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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, February 2017., Cataloged from PDF version of thesis., Includes bibliographical references., Post traumatic osteoarthritis (PTOA) refers to the progressive degradation of cartilage often triggered by a traumatic joint injury, such as a tear of the meniscus or anterior cruciate ligament (ACL). Such impact injuries lead to elevated levels of inflammatory cytokines in the synovial fluid of the joint, including IL-1, IL-6, and TNFa. In turn, these cytokines cause decreased matrix synthesis by chondrocytes and contribute to reprogramming of chondrocytes and synovial cells to increase release of matrix proteases. PTOA accounts for 12% of the OA population and typically affects younger individuals. The first part of this thesis focuses on developing a combination therapeutic which can address multiple aspects of cartilage degradation associated with the pathogenic responses to joint injury. We studied the combined use of insulin-like growth factor 1 (IGF-1) and dexamethasone (Dex) to block multiple degradative effects of cytokine challenge to articular cartilage. We found that in young bovine cartilage, the combination of IGF- 1 and Dex significantly inhibited the loss of sulfated glycosaminoglycans (sGAG) and collagen induced by IL-I. rescued the suppressed matrix biosynthesis, and inhibited the loss of chondrocyte viability caused by iL- 1 treatment. In adult human cartilage, only IGF- 1 rescued matrix biosynthesis and only Dex inhibited sGAG loss and improved cell viability. Thus, the combination of IGF-1+Dex together showed combined beneficial effects in human cartilage. Our findings suggest that the combination of IGF-I and Dex has greater beneficial effects than either molecule alone in preventing cytokine-mediated cartilage degradation in adult human and young bovine cartilage. In the second part of this thesis, a global phosphoproteomics approach was employed to determine the pathways that are activated upon cytokine challenge of adult human chondrocytes. We identified key regulatory kinases, p38, JNKI/2, ERKI/2, ERK5, JAK2, and STAT3 that were upregulated, by Yang Wang., Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, February 2017., Cataloged from PDF version of thesis., Includes bibliographical references., Post traumatic osteoarthritis (PTOA) refers to the progressive degradation of cartilage often triggered by a traumatic joint injury, such as a tear of the meniscus or anterior cruciate ligament (ACL). Such impact injuries lead to elevated levels of inflammatory cytokines in the synovial fluid of the joint, including IL-1, IL-6, and TNFa. In turn, these cytokines cause decreased matrix synthesis by chondrocytes and contribute to reprogramming of chondrocytes and synovial cells to increase release of matrix proteases. PTOA accounts for 12% of the OA population and typically affects younger individuals. The first part of this thesis focuses on developing a combination therapeutic which can address multiple aspects of cartilage degradation associated with the pathogenic responses to joint injury. We studied the combined use of insulin-like growth factor 1 (IGF-1) and dexamethasone (Dex) to block multiple degradative effects of cytokine challenge to articular cartilage. We found that in young bovine cartilage, the combination of IGF- 1 and Dex significantly inhibited the loss of sulfated glycosaminoglycans (sGAG) and collagen induced by IL-I. rescued the suppressed matrix biosynthesis, and inhibited the loss of chondrocyte viability caused by iL- 1 treatment. In adult human cartilage, only IGF- 1 rescued matrix biosynthesis and only Dex inhibited sGAG loss and improved cell viability. Thus, the combination of IGF-1+Dex together showed combined beneficial effects in human cartilage. Our findings suggest that the combination of IGF-I and Dex has greater beneficial effects than either molecule alone in preventing cytokine-mediated cartilage degradation in adult human and young bovine cartilage. In the second part of this thesis, a global phosphoproteomics approach was employed to determine the pathways that are activated upon cytokine challenge of adult human chondrocytes. We identified key regulatory kinases, p38, JNKI/2, ERKI/2, ERK5, JAK2, and STAT3 that were upregulated, by Yang Wang., Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2017., Cataloged from PDF version of thesis., Includes bibliographical references (pages 213-217)., Improving fuel economy of internal combustion engines is one of the major focuses in automotive industry. The piston ring friction contributes as much as 25% of total mechanical loss in internal combustion engines [1] and is an area of great interests to the automotive industry in their overall effort to improve engine efficiency. However, typical methods to reduce friction loss from piston ring pack, such as ring tension reduction, may cause additional oil consumption. A compromise between reduction of friction loss and control of gas leakage and oil consumption needs to be made, which requires a deep understanding of oil transport mechanism. This compromise gives rise to the interest in modeling work. Both experimental results and previous experience showed that oil film distribution on the piston varies significantly along the circumference and the oil leakage occurs locally. Therefore to predict oil transfer across different ring pack regions, one needs to integrate both global and local processes. This work is aimed at establishing an enduring framework for all the cycle-based processes at different length scales. As a first step, a multi-scale multi-physics piston ring pack model was developed by coupling the structural dynamics of the piston rings with gas flows and local interactions at ring-groove and ring-liner interfaces. A curved beam finite element method was adopted to calculate the ring structural response to interaction between the ring and the liner as well as the ring and the groove. Compared to a traditional straight beam finite element method, the curved beam separates the structural mesh and contact grid by utilizing the shape functions. In this work, a multi-length-scale ring pack model was, for the first time, successfully assembled. This model bears its fundamental values to truly reflect the integral results of all the relevant mechanisms. The significance of the current work is that it demonstrated such an integration of all the length scal, by Yang Liu., Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, February 2017., Cataloged from PDF version of thesis., Includes bibliographical references., Post traumatic osteoarthritis (PTOA) refers to the progressive degradation of cartilage often triggered by a traumatic joint injury, such as a tear of the meniscus or anterior cruciate ligament (ACL). Such impact injuries lead to elevated levels of inflammatory cytokines in the synovial fluid of the joint, including IL-1, IL-6, and TNFa. In turn, these cytokines cause decreased matrix synthesis by chondrocytes and contribute to reprogramming of chondrocytes and synovial cells to increase release of matrix proteases. PTOA accounts for 12% of the OA population and typically affects younger individuals. The first part of this thesis focuses on developing a combination therapeutic which can address multiple aspects of cartilage degradation associated with the pathogenic responses to joint injury. We studied the combined use of insulin-like growth factor 1 (IGF-1) and dexamethasone (Dex) to block multiple degradative effects of cytokine challenge to articular cartilage. We found that in young bovine cartilage, the combination of IGF- 1 and Dex significantly inhibited the loss of sulfated glycosaminoglycans (sGAG) and collagen induced by IL-I. rescued the suppressed matrix biosynthesis, and inhibited the loss of chondrocyte viability caused by iL- 1 treatment. In adult human cartilage, only IGF- 1 rescued matrix biosynthesis and only Dex inhibited sGAG loss and improved cell viability. Thus, the combination of IGF-1+Dex together showed combined beneficial effects in human cartilage. Our findings suggest that the combination of IGF-I and Dex has greater beneficial effects than either molecule alone in preventing cytokine-mediated cartilage degradation in adult human and young bovine cartilage. In the second part of this thesis, a global phosphoproteomics approach was employed to determine the pathways that are activated upon cytokine challenge of adult human chondrocytes. We identified key regulatory kinases, p38, JNKI/2, ERKI/2, ERK5, JAK2, and STAT3 that were upregulated, by Yang Wang., Ph. D.

Thesis: Ph. D., Massachusetts Institute of Technology, Sloan School of Management, 2015., Cataloged from PDF version of thesis., Includes bibliographical references (pages 157-163)., This thesis consists of three essays in corporate finance and capital markets. The first chapter estimates the effect of competition from low-cost index funds on fees in the money management industry. A difference-in-differences analysis exploiting the staggered entry of index funds finds that while actively managed funds sold directly to retail investors reduce fees by six percent, those sold through brokers increase fees by four percent. Additionally, actively managed funds, especially closet indexers, shift away from holding the index portfolio. The paper proposes a price-discrimination model to illustrate that the effect of low-cost passive fund competition depends on market segmentation. Beyond the price competition effect, the entry creates a selection effect that isolates the least-price-sensitive investors in the broker channel and results in a price increase for this group. Repeating the study using the entry of exchange-traded funds reveals similar but stronger finding. Overall, the results shed light on why aggregate mutual fund fees decline slowly despite increased competition from lower-cost passive alternatives. The second chapter, joint with Jean-Noel Barrot, examines the effects of imperfect investor risk adjustment on the behavior of mutual fund managers. We exploit a natural experiment when a major fund rating company changed its rating methodology. While in the old system, all equity funds were compared with one another in one pool, in the new algorithm, funds become compared within narrow peer groups. This algorithm revision increases the ability of retail investor to compare funds based on risk-adjusted returns, and it has an important impact on the fund mangers' compensation. The sensitivity of retail fund flows to systematic returns is eliminated. Using institutional funds as a control for retail funds in a difference-in-differences analysis, we find that this revision reduces fund managers risk taking behavior, in particular for funds in the, by Yang Sun., The effect of index fund competition on money management fees -- The effect of investor risk adjustment on fund manager incentives -- Dividend policy in the early twentieth century United States., Ph. D.

