Thesis or Fecis

It all comes down to this…

Archive for the ‘thesis’ Category

I Want You To Hit Me As Hard As You Can (with your words)

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With my thesis looming large on the horizon (less than 48 hours from now) and the amount of time I’ve spent editing and writing I’ve had lots of time to freak out about my research, the quality of it, the strength of my global conclusions, and finally the Rice faculty and graduate student’s opinion of my research quality. Because my mind loves to eat itself from the inside out I’ve extended this thought process to all things encompassing my life. And that brought me to thinking about whom I am and what my failings are.

Let’s pause for a second and get back to the Thesis. I am scheduled to defend my thesis on Wednesday, April 16th at 1:30pm. The location is Space Sciences Building room 106 (map). Here’s how it goes: I present my research for around 40 minutes. Following that, the committee will ask questions about my research no doubt exposing all the gaps in my knowledge, highlighting bad assumptions that formed the basis of my research and generally addressing the weak conclusions my research draws and the lack of impact my work will have on scaffold design and tissue engineering. Basically forcing me to face the honest failings of my past seven years.

No one likes to be publicly humiliated so you can probably see why I’d be concerned when several of my best friends and personal heroes expressed an interest in attending. Additionally, the probability of me breaking down into uncontrollable and embarrassing sobbing is nearly 1.0 for each of the three possible outcomes of Win, Lose or Weapons Grade FAIL. Add that to my fear of public humiliation and the result is that I don’t want anyone to attend my defense. But that’s not fair to myself or anyone that is genuinely interested in my research or supporting me. Oh also: people planning to attend only to see me be humiliated, I salute you slash fuck off.

The only way that I’m going to get over public humiliation is to put myself out there honestly and embrace what happens knowing that I did my best. And I will do that in my thesis and you are all invited to attend. I may even record video for those of you in other cities. But I need some practice getting honest appraisals. So this week I’m asking you to help me grow a thick skin.

I want you to be brutally honest with me.

For example: in a 2007 defamatory blog post, I was called a “would-be mogul,” a “snake oil salesman” and finally a “hard nosed motherfucker.” All hilarious terms but imagine arriving at SXSW to be on your first film panel and the ‘I’m Feeling Lucky’ hit for your name was a post entitled “A Hard Lesson in DIY – Matthew Wettergreen & The Dimes.” Micah Baldwin couldn’t ask for better press.

Now this was personally vindictive but I think you can come up with brutally honest things that are actually constructive. Tell me what my failings are as a human. Insult me. Tell me what bad things I’ve done and how they’ve affected you. Get creative, think of some really awful stuff. “You have the personal hygiene of a grue?” Boring. “Dollionaire philanderer?” Heard it. But what about things that I don’t even know about? Let’s cut to the quick here, folks. This is my coming of age.

If transparency is the new model (and I think I already show that if you’ve ever read my twitter stream) then here it is. Transparency about my entire life. My issues and problems put out there for everyone to see and digest so that I can see what I am and what I project myself as and what I fail at so that I can evaluate these things and become a better human. You want transparency? This post is fucking see-through.

Two ways you can participate.

Publicly: (for the brave) Leave a comment and as long as it won’t keep me out of office, I’ll approve it.

Privately: Anonymously email me using (remember not to put your email addy in the sender’s portion)

I’m being put through a professional coming of age ceremony on Wednesday. Think of this as my public trial. Everything after this sets the bar for my actions.




Written by Matthew Wettergreen

April 14, 2008 at 9:29 pm

Posted in thesis

6 – 5:33am, Thesis is done

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I finished my thesis. I don’t feel the glow of accomplishment. I don’t feel the pressure release from completion. I just feel mind fucked.

You can download the the whole thesis if you’re interested but I will warn you that it tops out at 248 pages. If you’re a fan of infoporn, check out the figures. The text is perfect if you are having problems sleeping; you won’t after reading a couple of pages of this document.

My thesis defense will be on Wednesday, April 16th at 1:30pm. This event is free and open to the public. Yes, you’re all invited in case you were waiting for that. I would love to share my research with you. Yes, there is also the possibility of public humiliation.

