Shearing in a Biomimetic Apatite-Protein Composite: Molecular Dynamics of Slip Zone Formation, Plastic Flow and Backcreep Mechanisms
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{"title"=>"Shearing in a biomimetic apatite-protein composite: Molecular dynamics of slip zone formation, plastic flow and backcreep mechanisms", "type"=>"journal", "authors"=>[{"first_name"=>"Dirk", "last_name"=>"Zahn", "scopus_author_id"=>"35739522200"}, {"first_name"=>"Erik", "last_name"=>"Bitzek", "scopus_author_id"=>"25723009400"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372838891", "scopus"=>"2-s2.0-84898636010", "pmid"=>"24691379", "sgr"=>"84898636010", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0093309"}, "id"=>"a05ddd31-df70-3c94-8059-3af5b861258f", "abstract"=>"We report molecular dynamics simulations of shear in a biomimetic hydroxyapatite-collagen composite. Our model exhibits elastic properties fully dominated by the inorganic component. However, beyond the elastic regime the biomolecules along with the hierarchical nature of the composite account for the formation of structure-inherent slip zones. These accommodate shear without compromising the overall structure and lead to the sliding of intrinsically defined rods at roughly constant restoring force. Upon releasing load, rod displacement is reversible and backcreep is observed as gradual ionic rearrangement in the slip zone, subjected to an activation barrier.", "link"=>"http://www.mendeley.com/research/shearing-biomimetic-apatiteprotein-composite-molecular-dynamics-slip-zone-formation-plastic-flow-bac", "reader_count"=>5, "reader_count_by_academic_status"=>{"Researcher"=>1, "Student > Ph. D. Student"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Researcher"=>1, "Student > Ph. D. Student"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>2, "Materials Science"=>1, "Physics and Astronomy"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1441591"], "description"=>"<p>For clarity, only the calcium ions and the collagen molecules (green) are shown. Calcium ions are colored in yellow, red and blue to illustrate full position constrains, z-coordinate constrains and unconstraint ions, respectively. Displacement of the central cylinder leads to elastic deformation up to about 3 Å. Plastic deformation is then observed as a local phenomenon starting at the protein-crystal interface (5 Å). The lower row shows the gradual merging of the disordered regions until a ‘complete’ slip zone is formed (9 Å) which embeds the displaced cylinder and facilitates further shearing. Note that the slip zone does not reflect the surface of the cylinder subjected to displacement, but follows the hexagonal pattern of the collagen matrix.</p>", "links"=>[], "tags"=>["biotechnology", "biomaterials", "chemistry", "computational chemistry", "molecular dynamics", "Materials Science", "Material properties", "Mechanical properties", "composite", "subjected", "periodic", "highlighting", "molecular", "simulations", "shearing", "elevated"], "article_id"=>979573, "categories"=>["Biological Sciences"], "users"=>["Dirk Zahn", "Erik Bitzek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093309.g001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshots_of_the_composite_model_subjected_to_periodic_boundary_conditions_in_all_directions_highlighting_molecular_dynamics_simulations_of_rod_shearing_at_elevated_temperature_/979573", "title"=>"Snapshots of the composite model subjected to periodic boundary conditions in all directions, highlighting molecular dynamics simulations of rod shearing at elevated temperature.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-01 02:45:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1441592"], "description"=>"<p>At high simulation temperature and displacement by about 10 Å, the single-crystalline model is observed to develop a less-ordered slip zone that facilitates further shearing at roughly constant opposing force leading to a flow stress of 1.4 GPa. The long-dashed curve indicates the elastic region (1.04 GPa / Å×z) whereas the dotted line refers to the average stress observed for the viscous flow regime.</p>", "links"=>[], "tags"=>["biotechnology", "biomaterials", "chemistry", "computational chemistry", "molecular dynamics", "Materials Science", "Material properties", "Mechanical properties", "stress-displacement", "composite", "300", "1000"], "article_id"=>979574, "categories"=>["Biological Sciences"], "users"=>["Dirk Zahn", "Erik Bitzek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093309.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Shear_stress_displacement_profile_for_the_composite_model_at_300_K_blue_curve_and_1000_K_red_curve_/979574", "title"=>"Shear stress-displacement profile for the composite model at 300 K (blue curve) and 1000 K (red curve).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-01 02:45:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1441597"], "description"=>"<p>Two typical snapshots are shown for a) quasi-elastic shearing with strain propagation into the slip zone, and b) inhomogeneous relaxation within the slip zone. Note that the slip zone may accommodate upwards and downwards displacements at the same time. For clarity, only calcium ions are shown.</p>", "links"=>[], "tags"=>["biotechnology", "biomaterials", "chemistry", "computational chemistry", "molecular dynamics", "Materials Science", "Material properties", "Mechanical properties", "inhomogeneous", "ionic", "displacements", "shearing"], "article_id"=>979577, "categories"=>["Biological Sciences"], "users"=>["Dirk Zahn", "Erik Bitzek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093309.g003", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Color_code_illustration_of_the_inhomogeneous_ionic_displacements_upon_shearing_the_central_rod_along_the_z_axis_/979577", "title"=>"Color-code illustration of the inhomogeneous ionic displacements upon shearing the central rod along the z-axis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-01 02:45:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1441598"], "description"=>"<p>The straight curves indicate double exponential fits with relaxation times of τ<sub>1</sub> = 4.8 ps and τ<sub>2</sub> = 9852, 192 and 24.6 ps, respectively. While the temperature-dependent picosecond-scale relaxation reflects elastic response, backcreep is related to an activation energy which was assessed as 21 kJ/mol from an Arrhenius plot (upper right).</p>", "links"=>[], "tags"=>["biotechnology", "biomaterials", "chemistry", "computational chemistry", "molecular dynamics", "Materials Science", "Material properties", "Mechanical properties", "displacement", "30", "observed", "unconstraint", "molecular", "simulations", "600", "1000"], "article_id"=>979578, "categories"=>["Biological Sciences"], "users"=>["Dirk Zahn", "Erik Bitzek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093309.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relaxation_after_rod_displacement_by_30_197_as_observed_from_unconstraint_molecular_dynamics_simulations_at_300_600_and_1000_K_shown_in_blue_green_and_red_respectively_/979578", "title"=>"Relaxation after rod displacement by 30 Å as observed from unconstraint molecular dynamics simulations at 300, 600 and 1000 K shown in blue, green and red, respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-01 02:45:41"}

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Relative Metric

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