Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture

[1]  Alberto Redaelli,et al.  Deformation rate controls elasticity and unfolding pathway of single tropocollagen molecules. , 2009, Journal of the mechanical behavior of biomedical materials.

[2]  Markus J. Buehler,et al.  Atomistic Modeling of Materials Failure , 2008 .

[3]  Markus J. Buehler,et al.  Elasticity, strength and resilience: A comparative study on mechanical signatures of α-Helix, β-sheet and tropocollagen domains , 2008 .

[4]  Markus J. Buehler,et al.  Hierarchical Coexistence of Universality and Diversity Controls Robustness and Multi-Functionality in Protein Materials , 2008 .

[5]  M. Buehler,et al.  Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling , 2008 .

[6]  Markus J Buehler,et al.  Asymptotic strength limit of hydrogen-bond assemblies in proteins at vanishing pulling rates. , 2008, Physical review letters.

[7]  M. Buehler Molecular architecture of collagen fibrils: A critical length scale for tough fibrils , 2008 .

[8]  Richard Weinkamer,et al.  Nature’s hierarchical materials , 2007 .

[9]  Markus J Buehler,et al.  Threshold crack speed controls dynamical fracture of silicon single crystals. , 2007, Physical review letters.

[10]  Markus J. Buehler,et al.  Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of α-helical and β-sheet protein domains , 2007, Proceedings of the National Academy of Sciences.

[11]  Markus J. Buehler,et al.  Fracture mechanics of protein materials , 2007 .

[12]  Markus J. Buehler,et al.  Nano- and micromechanical properties of hierarchical biological materials and tissues , 2007 .

[13]  Markus J. Buehler,et al.  Hierarchical chemo-nanomechanics of proteins: entropic elasticity, protein unfolding and molecular fracture , 2007 .

[14]  Markus J. Buehler,et al.  Molecular nanomechanics of nascent bone: fibrillar toughening by mineralization , 2007 .

[15]  Markus J. Buehler,et al.  Superelasticity, energy dissipation and strain hardening of vimentin coiled-coil intermediate filaments: atomistic and continuum studies , 2007, Journal of Materials Science.

[16]  Markus J Buehler,et al.  Entropic elasticity controls nanomechanics of single tropocollagen molecules. , 2007, Biophysical journal.

[17]  Derek N. Woolfson,et al.  Engineering nanoscale order into a designed protein fiber , 2007, Proceedings of the National Academy of Sciences.

[18]  Joanna I. Sulkowska,et al.  Mechanical stretching of proteins—a theoretical survey of the Protein Data Bank , 2007 .

[19]  Gerhard Hummer,et al.  Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. , 2007, Biophysical journal.

[20]  D. Makarov Unraveling individual molecules by mechanical forces: theory meets experiment. , 2007, Biophysical journal.

[21]  Jennifer C. Lee,et al.  Equilibrium unfolding of the poly(glutamic acid)20 helix. , 2007, Biopolymers.

[22]  B. Colombini,et al.  Characterization of actomyosin bond properties in intact skeletal muscle by force spectroscopy , 2007, Proceedings of the National Academy of Sciences.

[23]  K. Schulten,et al.  Single-Molecule Experiments in Vitro and in Silico , 2007, Science.

[24]  David A Calderwood,et al.  Forces and Bond Dynamics in Cell Adhesion , 2007, Science.

[25]  P. Fraser,et al.  Nuclear organization of the genome and the potential for gene regulation , 2007, Nature.

[26]  Justin L. MacCallum,et al.  Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding , 2007, Proceedings of the National Academy of Sciences.

[27]  Darrin J. Pochan,et al.  Polymer Nanocomposites for Biomedical Applications , 2007 .

[28]  David Taylor,et al.  Living with cracks: damage and repair in human bone. , 2007, Nature materials.

[29]  Syma Khalid,et al.  Coarse-grained molecular dynamics simulations of membrane proteins and peptides. , 2007, Journal of structural biology.

[30]  Ryan Day,et al.  Direct observation of microscopic reversibility in single-molecule protein folding. , 2007, Journal of molecular biology.

[31]  L. Serpell,et al.  Spider silk and amyloid fibrils: a structural comparison. , 2007, Macromolecular bioscience.

[32]  F. Barthelat,et al.  On the mechanics of mother-of-pearl: a key feature in the material hierarchical structure , 2007 .

[33]  Jane Clarke,et al.  Mechanical unfolding of proteins: insights into biology, structure and folding. , 2007, Current opinion in structural biology.

[34]  D. Brockwell Force Denaturation of Proteins - an Unfolding Story , 2007 .

[35]  R. Ruoff,et al.  Optimized adhesives for strong, lightweight, damage-resistant, nanocomposite materials: new insights from natural materials , 2007 .

[36]  Jianfeng Zang,et al.  Biocatalytic Generation of Ppy-Enzyme-CNT Nanocomposite: From Network Assembly to Film Growth , 2007 .

