160 
2023

cgNA+web : A visual interface to the cgNA+ sequencedependent statistical mechanics model of doublestranded nucleic acids
R. Sharma, A. Patelli, L. de Bruin, J.H Maddocks
Journal of Molecular Biology (2023)
DOI:https://doi.org/10.1016/j.jmb.2023.167978


159 
2023

Bending and Stretching in a Narrow Ribbon of Nematic Polymer Networks
Harmeet Singh and Epifanio G. Virga
Journal of Elasticity (2023)
DOI:10.1007/s10659022099781


158 
2022

Planar equilibria of an elastic rod wrapped around a circular capstan
H. Singh
Journal of Elasticity (2022)
DOI:10.1007/s10659022099398


157 
2022

Navigation of Concentric Tube Continuum Robots using Optimal Control
Dhanakoti, S.; Maddocks, J. and Weiser, M.
In Proceedings of the 19th International Conference on Informatics in Control, Automation and Robotics (2022), p. 9
DOI:10.5220/0011271000003271


156 
2022

Machine Learning for Musculoskeletal Modeling of Upper Extremity
Rahul Sharma, Abhishek Dasgupta, Runbei Cheng, Challenger Mishra, Vikranth H Nagaraja
IEEE Sensors Journal (2022)
DOI:10.1109/JSEN.2022.3197461


155 
2022

A computational framework to obtain nonlinearly elastic constitutive relations of special Cosserat rods with surface energy
Raushan Singh, Abhishek Arora, Ajeet Kumar
Computer Methods in Applied Mechanics and Engineering 398 (2022), p. 115256
DOI:10.1016/j.cma.2022.115256


154 
2020

The role of histone tails in nucleosome stability: An electrostatic perspective
A. Bendandi, A.S. Patelli, A. Diaspro, W. Rocchia
Computational and Structural Biotechnology Journal 18 (2020), p. 27992809
DOI:10.1016/j.csbj.2020.09.034


153 
2022

A Ribbon Model for Nematic Polymer Networks
H. Singh and E.G. Virga
Journal of Elasticity (2022)
DOI:10.1007/s10659022099009


152 
2022

Exciton decay mechanism in DNA single strands: backelectron transfer and ultrafast base motions
B. Bauer, R. Sharma, M. Chergui, M. Oppermann
Chemical Science (2022)
DOI:10.1039/d1sc06450a


151 
2022

Unraveling looping efficiency of stochastic Cosserat polymers
Giulio Corazza and Raushan Singh
Physical Review Research 4, no. 013071 (2022)
DOI:https://doi.org/10.1103/PhysRevResearch.4.013071


150 
2021

Sequence dependent structural properties of B DNA: what have we learned in 40 years?
G. da Rosa, L. Grille, V. Calzada. K. Ahmad. J.P. Arcon, F. Battistini, G. Bayarri, T. Bishop, P. Carloni,T. Cheatham III,R. Collepardo Guevara, J. Czub, J.R. Espinosa, R. Galindo Murillo, S.A. Harris, A. Hospital, C. Laughton, J.H. Maddocks, A. Noy, M. Orozco, M. Pasi, A. Pérez, D. Petkevičiūtė Gerlach, R. Sharma, R. Sun,P.D. Dans
Biophysical Reviews (2021)
DOI:https://doi.org/10.1007/s12551021008938


149 
2021

Pseudomomentum: origins and consequences
H. Singh and J.A. Hanna
Zeitschrift für angewandte Mathematik und Physik 72, no. 122 (2021)
DOI:https://doi.org/10.1007/s00033021015079


148 
2021

Mechanics of two filaments in tight orthogonal contact
P. Grandgeorge, C. Baek, H. Singh, P. Johanns, T.G. Sano, A. Flynn, J.H. Maddocks, and P.M. Reis
Proceedings of the National Academy of Sciences of the United States of America 118, no. 15 (2021), p. e2021684118
DOI:10.1073/pnas.2021684118