Matthew Wettergreen Thesis Defense

1:30 – ~3:00pm

Space Sciences 106 (

Parking available across the street from Space Sciences Building

Did you ever see that duck tales episode where Huey, Louie and Duey got ahold of that watch that would stop time? Every minute they had was like a second for the real world? I could use that watch right now cause I feel a Rip Van Winkle caliber nap bubbling up to the surface and tonight better be the LAST time I sleep in the Rice Library.

Written by Matthew Wettergreen

April 10, 2008 at 4:05 am

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21 – Chapter 2: Background (Part II) Bone Heirarchical Levels

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2.1 Bone Structure and Hierarchy {1}

Bone is a composite material that exists on at least 5 hierarchical levels: whole bone, architecture, tissue, lamellar, and ultrastructural level (Figure 1). The whole bone is at the greatest scale and represents the overall shape of the bone. This structure is composed of the architectural level, which contains the microstructure that defines the spatial distribution. Below the architectural level is the tissue level, which is inherent to the actual material properties of bone. The lamellar, or cellular level is below the tissue level and is composed of sheets of collagen and minerals deposited by osteoblasts [1]. The minimal scale level is the ultrastructural level which incorporates chemical and quantum interactions [2]. These five levels comprise structural differences in size magnitude between the subsequent levels, spanning from the whole bone to the chemical and quantum level [3]. In order for the research community to expedite a full characterization of bone, each separate constituent that contributes to the system as a whole must be evaluated. There are certain advantages that can be gained by separating the structure into microstructural organizational levels. By viewing bone at different hierarchical levels it is easy to compare different structures and tissues. Additionally, it is much simpler to define characteristic levels to use for analysis. Each level depends on the levels below it to provide function and structural support (Table 1).

{1} This section adopted from Liebschner MA, Wettergreen MA “Optimization of Bone Scaffold Engineering for Load Bearing Applications.” In Ferretti P., Ashammakhi N.: Topics in Tissue Engineering, e-book on tissue engineering, T. Waris & N. Ashammakhi, Chapter 22,, 2003.

Whole Bone Level

The top level of bone is the organ level, or whole bone level, and it represents the summation of the structural and material properties of all the levels of bone. At this level, the bone functions on the order of magnitude of the organism, providing structural support and aiding with locomotion. The mechanical characteristics of whole bone are a result of the complete structure’s geometry (Figure 2). Interaction between whole bone and other constituents of the body may include tendons, ligaments, muscles and other bones.

Bone Heirarchical Levels
Figure 1. Illustration of structures corresponding to hierarchical levels of bone. [4].
Bone Heirarchical Levels
Table 1. Structural Hierarchy and Mechanical Properties of Bone [4].
Optimization at this level is not seen in a shape change, but as a net mass change resulting from external/internal factors. Shape changes are minimal and the mechanical strength of the structure is derived from the total geometry of the bone and the distribution of tissue. Remodeling that may occur at lower levels is measured as percent increase or decrease in mass in the overall bone [6].
Femur, Whole Bone
Figure 2. Example of Whole Bone Level. Human Femur [5].

Architectural Level

The architectural level of bone relates to the characteristic micro-architecture of bone tissue, specifically cortical or trabecular bone (Figure 3). These structures serve to provide mechanical stability to the global structure of bone distributed throughout the osteons and/or trabeculae. This is the first level at which the remodeling of the organism can be visualized as a change in architecture. Architectural reorganization also affects the apparent properties of the structure. Two different architectures arise depending on anatomical site and loading conditions. Trabecular bone, contained in the ends of long bones and the site of bone marrow synthesis, exhibits anisotropy as a result of its rod and plate organization. Cortical bone is highly compact and orthotropic due to the circular nature of the osteons that make up its

Figure 3. On left, SEM of trabecular bone illustrating thinning of the trabecular in the center forefront. On right, photomicrograph of cortical bone illustrating the individual osteons and osteocytes [7, 8].