[37]  J. Clarke,et al.  Spectrin domains lose cooperativity in forced unfolding. , 2007, Biophysical journal.

[38]  Shuguang Zhang,et al.  Designer self-assembling peptide materials. , 2007, Macromolecular bioscience.

[39]  Laurent Kreplak,et al.  Biomechanical properties of intermediate filaments: from tissues to single filaments and back , 2007, BioEssays : news and reviews in molecular, cellular and developmental biology.

[40]  Lian Li,et al.  Design of superior spider silk: from nanostructure to mechanical properties. , 2006, Biophysical journal.

[41]  Sean X. Sun,et al.  Elasticity of alpha-helical coiled coils. , 2006, Physical review letters.

[42]  Wolfgang Wagermaier,et al.  Cooperative deformation of mineral and collagen in bone at the nanoscale , 2006, Proceedings of the National Academy of Sciences.

[43]  Joel W. Ager,et al.  Fracture and Ageing in Bone: Toughness and Structural Characterization , 2006 .

[44]  A. S. Argon,et al.  The strongest size , 2006 .

[45]  Markus J. Buehler,et al.  Mesoscale modeling of mechanics of carbon nanotubes: Self-assembly, self-folding, and fracture , 2006 .

[46]  G. Voth,et al.  Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules. , 2006, Biophysical journal.

[47]  Xiaojun Zhao,et al.  Molecular designer self-assembling peptides. , 2006, Chemical Society reviews.

[48]  S. Jarvis,et al.  Nanoscale Mechanical Characterisation of Amyloid Fibrils Discovered in a Natural Adhesive , 2006, Journal of biological physics.

[49]  Franz-Josef Ulm,et al.  Nanogranular origins of the strength of bone. , 2006, Nano letters.

[50]  H. Kreuzer,et al.  Breaking bonds in the atomic force microscope: theory and analysis. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[51]  Jan Feijen,et al.  Micromechanical testing of individual collagen fibrils. , 2006, Macromolecular bioscience.

[52]  Chwee Teck Lim,et al.  Experimental techniques for single cell and single molecule biomechanics , 2006 .

[53]  S. Sen,et al.  Matrix Elasticity Directs Stem Cell Lineage Specification , 2006, Cell.

[54]  Markus J. Buehler,et al.  Nature designs tough collagen: Explaining the nanostructure of collagen fibrils , 2006, Proceedings of the National Academy of Sciences.

[55]  Markus J. Buehler,et al.  Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and self-assembly , 2006 .

[56]  M. Kellermayer,et al.  Nanomechanical properties of desmin intermediate filaments. , 2006, Journal of structural biology.

[57]  U. Aebi,et al.  Exploring the mechanical properties of single vimentin intermediate filaments by atomic force microscopy. , 2006, Journal of molecular biology.

[58]  S. Jarvis,et al.  Explanation for the mechanical strength of amyloid fibrils , 2006 .

[59]  I. Rangelow,et al.  Hierarchical interconnections in the nano-composite material bone: Fibrillar cross-links resist fracture on several length scales , 2006 .

[60]  T. Irving,et al.  Microfibrillar structure of type I collagen in situ. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[61]  C. Dobson,et al.  Protein misfolding, functional amyloid, and human disease. , 2006, Annual review of biochemistry.

[62]  Baohua Ji,et al.  Cracking and adhesion at small scales: atomistic and continuum studies of flaw tolerant nanostructures , 2006, Modelling and Simulation in Materials Science and Engineering.

[63]  Hector H. Huang,et al.  Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Emanuele Paci,et al.  Mechanical unfolding revisited through a simple but realistic model. , 2006, The Journal of chemical physics.

[65]  Fritz Vollrath,et al.  Spider silk as archetypal protein elastomer. , 2006, Soft matter.

[66]  Kuan Wang,et al.  Coiled-Coil Nanomechanics and Uncoiling and Unfolding of the Superhelix and α-Helices of Myosin , 2006 .

[67]  M. Rief,et al.  Single molecule unzipping of coiled coils: sequence resolved stability profiles. , 2006, Physical Review Letters.

[68]  Gerhard Hummer,et al.  Intrinsic rates and activation free energies from single-molecule pulling experiments. , 2006, Physical review letters.

[69]  Markus J Buehler,et al.  Multiparadigm modeling of dynamical crack propagation in silicon using a reactive force field. , 2006, Physical review letters.

[70]  Klaus Schulten,et al.  Mechanical strength of the titin Z1Z2-telethonin complex. , 2006, Structure.

[71]  Huajian Gao,et al.  Application of Fracture Mechanics Concepts to Hierarchical Biomechanics of Bone and Bone-like Materials , 2006 .

[72]  H. Kahn,et al.  Nano measurements with micro-devices: mechanical properties of hydrated collagen fibrils , 2006, Journal of The Royal Society Interface.

[73]  D. Leckband,et al.  Lifetime measurements reveal kinetic differences between homophilic cadherin bonds. , 2006, Biophysical Journal.