147 
2021

The shapes of physical trefoil knots
P. Johanns, P. Grandgeorge, C. Baek, T.G. Sano, J.H. Maddocks, P.M. Reis
Extreme Mechanics Letters 43 (2021), p. 101172
DOI:10.1016/j.eml.2021.101172


146 
2020

Adhesion of a tape loop
T. Elder, T. Twohig, H. Singh, and A.B. Croll
Soft Matter 16 (2020), p. 1061110619
DOI:10.1039/D0SM01516D


145 
2020

Normalized Gaussian path integrals
Giulio Corazza and Matteo Fadel
Physical Review E 102, no. 2 (2020)
DOI:10.1103/PhysRevE.102.022135


144 
2019

The static and dynamic structural heterogeneities of BDNA: extending Calladine–Dickerson rules
P.D. Dans, A. Balaceanu, M. Pasi, A.S. Patelli, D. Petkevičiūtė, J. Walther, A. Hospital, G. Bayarri, R. Lavery, J.H. Maddocks, M. Orozco
Nucleic Acids Research (2019), p. 113
DOI:https://doi.org/10.1093/nar/gkz905


143 
2018

cgDNAweb: a web interface to the cgDNA sequencedependent coarsegrain model of doublestranded DNA
Lennart De Bruin, John H Maddocks
Nucleic Acids Research 46 (2018), p. W5  W10
DOI:10.1093/nar/gky351


142 
2017

SequenceDependent Persistence Lengths of DNA
J.S. Mitchell, J. Glowacki, A.E. Grandchamp, R.S. Manning, J.H. Maddocks
Journal of Chemical Theory and Computation 13 (2017), p. 15391555
DOI:10.1021/acs.jctc.6b00904


141 
2017

Absolute versus relative entropy parameter estimation in a coarsegrain model of DNA
O. Gonzalez, M. Pasi, D. Petkevičiūtė, J. Glowacki, J.H. Maddocks
Multiscale Modeling and Simulation 15, no. 3 (2017), p. 1073  1107
DOI:10.1137/16M1086091


140 
2017

Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles
M. Pasi, K. Zakrzewska, J.H. Maddocks, R. Lavery
Nucleic Acids Research 45, no. 7 (2017), p. 42694277
DOI:10.1093/nar/gkx092


139 
2016

Morphomechanical Innovation Drives Explosive Seed Dispersal
H. Hofhuis, D. Moulton, T. Lessinnes, A.L. RoutierKierzkowska, 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. 112
DOI:10.1016/j.cell.2016.05.002


138 
2015

Analyzing ion distributions around DNA: sequencedependence of potassium ion distributions from microsecond molecular dynamics
M. Pasi, J.H. Maddocks, R. Lavery
Nucleic Acid Research 43, no. 4 (2015), p. 2412–2423
DOI:10.1093/nar/gkv080


137 
2014

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in BDNA
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 sequencedependent coarsegrain free energies of Bform 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 KirchhoffLove Rod Model of Elastic Filaments
B. Ðurickovic, A. Goriely, J.H. Maddocks
Physical Review Letters 111 (2013), p. 108103 15
DOI:10.1103/PhysRevLett.111.108103


133 
2011

SecondOrder 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. 245250
DOI:10.1007/9783790827361_38


132 
2013

A sequencedependent rigidbase model of DNA
Oscar Gonzalez, Daiva Petkevičiūtė, and John H. Maddocks
Journal of Chemical Physics 138, no. 5 (2013), p. 055122 128
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/e201101523y


130 
2012

Adaptive conformational sampling based on replicas
J. Curuksu
J. Math. Biol. 64, no. 6 (2012), p. 917931
DOI:10.1007/s0028501104326


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. CottaRamusino, 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, no. 5 (2012), p. 1250057 114
DOI:10.1142/s0218216511010115


126 
2011

On spherefilling ropes
Henryk Gerlach, Heiko von der Mosel
American Math Monthly 118, no. 10 (2011), p. 863  876
DOI:10.4169/amer.math.monthly.118.10.863


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
DOI:10.1137/090765705


124 
2010

SecondOrder 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
DOI:10.1198/jasa.2010.tm09239