structure. One illustration of the micro-architectural differences between the two architectures is that cortical bone contains only microscopic channels through the center of the osteons whereas trabecular bone is highly porous (Figure 3) [9]. Mechanical function at the architectural level is to provide support for the overall bone structure and, specifically in trabecular bone, to act as a shock absorber and resist compressive loads [10]. The mechanical strength can be related to several geometric constraints such as trabecular thickness, bone mineral density, and bone surface to bone volume ratio. These constraints can be obtained from imaging techniques used to evaluate trabecular tissue [11]. Strain sensed in the bones at this architectural level causes the cells on lower hierarchical levels to remodel the gross arrangement of the micro-architecture at the surface [12]. Although gross reorganization of the bone micro-architecture is seen at this level as a change in geometry and architecture, the deposition and resorption occurs at the cellular level. Orientation and mechanical qualities change between anatomical sites and between bones as a result of dynamic loading and stress on bone tissue. The mechanical characteristics of the architectural level are largely due to the spatial distribution of the tissue (micro-architecture) and less so due to the properties of the material composing bone. The remodeling at this stage does not take an ordered path and thus may look random, but the structure that results from it is anything but unordered. The rods and plates that compose the trabecular bone follow a pattern of resorption and deposition according to the mechanotransduction principles of the bone. Due to the complexity of the bone, previous models have attempted to approximate the bone as simpler solids, such as open-celled foams or tetrakaidecagons [13, 14]. This will be discussed later in the mathematical approximation of trabecular bone.

Tissue Level

Below the architectural level of bone is the tissue level, which directly addresses the mechanical properties of the tissue. The material properties at this level provide support for the geometry of the architectural level above it. Remodeling of bone at this stage of the hierarchy alters the material properties of the bone tissue. Tissue properties are those that relate directly to the mechanical characteristics of the bone independent of the micro-architecture. Properties such as stiffness, Young’s Modulus, yield point, and energy to fracture can be dealt with on a fundamental material level. The optimization that occurs at this level is as a result of the modification of the material properties, and is responsible for the apparent properties of the architectural level.
Lamellar Level

Figure 4. Illustration of Lamellae.

Below the tissue level of bone is the lamellar level (Figure 4); the layers of bone deposited by single cells. Lone structures, the lamellae are laid on top of each other like composite board in directions that vary by up to 90 degrees. These laminations are the lowest form of bone and are deposited by the basic multicellular unit (BMU). This process involves the recruitment of osteoclasts that resorb bone; osteoblasts are then recruited to deposit bone; the process ends with the encapsulation of the osteoblasts in the bone matrix before they differentiate into mechanosensing osteocytes; finally, the osteoblasts deposit a layer of hydroxyapatite onto a woven bed of collagen [9, 15]. The sheets of lamellae are on the order of 3-20µm in thickness [3]. It is this process that produces all of the lamellar bone (Figure 4) in the body, which is a much stronger and better form of bone than embryonic or woven bone. The deposition and resorption of bone occurs only at the surface, however, the lowest layers of lamellae are not affected unless massive bone loss is experienced, as in osteoporosis.

Ultrastructural Level

The lowest level of the bone hierarchy considered in this review is the ultrastructural level. At this level chemical and quantum effects can be addressed. The order of magnitude for this level allows the analysis of the mechanics and architecture of the collagen fibers with the minerals [2]. The ultrastructural level is on the order of calcium and other minerals that are a part of bone, such as phosphate and magnesium. The advantage of viewing bone at this level is that it allows the study of an additional function of bone that cannot be addressed until this size. This function is the use of bone as mineral storage for the organism. Mineral storage and the effects of chemistry are the main functional points at the ultrastructural level as is the orientation of collagen in the lamellae [1]. The design of bone at this level illustrates how the micro-architecture of the structure must be evaluated as well as the nano-architecture. Several studies have been completed on the difference in ultrastructural mechanical properties as a result of the collagen orientation and the amount of mineral deposition on the collagen beds. The degree of mineralization will affect the final stiffness of the bone itself as well as the overall ash content [3].

