** This is a template input deck regarding the discrete-fiber model published in: **“Tissue loading and microstructure regulate the deformation of embedded nerve fibers: ** predictions from single-scale and multiscale simulations”. **Vahhab Zarei, Sijia Zhang, Beth A. Winkelstein, Victor H. Barocas **Journal of Royal Society Interface *Heading ** Job name: Template Model name: Template ** Generated by: Abaqus/CAE 6.11-1 *Preprint, echo=NO, model=NO, history=NO, contact=NO ** ** PARTS ** *Part, name=BLOCK ** Fiber network nodal coordinates *Node *include, input=FiberNodes.inp ** Node list of Boundaries of the network, FIX and MOVE are referred to opposite surfaces *Nset, nset=FIXX *include, input=FixX.inp *Nset, nset=FIXY *include, input=FixY.inp *Nset, nset=FIXZ *include, input=FixZ.inp *Nset, nset=MOVEX *include, input=MoveX.inp *Nset, nset=MOVEY *include, input=MoveY.inp *Nset, nset=MOVEZ *include, input=MoveZ.inp ** Section: Section-1-_PICKEDSET2 *End Part ** **The geometry of the axon (cylinder) *Part, name=Cylinder *Node *include, input=CylinderNodes.inp *Element, type=C3D8 *include, input=CylinderElements.inp *Nset, nset=_PickedSet2, internal, generate 1, 83817, 1 *Elset, elset=_PickedSet2, internal, generate 1, 76800, 1 ** Outer wall of the cylinder *Nset, nset=CYLWALLNODES *include, input=CylWallNodes.inp ** The node list of the end surfaces of the cylinder *Nset, nset=FIXZ *include, input=FixZCyl.inp *Nset, nset=MoveZ *include, input=MoveZCyl.inp ** Section: Section-1-_PICKEDSET2 *Solid Section, elset=_PickedSet2, material=Elastic , *End Part ** ** ** ASSEMBLY ** *Assembly, name=Assembly ** *Instance, name=BLOCK-1, part=BLOCK *End Instance ** *Instance, name=Cylinder-1, part=Cylinder 0., 0., -1.5 *End Instance ** *Element, type=CONN3D2 ** Fibers of the network *include, input=ConnFibers.inp ** Microtubules *include, input=MTFibers.inp ** Circular collagen fibers wrapping around the axon *include, input=CircFibers.inp ** Fibers representing the focal adhesions *include, input=AdjFibers.inp ** Set of collagen fibers sections - They need to be included in different sets because each of them has ** a different force-displacement relation *include, input=FiberSet.inp *Connector Section, elset=CircFibers, behavior=CONNSECTCIRC Axial, , "DATUM CSYS" *Elset, elset=CircFibers, internal, generate 200001, 300000, 1 *Connector Section, elset=AdjFibers, behavior=CONNSECTADJ Axial, , "DATUM CSYS" *Elset, elset=AdjFibers, internal, generate 300001, 400000, 1 *Connector Section, elset=MTFibers, behavior=CONNSECTMT Axial, , "DATUM CSYS" *Elset, elset=MTFibers, internal, generate 100001, 200000, 1 *Orientation, name="DATUM CSYS" 1., 0., 0., 0., 1., 0. 1, 0. *End Assembly ** Behavior of circular collagen fibers expressed as a force-displacement relationship ** Based on A=340e-09N and B=2.5 from the const. equation ** These fibers do not bear compressive load *Connector Behavior, name=CONNSECTCIRC, regularize=OFF, extrapolation=LINEAR *Connector Elasticity, nonlinear, component=1 -0.0, -1.0 0.000000000000000, 0.000000000000000 0.00000004633848400000, 0.005451963880645 0.00000011612849000000, 0.010903927761291 0.00000022355857800000, 0.016355891641936 0.00000039283664200000, 0.021807855522581 0.00000066619060600000, 0.027259819403227 0.00000111898275200000, 0.032711783283872 0.00000188889306200000, 0.038163747164517 0.00000323353970800000, 0.043615711045163 0.00000564686715200000, 0.049067674925808 ** Behavior of focal adhesion fibers expressed as a force-displacement relationship ** Based on A=170e-09N and B=2.5 from the const. equation ** These fibers do not bear compressive load *Connector Behavior, name=CONNSECTADJ, regularize=OFF, extrapolation=LINEAR *Connector Elasticity, nonlinear, component=1 -0.0, -1.0 0.000000000000000, 0.000000000000000 0.000000023169242, 0.005451963880645 0.000000058064245, 0.010903927761291 0.000000111779289, 0.016355891641936 0.000000196418321, 0.021807855522581 0.000000333095303, 0.027259819403227 0.000000559491376, 0.032711783283872 0.000000944446531, 0.038163747164517 0.000001616769854, 0.043615711045163 0.000002823433576, 0.049067674925808 ** Behavior of microtubules expressed as a force-displacement relations ship ** Based on spring constant of 0.942 k/m. Multiplied by e-6 because units of length are in micrometer ** These fibers do not bear compressive load *Connector Behavior, name=CONNSECTMT, regularize=OFF, extrapolation=LINEAR *Connector Elasticity, nonlinear, component=1 -0.0, -1.0 0.0, 0.0 9.42e-07, 1.0 ** Files containing the force-displacement behavior of all collagen fiber sections. ** Based on A = 340e-09N and B=2.5 *include, input=FiberBehaviors.inp ** ** MATERIALS ** ** Material used for non-microtubule part of the axon *Material, name=Elastic *Elastic 43.3e-08,0.48 ** ---------------------------------------------------------------- ** ** STEP: pull ** *Step, name=pull, nlgeom=YES, inc=10000 *Static 1e-02, 1., 1e-04, 3. ** ** BOUNDARY CONDITIONS ** Transverse loading up to 40 % stretch *Boundary BLOCK-1.FIXX, 1, 1, -1. *Boundary BLOCK-1.FIXX, 2, 2 *Boundary BLOCK-1.FIXX, 3, 3 *Boundary BLOCK-1.FIXY, 1, 1 *Boundary BLOCK-1.FIXY, 2, 2 *Boundary BLOCK-1.FIXY, 3, 3 *Boundary BLOCK-1.FIXZ, 3, 3 *Boundary Cylinder-1.FIXZ, 3, 3 *Boundary BLOCK-1.MOVEX, 1, 1, 1. *Boundary BLOCK-1.MOVEX, 2, 2 *Boundary BLOCK-1.MOVEX, 3, 3 *Boundary BLOCK-1.MOVEY, 1, 1 *Boundary BLOCK-1.MOVEY, 2, 2 *Boundary BLOCK-1.MOVEY, 3, 3 *Boundary BLOCK-1.MOVEZ, 3, 3 *Boundary Cylinder-1.MOVEZ, 3, 3 ** ** OUTPUT REQUESTS ** *Restart, write, frequency=0 ** ** FIELD OUTPUT: F-Output-1 ** *Output, field *Element Output, directions=YES E, MISES, S *Node Output RF, U, UR, UT, V, VR, VT ** ** HISTORY OUTPUT: H-Output-1 ** *End Step