123 
2009

A systematic molecular dynamics study of nearest neighbor effects on base pair and base pair step conformations and fluctuations in BDNA
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. 299313
DOI:10.1093/nar/gkp834


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
DOI:10.1039/b919565n


121 
2009

Bending modes of DNA directly addressed by cryoelectron 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
DOI:10.1093/nar/gkp137


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
DOI:10.1093/nar/gkp608


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
DOI:10.1007/s002050100390y


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
DOI:10.1142/s0218202509003668


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
DOI:10.1002/bip.20503


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
DOI:10.1073/pnas.0704594104


115 
2007

Around the Möbius band
John H. Maddocks
Nature Materials 6 (2007), p. 547  548
DOI:10.1038/nmat1960


114 
2008

A gauge finite element method for the 2D NavierStokes problem
Ph. Caussignac
Applied Numerical Mathematics 58 (2008), p. 1413  1433
DOI:10.1016/j.apnum.2007.08.002


113 
2007

Lowenergy effective theory for a RandallSundrum scenario with a moving bulk brane
Ludovica CottaRamusino and David Wands
Phys. Rev. D 75, no. 10 (2007), p. 104001 [9 pages]
DOI:10.1103/physrevd.75.104001


112 
2006

Formation and positioning of nucleosomes: Effect of sequencedependent longrange correlated structural disorder
C. Vaillant, B. Audit, C. Thermes, A. Arneodo
Eur. Phys. J. E 19 (2006), p. 263  277
DOI:10.1140/epje/i2005100533


111 
2007

Sequencedependent twiststretch coupling in DNA
T Lionnet, F Lankas
Biophysical Journal 92 (2007), p. L30  L32


110 
2006

3D reconstruction and comparison of shapes of DNA minicircles observed by cryoelectron 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: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
DOI:10.1016/j.str.2006.08.004


108 
2006

Helices
Nadia Chouaieb, Alain Goriely, and John H. Maddocks
Proceedings of the National Academy of Sciences USA 103 (2006), p. 9398  9403
DOI:10.1073/pnas.0508370103


107 
2008

Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to BDNA
Illia Horenko, Evelyn Dittmer, Filip Lankas, John Maddocks, Phillip Metzner, Christof Schütte
SIAM J. Applied Dynamical Systems 7, no. 2 (2008), p. 532560
DOI:10.1137/050630064


106 
2005

Thermodynamics of DNA Loops with LongRange Correlated Structural Disorder
C. Vaillant, B. Audit and A. Arneodo
Physical Review Letters 95, no. 6 (2005), p. 68101
DOI:10.1103/physrevlett.95.068101


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. L24L26
DOI:10.1529/biophysj.105.077974


104 
2006

Spatially confined polymer chains: implications of chromatin fibre flexibility and peripheral anchoring on telomeretelomere 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
DOI:10.1088/09538984/18/14/s09


103 
2005

Structural and dynamic effects of single 7hydro8oxoguanine 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
DOI:10.1016/j.bpc.2005.06.003


102 
2005

Scaling exponents and probability distributions of DNA endtoend distance
F. Valle, M. Favre, P. De Los Rios, A. Rosa, G. Dietler
Physical Review Letters 95 (2005), p. 158105 [4 pages]
DOI:10.1103/physrevlett.95.158105


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
DOI:10.1529/biophysj.105.067397


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
DOI:10.1088/09538984/18/14/s08


99 
2006

3D shape estimation of DNA molecules from stereo cryoelectron micrographs using a projectionsteerable snake
Mathews Jacob, Thierry Blu, Cedric Vaillant, John Maddocks, Michael Unser
IEEE Transactions on Image Processing 15, no. 1 (2006), p. 214  227
DOI:10.1109/TIP.2005.860310


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
DOI:10.1016/j.bpc.2004.12.030


97 
2004

The relative flexibility of BDNA and ARNA duplexes: database analysis
A. Perez, A. Noy, F Lankas, F. Javier Luque, M. Orozco
Nucleic Acids Res. 32 (2004), p. 6144  6151
DOI:10.1093/nar/gkh954