[74]  M. Rief,et al.  Single-molecule unfolding force distributions reveal a funnel-shaped energy landscape. , 2006, Biophysical journal.

[75]  D. Porter,et al.  Spider silk as a model biomaterial , 2006 .

[76]  T. Magin,et al.  Mutations in vimentin disrupt the cytoskeleton in fibroblasts and delay execution of apoptosis. , 2006, European journal of cell biology.

[77]  Amos Maritan,et al.  The origami of life , 2006 .

[78]  Huajian Gao,et al.  Dynamical fracture instabilities due to local hyperelasticity at crack tips , 2006, Nature.

[79]  Todd Sulchek,et al.  Strength of multiple parallel biological bonds. , 2005, Biophysical journal.

[80]  U Aebi,et al.  Exploring the mechanical behavior of single intermediate filaments. , 2005, Journal of molecular biology.

[81]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[82]  M. Horton,et al.  Atomic force microscopy of collagen structure in bone and dentine revealed by osteoclastic resorption. , 2005, Ultramicroscopy.

[83]  Andreas Mershin,et al.  A classic assembly of nanobiomaterials , 2005, Nature Biotechnology.

[84]  M. Tzaphlidou,et al.  Analysis of fibrous proteins from electron microscopy images. , 2005, Medical engineering & physics.

[85]  Himadri S. Gupta,et al.  Nanoscale deformation mechanisms in bone. , 2005, Nano letters.

[86]  D. Lacks,et al.  Energy barrier scalings in driven systems. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[87]  Jacqueline A. Cutroni,et al.  Sacrificial bonds and hidden length dissipate energy as mineralized fibrils separate during bone fracture , 2005, Nature materials.

[88]  J. Aizenberg,et al.  Skeleton of Euplectella sp.: Structural Hierarchy from the Nanoscale to the Macroscale , 2005, Science.

[89]  Ernesto Raúl Caffarena,et al.  Elastic properties, Young's modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics. , 2005, Journal of biomechanics.

[90]  R O Ritchie,et al.  Fracture in human cortical bone: local fracture criteria and toughening mechanisms. , 2005, Journal of biomechanics.

[91]  Rishi Gupta,et al.  Nanomanipulation and aggregation limitations of self-assembling structural proteins , 2005, Microelectron. J..

[92]  H. V. von Schroeder,et al.  Computational modeling of type I collagen fibers to determine the extracellular matrix structure of connective tissues. , 2005, Protein engineering, design & selection : PEDS.

[93]  Michael L Klein,et al.  Unfolding a linker between helical repeats. , 2005, Journal of molecular biology.

[94]  Michael Horton,et al.  Topography and mechanical properties of single molecules of type I collagen using atomic force microscopy. , 2005, Biophysical journal.

[95]  H. Lashuel,et al.  The Materials Science of Protein Aggregation , 2005 .

[96]  A. V. van Duin,et al.  Optimization and application of lithium parameters for the reactive force field, ReaxFF. , 2005, The journal of physical chemistry. A.

[97]  F. Glorieux Caffey disease: an unlikely collagenopathy. , 2005, The Journal of clinical investigation.

[98]  A. V. van Duin,et al.  Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field. , 2005, Journal of the American Chemical Society.

[99]  A. Redaelli,et al.  Molecular assessment of the elastic properties of collagen-like homotrimer sequences , 2005, Biomechanics and modeling in mechanobiology.

[100]  David A. Tirrell,et al.  Controlled Assembly of Macromolecular β-Sheet Fibrils , 2005 .

[101]  A. Nagy,et al.  Reversible Mechanical Unzipping of Amyloid β-Fibrils* , 2005, Journal of Biological Chemistry.

[102]  Arnab Bhattacharjee,et al.  Collagen Structure: The Madras Triple Helix and the Current Scenario , 2005, IUBMB life.

[103]  A. V. van Duin,et al.  Thermal decomposition of RDX from reactive molecular dynamics. , 2005, The Journal of chemical physics.

[104]  Hualiang Jiang,et al.  Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. , 2005, Biophysical journal.

[105]  A. V. van Duin,et al.  Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes. , 2005, The journal of physical chemistry. A.

[106]  A. V. van Duin,et al.  ReaxFF(MgH) reactive force field for magnesium hydride systems. , 2005, The journal of physical chemistry. A.

[107]  J. Ramshaw,et al.  Electrostatic interactions involving lysine make major contributions to collagen triple-helix stability. , 2005, Biochemistry.

[108]  Gerhard Hummer,et al.  Free energy surfaces from single-molecule force spectroscopy. , 2005, Accounts of chemical research.

[109]  Ueli Aebi,et al.  Molecular mechanisms underlying the assembly of intermediate filaments. , 2004, Experimental cell research.

[110]  M. Omary,et al.  Intermediate filament proteins and their associated diseases. , 2004, The New England journal of medicine.

[111]  Kai-Nan An,et al.  Stretching type II collagen with optical tweezers. , 2004, Journal of biomechanics.

