Computational Modeling in Bioengineering and Bioinformatics

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COMPUTATIONAL
MODELING IN
BIOENGINEERING
AND
BIOINFORMATICS
Copyright
About the author
Preface
1
Computational modeling of atherosclerosis
	Theoretical background
	Methods
		Blood flow simulation
		Plaque formation and progression modeling-Continuum approach
		Discrete approach
		DPD modeling of oxidized LDL particle adhesion to the wall
	Results
		Animal pig experiments
		Comparison experimental and numerical results for pigs data
		Fitting parameters of ODE model for pigs
			Hybrid genetic algorithm
			Results for fitting model
				HHF pigs
		Coupled model of atherosclerosis
		Plaque concentration distribution in the coronary artery
	Conclusions
	Acknowledgments
	References
	Further reading
2
Machine learning approach for breast cancer prognosis prediction
	Introduction
	Machine learning applications for prediction of breast cancer prognosis
	Methodological framework for machine learning techniques
		Preprocessing
		Imbalanced data sets
		Feature selection
		Classification models and evaluation of performances
	To what extent can we trust a prediction model?
	Findings
		Data source
		Prognosis on survivability
		Prognosis on breast cancer recurrence
		Estimation of reliability for individual predictions
	Conclusions and future trends
	References
3
Topological and parametric optimization of stent design based on numerical methods
	Introduction
	Endovascular prosthesis: Stent
	History of endovascular prosthesis: STENT
	Classification of stents
	Stent modeling
		Computer methods for stent design
			Modern CAD/CAM/CAE
		Introduction to modeling
		FEM analysis of stent spreading
			Analysis of the initial design
		UMAT (Abaqus) material model
	Stent geometry optimization
	Nonparametric optimization of the model
	Parametric optimization
	Creation of a 3D model of the whole stent
	Conclusion
	References
4
Lung on a chip and epithelial lung cells modeling
	Introduction
	Model of the bioreactor for organ-on-a-chip usage
		Modeling of monocytes distribution inside the bioreactor
		Mathematical derivation of the bioreactor model
		Application of the finite element method to model of the bioreactor
		Results of the bioreactor model
	Model of the A549 lung epithelial cell line
		Modeling of A549 cell behavior and barrier formation
		Mathematical derivation of the A549 cell model
		Application of the finite element method to the A549 cells model
		Results of the A549 cell model
	Discussion and conclusions
	Acknowledgments
	References
5
Aortic dissection: Numerical modeling and virtual surgery
	Introduction
	Aortic dissection
		History of aortic dissection
		Classification of aortic dissection
	Diagnostic techniques
		Transthoracic and transesophageal echocardiography
		Computerized tomography
		Magnetic resonance
		Aortography
		Intravascular ultrasound
	Treatment of acute aortic dissection
		Treatment with medicaments
		Surgical treatment
		Surgical intervention in acute aortic dissection of type A (type I and II)
		Surgical intervention in acute aortic dissection type B (type III)
		Interventional techniques
	Solution of nonalinear problems with the final elements method
	Basic equations of fluid flow
		Continuity equation
		Navier-Stokes equations
	Basic equations of solid motion
	Solid fluid interaction
	3D modeling of aortic dissection
		Introduction
	3D reconstruction using Materialize Mimics 10.01
	Geometric 3D modeling using Geomagic Studio 10.0
	Virtual surgery
	Results of numerical analysis
	Results of the simulation of preoperative models
	Results of simulation of postoperative models
	Results of simulation of the wall shear stress on the false lumen of preoperative models
	Conclusion
	References
6
The biomechanics of lower human extremities
	Introduction
	Anatomy of lower extremities
		Hip joint anatomy
		Knee joint anatomy
		Ankle joint anatomy
	Finite element method application in biomechanics
		Hip joint
		Knee Joint
		Ankle joint
	3D model development
	Material properties
		Bone
			Cortical bone
			Cancellous bone
		Cartilage
		Ligaments
		Menisci
	Boundary conditions
		Hip joint
		Knee joint
		Ankle joint
	Finite element analysis of the knee joint with ruptured anterior cruciate ligament
		Step 1: Three-dimensional model development
		Step 2: Material properties
		Step 3: Boundary conditions
