Table Of ContentSuvranu De · Wonmuk Hwang
Ellen Kuhl Editors
Multiscale
Modeling in
Biomechanics
and
Mechanobiology
Multiscale Modeling in Biomechanics
and Mechanobiology
Suvranu De Wonmuk Hwang
(cid:129)
Ellen Kuhl
Editors
Multiscale Modeling
in Biomechanics
and Mechanobiology
123
Editors
Suvranu De Ellen Kuhl
Department of Mechanical, Aerospace, Departments of Mechanical Engineering,
andNuclear Engineering Bioengineering andCardiothoracic
Rensselaer Polytechnic Institute Surgery
Troy,NY Stanford University
USA Stanford,CA
USA
WonmukHwang
Department of BiomedicalEngineering
Texas A&MUniversity
College Station, TX
USA
ISBN 978-1-4471-6598-9 ISBN 978-1-4471-6599-6 (eBook)
DOI 10.1007/978-1-4471-6599-6
LibraryofCongressControlNumber:2014951146
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Preface
Biological systems are arguably the most complex subjects in scientific research,
especiallyregardingtheenormousrangeoflengthandtimescalesinvolved.Atthe
molecular level, structures and dynamics involving biomolecules are highly
sophisticatedandstochastic.Atthecellularlevel,numerousmolecularcomponents,
manyofwhichareunidentified,interactandorganizeinspaceandtime,fromwhich
nonequilibrium physiological processes emerge at the tissue and organ levels, and
beyond. While vast knowledge is accumulating for any given biological system,
establishing quantitative relations between systems defined at different scales
requires an integrative approach such as Multiscale Modeling (MSM).
Thisbookisintended asafieldmanualforMSMmethodsthatlinkatleasttwo
scales. Given the extreme diversity of the topic, the best way to learn MSM is via
system-specific case studies. A quick approach toward developing a multiscale
modelwouldbetolinkthescalesphenomenologically.Here,however,wesuggest
a more holistic approach, where real physical and structural information is passed
across the scales. This information is becoming increasingly available via rapid
advances in imaging and other measurement techniques. Furthermore, physical
modeling is inevitable when considering mechanical phenomena in biology, as
forces are intrinsically coupled to spatial variables in any physical process.
Among the many possible topics of MSM, our focus is on biomechanics and
mechanobiology. The two terms are subtly different, yet closely correlated: Bio-
mechanics is the study of biological systems by means of mechanical tools. It is
thus often associated with the “passive” nature of a biological system including
strain, stress, and stiffness. Mechanobiology is the study of the role of mechanical
forcesinmodulatingbiologicalsystems.Itisassociatedwiththe“active”response
of a living system including mechanoreception, signal transduction, and target
activation. For a complete understanding of living systems, we have to understand
both aspects equally.
The organization of this book naturally follows the biological hierarchy. At the
molecular level, we focus on linking discrete and continuum descriptions of bio-
filaments, molecular motors, and biofilament assemblies. At the cellular level,
major topicsaretheemergenceofmotilebehavior,filament network-to-continuum
v
vi Preface
transition, and transport phenomena. At the organ level, we review specific organ
systems including tendonsandligaments,arteries,andheartvalves.Throughthese
casestudies,wehopethatthereaderwilldevelop“numericalinstincts”toadvance
methods and tools and to generalize MSM to other living systems.
We would like to extend our thanks to all contributing authors whose expert
contributionsmadethismonographpossible.WewouldalsoliketothanktheU.S.
InteragencyModelingandAnalysisGroup(IMAG),inparticular,Dr.GracePengat
the National Institutes of Health, interaction with whom and the IMAG activities
were one of the catalyzing factors for conceiving this edited volume. Finally, we
wishtoexpressourdeepestgratitudetoMs.GabriellaAndersonandhercolleagues
at Springer, who provided us with the encouragement and technical assistance
essential to the success of this project.