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015., Cataloged from PDF version of thesis. Volume 1 (page 1 to page 510) ; Volume 2 (page 511 to 881). Duplicated pages for pages 195 to 240 are bound after page 881., Includes bibliographical references., Part I. Palladium-Catalyzed Carbon-Carbon Bond Forming Cross-Couplings Chapter 1. Ligand-Controlled Palladium-Catalyzed Regiodivergent Suzuki-Miyaura Cross-Coupling of Allylboronates and Aryl Halides An orthogonal set of catalyst systems based on the use of two biarylphosphine ligands has been developed for the Suzuki-Miyaura coupling of 3,3-disubstituted and 3-monosubstituted allylboronates with (hetero)aryl halides. These methods allow for the regiodivergent preparation of either the ct- or the [gamma]-isomeric coupling product with high levels of site selectivity using a common allylboron building block. Preliminary investigations have demonstrated the feasibility of an enantioselective variant for the [gamma]-selective cross-coupling using chiral monodentate biarylphosphine ligands. Chapter 2. Palladium-Catalyzed Completely Linear-Selective Negishi Coupling of 3,3-Disubstituted Organozinc Reagents with Aryl and Vinyl Electrophiles A palladium-catalyzed general and completely linear-selective Negishi coupling of 3,3- disubstituted allyl organozinc reagents with (hetero)aryl and vinyl electrophiles has been developed. This method provided an effective means for accessing highly functionalized aromatic and heteroaromatic compounds bearing prenyl-type side chains. The utility of the current protocol was further illustrated in the concise synthesis of the anti-HIV natural product siamenol. Chapter 3. Palladium-Catalyzed Highly Selective Negishi Cross-Coupling of Secondary Alkylzinc Reagents with Aryl and Heteroaryl Halides The palladium-catalyzed Negishi cross-coupling of secondary alkylzinc reagents and heteroaryl halides with high levels of regioisomeric retention has been described. The development of a series of biarylphosphine ligands has led to the identification of an improved catalyst for the coupling of electron-deficient heterocyclic substrates. Preparation and characterization of oxidative addition complex (L)Pd(Ar)(Br) provided insight into the unique rea, by Yang Yang., Ph. D. in Organic Chemistry

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015., Cataloged from PDF version of thesis. Volume 1 (page 1 to page 510) ; Volume 2 (page 511 to 881). Duplicated pages for pages 195 to 240 are bound after page 881., Includes bibliographical references., Part I. Palladium-Catalyzed Carbon-Carbon Bond Forming Cross-Couplings Chapter 1. Ligand-Controlled Palladium-Catalyzed Regiodivergent Suzuki-Miyaura Cross-Coupling of Allylboronates and Aryl Halides An orthogonal set of catalyst systems based on the use of two biarylphosphine ligands has been developed for the Suzuki-Miyaura coupling of 3,3-disubstituted and 3-monosubstituted allylboronates with (hetero)aryl halides. These methods allow for the regiodivergent preparation of either the ct- or the [gamma]-isomeric coupling product with high levels of site selectivity using a common allylboron building block. Preliminary investigations have demonstrated the feasibility of an enantioselective variant for the [gamma]-selective cross-coupling using chiral monodentate biarylphosphine ligands. Chapter 2. Palladium-Catalyzed Completely Linear-Selective Negishi Coupling of 3,3-Disubstituted Organozinc Reagents with Aryl and Vinyl Electrophiles A palladium-catalyzed general and completely linear-selective Negishi coupling of 3,3- disubstituted allyl organozinc reagents with (hetero)aryl and vinyl electrophiles has been developed. This method provided an effective means for accessing highly functionalized aromatic and heteroaromatic compounds bearing prenyl-type side chains. The utility of the current protocol was further illustrated in the concise synthesis of the anti-HIV natural product siamenol. Chapter 3. Palladium-Catalyzed Highly Selective Negishi Cross-Coupling of Secondary Alkylzinc Reagents with Aryl and Heteroaryl Halides The palladium-catalyzed Negishi cross-coupling of secondary alkylzinc reagents and heteroaryl halides with high levels of regioisomeric retention has been described. The development of a series of biarylphosphine ligands has led to the identification of an improved catalyst for the coupling of electron-deficient heterocyclic substrates. Preparation and characterization of oxidative addition complex (L)Pd(Ar)(Br) provided insight into the unique rea, by Yang Yang., Ph. D. in Organic Chemistry

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015., Cataloged from PDF version of thesis. Volume 1 (page 1 to page 510) ; Volume 2 (page 511 to 881). Duplicated pages for pages 195 to 240 are bound after page 881., Includes bibliographical references., Part I. Palladium-Catalyzed Carbon-Carbon Bond Forming Cross-Couplings Chapter 1. Ligand-Controlled Palladium-Catalyzed Regiodivergent Suzuki-Miyaura Cross-Coupling of Allylboronates and Aryl Halides An orthogonal set of catalyst systems based on the use of two biarylphosphine ligands has been developed for the Suzuki-Miyaura coupling of 3,3-disubstituted and 3-monosubstituted allylboronates with (hetero)aryl halides. These methods allow for the regiodivergent preparation of either the ct- or the [gamma]-isomeric coupling product with high levels of site selectivity using a common allylboron building block. Preliminary investigations have demonstrated the feasibility of an enantioselective variant for the [gamma]-selective cross-coupling using chiral monodentate biarylphosphine ligands. Chapter 2. Palladium-Catalyzed Completely Linear-Selective Negishi Coupling of 3,3-Disubstituted Organozinc Reagents with Aryl and Vinyl Electrophiles A palladium-catalyzed general and completely linear-selective Negishi coupling of 3,3- disubstituted allyl organozinc reagents with (hetero)aryl and vinyl electrophiles has been developed. This method provided an effective means for accessing highly functionalized aromatic and heteroaromatic compounds bearing prenyl-type side chains. The utility of the current protocol was further illustrated in the concise synthesis of the anti-HIV natural product siamenol. Chapter 3. Palladium-Catalyzed Highly Selective Negishi Cross-Coupling of Secondary Alkylzinc Reagents with Aryl and Heteroaryl Halides The palladium-catalyzed Negishi cross-coupling of secondary alkylzinc reagents and heteroaryl halides with high levels of regioisomeric retention has been described. The development of a series of biarylphosphine ligands has led to the identification of an improved catalyst for the coupling of electron-deficient heterocyclic substrates. Preparation and characterization of oxidative addition complex (L)Pd(Ar)(Br) provided insight into the unique rea, by Yang Yang., Ph. D. in Organic Chemistry

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015., Cataloged from PDF version of thesis. Volume 1 (page 1 to page 510) ; Volume 2 (page 511 to 881). Duplicated pages for pages 195 to 240 are bound after page 881., Includes bibliographical references., Part I. Palladium-Catalyzed Carbon-Carbon Bond Forming Cross-Couplings Chapter 1. Ligand-Controlled Palladium-Catalyzed Regiodivergent Suzuki-Miyaura Cross-Coupling of Allylboronates and Aryl Halides An orthogonal set of catalyst systems based on the use of two biarylphosphine ligands has been developed for the Suzuki-Miyaura coupling of 3,3-disubstituted and 3-monosubstituted allylboronates with (hetero)aryl halides. These methods allow for the regiodivergent preparation of either the ct- or the [gamma]-isomeric coupling product with high levels of site selectivity using a common allylboron building block. Preliminary investigations have demonstrated the feasibility of an enantioselective variant for the [gamma]-selective cross-coupling using chiral monodentate biarylphosphine ligands. Chapter 2. Palladium-Catalyzed Completely Linear-Selective Negishi Coupling of 3,3-Disubstituted Organozinc Reagents with Aryl and Vinyl Electrophiles A palladium-catalyzed general and completely linear-selective Negishi coupling of 3,3- disubstituted allyl organozinc reagents with (hetero)aryl and vinyl electrophiles has been developed. This method provided an effective means for accessing highly functionalized aromatic and heteroaromatic compounds bearing prenyl-type side chains. The utility of the current protocol was further illustrated in the concise synthesis of the anti-HIV natural product siamenol. Chapter 3. Palladium-Catalyzed Highly Selective Negishi Cross-Coupling of Secondary Alkylzinc Reagents with Aryl and Heteroaryl Halides The palladium-catalyzed Negishi cross-coupling of secondary alkylzinc reagents and heteroaryl halides with high levels of regioisomeric retention has been described. The development of a series of biarylphosphine ligands has led to the identification of an improved catalyst for the coupling of electron-deficient heterocyclic substrates. Preparation and characterization of oxidative addition complex (L)Pd(Ar)(Br) provided insight into the unique rea, by Yang Yang., Ph. D. in Organic Chemistry