[112]  D. Bader,et al.  Local Strain Measurement within Tendon , 2004 .

[113]  U. Aebi,et al.  Crystal structure of the human lamin A coil 2B dimer: implications for the head-to-tail association of nuclear lamins. , 2004, Journal of molecular biology.

[114]  P. Fratzl,et al.  Synchrotron diffraction study of deformation mechanisms in mineralized tendon. , 2004, Physical review letters.

[115]  Alexander D. MacKerell Empirical force fields for biological macromolecules: Overview and issues , 2004, J. Comput. Chem..

[116]  Wei-Jing Zhu,et al.  Surface energetics of hydroxyapatite: a DFT study , 2004 .

[117]  D. Makarov,et al.  Simulation of the mechanical unfolding of ubiquitin: probing different unfolding reaction coordinates by changing the pulling geometry. , 2004, The Journal of chemical physics.

[118]  P. B. Warren,et al.  Multiscale modelling of human hair , 2004, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[119]  F. Silver,et al.  Elastic energy storage in unmineralized and mineralized extracellular matrices (ECMs): a comparison between molecular modeling and experimental measurements. , 2004, Journal of theoretical biology.

[120]  I. Meier,et al.  Scaffolds, levers, rods and springs: diverse cellular functions of long coiled-coil proteins , 2004, Cellular and Molecular Life Sciences CMLS.

[121]  Michael F. Ashby,et al.  The mechanical efficiency of natural materials , 2004 .

[122]  Himadri S. Gupta,et al.  Structure and mechanical quality of the collagen–mineral nano-composite in bone , 2004 .

[123]  Jonathan A. Zimmerman,et al.  Calculation of stress in atomistic simulation , 2004 .

[124]  Eric A. Stach,et al.  Characteristic dimensions and the micro-mechanisms of fracture and fatigue in `nano' and `bio' materials , 2004 .

[125]  Huajian Gao,et al.  Deformation Mechanisms of Very Long Single-Wall Carbon Nanotubes Subject to Compressive Loading , 2004 .

[126]  Ueli Aebi,et al.  Molecular and biophysical characterization of assembly-starter units of human vimentin. , 2004, Journal of molecular biology.

[127]  J. Engel,et al.  Design and crystal structure of bacteriophage T4 mini-fibritin NCCF. , 2004, Journal of molecular biology.

[128]  P. Janmey,et al.  Nonlinear elasticity in biological gels , 2004, Nature.

[129]  Subra Suresh,et al.  Large deformation of living cells using laser traps , 2004 .

[130]  R. Langer,et al.  Designing materials for biology and medicine , 2004, Nature.

[131]  A. Kishimoto,et al.  beta-Helix is a likely core structure of yeast prion Sup35 amyloid fibers. , 2004, Biochemical and biophysical research communications.

[132]  Valerio Bertolasi,et al.  Covalent versus electrostatic nature of the strong hydrogen bond: discrimination among single, double, and asymmetric single-well hydrogen bonds by variable-temperature X-ray crystallographic methods in beta-diketone enol RAHB systems. , 2004, Journal of the American Chemical Society.

[133]  J. Gosline,et al.  Molecular design of the α–keratin composite: insights from a matrix–free model, hagfish slime threads , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[134]  J Langowski,et al.  Assessing the flexibility of intermediate filaments by atomic force microscopy. , 2004, Journal of molecular biology.

[135]  U. Schwarz,et al.  Stability of adhesion clusters under constant force. , 2004, Physical review letters.

[136]  B. Helfand,et al.  Intermediate filaments are dynamic and motile elements of cellular architecture , 2004, Journal of Cell Science.

[137]  C. Dobson Protein folding and misfolding , 2003, Nature.

[138]  P. Dobson,et al.  Length preferences and periodicity in β‐strands. Antiparallel edge β‐sheets are more likely to finish in non‐hydrogen bonded rings , 2003 .

[139]  Markus Gruber,et al.  Historical review: another 50th anniversary--new periodicities in coiled coils. , 2003, Trends in biochemical sciences.

[140]  Klaus Schulten,et al.  Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[141]  Huajian Gao,et al.  Hyperelasticity governs dynamic fracture at a critical length scale , 2003, Nature.

[142]  C. Lim,et al.  Mechanics of the human red blood cell deformed by optical tweezers , 2003 .

[143]  S. Suresh,et al.  Cell and molecular mechanics of biological materials , 2003, Nature materials.

[144]  D J Mooney,et al.  Regulating Bone Formation via Controlled Scaffold Degradation , 2003, Journal of dental research.

[145]  D. Makarov,et al.  Theoretical studies of the mechanical unfolding of the muscle protein titin: Bridging the time-scale gap between simulation and experiment , 2003 .

[146]  Sheh-Yi Sheu,et al.  Energetics of hydrogen bonds in peptides , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[147]  Simon R. Phillpot,et al.  Deformation mechanism and inverse Hall–Petch behavior in nanocrystalline materials , 2003 .