1. Majeska, R., Cell Biology of Bone, in Bone Biomechanics Handbook, S.C. Cowin, Editor. 2001, CRC Press LLC: Boca Raton. p. (2)1-(2)-24.
2. van der Linden, J.C., et al., Trabecular bone’s mechanical properties are affected by its non-uniform mineral distribution. J Biomech, 2001. 34(12): p. 1573-80.
3. Lucchinetti, E., Composite Models of Bone Properties, in Bone Biomechanics Handbook, S.C. Cowin, Editor. 2001, CRC Press LLC: Boca Raton. p. (12)1-(12)19.
4. Liebschner, M.A.K. and M.A. Wettergreen, Optimization of Bone Scaffold
Engineering for Load Bearing
Applications, in Topics In Tissue Engineering, N. Ashammakhi and P. Ferretti, Editors. 2003.
5. Wikipedia. Femur. 2008 [cited; Available from:
6. Yaszemski, M.J., et al., Evolution of bone transplantation: molecular, cellular and tissue strategies to engineer human bone. Biomaterials, 1996. 17(2): p. 175-85.
7. Blue Histology. 2003 [cited 2003 12.2]; Available from:
8. Hollister, S.J. Bone Structure. 2003 [cited 2003 12.2]; Available from:
9. Jee, W., Integrated Bone Tissue Physiology: Anatomy and Physiology, in Bone Biomechanics Handbook, S.C. Cowin, Editor. 2001, CRC Press LLC: Boca Raton. p. (1)1-(1)68.
10. Borah, B., et al., Three-dimensional microimaging (MRmicroI and microCT), finite element modeling, and rapid prototyping provide unique insights into bone architecture in osteoporosis. Anat Rec, 2001. 265(2): p. 101-10.
11. Kopperdahl, D.L. and T.M. Keaveny, Yield strain behavior of trabecular bone. J Biomech, 1998. 31(7): p. 601-8.
12. Smith, T.S., et al., Surface remodeling of trabecular bone using a tissue level model. J Orthop Res, 1997. 15(4): p. 593-600.
13. Gibson, L.J. and M.F. Ashby, Cellular Solids: Structure and Properties. 1988, New York: Pergamon Press. 357.
14. Pearce, P., Structure in nature is a strategy for design. 1990, Cambridge, Massachusetts: MIT Press. 245.
15. Sikavitsas, V.I., J.S. Temenoff, and A.G. Mikos, Biomaterials and bone mechanotransduction. Biomaterials, 2001. 22(19): p. 2581-93.

Written by Matthew Wettergreen

March 26, 2008 at 9:33 am

Posted in thesis

23 – Thesis Title

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It has recently been brought to my attention that the title of my blog is too long. “The Effect of Material Organization on the Structural Properties of Porous Architectures? What does that even mean? Who do you want to read this thing? What are you putting it up for?”

This person was on vicodin.

Right after this conversation she congratulated me for another brilliant post on Stuff White People Like, saying “San Francisco! That’s so funny. You are so white! You’re in grad school and you like The Wire and Eternal Sunshine… and you do crosswords every day. I’m sure that you write that blog, c’mon admit it!”

Drugs aside, it got me thinking why I’m doing this blog: for myself. I don’t care who reads it, I’m not jumping up and down clamoring for people to pore over the inanity of my work from the past seven years, I already abuse twitter heavily enough for that. I’ve got less than 30 days til I defend, I stopped writing in my gurnal over a year ago (So what if I’m not as smart as you!), there needs to be a document of last days…this is it.

But if you do stumble upon this and want to know wtf “The Effect of Material Organization on the Structural Properties of Porous Architectures” means, let’s break it down:

Porosity is a measure of the amount of void space in any unit volume. If you have an empty box and you put something in it, the porosity, which used to be 100% has now been reduced by the volume of material in that box. Bone is around 80 – 90 % porous. It’s on the 90% side if you have osteoporosis where if you fall you shatter like glass, like my mother. It’s on the 80% side if you are a fine shining example of a fit and healthy human like that pitcher guy whose wife took all those steroids for him. The architectures that I work with are ranged in porosity between 50% and 90%. When you change porosity, you change the strength of an architecture: less material, less strength. The exciting part is that if you use the same architecture, you can compare the effects of material arrangement alone:

Von Mises Distribution - Rhombitruncated Cuboctahedron
The porous architecture, Rhombitruncated Cuboctahedron, at five porosities, left to right, 50% through 90%

By “Material Organization” I mean the arrangement of material in any configuration. You have 100 lego bricks and you arrange them into some configuration and then crush them. It’s got a certain strength, say x. Then, you arrange those 100 legos into a completely different arrangement and again, crush it. It has a strength, say y. Unless you know what you’re doing or are extremely lucky, xy. And the difference is the “material organization” not the porosity, since you used the same amount of bricks thus you have the same amount of porosity. Material properties are the characteristics of the construction material: playdoh, steel, clay, plastic. The specific heat, tensile strength, ultimate strength (crushing strength as a friend would understand it), and stiffness. These properties all have to do with the material itself. When you arrange that material into a shape, say a porous architecture, and crush it, you get the structural properties of that architecture.