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015., Cataloged from PDF version of thesis. Volume 1 (page 1 to page 510) ; Volume 2 (page 511 to 881). Duplicated pages for pages 195 to 240 are bound after page 881., Includes bibliographical references., Part I. Palladium-Catalyzed Carbon-Carbon Bond Forming Cross-Couplings Chapter 1. Ligand-Controlled Palladium-Catalyzed Regiodivergent Suzuki-Miyaura Cross-Coupling of Allylboronates and Aryl Halides An orthogonal set of catalyst systems based on the use of two biarylphosphine ligands has been developed for the Suzuki-Miyaura coupling of 3,3-disubstituted and 3-monosubstituted allylboronates with (hetero)aryl halides. These methods allow for the regiodivergent preparation of either the ct- or the [gamma]-isomeric coupling product with high levels of site selectivity using a common allylboron building block. Preliminary investigations have demonstrated the feasibility of an enantioselective variant for the [gamma]-selective cross-coupling using chiral monodentate biarylphosphine ligands. Chapter 2. Palladium-Catalyzed Completely Linear-Selective Negishi Coupling of 3,3-Disubstituted Organozinc Reagents with Aryl and Vinyl Electrophiles A palladium-catalyzed general and completely linear-selective Negishi coupling of 3,3- disubstituted allyl organozinc reagents with (hetero)aryl and vinyl electrophiles has been developed. This method provided an effective means for accessing highly functionalized aromatic and heteroaromatic compounds bearing prenyl-type side chains. The utility of the current protocol was further illustrated in the concise synthesis of the anti-HIV natural product siamenol. Chapter 3. Palladium-Catalyzed Highly Selective Negishi Cross-Coupling of Secondary Alkylzinc Reagents with Aryl and Heteroaryl Halides The palladium-catalyzed Negishi cross-coupling of secondary alkylzinc reagents and heteroaryl halides with high levels of regioisomeric retention has been described. The development of a series of biarylphosphine ligands has led to the identification of an improved catalyst for the coupling of electron-deficient heterocyclic substrates. Preparation and characterization of oxidative addition complex (L)Pd(Ar)(Br) provided insight into the unique rea, by Yang Yang., Ph. D. in Organic Chemistry

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2015., Cataloged from PDF version of thesis., Includes bibliographical references (pages 153-160)., The goal of this thesis is to better understand the design practice employed by the desalination industry from a systems-level viewpoint and offer recommendations to improve the process of design. A human-centered design research approach is used, in which industry practitioners were interviewed about the design strategies they employ for industrial desalination systems. A common theme from the interviews is that long term performance of desalination systems needs to be emphasized during the design process. Based on this observation, a novel design framework is proposed that incorporates health monitoring and maintenance in the design stage. The proposed framework is shown to make the design process more effective and can result in more optimal design over the lifecycle of a plant. The interviews also suggest open questions about how designers use computational tools for the design of desalination system. An investigation of how designers respond to the complexity of desalination parameter design problems was conducted. The behavior of designers during a series of simulated design processes involving seawater reverse osmosis (SWRO) plants was observed. The experiments revealed that desalination knowledge seemed to lead to better performance, but the results also showed that subjects with limited desalination knowledge could perform worse than subjects with no desalination knowledge. It was also observed that human designers had difficulties understanding the sensitivity of coupled variables, which can lead to poor performance on parameter design problems. Additionally, the top-performance-ranked subjects were observed to behavior very differently from the bottom-ranked. The problem-solving profiles of best performing subjects resembled a well-tuned simulated annealing algorithm while the worst performing subjects used a pseudo random search strategy., by Bo Yang Yu., Ph. D.

We have investigated the molecular environment of the semicircular composite supernova remnant (SNR) 3C 396 and performed a Chandra spatially resolved thermal X-ray spectroscopic study of this young SNR. With our CO millimeter observations, we find that the molecular clouds (MCs) at V[subscript LSR]~ 84 km s[superscript –1] can better explain the multiwavelength properties of the remnant than the V [subscript LSR] = 67-72 km s[superscript –1] MCs that are suggested by Lee et al. At around 84 km s[superscript –1], the western boundary of the SNR is perfectly confined by the western molecular wall. The CO emission fades out from west to east, indicating that the eastern region is of low gas density. In particular, an intruding finger/pillar-like MC, which may be shocked at the tip, can well explain the X-ray and radio enhancement in the southwest and some infrared filaments there. The SNR-MC interaction is also favored by the relatively elevated [superscript 12]CO J = [2-1 over J] = 1-0 line ratios in the southwestern "pillar tip" and the molecular patch on the northwestern boundary. The redshifted [superscript 12]CO (J = 1-0 and J = 2-1) wings (86-90 km s[superscript –1]) of an eastern 81 km s[superscript –1] molecular patch may be the kinematic evidence for shock-MC interaction. We suggest that the 69 km s[superscript –1] MCs are in the foreground based on H I self-absorption while the 84 km s[superscript –1] MCs at a distance of 6.2 kpc (the tangent point) are in physical contact with SNR 3C 396. The X-ray spectral analysis suggests an SNR age of ~3 kyr. The metal enrichment of the X-ray emitting gas in the north and south implies a 13-15 M [subscript ☉] B1-B2 progenitor star., National Natural Science Foundation (China) (Grant 10621303), National Natural Science Foundation (China) (Grant 10725312), National Natural Science Foundation (China) (973 Program Grant 2009CB824800)