[148]  Shuguang Zhang Fabrication of novel biomaterials through molecular self-assembly , 2003, Nature Biotechnology.

[149]  Christian Riekel,et al.  The mechanical properties of hydrated intermediate filaments: insights from hagfish slime threads. , 2003, Biophysical journal.

[150]  Hui Lu,et al.  The mechanical stability of ubiquitin is linkage dependent , 2003, Nature Structural Biology.

[151]  A. V. van Duin,et al.  Shock waves in high-energy materials: the initial chemical events in nitramine RDX. , 2003, Physical review letters.

[152]  Emanuele Paci,et al.  Pulling geometry defines the mechanical resistance of a β-sheet protein , 2003, Nature Structural Biology.

[153]  Gerhard Hummer,et al.  Kinetics from nonequilibrium single-molecule pulling experiments. , 2003, Biophysical journal.

[154]  Huajian Gao,et al.  Materials become insensitive to flaws at nanoscale: Lessons from nature , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[155]  Meital Reches,et al.  Casting Metal Nanowires Within Discrete Self-Assembled Peptide Nanotubes , 2003, Science.

[156]  A. V. Duin,et al.  ReaxFFSiO Reactive Force Field for Silicon and Silicon Oxide Systems , 2003 .

[157]  H. Jaeger,et al.  Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[158]  P. Janmey,et al.  Assembly and structure of neurofilaments , 2003 .

[159]  Ueli Aebi,et al.  Molecular architecture of intermediate filaments , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[160]  R. Ritchie,et al.  Mechanistic fracture criteria for the failure of human cortical bone , 2003, Nature materials.

[161]  R O Ritchie,et al.  Effect of orientation on the in vitro fracture toughness of dentin: the role of toughening mechanisms. , 2003, Biomaterials.

[162]  Ueli Aebi,et al.  Intermediate filaments: molecular structure, assembly mechanism, and integration into functionally distinct intracellular Scaffolds. , 2003, Annual review of biochemistry.

[163]  D. Parry,et al.  Modeling α‐helical coiled‐coil interactions: The axial and azimuthal alignment of 1B segments from vimentin intermediate filaments , 2002, Proteins.

[164]  Klaus Schulten,et al.  Unfolding of titin domains studied by molecular dynamics simulations , 2002, Journal of Muscle Research & Cell Motility.

[165]  M. Goh,et al.  Hierarchical assembly and the onset of banding in fibrous long spacing collagen revealed by atomic force microscopy. , 2002, Matrix biology : journal of the International Society for Matrix Biology.

[166]  Matthias Rief,et al.  The myosin coiled-coil is a truly elastic protein structure , 2002, Nature materials.

[167]  Hugh A. Bruck,et al.  The role of mechanics in biological and biologically inspired materials , 2002 .

[168]  H. Kitano,et al.  Computational systems biology , 2002, Nature.

[169]  Sean D Mooney,et al.  Structural Models of Osteogenesis Imperfecta-associated Variants in the COL1A1 Gene* , 2002, Molecular & Cellular Proteomics.

[170]  Rajiv K. Kalia,et al.  ATOMISTIC ASPECTS OF CRACK PROPAGATION IN BRITTLE MATERIALS: Multimillion Atom Molecular Dynamics Simulations , 2002 .

[171]  F. Vollrath,et al.  Amyloidogenic nature of spider silk. , 2002, European journal of biochemistry.

[172]  B. Meier,et al.  The molecular structure of spider dragline silk: Folding and orientation of the protein backbone , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[173]  Kai-Nan An,et al.  Direct quantification of the flexibility of type I collagen monomer. , 2002, Biochemical and biophysical research communications.

[174]  Sean D Mooney,et al.  Conformational preferences of substituted prolines in the collagen triple helix. , 2002, Biopolymers.

[175]  John D. Currey,et al.  Bones: Structure and Mechanics , 2002 .

[176]  H. Hansma,et al.  Segmented nanofibers of spider dragline silk: Atomic force microscopy and single-molecule force spectroscopy , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[177]  J T Finch,et al.  Amyloid fibers are water-filled nanotubes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[178]  U. Aebi,et al.  Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly , 2002, The EMBO journal.

[179]  Helmut Grubmüller,et al.  Force spectroscopy of single biomolecules. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.

[180]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[181]  P. Fratzl,et al.  Viscoelastic properties of collagen: synchrotron radiation investigations and structural model. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[182]  Fumio Arisaka,et al.  Structure of the cell-puncturing device of bacteriophage T4 , 2002, Nature.

[183]  Donald W. Brenner,et al.  A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons , 2002 .

[184]  D. Boal,et al.  Mechanics of the cell , 2001 .

[185]  Paul K. Hansma,et al.  Bone indentation recovery time correlates with bond reforming time , 2001, Nature.

[186]  Marek Cieplak,et al.  Thermal folding and mechanical unfolding pathways of protein secondary structures , 2001, Proteins.