Structural Properties work the same as Material Properties (stiffness, modulus, ultimate strength, etc. etc.) but they are solely due to the arrangement of the material the architecture is built with. You build a tower out of steel and that steel has its own material properties. The structure that you build then has its own structural properties.

So let’s recap “The Effect of Material Organization on the Structural Properties of Porous Architectures”
I study polyhedra which are “porous architectures”.
There are several polyhedra in the set that I study, each one has a different “material organization”.
Each polyhedra is built with the same material but has a different architecture which means they all have different “structural properties”.
I am looking to create rules which govern how a material organization can result in a tailored structural property.
The application of this is tailored patient implants for spinal repair.

So after all this I’ve decided to change the title to “Thesis or Fecis”

…it all comes down to this.

Written by Matthew Wettergreen

March 24, 2008 at 10:19 am

24 – Chapter 2: Background (Part I)

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The inability of bone to regenerate itself in cases of gross trauma poses a problem still unsolved. The complexity of bone tissue itself is compounded by the requirement that it provide structural support for the patient. Successful treatment should stimulate new bone growth resulting, at the end state, in native bone tissue with no trace of the regenerative device. Bone scaffolds have shown promise in regenerating some critical size defects in non-load bearing anatomic sites but results vary with anatomy and species [1]. Additionally, problems arise in load bearing sites where the scaffold must endure a modicum of mechanical loading. Success requires insight into the mechanisms that dictate bone growth as well as thorough characterization of the intended implanted scaffold. Currently, research has begun to characterize input parameters such as architecture, porosity, permeability and their effect on the resulting tissue ingrowth [2, 3]. The use of techniques such as Computer Aided Tissue Engineering (CATE) may in the future promote the regeneration of a functional bone system where a defect once lay [4]. The following sections will illustrate the importance of structure for function in nature and more specifically in bone. The subsequent architectural discussion will be framed in the effects of specific parameters of architecture and the past work that has attempted to incorporate these concepts into scaffold design.



1. Liebschner, M.A., Biomechanical considerations of animal models used in tissue engineering of bone. Biomaterials, 2004. 25(9): p. 1697-714.

2. Li, S.H., et al., Accurate geometric characterization of macroporous scaffold of tissue engineering. Key Engineering Materials, 2003. 240-242: p. 541-546.

3. Hollister, S.J., et al., Engineering craniofacial scaffolds. Orthod Craniofac Res, 2005. 8(3): p. 162-73.

4. Sun W, D.A., Starly B, Nam J, Computer-Aided Tissue Engineering:Overview, Scope, and Challenges. Biotechnology and Applied Biochemistry, 2004. 39: p. 29-47.




Written by Matthew Wettergreen

March 23, 2008 at 8:00 am

26 – Chapter 1: Introduction and Objectives

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Chapter 1: Introduction and Objectives

1.1 Introduction

The overall goal of this research is to determine relationships that govern the apparent properties of architectures evaluated solely from a material arrangement standpoint. This work specifically evaluates the structural and material properties of regular architectures that exhibit symmetry, homogeneity, and order. Additionally, this work will evaluate the apparent properties of architectures composed of random pore distributions. These properties and their relationships will be determined through modulation of the solid material and manipulation of the void space. Characterization of these structures will be used in the application of computer aided tissue engineering for the design of novel implants and tailored solutions to clinical problems stemming from tissue defects. Applied focus will be on the design of implants for bone regenerative scaffolds or other mechanically modulated systems. Numerous studies have demonstrated effects of specific scaffold architecture on tissue ingrowth [1-15]. As of yet, no rules have been generated to explain the exact structure’s exact effect nor has any quantifiable difference ever been demonstrated for given architectures as a result of their material organization [16]. Therefore, the global hypothesis of this research is that organization of material affects the structural and material properties of that architecture [17] and ultimately, the success of the implant. Furthermore, the use of design principles to create structures and scaffolds with specific architectures may be used to characterize mechanisms that dictate tissue regeneration in therapeutic scaffolds.

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Written by Matthew Wettergreen

March 22, 2008 at 5:00 am