3C 397 is a radio and X-ray bright Galactic supernova remnant (SNR) with an unusual rectangular morphology. Our CO observation obtained with the Purple Mountain Observatory at Delingha, Qinghai Province, China reveals that the remnant is well confined in a cavity of molecular gas and embedded at the edge of a molecular cloud (MC) at the local standard of rest systemic velocity of ~32 km s[superscript –1]. The cloud has a column density gradient increasing from southeast to northwest, perpendicular to the Galactic plane, in agreement with the elongation direction of the remnant. This systemic velocity places the cloud and SNR 3C 397 at a kinematic distance of ~10.3 kpc. The derived mean molecular density (~10-30 cm[superscript –3]) explains the high volume emission measure of the X-ray emitting gas. A [superscript 12]CO line broadening of the ~32 km s[superscript –1] component is detected at the westmost boundary of the remnant, which provides direct evidence of the SNR-MC interaction and suggests multi-component gas there with dense (~10[superscript 4] cm[superscript –3]) molecular clumps. We confirm the previous detection of an MC at ~38 km s[superscript –1] to the west and south of the SNR and argue, based on H I self-absorption, that the cloud is located in the foreground of the remnant. A list of Galactic SNRs presently known and suggested to be in physical contact with environmental MCs is appended in this paper., National Natural Science Foundation (China) (grant 10725312), National Natural Science Foundation (China) (973 Program grant 2009CB824800), National Natural Science Foundation (China) (grant 10673003), Natural Sciences and Engineering Research Council of Canada, Canada Research Chairs (Program)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2010., Cataloged from PDF version of thesis., Includes bibliographical references (p. 91-104) and index., Water is the most ubiquitous substance on earth, and is essential to sustain all known forms of life. However, despite centuries of research, a coherent picture of the unusual phase behavior of water is so far lacking. The most promising theory under scrutiny relies on the hypothetical existence of a liquid-liquid phase transition and an associated liquid-liquid critical point hidden in the region of supercooled temperatures and elevated pressures, where bulk water does not exist in liquid state. Therefore it is a grand experimental challenge to investigate the properties of water, both thermodynamic and dynamic, in the relative region of the phase diagram. A combination of neutron triple-axis spectrometer and small-angle neutron scattering instrument are used to measure the density of water confined in a nanoporous silica matrix MCM-41-S in a Temperature-Pressure range inaccessible for the bulk (300-130 K and 1-2900 bar), namely, the equation of state p(T, P). The measured isobaric density profiles clearly show a change of behavior around 1500 bar. This experiment provides the most direct evidence supporting the existence of a liquid-liquid critical point in such confined water. The experimental result further implies that the nature of the liquid-liquid critical point of water might be of a tricritical type. Moreover, the reported density data of confined water under extreme conditions are valuable for the vast communities in biological, geological and planetary sciences. Parallel to the density measurement, the dynamics of water in confined geometry, such as aged cement paste and the vicinity of protein surfaces, are also investigated using a variety of quasi-elastic and inelastic neutron scattering spectrometers. A wide range of pre-glass-transition phenomena, such as dynamic crossover, dynamic heterogeneity and boson peak, are observed above the conventional glass-transition temperature. Possible explanations are discussed in the frameworks of the liquidliquid, by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 168-175)., A modern engineering system, e.g. the Internet, faces challenges from both the strategic behavior of its self-interested participants and the inherent computational intractability of large systems. Responding to this challenge, a new field, Algorithmic Mechanism Design, has emerged. One of the most fundamental problems in this field is How to optimize revenue in an auction? In his seminal paper [Mye81], Myerson gives a partial solution to this problem by providing a revenue-optimal auction for a seller who is looking to sell a single item to muLtiple bidders. Extending this auction to simultaneously selling multiple heterogeneous items has been one of the central open problems in Mathematical Economics. We provide such an extension that is also computationally efficient. Our solution proposes a novel framework for mechanism design by reducing mechanism design problems (where one optimizes an objective function on "rational inputs" ) to algorithm design problems (where one optimizes an objective function on "honest inputs"). Our reduction is generic and provides a framework for many other mechanism design problems., by Yang Cai., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2010., Cataloged from PDF version of thesis., Includes bibliographical references (p. 91-104) and index., Water is the most ubiquitous substance on earth, and is essential to sustain all known forms of life. However, despite centuries of research, a coherent picture of the unusual phase behavior of water is so far lacking. The most promising theory under scrutiny relies on the hypothetical existence of a liquid-liquid phase transition and an associated liquid-liquid critical point hidden in the region of supercooled temperatures and elevated pressures, where bulk water does not exist in liquid state. Therefore it is a grand experimental challenge to investigate the properties of water, both thermodynamic and dynamic, in the relative region of the phase diagram. A combination of neutron triple-axis spectrometer and small-angle neutron scattering instrument are used to measure the density of water confined in a nanoporous silica matrix MCM-41-S in a Temperature-Pressure range inaccessible for the bulk (300-130 K and 1-2900 bar), namely, the equation of state p(T, P). The measured isobaric density profiles clearly show a change of behavior around 1500 bar. This experiment provides the most direct evidence supporting the existence of a liquid-liquid critical point in such confined water. The experimental result further implies that the nature of the liquid-liquid critical point of water might be of a tricritical type. Moreover, the reported density data of confined water under extreme conditions are valuable for the vast communities in biological, geological and planetary sciences. Parallel to the density measurement, the dynamics of water in confined geometry, such as aged cement paste and the vicinity of protein surfaces, are also investigated using a variety of quasi-elastic and inelastic neutron scattering spectrometers. A wide range of pre-glass-transition phenomena, such as dynamic crossover, dynamic heterogeneity and boson peak, are observed above the conventional glass-transition temperature. Possible explanations are discussed in the frameworks of the liquidliquid, by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 168-175)., A modern engineering system, e.g. the Internet, faces challenges from both the strategic behavior of its self-interested participants and the inherent computational intractability of large systems. Responding to this challenge, a new field, Algorithmic Mechanism Design, has emerged. One of the most fundamental problems in this field is How to optimize revenue in an auction? In his seminal paper [Mye81], Myerson gives a partial solution to this problem by providing a revenue-optimal auction for a seller who is looking to sell a single item to muLtiple bidders. Extending this auction to simultaneously selling multiple heterogeneous items has been one of the central open problems in Mathematical Economics. We provide such an extension that is also computationally efficient. Our solution proposes a novel framework for mechanism design by reducing mechanism design problems (where one optimizes an objective function on "rational inputs" ) to algorithm design problems (where one optimizes an objective function on "honest inputs"). Our reduction is generic and provides a framework for many other mechanism design problems., by Yang Cai., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 301-319)., Polygeneration is a concept where multiple energy products are generated in a single plant by tightly integrating multiple processes into one system. Compared to conventional single-product systems, polygeneration systems have many economic advantages, such as potentially high profitability and high viability when exposed to market fluctuations. The optimal design of an energy polygeneration system that converts coal and biomass to electricity, liquid fuels (naphtha and diesel) and chemical products (methanol) with carbon dioxide (CO²) capture under different economic scenarios is investigated. In this system, syngas is produced by gasification of coal and/or biomass; purified by a cleaning process to remove particles, mercury, sulfur and CO²; and then split to different downstream sections such as the gas turbine, FT process and the methanol process. In this thesis, the optimal design with the highest net present value (NPV) is determined by optimizing equipment capacities, stream flow rates and stream split fractions. The case study results for static polygeneration systems reveal that the optimal design of polygeneration systems is strongly influenced by economic conditions such as feedstock prices, product prices, and potential emissions penalties for CO². Over the range of economic scenarios considered, it can be optimal to produce a mixture of electricity, liquid fuels, and methanol; only one each; or mixtures in-between. The optimal biomass/coal feed ratio significantly increases when the carbon tax increases or the biomass price decreases. An economic analysis of the optimal static polygeneration designs yielded a slightly higher NPV than comparable single-product plants. The flexible operation is then considered for the energy polygeneration system. In real applications, product prices can fluctuate significantly seasonally or even daily. The profitability of the polygeneration system can potentially be increased if some operational flexibility is introduce, by Yang Chen., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 301-319)., Polygeneration is a concept where multiple energy products are generated in a single plant by tightly integrating multiple processes into one system. Compared to conventional single-product systems, polygeneration systems have many economic advantages, such as potentially high profitability and high viability when exposed to market fluctuations. The optimal design of an energy polygeneration system that converts coal and biomass to electricity, liquid fuels (naphtha and diesel) and chemical products (methanol) with carbon dioxide (CO²) capture under different economic scenarios is investigated. In this system, syngas is produced by gasification of coal and/or biomass; purified by a cleaning process to remove particles, mercury, sulfur and CO²; and then split to different downstream sections such as the gas turbine, FT process and the methanol process. In this thesis, the optimal design with the highest net present value (NPV) is determined by optimizing equipment capacities, stream flow rates and stream split fractions. The case study results for static polygeneration systems reveal that the optimal design of polygeneration systems is strongly influenced by economic conditions such as feedstock prices, product prices, and potential emissions penalties for CO². Over the range of economic scenarios considered, it can be optimal to produce a mixture of electricity, liquid fuels, and methanol; only one each; or mixtures in-between. The optimal biomass/coal feed ratio significantly increases when the carbon tax increases or the biomass price decreases. An economic analysis of the optimal static polygeneration designs yielded a slightly higher NPV than comparable single-product plants. The flexible operation is then considered for the energy polygeneration system. In real applications, product prices can fluctuate significantly seasonally or even daily. The profitability of the polygeneration system can potentially be increased if some operational flexibility is introduce, by Yang Chen., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2010., Cataloged from PDF version of thesis., Includes bibliographical references (p. 91-104) and index., Water is the most ubiquitous substance on earth, and is essential to sustain all known forms of life. However, despite centuries of research, a coherent picture of the unusual phase behavior of water is so far lacking. The most promising theory under scrutiny relies on the hypothetical existence of a liquid-liquid phase transition and an associated liquid-liquid critical point hidden in the region of supercooled temperatures and elevated pressures, where bulk water does not exist in liquid state. Therefore it is a grand experimental challenge to investigate the properties of water, both thermodynamic and dynamic, in the relative region of the phase diagram. A combination of neutron triple-axis spectrometer and small-angle neutron scattering instrument are used to measure the density of water confined in a nanoporous silica matrix MCM-41-S in a Temperature-Pressure range inaccessible for the bulk (300-130 K and 1-2900 bar), namely, the equation of state p(T, P). The measured isobaric density profiles clearly show a change of behavior around 1500 bar. This experiment provides the most direct evidence supporting the existence of a liquid-liquid critical point in such confined water. The experimental result further implies that the nature of the liquid-liquid critical point of water might be of a tricritical type. Moreover, the reported density data of confined water under extreme conditions are valuable for the vast communities in biological, geological and planetary sciences. Parallel to the density measurement, the dynamics of water in confined geometry, such as aged cement paste and the vicinity of protein surfaces, are also investigated using a variety of quasi-elastic and inelastic neutron scattering spectrometers. A wide range of pre-glass-transition phenomena, such as dynamic crossover, dynamic heterogeneity and boson peak, are observed above the conventional glass-transition temperature. Possible explanations are discussed in the frameworks of the liquidliquid, by Yang Zhang., Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 107-109)., Nowadays, a rapid growth of internal combustion (IC) engines is considered to be a major contributor to energy crisis. About 20% of the mechanical loss in internal combustion engines directly goes to the friction loss between piston ring pack and liner finish. A twin-land oil control ring (TLOCR) deterministic model was developed by Chen et al. and it helps the automotive companies investigate the effects of liner finish, rings, and lubricants on friction and oil control of the TLOCR [2]. This work focuses on application of the TLOCR model and extension of the deterministic model to the top two rings. First, there are some practical challenges in the application of Chen's TLOCR deterministic model. Due to different wear condition on the same liner, surface roughness varies from spot to spot. A small patch of measurement cannot provide enough information and the change of plateau roughness makes the contact model unreliable. As a result, a multi-point correlation method was proposed to combine the information of different spots from the same liner and this method was shown to give better match to the experimental results. A top-two-ring lubrication cycle model was developed based on the multiphase deterministic model by Li. et al [30] and previous top-two-ring lubrication model by Chen. Et al [2][31]. The model is composed with two parts. First, the deterministic model is used to generate a correlation between the hydrodynamic pressure/friction and the minimum clearance with prescribed oil supply from the deterministic oil control ring model. It was found that within reasonable accuracy, the gas pressure effect on the hydrodynamic lubrication of the top two rings can be decoupled from the hydrodynamic lubrication. Thus, only single-phase deterministic model was needed to generate the correlation. This decoupling significantly reduces the computation time. Then, a cycle model was developed utilizing the correlation of hydrodynamic pressure/friction and the minimum cle, by Yang Liu., S.M.

