks
Systems of Nonlinear Partial Differential Equations - Proc. of NATO/London Math. Soc. Advanced Study Institute, Eds. J.M. Ball, Reidel (1983), p. 311 - 322
# Year Publication name
14 2016 Computation and Visualization in Multiscale Modelling of DNA Mechanics
Jaroslaw Glowacki
PhD dissertation #7062 (EPFL)
13 2016 On the statistical physics of chains and rods, with application to multi-scale sequence dependend DNA modelling
Alexandre Grandchamp
PhD dissertation #6977 (EPFL)
12 2012 A DNA Coarse-Grain Rigid Base Model and Parameter Estimation from Molecular Dynamics Simulations
Daiva Petkevičiūtė
PhD dissertation #5520 (EPFL)
11 2010 Computation and visualization of ideal knot shapes
Mathias Carlen
PhD dissertation #4621 (EPFL)
10 2010 Ideal Knots and Other Packing Problems of Tubes
Henryk Gerlach
PhD dissertation #4601 (EPFL)
9 2008 A path-integral formalism of DNA looping probability
Ludovica Cotta-Ramusino
PhD dissertation #4017 (EPFL)
8 2007 Effects of Base-Pair Sequence, Nicks and Gaps on DNA Minicircle Shapes: Analysis and Experiment
Arnaud Amzallag
PhD dissertation #3995 (EPFL)
7 2004 Global Radii of Curvature, and the Biarc Approximation of Space Curves: In Pursuit of Ideal Knot Shapes
Jana Smutny
PhD dissertation #2981 (EPFL)
6 2003 Kirchhoff's Problem of Helical Solutions of Uniform Rods and Their Stability Properties
Nadia Chouaïeb
PhD dissertation #2717 (EPFL)
5 2002 Symmetry breaking, averaging and elastic rods with high intrinsic twist
Stéphane Rey
PhD dissertation #2646 (EPFL)
4 1999 Mathematical Visualization, Parameter Continuation and Steered Computations
Randy Clinton Paffenroth
PhD dissertation (University of Maryland)
3 1997 Stability Exchange in Parameter-Dependent Constrained Variational Principles with Applications to Elastic Rod Models of DNA Minicircles
Kathleen Ann Rogers-Hoffman
PhD dissertation (University of Maryland)
2 1997 Hamiltonian Formulations of the Equilibrium Conditions Governing Elastic Rods: Qualitative Analysis and Effective Properties
Stefan Kehrbaum
PhD dissertation (University of Maryland)
1 1994 Hamiltonian Dynamics of a Spatial Elastica and the Stability of Solitary Waves
Donald James Dichmann
PhD dissertation (University of Maryland)
# Year Publication name
8 2016 Sequence-dependent equilibrium distributions of DNA within the cgDNA coarse grain model
Mélissa Nicollier
Master's thesis (EPFL)
7 2013 Generalized Load-Displacement Relations for Helical Structures
Pauline Rüegg-Reymond
Master's thesis (EPFL)
6 2011 Méthodes numériques pour un problème inverse
Maxime Mogé
Master's thesis (EPFL)
5 2011 Equilibrium Birod Theory, High Twist and Coarse Grain DNA Models
Alexandre Grandchamp
Master's thesis (EPFL)
4 2011 Spectral analysis of a coarse-grain model of DNA
Julien Delafontaine
Master's thesis (EPFL)
3 2006 Numerical investigation of solutions of Langevin equations
Nikki Vercauteren
Master's thesis (Freie Universität Berlin, EPFL)
2 2005 Analysis and Simulation of Stokes Flow of Knotted Filaments?
Mathias Carlen
Master's thesis (EPFL)
1 1997 Numerical Simulations of Elastic Rods
Jeremy A. Warner
Master's thesis (University of Maryland)