[187]  R. Moir,et al.  The structure and function of nuclear lamins: implications for disease , 2001, Cellular and Molecular Life Sciences CMLS.

[188]  A. V. Duin,et al.  ReaxFF: A Reactive Force Field for Hydrocarbons , 2001 .

[189]  K. An,et al.  Stretching short biopolymers using optical tweezers. , 2001, Biochemical and biophysical research communications.

[190]  Seiji Takeda,et al.  Insight into conformational changes of a single α-helix peptide molecule through stiffness measurements , 2001 .

[191]  Allen J. Bailey,et al.  Molecular mechanisms of ageing in connective tissues , 2001, Mechanisms of Ageing and Development.

[192]  Peter Gumbsch,et al.  Dislocation sources in discrete dislocation simulations of thin-film plasticity and the Hall-Petch relation , 2001 .

[193]  C. A. Miles,et al.  Thermally labile domains in the collagen molecule. , 2001, Micron.

[194]  H. Güntherodt,et al.  Quantitative Measurement of Short-Range Chemical Bonding Forces , 2001, Science.

[195]  Fritz Vollrath,et al.  Liquid crystalline spinning of spider silk , 2001, Nature.

[196]  G. Hummer,et al.  Free energy reconstruction from nonequilibrium single-molecule pulling experiments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[197]  Evan Evans,et al.  Chemically distinct transition states govern rapid dissociation of single L-selectin bonds under force , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[198]  K. Wilson,et al.  Lamins and Disease Insights into Nuclear Infrastructure , 2001, Cell.

[199]  P. Kollman,et al.  Computed free energy differences between point mutations in a collagen-like peptide. , 2001, Biopolymers.

[200]  Ye-Sho Chen,et al.  Decision Criteria Consolidation: A Theoretical Foundation of Pareto Principle to Porter's Competitive Forces , 2001, J. Organ. Comput. Electron. Commer..

[201]  P. Fratzl,et al.  Mineralized collagen fibrils: a mechanical model with a staggered arrangement of mineral particles. , 2000, Biophysical journal.

[202]  D. Wirtz,et al.  The 'ins' and 'outs' of intermediate filament organization. , 2000, Trends in cell biology.

[203]  H. Berman,et al.  Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair. , 2000, Journal of molecular biology.

[204]  P Kolb,et al.  Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy. , 2000, Biochemistry.

[205]  K. Schulten,et al.  The key event in force-induced unfolding of Titin's immunoglobulin domains. , 2000, Biophysical journal.

[206]  H. Grubmüller,et al.  Dynamic force spectroscopy of molecular adhesion bonds. , 2000, Physical review letters.

[207]  E M Arruda,et al.  Finite element modeling of human skin using an isotropic, nonlinear elastic constitutive model. , 2000, Journal of biomechanics.

[208]  S. Smith,et al.  Single-molecule studies of DNA mechanics. , 2000, Current opinion in structural biology.

[209]  R. Kisilevsky Review: amyloidogenesis-unquestioned answers and unanswered questions. , 2000, Journal of structural biology.

[210]  A Ikai,et al.  Dynamic measurement of single protein's mechanical properties. , 2000, Biochemical and biophysical research communications.

[211]  S. Stuart,et al.  A reactive potential for hydrocarbons with intermolecular interactions , 2000 .

[212]  M. Steinmetz,et al.  The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of interhelical and intrahelical salt bridges. , 2000, Structure.

[213]  U. Seifert,et al.  Rupture of multiple parallel molecular bonds under dynamic loading. , 2000, Physical review letters.

[214]  Mark A. Lantz,et al.  Stretching the α-helix: a direct measure of the hydrogen-bond energy of a single-peptide molecule , 1999 .

[215]  E. Evans,et al.  Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy. , 1999, Biophysical chemistry.

[216]  Klaus Schulten,et al.  Mechanical unfolding intermediates in titin modules , 1999, Nature.

[217]  A. Oberhauser,et al.  The study of protein mechanics with the atomic force microscope. , 1999, Trends in biochemical sciences.

[218]  U. Aebi,et al.  Intermediate filament assembly: temperature sensitivity and polymorphism , 1999, Cellular and Molecular Life Sciences CMLS.

[219]  Mario Viani,et al.  Molecular mechanistic origin of the toughness of natural adhesives, fibres and composites , 1999, Nature.

[220]  R. Lavery,et al.  Unraveling proteins: a molecular mechanics study. , 1999, Biophysical journal.

[221]  M. Rief,et al.  How strong is a covalent bond? , 1999, Science.

[222]  K. Broberg Cracks and Fracture , 1999 .

[223]  M. Rief,et al.  Single molecule force spectroscopy of spectrin repeats: low unfolding forces in helix bundles. , 1999, Journal of molecular biology.

[224]  R. Merkel,et al.  Energy landscapes of receptor–ligand bonds explored with dynamic force spectroscopy , 1999, Nature.