Thesis (Ph. D. in Urban and Regional Planning)--Massachusetts Institute of Technology, Dept. of Urban Studies and Planning, 2012., Cataloged from PDF version of thesis., Includes bibliographical references (p. 203-214)., China and the rest of the world are facing the challenge of meeting energy demand sustainably. Household-level energy consumption is a large ultimate driving force of a nation's energy use. Realizing a sustainable energy future will require behavioral change on the consumption side. In this context, examining the role of neighborhoods is important since neighborhoods are the building blocks of China's urban growth and the neighborhoods we build now will have a long-lasting effect on households' lifestyles of energy consumption. This research uses Jinan as a context for Chinese cities, and tries to understand how neighborhood design influences households' direct energy consumption, including travel and in-home energy use, through the influence on urban households' lifestyle. This research utilized an approach combining qualitative and quantitative methods, and finds that: (1) Household residential and vehicle ownership choice is made as a bundle reflecting the chosen lifestyle, making the combined evaluation of both travel and residential energy use possible; (2) Households belonging to different lifestyle groups have different decision-making mechanisms, suggesting the need for targeted design and policies; and, (3) Neighborhood design influences household direct energy consumption both through the ownership component choice and the usage component. By enabling more lifestyle bundle choices and providing new experiences and feedback, breaking old habits and creating new ones, energy-efficient neighborhood design can "lock in" households' lifestyles for a longer period of time via the lifestyle bundle choice effect. Design, therefore, likely has a larger and more robust impact in the long run than one-time or short-term incentives. This qualitative-quantitative mixed-method study contributes to a bridging of the literatures on consumer behavior, lifestyle, built environment and travel behavior, residential energy consumption, and energy demand analysis. It also provi, by Yang Chen., Ph.D.in Urban and Regional Planning

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013., Cataloged from PDF version of thesis., Includes bibliographical references., The degradation of articular cartilage is the hallmark in the pathogenesis of osteoarthritis (OA). It still remains largely unknown which precise mechanisms initiate cartilage degradation. However, risks factors include traumatic joint injury that results in immediate upregulation of inflammatory cytokines within the joint, as well as direct mechanical damage to the cartilage, factors known to contribute to the onset of OA and its progression. The first aim of this thesis focused on elucidating the importance of post-injury mechanical loading of cartilage. An in vitro model was used to simulate aspects of joint injury: mechanically damaged cartilage was co-cultured in the presence of inflammatory cytokines (TNF-Q and IL-6). Intermittent dynamic compression was then applied to simulate different strain levels known to exist in vivo after joint injury. Strain-dependent modulation of aggrecan biosynthesis and degradation, aggrecanase cleavage of aggrecan, chondrocyte gene expression profiles and changes in cell viability (apoptosis) were observed. Results imply that appropriate biomechanical stimuli can be beneficial during rehabilitation for post traumatic OA (PTOA) treatment. In the second aim, a combination therapy of insulin-like growth factor-1 (IGF-1) and the glucocorticoid dexamethasone (Dex) was tested as a potential therapeutic for PTOA. The effects of this combination were examined at the transcriptional and protein levels in the presence of IL-i a. Our results showed that the combination of IGF- 1 and Dex significantly improved aggrecan biosynthesis, blocked aggrecan and collagen proteolysis and loss, and rescued cell viability. These dramatic results could not be achieved by using either IGF-1 or Dex alone, thus providing strong support for the concept and use of a combination therapy for PTOA treatment. Dex is used to relieve inflammation and pain for short term OA treatment; however, it has not been studied as a potential disease-modifying drug for OA. In, by Yang Li., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 168-175)., A modern engineering system, e.g. the Internet, faces challenges from both the strategic behavior of its self-interested participants and the inherent computational intractability of large systems. Responding to this challenge, a new field, Algorithmic Mechanism Design, has emerged. One of the most fundamental problems in this field is How to optimize revenue in an auction? In his seminal paper [Mye81], Myerson gives a partial solution to this problem by providing a revenue-optimal auction for a seller who is looking to sell a single item to muLtiple bidders. Extending this auction to simultaneously selling multiple heterogeneous items has been one of the central open problems in Mathematical Economics. We provide such an extension that is also computationally efficient. Our solution proposes a novel framework for mechanism design by reducing mechanism design problems (where one optimizes an objective function on "rational inputs" ) to algorithm design problems (where one optimizes an objective function on "honest inputs"). Our reduction is generic and provides a framework for many other mechanism design problems., by Yang Cai., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 168-175)., A modern engineering system, e.g. the Internet, faces challenges from both the strategic behavior of its self-interested participants and the inherent computational intractability of large systems. Responding to this challenge, a new field, Algorithmic Mechanism Design, has emerged. One of the most fundamental problems in this field is How to optimize revenue in an auction? In his seminal paper [Mye81], Myerson gives a partial solution to this problem by providing a revenue-optimal auction for a seller who is looking to sell a single item to muLtiple bidders. Extending this auction to simultaneously selling multiple heterogeneous items has been one of the central open problems in Mathematical Economics. We provide such an extension that is also computationally efficient. Our solution proposes a novel framework for mechanism design by reducing mechanism design problems (where one optimizes an objective function on "rational inputs" ) to algorithm design problems (where one optimizes an objective function on "honest inputs"). Our reduction is generic and provides a framework for many other mechanism design problems., by Yang Cai., Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013., Cataloged from PDF version of thesis., Includes bibliographical references (p. 107-109)., Nowadays, a rapid growth of internal combustion (IC) engines is considered to be a major contributor to energy crisis. About 20% of the mechanical loss in internal combustion engines directly goes to the friction loss between piston ring pack and liner finish. A twin-land oil control ring (TLOCR) deterministic model was developed by Chen et al. and it helps the automotive companies investigate the effects of liner finish, rings, and lubricants on friction and oil control of the TLOCR [2]. This work focuses on application of the TLOCR model and extension of the deterministic model to the top two rings. First, there are some practical challenges in the application of Chen's TLOCR deterministic model. Due to different wear condition on the same liner, surface roughness varies from spot to spot. A small patch of measurement cannot provide enough information and the change of plateau roughness makes the contact model unreliable. As a result, a multi-point correlation method was proposed to combine the information of different spots from the same liner and this method was shown to give better match to the experimental results. A top-two-ring lubrication cycle model was developed based on the multiphase deterministic model by Li. et al [30] and previous top-two-ring lubrication model by Chen. Et al [2][31]. The model is composed with two parts. First, the deterministic model is used to generate a correlation between the hydrodynamic pressure/friction and the minimum clearance with prescribed oil supply from the deterministic oil control ring model. It was found that within reasonable accuracy, the gas pressure effect on the hydrodynamic lubrication of the top two rings can be decoupled from the hydrodynamic lubrication. Thus, only single-phase deterministic model was needed to generate the correlation. This decoupling significantly reduces the computation time. Then, a cycle model was developed utilizing the correlation of hydrodynamic pressure/friction and the minimum cle, by Yang Liu., S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Nuclear Science and Engineering, 2010., Cataloged from PDF version of thesis., Includes bibliographical references (p. 91-104) and index., Water is the most ubiquitous substance on earth, and is essential to sustain all known forms of life. However, despite centuries of research, a coherent picture of the unusual phase behavior of water is so far lacking. The most promising theory under scrutiny relies on the hypothetical existence of a liquid-liquid phase transition and an associated liquid-liquid critical point hidden in the region of supercooled temperatures and elevated pressures, where bulk water does not exist in liquid state. Therefore it is a grand experimental challenge to investigate the properties of water, both thermodynamic and dynamic, in the relative region of the phase diagram. A combination of neutron triple-axis spectrometer and small-angle neutron scattering instrument are used to measure the density of water confined in a nanoporous silica matrix MCM-41-S in a Temperature-Pressure range inaccessible for the bulk (300-130 K and 1-2900 bar), namely, the equation of state p(T, P). The measured isobaric density profiles clearly show a change of behavior around 1500 bar. This experiment provides the most direct evidence supporting the existence of a liquid-liquid critical point in such confined water. The experimental result further implies that the nature of the liquid-liquid critical point of water might be of a tricritical type. Moreover, the reported density data of confined water under extreme conditions are valuable for the vast communities in biological, geological and planetary sciences. Parallel to the density measurement, the dynamics of water in confined geometry, such as aged cement paste and the vicinity of protein surfaces, are also investigated using a variety of quasi-elastic and inelastic neutron scattering spectrometers. A wide range of pre-glass-transition phenomena, such as dynamic crossover, dynamic heterogeneity and boson peak, are observed above the conventional glass-transition temperature. Possible explanations are discussed in the frameworks of the liquidliquid, by Yang Zhang., Ph.D.