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
DOI:10.1016/j.jmb.2004.07.048


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
DOI:10.1529/biophysj.104.045252


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]
DOI:10.1103/physreve.71.066109


93 
2004

Kirchhoff's Problem of Helical Equilibria of Uniform Rods
N. Chouaieb, J. H. Maddocks
Journal of Elasticity 77 (2004), p. 221247
DOI:10.1007/s106590050931z


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
DOI:10.1140/epje/i2004100397


91 
2005

NonPoisson 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
DOI:10.1016/j.physa.2004.08.004


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
DOI:10.1021/ja0390449


89 
2004

DNA Sequencedependent Deformability  Insights from Computer Simulations
F. Lankas
Biopolymers 73 (2004), p. 327  339
DOI:10.1002/bip.10542


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
DOI:10.1016/s00063495(03)747109


87 
2004

Extracting DNA twist rigidity from experimental supercoiling data
Sébastien Neukirch
Physical Review Letters 93, no. 19 (2004), p. 198107 [4 pages]
DOI:10.1103/physrevlett.93.198107


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
DOI:10.1023/b:jobp.0000016438.86794.8e


85 
2003

Extracting structural and dynamical informations from waveletbased analysis of DNA sequences.
A. Arnéodo, B. Audit, C. Vaillant, Y. d'AubentonCarafa, 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
DOI:10.1103/physreve.67.032901


83 
2003

A constructive approach to modelling the tight shapes of some linked structures
E. L. Starostin
Forma 18 (2003), p. 263  293
DOI:10.1002/pamm.200310509


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 (2005), p. 75  108
DOI:10.1142/9789812703460_0005


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 (2004), p. 113  136
DOI:10.1007/9789401704274_7


80 
2005

A doublestrand elastic rod theory
Maher Moakher, John H. Maddocks
Arch. Rational Mech. Anal. 177 (2005), p. 53  91
DOI:10.1007/s002050050360y


79 
2002

Geometry and mechanics of uniform nplies: from engineering ropes to biological filaments
Sébastien Neukirch, Gert van der Heijden
Journal of Elasticity 69 (2002), p. 41  72
DOI:10.1023/a:1027390700610


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. 133160
DOI:10.1017/S0022112004001284


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
DOI:10.1142/s0218127404009971


76 
2004

Symmetric equilibria of a thin elastic rod with selfcontacts
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
DOI:10.1002/bip.10430


73 
2005

A differential geometric approach to the geometric mean of symmetric positivedefinite matrices
M. Moakher
SIAM Journal on Matrix Analysis and Applications 26, no. 3 (2005), p. 735  747
DOI:10.1137/s0895479803436937


72 
2005

On the writhing number of nonclosed curves
E. L. Starostin
Physical and Numerical Models in Knot Theory and Their Application to the Life Sciences (2005), p. 525  545
DOI:10.1142/9789812703460_0026


71 
2003

Instability and selfcontact 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
DOI:10.1016/s00207403(02)001832


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
DOI:10.1177/107754603030746


69 
2002

Equilibrium configurations of a thin elastic rod with selfcontacts
E. L. Starostin
PAMM, Proc. Appl. Math. Mech. 1 (2002), p. 137  138
DOI:10.1002/16177061(200203)1:1<137::AIDPAMM137>3.0.CO;2B


68 
2002

Comment on 'Cyclic rotations, contractibility and GaussBonnet'
E. L. Starostin
J. of Physics A: Math. & Gen. 35 (2002), p. 6183  6190
DOI:10.1088/03054470/35/29/401


67 
2002

Supercoiling of DNA plasmids: mechanics of the generalized ply
J. M. T Thompson, G. H. M van der Heijden, S. Neukirch
Proceedings of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences 458 (2002), p. 959985
DOI:10.1098/rspa.2001.0901


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
DOI:10.1016/s00225096(01)001302


65 
2002

Curves, Circles, and Spheres
O. Gonzalez, J. H. Maddocks, J. Smutny
Contemporary Mathematics (AMS) 304 (2002), p. 195  215
DOI:10.1090/conm/304/05195