[225]  M. Rief,et al.  The mechanical stability of immunoglobulin and fibronectin III domains in the muscle protein titin measured by atomic force microscopy. , 1998, Biophysical journal.

[226]  Matthias Rief,et al.  Elastically Coupled Two-Level Systems as a Model for Biopolymer Extensibility , 1998 .

[227]  Steve Weiner,et al.  THE MATERIAL BONE: Structure-Mechanical Function Relations , 1998 .

[228]  K. Schulten,et al.  Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. , 1998, Biophysical journal.

[229]  D. Wirtz,et al.  Reversible hydrogels from self-assembling artificial proteins. , 1998, Science.

[230]  J. Waite,et al.  The peculiar collagens of mussel byssus. , 1998, Matrix biology : journal of the International Society for Matrix Biology.

[231]  Andres F. Oberhauser,et al.  The molecular elasticity of the extracellular matrix protein tenascin , 1998, Nature.

[232]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[233]  R. Lewis,et al.  Evidence from flagelliform silk cDNA for the structural basis of elasticity and modular nature of spider silks. , 1998, Journal of molecular biology.

[234]  Sidney Yip,et al.  Nanocrystals: The strongest size , 1998, Nature.

[235]  P. Ball Made to Measure , 1997 .

[236]  N. Sasaki,et al.  Measurement of partition of stress between mineral and collagen phases in bone using X-ray diffraction techniques. , 1997, Journal of biomechanics.

[237]  C. Jarzynski Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach , 1997, cond-mat/9707325.

[238]  M. Rief,et al.  Reversible unfolding of individual titin immunoglobulin domains by AFM. , 1997, Science.

[239]  E. Evans,et al.  Dynamic strength of molecular adhesion bonds. , 1997, Biophysical journal.

[240]  Laxmikant V. Kalé,et al.  NAMD: a Parallel, Object-Oriented Molecular Dynamics Program , 1996, Int. J. High Perform. Comput. Appl..

[241]  A. Warshel,et al.  Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[242]  C. Jarzynski Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[243]  D. Parry,et al.  Heptad breaks in α‐helical coiled coils: Stutters and stammers , 1996 .

[244]  N. Sasaki,et al.  Elongation mechanism of collagen fibrils and force-strain relations of tendon at each level of structural hierarchy. , 1996, Journal of biomechanics.

[245]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[246]  Peter A. Kollman,et al.  AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .

[247]  D J Prockop,et al.  Radial packing, order, and disorder in collagen fibrils. , 1995, Biophysical journal.

[248]  M. Osteaux,et al.  Cortical mineral content of the radius assessed by peripheral QCT predicts compressive strength on biomechanical testing. , 1995, Bone.

[249]  Y. Termonia Molecular modeling of spider silk elasticity , 1994 .

[250]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[251]  Ye-Sho Chen,et al.  Mathematical and computer modelling of the Pareto principle , 1994 .

[252]  M. Yoder,et al.  Unusual structural features in the parallel β-helix in pectate lyases , 1993 .

[253]  Ye-Sho Chen,et al.  Theoretical foundation of the 80/20 rule , 1993, Scientometrics.

[254]  J. B. Adams,et al.  Interatomic Potentials from First-Principles Calculations: The Force-Matching Method , 1993, cond-mat/9306054.

[255]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[256]  R. Lakes Materials with structural hierarchy , 1993, Nature.

[257]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[258]  Jeffrey Wadsworth,et al.  Hall-petch relation in nanocrystalline solids , 1991 .

[259]  P. Janmey,et al.  Viscoelastic properties of vimentin compared with other filamentous biopolymer networks , 1991, The Journal of cell biology.

[260]  D. Kaplan,et al.  Liquid crystallinity of natural silk secretions , 1991, Nature.

[261]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[262]  PRIYA VASHISHTA,et al.  Large-scale atomistic simulations of dynamic fracture , 1989, Comput. Sci. Eng..

[263]  Benoit B. Mandelbrot,et al.  Fractal geometry: what is it, and what does it do? , 1989, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[264]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[265]  J Engel,et al.  Localization of flexible sites in thread-like molecules from electron micrographs. Comparison of interstitial, basement membrane and intima collagens. , 1984, Journal of molecular biology.

[266]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[267]  J. Karn,et al.  Periodic features in the amino acid sequence of nematode myosin rod. , 1983, Journal of molecular biology.

[268]  S Cusack,et al.  Determination of the elastic constants of collagen by Brillouin light scattering. , 1979, Journal of molecular biology.

[269]  D. H. Tsai The virial theorem and stress calculation in molecular dynamics , 1979 .

[270]  G. I. Bell Models for the specific adhesion of cells to cells. , 1978, Science.

[271]  D. Parry Fibrinogen: A preliminary analysis of the amino acid sequences of the portions of the α, β and γ-chains postulated to form the interdomainal link between globular regions of the molecule , 1978 .

[272]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[273]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[274]  J. White,et al.  Phonons and the elastic moduli of collagen and muscle , 1977, Nature.