Dynamic Traffic Assignment (DTA) system [Ben-Akiva et al., 1991] [Mahmassani, 2001] benefits travelers by providing accurate estimate of current traffic conditions, consistent anticipatory network information as well as reliable route guidance. Over the years, two types of model adjustment schemes have been studied - DTA off-line calibration [Balakrishna, 2006] [Toledo et al., 2003] [van der Zijpp, 1997] and DTA on-line calibration [Antoniou et al., 2007] [Wang et al., 2007] [Ashok and Ben-Akiva, 2000]. The on-line calibration of DTA system allows real-time model self-corrections and has proven to be a useful complement to off-line calibration. In this paper, we explore distributed gradient calculations for the speed-up of on-line calibration of Dynamic Traffic Assignment (DTA) systems. Extended Kalman Filter (EKF) and Stochastic Gradient Descent (GD) are examined and their corresponding distributed versions (Para-EKF and Para-GD) are proposed. A case study is performed on a 25-km expressway in Western Portugal. We empirically show that the application of distributed gradient calculation significantly reduce the computational time of on-line calibration and thus provide attractive alternatives for speed-critical real-time DTA systems., MIT-Portugal Program

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2010., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student-submitted PDF version of thesis., Includes bibliographical references (p. 169-181)., In this thesis, we use the X-ray CT images of Berea sandstones to carry out the numerical study of the effects of wave-induced fluid motion on seismic velocity and attenuation in porous rocks. In numerical modeling, it is possible to control the factors and inputs that are hard to accomplish in laboratory measurements and isolate those of interest that have significant impact on the seismic responses; this can help in understanding the fundamental physics of seismic waves propagating in saturated porous rocks. The ultimate goal of computational rock physics is to supplement the traditional laboratory measurements, that are time consuming and costly, with cheaper numerical experiments that allow the parameter space to be explored more thoroughly. For this purpose, in this thesis we develop a computational method for time domain simulation of wave propagation in poroelastic medium. The medium is composed of an elastic matrix saturated with a Newtonian fluid. The method operates on a digitized representation of the medium where a distinct material phase and properties are specified at each volume cell. The dynamic response to an acoustic excitation is modeled mathematically with a coupled system of equations: elastic wave equation in the solid matrix and linearized Navier-Stokes equation in the fluid. Implementation of the solution is simplified by introducing a common numerical form for both solid and fluid cells and using a rotated-staggered-grid finite-difference scheme which allows stable solutions without explicitly handling the fluid-solid boundary conditions. A stability analysis is incorporated and can be used to select gridding and time step size as a function of material properties. The numerical results are shown to agree with the analytical solution for an idealized porous medium of periodically alternating solid and fluid layers. When applying the linear solver to compute the effective elastic properties of 3D digitized porous rocks, we find discrepancies, by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2010., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student-submitted PDF version of thesis., Includes bibliographical references (p. 169-181)., In this thesis, we use the X-ray CT images of Berea sandstones to carry out the numerical study of the effects of wave-induced fluid motion on seismic velocity and attenuation in porous rocks. In numerical modeling, it is possible to control the factors and inputs that are hard to accomplish in laboratory measurements and isolate those of interest that have significant impact on the seismic responses; this can help in understanding the fundamental physics of seismic waves propagating in saturated porous rocks. The ultimate goal of computational rock physics is to supplement the traditional laboratory measurements, that are time consuming and costly, with cheaper numerical experiments that allow the parameter space to be explored more thoroughly. For this purpose, in this thesis we develop a computational method for time domain simulation of wave propagation in poroelastic medium. The medium is composed of an elastic matrix saturated with a Newtonian fluid. The method operates on a digitized representation of the medium where a distinct material phase and properties are specified at each volume cell. The dynamic response to an acoustic excitation is modeled mathematically with a coupled system of equations: elastic wave equation in the solid matrix and linearized Navier-Stokes equation in the fluid. Implementation of the solution is simplified by introducing a common numerical form for both solid and fluid cells and using a rotated-staggered-grid finite-difference scheme which allows stable solutions without explicitly handling the fluid-solid boundary conditions. A stability analysis is incorporated and can be used to select gridding and time step size as a function of material properties. The numerical results are shown to agree with the analytical solution for an idealized porous medium of periodically alternating solid and fluid layers. When applying the linear solver to compute the effective elastic properties of 3D digitized porous rocks, we find discrepancies, by Yang Zhang., Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010., Cataloged from PDF version of thesis., Includes bibliographical references (p. 47-48)., We prove a generalization of von Neumann's minmax theorem to the class of separable multiplayer zero-sum games, introduced in [Bregman and Fokin 1998]. These games are polymatrix-that is, graphical games in which every edge is a two-player game between its endpoints-in which every outcome has zero total sum of players' payoffs. Our generalization of the minmax theorem implies convexity of equilibria, polynomial-time tractability, and convergence of no-regret learning algorithms to Nash equilibria. Given that three player zero-sum games are already PPAD-complete, this class of games, i.e. with pairwise separable utility functions, defines essentially the broadest class of multi-player constants sum games to which we can hope to push tractability results. Our result is obtained by establishing a certain game-class collapse, showing that separable constant-sum games are payoff equivalent to pairwise constant-sum polymatrix games-polymatrix games in which all edges are constant-sum games, and invoking a recent result of [Daskalakis, Papadimitriou 2009] for these games. We also explore generalizations to classes of non- constant-sum multi-player games. A natural candidate is polymatrix games with strictly competitive games on their edges. In the two player setting, such games are minmax solvable and recent work has shown that they are merely affine transformations of zero-sum games [Adler, Daskalakis, Papadimitriou 2009]. Surprisingly we show that a polymatrix game comprising of strictly competitive games on its edges is PPAD-complete to solve, proving a striking difference in the complexity of networks of zero-sum and strictly competitive games. Finally, we look at the role of coordination in networked interactions, studying the complexity of polymatrix games with a mixture of coordination and zero-sum games. We show that finding a pure Nash equilibrium in coordination-only polymatrix games is PLS-complete; hence, computing a mixed Nash equilibrium is in PLS n PPAD, but, by Yang Cai., S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2010., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student-submitted PDF version of thesis., Includes bibliographical references (p. 169-181)., In this thesis, we use the X-ray CT images of Berea sandstones to carry out the numerical study of the effects of wave-induced fluid motion on seismic velocity and attenuation in porous rocks. In numerical modeling, it is possible to control the factors and inputs that are hard to accomplish in laboratory measurements and isolate those of interest that have significant impact on the seismic responses; this can help in understanding the fundamental physics of seismic waves propagating in saturated porous rocks. The ultimate goal of computational rock physics is to supplement the traditional laboratory measurements, that are time consuming and costly, with cheaper numerical experiments that allow the parameter space to be explored more thoroughly. For this purpose, in this thesis we develop a computational method for time domain simulation of wave propagation in poroelastic medium. The medium is composed of an elastic matrix saturated with a Newtonian fluid. The method operates on a digitized representation of the medium where a distinct material phase and properties are specified at each volume cell. The dynamic response to an acoustic excitation is modeled mathematically with a coupled system of equations: elastic wave equation in the solid matrix and linearized Navier-Stokes equation in the fluid. Implementation of the solution is simplified by introducing a common numerical form for both solid and fluid cells and using a rotated-staggered-grid finite-difference scheme which allows stable solutions without explicitly handling the fluid-solid boundary conditions. A stability analysis is incorporated and can be used to select gridding and time step size as a function of material properties. The numerical results are shown to agree with the analytical solution for an idealized porous medium of periodically alternating solid and fluid layers. When applying the linear solver to compute the effective elastic properties of 3D digitized porous rocks, we find discrepancies, by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2010., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student-submitted PDF version of thesis., Includes bibliographical references (p. 169-181)., In this thesis, we use the X-ray CT images of Berea sandstones to carry out the numerical study of the effects of wave-induced fluid motion on seismic velocity and attenuation in porous rocks. In numerical modeling, it is possible to control the factors and inputs that are hard to accomplish in laboratory measurements and isolate those of interest that have significant impact on the seismic responses; this can help in understanding the fundamental physics of seismic waves propagating in saturated porous rocks. The ultimate goal of computational rock physics is to supplement the traditional laboratory measurements, that are time consuming and costly, with cheaper numerical experiments that allow the parameter space to be explored more thoroughly. For this purpose, in this thesis we develop a computational method for time domain simulation of wave propagation in poroelastic medium. The medium is composed of an elastic matrix saturated with a Newtonian fluid. The method operates on a digitized representation of the medium where a distinct material phase and properties are specified at each volume cell. The dynamic response to an acoustic excitation is modeled mathematically with a coupled system of equations: elastic wave equation in the