64 
2002

La triple hélice : vers une mécanique du collagène
S. Neukirch & G.H.M. van der Heijden
Rencontre du NonLinéaire (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

Selfinteractions of strands and sheets
J.R. Banavar, O. Gonzalez, J.H. Maddocks, A. Maritan
Journal of Statistical Physics 110 (2003), p. 35  50
DOI:10.1023/a:1021010526495


61 
2002

Global curvature and selfcontact 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 selfcontacts
E. L. Starostin
Proceedings of the 16th IMACS World Congress 2000 , Lausanne, August 2125 (2000)
DOI:10.1002/16177061(200203)1:1<137::aidpamm137>3.0.co;2b


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
DOI:10.1142/s0218202502002033


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
DOI:10.1109/eguk.2002.1011285


57 
2000

Best packing in proteins and DNA
Andrzej Stasiak, John H. Maddocks
Nature 406 (2000), p. 251  252
DOI:10.1038/35018674


56 
2001

Extracting parameters for basepair level models of DNA
Oscar Gonzalez, John H. Maddocks
Theoretical Chemistry Accounts 106 (2001), p. 76  82
DOI:10.1007/s002140100256


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
DOI:10.1002/15222616(200011)219:1<109::aidmana109>3.0.co;21


52 
2001

MultiMultiplier 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
DOI:10.1007/s002050100134


51 
2000

DNA Rings with Multiple Energy Minima
Patrick B. Furrer, Robert S. Manning, John H. Maddocks
Biophysical Journal 79 (2000), p. 116  136
DOI:10.1016/s00063495(00)762771


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
GECCO99 (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
DOI:10.1126/science.283.5408.1641c


47 
1999

Mechanical Systems Subject to Holonomic Constraints: DifferentialAlgebraic Formulations and Conservative Integration
O. Gonzalez
Physica D 132 (1999), p. 165  174
DOI:10.1016/s01672789(99)000548


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
DOI:10.1093/imanum/19.2.169


45 
1999

An EnergyTransport 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
DOI:10.1108/03321649910236993


44 
1999

Structural Effect of Complete [Rp]Phosphorothioate and Phosphorodithioate Substitutions in the DNA Strand of a Model Antisense InhibitorTarget 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
DOI:10.1006/jmbi.1998.2305


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
DOI:10.1073/pnas.96.9.4769


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
DOI:10.1016/s00457825(98)00200x


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 FarrJones, 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/bk19980682.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
DOI:10.1016/s03064573(98)000156


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
DOI:10.1109/70.720342


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
DOI:10.1098/rspa.1998.0291


35 
1997

On the Qualitative Properties of Modified Equations
O. Gonzalez & A.M. Stuart
Foundations of Computational Mathematics (1997), p. 169  179
DOI:10.1007/9783642605390_12


34 
1997

Opposite Effect of Counterions on the Persistence Length of Nicked and Nonnicked DNA
Patrick Furrer, Jan Bednar, Alicja Z. Stasiak, Vsevolod Katritch, Didier Michoud, Andrzej Stasiak, Jacques Dubochet
J. Mol. Biol. 266 (1997), p. 711  721
DOI:10.1006/jmbi.1996.0825


33 
1997

The Calogero  Sutherland  Moser (csm) model as a quantum billiard
Stéphane Rey, Philippe Choquard
Eur.J. Phys. 18 (1997), p. 94  98
DOI:10.1088/01430807/18/2/007


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
DOI:10.1142/s0218202597000566


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
DOI:10.1098/rsta.1997.0113


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
DOI:10.1142/s0218127497001333


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
DOI:10.1007/9781461240662_6


27 
1996

A Continuum Rod Model of SequenceDependent DNA Structure
R.S. Manning, J.H. Maddocks, J.D. Kahn
J. Chem. Phys. 105 (1996), p. 5626  5646
DOI:10.1063/1.472373