[275]  A. Bailey,et al.  The chemistry of the collagen cross-links. The mechanism of stabilization of the reducible intermediate cross-links. , 1975, The Biochemical journal.

[276]  A. Bailey,et al.  The chemistry of the collagen cross-links. The characterization of fraction C, a possible artifact produced during the reduction of collagen fibres with borohydride. , 1973, The Biochemical journal.

[277]  P. Byers,et al.  Defect in Conversion of Procollagen to Collagen in a Form of Ehlers-Danlos Syndrome , 1973, Science.

[278]  H. Kramers Brownian motion in a field of force and the diffusion model of chemical reactions , 1940 .

[279]  M. Buehler Nanomechanics of collagen fibrils under varying cross-link densities: atomistic and continuum studies. , 2008, Journal of the mechanical behavior of biomedical materials.

[280]  M. Buehler Hierarchical Nanomechanics of Collagen Fibrils: Atomistic and Molecular Modeling , 2008 .

[281]  Peter Fratzl,et al.  Collagen : structure and mechanics , 2008 .

[282]  Markus J Buehler,et al.  Geometric confinement governs the rupture strength of H-bond assemblies at a critical length scale. , 2008, Nano letters.

[283]  Markus J Buehler,et al.  Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains. , 2007, Proceedings of the National Academy of Sciences of the United States of America.

[284]  Paul Roschger,et al.  From brittle to ductile fracture of bone , 2006, Nature materials.

[285]  A. V. Duin,et al.  Multi-paradigm modeling of dynamical crack propagation in silicon using the ReaxFF reactive force field , 2006 .

[286]  S. Radford,et al.  Mechanical resistance of proteins explained using simple molecular models. , 2006, Biophysical journal.

[287]  Chwee Teck Lim,et al.  Connections between single-cell biomechanics and human disease states: gastrointestinal cancer and malaria. , 2005, Acta biomaterialia.

[288]  William A. Goddard,et al.  A Perspective of Materials Modeling , 2005 .

[289]  A. V. Duin,et al.  The Computational Materials Design Facility (CMDF): A powerful framework for multi-paradigm multi-scale simulations , 2005 .

[290]  R O Ritchie,et al.  Mechanistic aspects of fracture and R-curve behavior in human cortical bone. , 2005, Biomaterials.

[291]  Sidney Yip,et al.  Handbook of Materials Modeling , 2005 .

[292]  Peter S. Lomdahl,et al.  LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES , 2004 .

[293]  Kai-Nan An,et al.  Flexibility of type I collagen and mechanical property of connective tissue. , 2004, Biorheology.

[294]  Ning Wang,et al.  Mechanics of vimentin intermediate filaments , 2004, Journal of Muscle Research & Cell Motility.

[295]  T. M. Parker,et al.  Mechanics of elastin: molecular mechanism of biological elasticity and its relationship to contraction , 2003 .

[296]  Martine Pithioux,et al.  Numerical damage models using a structural approach: application in bones and ligaments , 2002 .

[297]  P. Kollman,et al.  Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. , 2001, Annual review of biophysics and biomolecular structure.

[298]  E. Evans Probing the relation between force--lifetime--and chemistry in single molecular bonds. , 2001, Annual review of biophysics and biomolecular structure.

[299]  H. Heslot Artificial fibrous proteins: a review. , 1998, Biochimie.

[300]  R. Lewis,et al.  Structural studies of spider silk proteins in the fiber , 1997, Journal of molecular recognition : JMR.

[301]  John H. Holland,et al.  Hidden Order: How Adaptation Builds Complexity , 1995 .

[302]  H. Fawcett Manual of Political Economy , 1995 .

[303]  Borel Jp,et al.  [Collagens: why such a structural complexity?]. , 1993 .

[304]  A Leith,et al.  Mineral and organic matrix interaction in normally calcifying tendon visualized in three dimensions by high-voltage electron microscopic tomography and graphic image reconstruction. , 1993, Journal of structural biology.

[305]  C. Branden,et al.  Introduction to protein structure , 1991 .

[306]  P. Hansma,et al.  Atomic force microscopy , 1990, Nature.

[307]  W. Hayes,et al.  Mechanical properties of trabecular bone from the proximal femur: a quantitative CT study. , 1990, Journal of computer assisted tomography.

[308]  H. Lodish Molecular Cell Biology , 1986 .

[309]  H. Saunders,et al.  Introduction to fracture mechanics , 1984 .

[310]  Jens Lothe John Price Hirth,et al.  Theory of Dislocations , 1968 .

[311]  G. N. Ramachandran,et al.  Structure of Collagen , 1955, Nature.

[312]  S. Timoshenko Theory of Elastic Stability , 1936 .

[313]  William Thomas Astbury,et al.  X-Ray Studies of the Structure of Hair, Wool, and Related Fibres. I. General , 1932 .

[314]  A. A. Griffith The Phenomena of Rupture and Flow in Solids , 1921 .