		Step 4: Results and discussion
	Conclusion
	Acknowledgment
	References
7
Different theoretical approaches in the study of antioxidative mechanisms
	Prevention of oxidative stress
	Characteristics of good antioxidants in general
	The proposed reaction mechanisms
		Hydrogen-atom transfer versus proton-coupled electron transfer
		Single electron transfer
		Single electron transfer-proton transfer
		Sequential proton-loss electron transfer
		Sequential proton loss hydrogen atom transfer mechanism
	Radical adduct formation
		Thermodynamical parameters for evaluation of antioxidative mechanisms
		Influence of different free radicals on scavenging potency of various antioxidants
	Mechanistic approach
		Electron-transfer reaction rate constant calculation
	Thermodynamical parameters for quercetin, gallic acid, and DHBA
	Antiradical mechanisms in the presence of different free radicals
	Mechanistic approach to analysis of the antioxidant action
		Reaction of quercetin via HAT mechanism
		Reaction of quercetin via SET-PT mechanism
			Mechanism Q+ with the hydroxide anion in the gaseous and aqueous phases
			Mechanism Q+ with the MeS anion
			Mechanism Q+ with the methylamine
	Kinetics of HAT and PCET mechanism
	Radical adduct formation (RAF) mechanism
		Electron-transfer reaction of quercetin
		Electron-transfer mechanism of GA
	Conclusion
	References
	Further reading
8
Computational modeling of dry-powder inhalers for pulmonary drug delivery
	Theoretical background
		Introduction
		Dry-powder inhalers (DPIs)
			Aerolizer
		Clinical efficacy of inhalation dry powders
		Forces during inhalation
	Literature review: Particle engineering strategies for pulmonary drug delivery
	Simulations performed on dry-powder inhaler Aerolizer
		Geometry
		Meshing
		Simulation assumptions and boundary conditions
		Results and discussion
	Conclusions and recommendations
	Acknowledgments
	References
9
Computer modeling of cochlear mechanics
	Introduction
	Concepts of modeling
	Solid model
	Fluid model
	Loose coupling algorithm
	Strong coupling algorithm
	Finite element modeling
	Finite element models
		Cochlea-Box model
		Cochlea-Tapered model
		Cochlea-Coiled model
		Middle ear model
		Coupled model
	Model of cochlea including feedforward and feedbackward forces
		Feedforward and feedbackward OHC forces
	Conclusion
	Acknowledgment
	References
	Further reading
10
Numerical modeling of cell separation in microfluidic chips
	Introduction
	Numerical model
		Modeling fluid flow
		Modeling solid deformation
			Modeling reaction to the surface strain of the membrane
			Modeling the reaction to the change of volume
			Modeling the reaction to the change of surface area of the membrane
			Modeling the reaction to the bending of the membrane
		Modeling solid-fluid interaction
	Numerical simulations
	Conclusion
	Acknowledgments
	References
11
Computational analysis of abdominal aortic aneurysm before and after endovascular aneurysm repair
	Introduction
	Risk factors and surgical treatments for AAA
	Computational methods applied for AAA
	Geometrical model of AAA
		Creation of 3D geometry based on 2D images data
		Creation of the 3D models with smooth surfaces
		Creation of the volumetric 3D models
	Numerical model of AAA
		Material properties
		Boundary conditions
	Finite element procedure and fluid-structure interaction
		Shear stress calculation
		Modeling the deformation of blood vessels
		FSI interaction
	Results
		Unstented AAA
		Stented AAA
	Discussion
	Conclusion
	Acknowledgment
	References
12
Sport biomechanics: Experimental and computer simulation of knee joint during jumping and walking
	Introduction
	Methods
		Geometry of the model
		Material properties
		Boundary conditions
		Mechanical model of knee joint and assessment of cartilage stress distribution
		Spring-damper-mass model
		Finite element method for numerical calculation
		Caption motion system
		Force measurement
		Motion capture system
		Foot pressure distribution measurement
		Force plate measurement
		Inverse dynamics
	Results
		Definition of knee geometry from medical images
		Noninvasive determination of knee cartilage deformation
		Computer simulation in the jumping force analysis
	Discussion and Conclusion
	References
	Further reading
Index
	A
	B
	C
	D
	E
	F
	G
	H
	I
	J
	K
	L
	M
	N
	O
	P
	Q
	R
	S
	T
	V
	W
	Z
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