Mechanics of growth 13 - living matter lab

(Difference between revisions)

Latest revision as of 21:40, 6 March 2013

1 winter 13 - me337 - mechanics of growth
2 goals
3 journal club
4 class papers
5 grading
6 syllabus
7 final project
8 matlab files
9 additional reading

winter 13 - me337 - mechanics of growth

ellen kuhl, alexander zollner
office hours thu 2:00-3:00, durand 217
course announcement

winter 2013
tue thu 11:00-12:15
530-127

goals

in contrast to traditional engineering structures living structures show the fascinating ability to grow and adapt their form, shape and microstructure to a given mechanical environment. this course addresses the phenomenon of growth on a theoretical and computational level and applies the resulting theories to classical biomechanical problems like bone remodeling, hip replacement, wound healing, atherosclerosis or in stent restenosis. this course will illustrate how classical engineering concepts like continuum mechanics, thermodynamics or finite element modeling have to be rephrased in the context of growth. having attended this course, you will be able to develop your own problem-specific finite element based numerical solution techniques and interpret the results of biomechanical simulations with the ultimate goal of improving your understanding of the complex interplay between form and function.

journal club

mechanics of growth on imechanica

class papers

zöllner am, abilez oj, böl m, kuhl e. stretching skeletal muscle - chronic muscle lengthening through sarcomerogenesis. plos one, 2012;7(10):e45661. (download) (online)

pang h, shiwalkar ap, madormo cm, taylor re, andriacchi tp, kuhl e. computational modeling of bone density profiles in response to gait: a subject-specific approach. biomech model mechanobio, 2012;11:379-390. (download)

buganza tepole a, ploch cj, wong j, gosain ak, kuhl e. growing skin - a computational model for skin expansion in reconstructive surgery. j mech phys solids, 2011;59:2177-2190. (download)

taylor re, zheng ch, jackson pr, doll jc, chen jc, holzbaur krs, besier t, kuhl e. the phenomenon of twisted growth: humeral torsion in dominant arms of high performance tennis players. comp meth biomech biomed eng, 2009;12:83-93. (download)

grading

30 % homework - 3 homework assignments, 10% each
30 % midterm - closed book, closed notes, one single page cheat sheet
20 % final project oral presentations - graded by the class
20 % final project essay - graded by instructor

syllabus

day	date		topic	slides	homework
tue	jan	08	motivation - everything grows!	s01
thu	jan	10	basics maths - notation and tensors	s02	h01
tue	jan	15	basic kinematics - large deformation and growth	s03
thu	jan	17	kinematics - growing hearts	s04
tue	jan	22	guest lecture - growing surfaces	s05
thu	jan	24	kinematics - growing leaflets	s06
tue	jan	29	basic balance equations - closed and open systems	s07
thu	jan	31	basic constitutive equations - growing muscle	s08	h02
tue	feb	05	basic constitutive equations - growing tumors	s09
thu	feb	07	volume growth - finite elements for growth - theory	s10
tue	feb	12	volume growth - finite elements for growth - matlab	s11
thu	feb	14	volume growth - growing skin	s12
tue	feb	19	basic constitutive equations - growing bones	s13
thu	feb	21	density growth - finite elements for growth	s14	h03
tue	feb	26	density growth - growing bones	s15
thu	feb	28	everything grows! - midterm summary	s16
tue	mar	05	midterm
thu	mar	07	remodeling - remodeling arteries and tendons	s18
tue	mar	12	class project - discussion, presentation, evaluation	s19	h04
thu	mar	14	class project - discussion, presentation, evaluation
thu	mar	14	written part of final projects due

final project

buganza a, wong j, kuhl e. computational modeling of mechanically driven skin growth due to different expander geometries, farmington, pennsylvania, 2011

matlab files

finally... here's the matlab code for growth

additional reading

(1) taber l. biomechanics of growth, remodeling, and morphogenesis, appl mech rew 48, 487-545, 1995
(2) kuhl e, menzel a, steinmann p. computational modeling of growth - a critical review, a classification and two new consistent approaches, computational mechanics 32, 71-88, 2003
(3) rodriguez ek, hoger a, mc culloch a. stress-dependent finite growth in soft elastic tissues, j biomechanics 27, 455-467, 1994
(4) kuhl e, maas r, himpel g, menzel a. computational modeling of arterial wall growth - attempts towards patient-specific simulations based on computer tomography, biomech model mechanobio 6, 321-331, 2007
(5) göktepe s, abilez oj, parker kk, kuhl e. a multiscale model for eccentric and concentric cardiac growth through sarcomerogenesis.j theor bio 265: 433-442, 2010
(6) ambrosi d, ateshian ga, arruda em, cowin sc, dumais j, goriely a, holzapfel ga, humphrey jd, kemkemer r, kuhl e, olberding je, taber la, garikipati k. perspectives on biological growth and remodeling.j mech phys solids 59: 863-883, 2011
(7) zöllner am, buganza tepole A, kuhl e. on the biomechanics and mechanobiology of growing skin. j theor bio 297, 166-175, 2012
(8) menzel a, kuhl e. frontiers in growth and remodeling. mech res comm 42,1-14, 2012