26 
1996

An ImpetusStriction Simulation of the Dynamics of an Elastica
D.J. Dichmann, J.H. Maddocks
J. Nonlinear Science 6 (1996), p. 271  292
DOI:10.1007/bf02439312


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
DOI:10.1007/bf02198477


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. 12561257
DOI:10.1137/0519091


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
DOI:10.1007/9781461384489_17


22 
1995

Stability Theory for Dissipatively Perturbed Hamiltonian Systems
J.H. Maddocks, M.L. Overton
Commun. On Pure and Applied Math. (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
DOI:10.1007/bf02099446


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
DOI:10.1177/027836499401300207


19 
1994

Conservation laws in the dynamics of rods
J.H. Maddocks, D.J. Dichmann
J. of Elasticity 34 (1994), p. 83  96
DOI:10.1007/bf00042427


18 
1993

On the stability of KdV multisolitons
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 frictiondominated motion of a pushed object
J.C. Alexander, J.H. Maddocks
Int. J. of Robotics Research 12, no. 3 (1993), p. 231  248
DOI:10.1177/027836499301200303


16 
1992

On the dynamics of chains
D. Jacobson, J.H. Maddocks
SIAM J. Applied Math. 52 (1992), p. 1563  1583
DOI:10.1137/0152090


15 
1992

Steady rigidbody motions in a central gravitational field
LS. Wang, J.H. Maddocks, P.K. Krishnaprasad
J. of the Astronautical Sciences 40, no. 4 (1992), p. 449  478


14 
1992

SteadyState shearbands in thermo plasticity, Part I: vanishing yield stress
J.H. Maddocks, R. MalekMadani
Int. J. Solids Structures 29, no. 16 (1992), p. 2063  2076
DOI:10.1016/00207683(92)90193w


13 
1991

Hamiltonian dynamics of a rigid body in a central gravitational field
LS. Wang, P.K. Krishnaprasad, J.H. Maddocks
Celestial Mechanics and Dynamical Astronomy 50 (1991), p. 59  96
DOI:10.1007/bf02426678


12 
1991

On the stability of relative equilibria
J.H. Maddocks
IMA J. Applied Math. 46 (1991), p. 71  99
DOI:10.1093/imamat/46.12.71


11 
1989

On the kinematics of wheeled mobile robots
J.C. Alexander, J.H. Maddocks
Int. J. Robotics Research 8 (1989), p. 15  27
DOI:10.1177/027836498900800502


10 
1988

Restricted quadratic forms, inertia theorems, and the Schur complement
J.H. Maddocks
Linear Algebra and Appl. 108 (1988), p. 1  36
DOI:10.1016/00243795(88)901772


9 
1988

On the maneuvering of vehicles
J.C. Alexander, J.H. Maddocks
SIAM J. Appl. Math. 48, no. 1 (1988), p. 3852
DOI:10.1137/0148002


8 
1987

Ropes in equilibrium
J.H. Maddocks, J.B. Keller
SIAM J.Appl. Math. 47, no. 6 (1987), p. 1185  1200
DOI:10.1137/0147080


7 
1987

A model for disclinations in nematic liquid crystal
J.H. Maddocks
IMA Volumes in Mathematics and Its Applications (1987), p. 255  269
DOI:10.1007/9781461387435_13


6 
1987

Stability and folds
J.H. Maddocks
Arch. Rat. Mech. Anal. 99 (1987), p. 301  328
DOI:10.1007/bf00282049


5 
1986

A model for twinning
J.H. Maddocks, G.P. Parry
J. Elasticity 16 (1986), p. 113  133
DOI:10.1007/bf00043580


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
DOI:10.1137/0516004


3 
1984

Nonlinear dynamical theory of the elastica
R.E. Caflisch, J.H. Maddocks
Proc. Roy. Soc. Edinburgh 99A (1984), p. 1  23
DOI:10.1017/s0308210500025920


2 
1984

Stability of nonlinearly elastic rods
J.H. Maddocks
Arch. Rat. Mech. Anal. 85 (1984), p. 311  354
DOI:10.1007/bf00275737


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) (1983)
DOI:10.1007/9789400971899_17