Suvranu De
Wonmuk Hwang
Ellen Kuhl
Contents
Part I Multiscale Modeling Around the Molecular Level
1 Proteins: Ssp DnaE Intein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Albert K. Dearden and Saroj K. Nayak
2 Protein Crystals: Molecular to Continuum Level Models
Based on Crystal Plasticity Theory . . . . . . . . . . . . . . . . . . . . . . . 13
Suvranu De and Amir Reza Zamiri
3 Molecular Motors: Cooperative Phenomena of Multiple
Molecular Motors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Stefan Klumpp, Corina Keller, Florian Berger
and Reinhard Lipowsky
4 Biofilament Dynamics: Line-to-Rod-Level Descriptions. . . . . . . . . 63
Wonmuk Hwang
Part II Multiscale Modeling Around the Cellular and Tissue Level
5 Multiscale Modeling of Primary Cilia . . . . . . . . . . . . . . . . . . . . . 87
Y.-N. Young, Lina C. Espinha, An M. Nguyen
and Christopher R. Jacobs
6 Reduced-Order Network Models for Biological Scaffolding. . . . . . 111
T.I. Zohdi
7 Transport Phenomena: Computational Models for Convective
and Diffusive Transport in Capillaries and Tissue . . . . . . . . . . . . 131
Milos Kojic, Miljan Milosevic, Nikola Kojic, Velibor Isailovic,
Dejan Petrovic, Nenad Filipovic, Mauro Ferrari and Arturas Ziemys
vii
viii Contents
Part III Multiscale Modeling Around the Organ Level
8 Tendons and Ligaments: Current State and Future Directions . . . 159
Shawn P. Reese and Jeffrey A. Weiss
9 Arteries: Mechanics, Mechanobiology, and the Need
for a New Class of Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
J.D. Humphrey and J.S. Wilson
10 Mitral Valves: A Computational Framework. . . . . . . . . . . . . . . . 223
Chung-Hao Lee, Rouzbeh Amini, Yusuke Sakamoto,
Christopher A. Carruthers, Ankush Aggarwal,
Robert C. Gorman, Joseph H. Gorman III and Michael S. Sacks
11 Biological Systems: Multiscale Modeling Based
on Mixture Theory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Yusheng Feng, Sarah J. Boukhris, Rakesh Ranjan
and Raul A. Valencia
Part I
Multiscale Modeling Around
the Molecular Level
Chapter 1
Proteins: Ssp DnaE Intein
AlbertK.DeardenandSarojK.Nayak
Abstract During the twentieth century, there have been many rapid advances in
scientificunderstandingaboutthenaturalworld.Oftheseadvances,ourunderstand-
ingofmolecularbiologyhastakengreatleaps,startingwiththefirstdescriptionofthe
DNAdoublehelixasdescribedinascientificarticleinAprilof1953.Sincethen,vast
numbersofresearcharticleshavebeenwrittenallinanefforttobetterunderstandour
worldfromamolecularstandpoint.However,despitethislargeeffort,specificdetails
aboutthemechanicsofmolecularinteractionsattheatomisticscaleremainelusive.
Onemethodtoilluminatedetailsoftheseinteractionsisthroughtheuseofquantum
mechanical computer simulations based on basic physical principles. Through the
useofcomputationalmodels,newinsightsintothemechanisticbehaviorofprotein
interactions at an atomic scale can be discovered, furthering our understanding of
biologicalsystems.
Sincetheirdiscoveryin1987[1–3],inteinshavebeenfoundtoexistinalldomains
oflife.Theyhaveprovenusefulformanybiotechnologyapplicationsaswellashave
been found in various forms of cancer and infections like tuberculosis. Thus, the
ability to control the functions of inteins would be beneficial over a wide range
of areas.s However, although it is generally understood that for protein splicing
to take place, in which an intein must first self-cleave off the flanking N and C
extein polypeptides, a detailed understanding of the mechanics of this process is
still not understood. In this aspect, computational simulations with foundations in
basicphysicalprinciplesallowfornewinsightsintobiologicalproblemsfacedtoday.
UsingDensityFunctionalTheory(DFT)[4,5],agreaterunderstandingofbiological
systemsismadepossiblethroughinvestigationsintothespecificinteractionswithin
thesesystems.
Inthecontextofthiswork,theSynechocystissp.StrainPCC6803DnaEinteinwas
examinedbyBelfortetal.[6].Intheirexperiment,theirgoalwastoobtaincontrol
B
A.K.Dearden( )
DepartmentofPhysics,AppliedPhysics,andAstronomy,
RensselaerPolytechnicInstitute,Troy,NY12180,USA
e-mail:[email protected]
S.K.Nayak
SchoolofBasicSciences,IndianInstituteofTechnology,Bhubaneswar,India
©Springer-VerlagLondon2015 3
S.Deetal.(eds.),MultiscaleModelinginBiomechanics
andMechanobiology,DOI10.1007/978-1-4471-6599-6_1