solid matrix and linearized Navier-Stokes equation in the fluid. Implementation of the solution is simplified by introducing a common numerical form for both solid and fluid cells and using a rotated-staggered-grid finite-difference scheme which allows stable solutions without explicitly handling the fluid-solid boundary conditions. A stability analysis is incorporated and can be used to select gridding and time step size as a function of material properties. The numerical results are shown to agree with the analytical solution for an idealized porous medium of periodically alternating solid and fluid layers. When applying the linear solver to compute the effective elastic properties of 3D digitized porous rocks, we find discrepancies, by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2009., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student submitted PDF version of thesis., Includes bibliographical references (p. 257-266)., In this thesis, the influence of boundary layer processes and seasonal forcing on baroclinic eddy equilibration is studied to understand how the baroclinic adjustment is modified when taking into account these two factors. A modified [beta] plane multilevel quasi-geostrophic (QG) model with an interactive stratification and a simplified parameterization of atmospheric boundary layer physics is used as the atmospheric model in this study. Comparisons between experiments with the modified QG model and the traditional QG model with fixed stratification show that it is necessary to include the interaction between vertical eddy heat flux and stratification to obtain a realistic equilibrated state, i.e. robust isentropic slope. A slab surface model is also coupled with the atmospheric model to provide an interactive surface temperature distribution in some experiments in this study. The effect of boundary layer processes is first studied under the situation with fixed underlying surface temperature. The boundary layer vertical thermal diffusion, along with the surface heat exchange, is found primarily responsible for the limitation of the PV homogenization in the boundary layer. The boundary layer processes can influence the eddy activity in at least two competing ways. First, in the eddy energy budget, all the boundary layer processes act to damp the eddy energy directly. On the other hand, the boundary layer processes also influence the mean flow, which can further influence the eddy behavior. For the boundary layer thermal damping, the indirect effect on the eddy activity becomes dominant., (cont.) Stronger boundary layer thermal forcing results in stronger meridional temperature gradients and eddy heat fluxes. For the frictional dissipation, the resulting changes in the zonal wind and in the location of the critical latitude lead to a meridional variation of the eddy forcing, which can further result in a non-monotonic response of the mean flow. The role of the boundary layer processes in the baroclinic eddy equilibration is further studied using a simple air-sea thermally coupled model. Although in the coupled system, each boundary layer process has more and different ways to influence the equilibrium state, their effect on the lower level PV homogenization is very robust. Surface friction and surface 3 heat flux all act to damp the lower level PV mixing and stronger surface damping prevents the PV homogenization more strongly, but the way in which each boundary layer process affects the PV homogenization is very different. Baroclinic eddy equilibration under seasonal forcing is studied in both the atmospheric model and the coupled model. In the situation with specified seasonal variation of the underlying surface temperature, a Northern-Hemisphere like seasonal variation of the surface temperature is used to act on the atmospheric flow through the boundary layer processes and the radiative-convective heating., (cont.) Under slowly varying seasonal forcing, the eddy and the mean flow behavior is characterized by four clearly divided time intervals: an eddy inactive time interval in the summer, a mainly dynamically determined eddy spinup time interval starting from mid-fall and lasting less than one month, a quasi-equilibrium time interval for the zonal mean flow available potential energy from late fall to late spring and a mainly external forcing determined eddy spindown time interval from late winter to late spring. In spite of the strong seasonality of the eddy activity, a robust PV structure is still observed through all the seasons. It is found that besides baroclinic eddies, the boundary layer thermal forcing as well as the moist convection all can help maintain the lower level PV structure. The sensitivity study of the eddy equilibration to the time scale of the external forcing also indicates that the time scale separation between the baroclinic adjustment and the external forcing in midlatitudes is only visible for external forcing cycle one year and longer. The seasonality study with the coupled model confirms the conclusions obtained in the uncoupled model., by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2009., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student submitted PDF version of thesis., Includes bibliographical references (p. 257-266)., In this thesis, the influence of boundary layer processes and seasonal forcing on baroclinic eddy equilibration is studied to understand how the baroclinic adjustment is modified when taking into account these two factors. A modified [beta] plane multilevel quasi-geostrophic (QG) model with an interactive stratification and a simplified parameterization of atmospheric boundary layer physics is used as the atmospheric model in this study. Comparisons between experiments with the modified QG model and the traditional QG model with fixed stratification show that it is necessary to include the interaction between vertical eddy heat flux and stratification to obtain a realistic equilibrated state, i.e. robust isentropic slope. A slab surface model is also coupled with the atmospheric model to provide an interactive surface temperature distribution in some experiments in this study. The effect of boundary layer processes is first studied under the situation with fixed underlying surface temperature. The boundary layer vertical thermal diffusion, along with the surface heat exchange, is found primarily responsible for the limitation of the PV homogenization in the boundary layer. The boundary layer processes can influence the eddy activity in at least two competing ways. First, in the eddy energy budget, all the boundary layer processes act to damp the eddy energy directly. On the other hand, the boundary layer processes also influence the mean flow, which can further influence the eddy behavior. For the boundary layer thermal damping, the indirect effect on the eddy activity becomes dominant., (cont.) Stronger boundary layer thermal forcing results in stronger meridional temperature gradients and eddy heat fluxes. For the frictional dissipation, the resulting changes in the zonal wind and in the location of the critical latitude lead to a meridional variation of the eddy forcing, which can further result in a non-monotonic response of the mean flow. The role of the boundary layer processes in the baroclinic eddy equilibration is further studied using a simple air-sea thermally coupled model. Although in the coupled system, each boundary layer process has more and different ways to influence the equilibrium state, their effect on the lower level PV homogenization is very robust. Surface friction and surface 3 heat flux all act to damp the lower level PV mixing and stronger surface damping prevents the PV homogenization more strongly, but the way in which each boundary layer process affects the PV homogenization is very different. Baroclinic eddy equilibration under seasonal forcing is studied in both the atmospheric model and the coupled model. In the situation with specified seasonal variation of the underlying surface temperature, a Northern-Hemisphere like seasonal variation of the surface temperature is used to act on the atmospheric flow through the boundary layer processes and the radiative-convective heating., (cont.) Under slowly varying seasonal forcing, the eddy and the mean flow behavior is characterized by four clearly divided time intervals: an eddy inactive time interval in the summer, a mainly dynamically determined eddy spinup time interval starting from mid-fall and lasting less than one month, a quasi-equilibrium time interval for the zonal mean flow available potential energy from late fall to late spring and a mainly external forcing determined eddy spindown time interval from late winter to late spring. In spite of the strong seasonality of the eddy activity, a robust PV structure is still observed through all the seasons. It is found that besides baroclinic eddies, the boundary layer thermal forcing as well as the moist convection all can help maintain the lower level PV structure. The sensitivity study of the eddy equilibration to the time scale of the external forcing also indicates that the time scale separation between the baroclinic adjustment and the external forcing in midlatitudes is only visible for external forcing cycle one year and longer. The seasonality study with the coupled model confirms the conclusions obtained in the uncoupled model., by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences, 2009., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Cataloged from student submitted PDF version of thesis., Includes bibliographical references (p. 257-266)., In this thesis, the influence of boundary layer processes and seasonal forcing on baroclinic eddy equilibration is studied to understand how the baroclinic adjustment is modified when taking into account these two factors. A modified [beta] plane multilevel quasi-geostrophic (QG) model with an interactive stratification and a simplified parameterization of atmospheric boundary layer physics is used as the atmospheric model in this study. Comparisons between experiments with the modified QG model and the traditional QG model with fixed stratification show that it is necessary to include the interaction between vertical eddy heat flux and stratification to obtain a realistic equilibrated state, i.e. robust isentropic slope. A slab surface model is also coupled with the atmospheric model to provide an interactive surface temperature distribution in some experiments in this study. The effect of boundary layer processes is first studied under the situation with fixed underlying surface temperature. The boundary layer vertical thermal diffusion, along with the surface heat exchange, is found primarily responsible for the limitation of the PV homogenization in the boundary layer. The boundary layer processes can influence the eddy activity in at least two competing ways. First, in the eddy energy budget, all the boundary layer processes act to damp the eddy energy directly. On the other hand, the boundary layer processes also influence the mean flow, which can further influence the eddy behavior. For the boundary layer thermal damping, the indirect effect on the eddy activity becomes dominant., (cont.) Stronger boundary layer thermal forcing results in stronger meridional temperature gradients and eddy heat fluxes. For the frictional dissipation, the resulting changes in the zonal wind and in the location of the critical latitude lead to a