Retrieved from "http://biomechanics.stanford.edu/cgi-bin/index.php?title=Mechanics_of_growth_13&oldid=5735"

@@ Line 1: / Line 1: @@
-==winter 12 - me337 - mechanics of growth==
+==winter 13 - me337 - mechanics of growth==
 <div>
-[[Image:growth2012a.jpg|200px|left]]
+[[Image:growth2013d.jpg|200px|left]]
-[[Image:growth2012b.jpg|200px|right]]
+[[Image:growth2013c.jpg|200px|right]]
 {|
 |-
 |
-me 337 - [[mechanics of growth 12]] <br>
 [http://biomechanics.stanford.edu/People ellen kuhl], [mailto:azoell@stanford.edu alexander zollner]<br>
-office hours thu 11-12:30, durand 217<br>
+office hours thu 2:00-3:00, durand 217<br>
-[http://biomechanics.stanford.edu/me337_12/ME337_announcement.pdf course announcement]<br>
+[http://biomechanics.stanford.edu/me337_13/ME337_announcement.pdf course announcement]<br>
-winter 2012 <br>
+winter 2013 <br>
-tue thu 09:30-10:45 <br>
+tue thu 11:00-12:15 <br>
--020
+-127
 |}
 </div>
+<div class="spacer">&nbsp;</div>
 ==goals==
@@ Line 28: / Line 28: @@
 ==class papers==
+z&ouml;llner am, abilez oj, b&ouml;l m, kuhl e.
+stretching skeletal muscle - chronic muscle lengthening through sarcomerogenesis.
+plos one, 2012;7(10):e45661.
+[http://biomechanics.stanford.edu/paper/PLOS12.pdf (download)]
+[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0045661 (online)]
 pang h, shiwalkar ap, madormo cm, taylor re, andriacchi tp, kuhl e.
 computational modeling of bone density profiles in response to gait: a subject-specific approach.
-biomech model mechanobio, 2012;doi:10.1007/s10237-011-0318-y.
+biomech model mechanobio, 2012;11:379-390.
 [http://biomechanics.stanford.edu/paper/BMMB11.pdf (download)]
@@ Line 56: / Line 62: @@
 ! day !! date !! !! topic !! slides !! homework
 |-
-| tue || jan || 10 || motivation - everything grows! || [http://biomechanics.stanford.edu/me337_12/me337_s01.pdf s01] ||
+| tue || jan || 08 || motivation - everything grows! || [http://biomechanics.stanford.edu/me337_13/me337_s01.pdf s01] ||
 |-
-| thu || jan || 12 || basics maths - notation and tensors || [http://biomechanics.stanford.edu/me337_12/me337_s02.pdf s02] || [http://biomechanics.stanford.edu/me337_12/me337_h01.pdf h01]
+| thu || jan || 10 || basics maths - notation and tensors || [http://biomechanics.stanford.edu/me337_13/me337_s02.pdf s02] || [http://biomechanics.stanford.edu/me337_13/me337_h01.pdf h01]
 |-
-| tue || jan || 17 || basic kinematics - large deformation and growth ||  [http://biomechanics.stanford.edu/me337_12/me337_s03.pdf s03] ||
+| tue || jan || 15 || basic kinematics - large deformation and growth ||  [http://biomechanics.stanford.edu/me337_13/me337_s03.pdf s03] ||
 |-
-| thu || jan || 19 || kinematics - growing hearts || [http://biomechanics.stanford.edu/me337_12/me337_s04.pdf s04] ||
+| thu || jan || 17 || kinematics - growing hearts || [http://biomechanics.stanford.edu/me337_13/me337_s04.pdf s04] ||
 |-
-| tue || jan || 24 || guest lecture - growing skin || [http://biomechanics.stanford.edu/me337_12/me337_s03.pdf s05] ||
+| tue || jan || 22 || guest lecture - growing surfaces || [http://biomechanics.stanford.edu/me337_13/me337_s05.pdf s05] ||
 |-
-| thu || jan || 26 || guest lecture - growing leaflets || [http://biomechanics.stanford.edu/me337_12/me337_s06.pdf s06]||
+| thu || jan || 24 || kinematics - growing leaflets || [http://biomechanics.stanford.edu/me337_13/me337_s06.pdf s06]||
 |-
-| tue || jan || 31 || basic balance equations - closed and open systems  || [http://biomechanics.stanford.edu/me337_12/me337_s07.pdf s07] ||
+| tue || jan || 29 || basic balance equations - closed and open systems  || [http://biomechanics.stanford.edu/me337_13/me337_s07.pdf s07] ||
 |-
-| thu || feb || 02 || basic constitutive equations - growing tumors  || [http://biomechanics.stanford.edu/me337_12/me337_s08.pdf s08] || [http://biomechanics.stanford.edu/me337_12/me337_h02.pdf h02]
+| thu || jan || 31 || basic constitutive equations - growing muscle  || [http://biomechanics.stanford.edu/me337_13/me337_s08.pdf s08] || [http://biomechanics.stanford.edu/me337_13/me337_h02.pdf h02]
 |-
-| tue || feb || 07 || volume growth - finite elements for growth || [http://biomechanics.stanford.edu/me337_12/me337_s09.pdf s09] ||
+| tue || feb || 05 || basic constitutive equations - growing tumors || [http://biomechanics.stanford.edu/me337_13/me337_s09.pdf s09] ||
 |-
-| thu || feb || 09 || volume growth - growing arteries ||  [http://biomechanics.stanford.edu/me337_12/me337_s10.pdf s10]||
+| thu || feb || 07 || volume growth - finite elements for growth - theory ||  [http://biomechanics.stanford.edu/me337_13/me337_s10.pdf s10]||
 |-
-| tue || feb || 14 || volume growth - growing skin || [http://biomechanics.stanford.edu/me337_12/me337_s11.pdf s11] ||
+| tue || feb || 12 || volume growth - finite elements for growth - matlab || [http://biomechanics.stanford.edu/me337_13/me337_s11.pdf s11] ||
 |-
-| thu || feb || 16 || volume growth - growing hearts  || [http://biomechanics.stanford.edu/me337_12/me337_s12.pdf s12]||
+| thu || feb || 14 || volume growth - growing skin  || [http://biomechanics.stanford.edu/me337_13/me337_s12.pdf s12]||
 |-
-| tue || feb || 21 || basic constitutive equations - growing bones  ||  [http://biomechanics.stanford.edu/me337_12/me337_s13.pdf s13] ||
+| tue || feb || 19 || basic constitutive equations - growing bones  ||  [http://biomechanics.stanford.edu/me337_13/me337_s13.pdf s13] ||
 |-
-| thu || feb || 23 || density growth - finite elements for growth  || [http://biomechanics.stanford.edu/me337_12/me337_s14.pdf s14] || [http://biomechanics.stanford.edu/me337_12/me337_h03.pdf h03]
+| thu || feb || 21 || density growth - finite elements for growth  || [http://biomechanics.stanford.edu/me337_13/me337_s14.pdf s14] || [http://biomechanics.stanford.edu/me337_13/me337_h03.pdf h03]
 |-
-| tue || feb || 28 || density growth - growing bones || [http://biomechanics.stanford.edu/me337_12/me337_s15.pdf s15] ||
+| tue || feb || 26 || density growth - growing bones || [http://biomechanics.stanford.edu/me337_13/me337_s15.pdf s15] ||
 |-
-| thu || mar || 01 || everything grows! - midterm summary ||  [http://biomechanics.stanford.edu/me337_12/me337_s16.pdf s16]  ||
+| thu || feb || 28 || everything grows! - midterm summary ||  [http://biomechanics.stanford.edu/me337_13/me337_s16.pdf s16]  ||
 |-
-| tue || mar || 06 || midterm ||    ||
+| tue || mar || 05 || midterm ||    ||
 |-
-| thu || mar || 08 || remodeling - remodeling arteries and tendons ||  [http://biomechanics.stanford.edu/me337_12/me337_s18.pdf s18] ||
+| thu || mar || 07 || remodeling - remodeling arteries and tendons ||  [http://biomechanics.stanford.edu/me337_13/me337_s18.pdf s18] ||
 |-
-| tue || mar || 13 || class project - discussion, presentation, evaluation || [http://biomechanics.stanford.edu/me337_12/me337_s19.pdf s19]  ||
+| tue || mar || 12 || class project - discussion, presentation, evaluation || [http://biomechanics.stanford.edu/me337_12/me337_s19.pdf s19]  || [http://biomechanics.stanford.edu/me337_13/me337_sample.doc h04]
 |-
-| thu || mar || 15 || class project - discussion, presentation, evaluation ||  ||