meridional variation of the eddy forcing, which can further result in a non-monotonic response of the mean flow. The role of the boundary layer processes in the baroclinic eddy equilibration is further studied using a simple air-sea thermally coupled model. Although in the coupled system, each boundary layer process has more and different ways to influence the equilibrium state, their effect on the lower level PV homogenization is very robust. Surface friction and surface 3 heat flux all act to damp the lower level PV mixing and stronger surface damping prevents the PV homogenization more strongly, but the way in which each boundary layer process affects the PV homogenization is very different. Baroclinic eddy equilibration under seasonal forcing is studied in both the atmospheric model and the coupled model. In the situation with specified seasonal variation of the underlying surface temperature, a Northern-Hemisphere like seasonal variation of the surface temperature is used to act on the atmospheric flow through the boundary layer processes and the radiative-convective heating., (cont.) Under slowly varying seasonal forcing, the eddy and the mean flow behavior is characterized by four clearly divided time intervals: an eddy inactive time interval in the summer, a mainly dynamically determined eddy spinup time interval starting from mid-fall and lasting less than one month, a quasi-equilibrium time interval for the zonal mean flow available potential energy from late fall to late spring and a mainly external forcing determined eddy spindown time interval from late winter to late spring. In spite of the strong seasonality of the eddy activity, a robust PV structure is still observed through all the seasons. It is found that besides baroclinic eddies, the boundary layer thermal forcing as well as the moist convection all can help maintain the lower level PV structure. The sensitivity study of the eddy equilibration to the time scale of the external forcing also indicates that the time scale separation between the baroclinic adjustment and the external forcing in midlatitudes is only visible for external forcing cycle one year and longer. The seasonality study with the coupled model confirms the conclusions obtained in the uncoupled model., by Yang Zhang., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2009., Includes bibliographical references (p. 163-174)., This research develops a systematic approach to analyze the computational performance of Dynamic Traffic Assignment (DTA) models and provides solution techniques to improve their scalability for on-line applications for large-scale networks. DTA models for real-time use provide short-term predictions of network status and generate route guidance for travelers. The computational performance of such systems is a critical concern. Existing methodologies, which have limited capabilities for online large-scale applications, use single-processor configurations that are less scalable, and rely primarily on trade-offs that sacrifice accuracy for improved computational efficiency. In the proposed scalable methodology, algorithmic analyses are first used to identify the system bottlenecks for large-scale problems. Our analyses show that the computation time of DTA systems for a given time interval depends largely on a small set of parameters. Important parameters include the number of origin-destination (OD) pairs, the number of sensors, the number of vehicles, the size of the network, and the number of time-steps used by the simulator. Then scalable approaches are developed to solve the bottlenecks. A constraint generalized least-squares solution enabling efficient use of the sparse-matrix property is applied to the dynamic OD estimation, replacing the Kalman-Filter solution or other full-matrix algorithms. Parallel simulation with an adaptive network decomposition framework is proposed to achieve better load-balancing and improved efficiency. A synchronization-feedback mechanism is designed to ensure the consistency of traffic dynamics across processors while keeping communication overheads minimal. The proposed methodology is implemented in DynaMIT, a state-of-the-art DTA system. Profiling studies are used to validate the algorithmic analysis of the system bottlenecks., (cont.) The new system is evaluated on two real-world networks under various scenarios. Empirical results of the case studies show that the proposed OD estimation algorithm is insensitive to an increase in the number of OD pairs or sensors, and the computation time is reduced from minutes to a few seconds. The parallel simulation is found to maintain accurate output as compared to the sequential simulation, and with adaptive load-balancing, it considerably speeds up the network models even under non-recurrent incident scenarios. The results demonstrate the practical nature of the methodology and its scalability to large-scale real-world problems., by Yang Wen., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2009., Includes bibliographical references (p. 163-174)., This research develops a systematic approach to analyze the computational performance of Dynamic Traffic Assignment (DTA) models and provides solution techniques to improve their scalability for on-line applications for large-scale networks. DTA models for real-time use provide short-term predictions of network status and generate route guidance for travelers. The computational performance of such systems is a critical concern. Existing methodologies, which have limited capabilities for online large-scale applications, use single-processor configurations that are less scalable, and rely primarily on trade-offs that sacrifice accuracy for improved computational efficiency. In the proposed scalable methodology, algorithmic analyses are first used to identify the system bottlenecks for large-scale problems. Our analyses show that the computation time of DTA systems for a given time interval depends largely on a small set of parameters. Important parameters include the number of origin-destination (OD) pairs, the number of sensors, the number of vehicles, the size of the network, and the number of time-steps used by the simulator. Then scalable approaches are developed to solve the bottlenecks. A constraint generalized least-squares solution enabling efficient use of the sparse-matrix property is applied to the dynamic OD estimation, replacing the Kalman-Filter solution or other full-matrix algorithms. Parallel simulation with an adaptive network decomposition framework is proposed to achieve better load-balancing and improved efficiency. A synchronization-feedback mechanism is designed to ensure the consistency of traffic dynamics across processors while keeping communication overheads minimal. The proposed methodology is implemented in DynaMIT, a state-of-the-art DTA system. Profiling studies are used to validate the algorithmic analysis of the system bottlenecks., (cont.) The new system is evaluated on two real-world networks under various scenarios. Empirical results of the case studies show that the proposed OD estimation algorithm is insensitive to an increase in the number of OD pairs or sensors, and the computation time is reduced from minutes to a few seconds. The parallel simulation is found to maintain accurate output as compared to the sequential simulation, and with adaptive load-balancing, it considerably speeds up the network models even under non-recurrent incident scenarios. The results demonstrate the practical nature of the methodology and its scalability to large-scale real-world problems., by Yang Wen., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2009., Includes bibliographical references (p. 163-174)., This research develops a systematic approach to analyze the computational performance of Dynamic Traffic Assignment (DTA) models and provides solution techniques to improve their scalability for on-line applications for large-scale networks. DTA models for real-time use provide short-term predictions of network status and generate route guidance for travelers. The computational performance of such systems is a critical concern. Existing methodologies, which have limited capabilities for online large-scale applications, use single-processor configurations that are less scalable, and rely primarily on trade-offs that sacrifice accuracy for improved computational efficiency. In the proposed scalable methodology, algorithmic analyses are first used to identify the system bottlenecks for large-scale problems. Our analyses show that the computation time of DTA systems for a given time interval depends largely on a small set of parameters. Important parameters include the number of origin-destination (OD) pairs, the number of sensors, the number of vehicles, the size of the network, and the number of time-steps used by the simulator. Then scalable approaches are developed to solve the bottlenecks. A constraint generalized least-squares solution enabling efficient use of the sparse-matrix property is applied to the dynamic OD estimation, replacing the Kalman-Filter solution or other full-matrix algorithms. Parallel simulation with an adaptive network decomposition framework is proposed to achieve better load-balancing and improved efficiency. A synchronization-feedback mechanism is designed to ensure the consistency of traffic dynamics across processors while keeping communication overheads minimal. The proposed methodology is implemented in DynaMIT, a state-of-the-art DTA system. Profiling studies are used to validate the algorithmic analysis of the system bottlenecks., (cont.) The new system is evaluated on two real-world networks under various scenarios. Empirical results of the case studies show that the proposed OD estimation algorithm is insensitive to an increase in the number of OD pairs or sensors, and the computation time is reduced from minutes to a few seconds. The parallel simulation is found to maintain accurate output as compared to the sequential simulation, and with adaptive load-balancing, it considerably speeds up the network models even under non-recurrent incident scenarios. The results demonstrate the practical nature of the methodology and its scalability to large-scale real-world problems., by Yang Wen., Ph.D.

The interaction between protein and water is of fundamental importance for processes ranging from protein folding and enzymatic activity to anhydrobiosis. In this letter we bring together results from diverse types of measurements to give a unified picture of the hydration process for lysozyme. The data come principally from experiments with protein films and powders. The principal aim is to examine the relationship between the sites of water interaction, the extent of coverage, and the enzymatic activity, thus providing a better understanding of the relationship between water and enzyme dynamics.

The interaction between protein and water is of fundamental importance for processes ranging from protein folding and enzymatic activity to anhydrobiosis. In this letter we bring together results from diverse types of measurements to give a unified picture of the hydration process for lysozyme. The data come principally from experiments with protein films and powders. The principal aim is to examine the relationship between the sites of water interaction, the extent of coverage, and the enzymatic activity, thus providing a better understanding of the relationship between water and enzyme dynamics.