+| thu || mar || 14 || class project - discussion, presentation, evaluation ||  ||
 |-
-| thu || mar || 15 || written part of final projects due ||  ||
+| thu || mar || 14 || written part of final projects due ||  ||
 |}
@@ Line 112: / Line 118: @@
 ==additional reading==
-[http://biomechanics.stanford.edu/paper/CMBBE08.pdf (1)] taylor re, zheng c, jackson rp, doll jc, chen jc, holzbaur krs, besier t, kuhl e. the phenomenon of twisted growth: humeral torsion in dominant arms of high performance tennis players, comp meth biomech biomed eng, 2009;12:83-93. <br>
+[http://biomechanics.stanford.edu/me337/taber95.pdf (1)] taber l. biomechanics of growth, remodeling, and morphogenesis, appl mech rew 48, 487-545, 1995 <br>
-[http://biomechanics.stanford.edu/me337/taber95.pdf (2)] taber l. biomechanics of growth, remodeling, and morphogenesis, appl mech rew 48, 487-545, 1995 <br>
+[http://biomechanics.stanford.edu/me337/kuhl03.pdf (2)] kuhl e, menzel a, steinmann p. computational modeling of growth - a critical review, a classification and two new consistent approaches, computational mechanics 32, 71-88, 2003 <br>
-[http://biomechanics.stanford.edu/me337/jacobs95.pdf (3)] jacobs cr, levenston me, beaupre gs, simo jc, carter dr. numerical instabilities in bone remodeling simulations: the advantages of a node-based finite element approach, j biomechanics 28, 449-459, 1995 <br>
+[http://biomechanics.stanford.edu/me337/rodriguez94.pdf (3)] rodriguez ek, hoger a, mc culloch a. stress-dependent finite growth in soft elastic tissues, j biomechanics 27, 455-467, 1994 <br>
-[http://biomechanics.stanford.edu/me337/kuhl03.pdf (4)] kuhl e, menzel a, steinmann p. computational modeling of growth - a critical review, a classification and two new consistent approaches, computational mechanics 32, 71-88, 2003 <br>
+[http://biomechanics.stanford.edu/me337/kuhl06.pdf (4)] kuhl e, maas r, himpel g, menzel a. computational modeling of arterial wall growth - attempts towards patient-specific simulations based on computer tomography, biomech model mechanobio 6, 321-331, 2007 <br>
-[http://biomechanics.stanford.edu/me337/rodriguez94.pdf (5)] rodriguez ek, hoger a, mc culloch a. stress-dependent finite growth in soft elastic tissues, j biomechanics 27, 455-467, 1994 <br>
+[http://biomechanics.stanford.edu/paper/JTBIO10.pdf (5)] g&ouml;ktepe s, abilez oj, parker kk, kuhl e. a multiscale model for eccentric and concentric cardiac growth
-[http://biomechanics.stanford.edu/me337/kuhl06.pdf (6)] kuhl e, maas r, himpel g, menzel a. computational modeling of arterial wall growth - attempts towards patient-specific simulations based on computer tomography, biomech model mechanobio 6, 321-331, 2007 <br>
+through sarcomerogenesis.j theor bio 265: 433-442, 2010 <br>
+[http://biomechanics.stanford.edu/paper/JMPS11.pdf (6)] ambrosi d, ateshian ga, arruda em, cowin sc, dumais j, goriely a, holzapfel ga, humphrey jd, kemkemer r, kuhl e, olberding je, taber la, garikipati k. perspectives on biological growth and remodeling.j mech phys solids 59: 863-883, 2011 <br>
 [http://biomechanics.stanford.edu/paper/JTBIO12.pdf (7)]
-z&ouml;llner am, buganza tepole A, kuhl e.
+z&ouml;llner am, buganza tepole A, kuhl e. on the biomechanics and mechanobiology of growing skin. j theor bio 297, 166-175, 2012 <br>
-on the biomechanics and mechanobiology of growing skin.
+[http://biomechanics.stanford.edu/paper/MRCOM12.pdf (8)] menzel a, kuhl e. frontiers in growth and remodeling. mech res comm 42,1-14, 2012
-j theor bio 297, 166-175 , 2012