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Steepest-entropy-ascent quantum thermodynamics (SEAQT) is a mathematical and theoretical framework for intrinsic quantum thermodynamics (IQT), a unified theory of quantum mechanics and thermodynamics. In the theoretical framework, entropy is viewed as a measure of energy load sharing among available energy eigenlevels, and a unique relaxation path of a system from an initial non-equilibrium state to a stable equilibrium is determined from the greatest entropy generation viewpoint. The SEAQT modeling has seen a great development recently. However, the applications have mainly focused on gas phases, where a simple energy eigenstructure (a set of energy eigenlevels) can be constructed from appropriate quantum models by assuming that gas-particles behave independently. The focus of this research is to extend the applicability to solid phases, where interactions between constituent particles play a definitive role in their properties so that an energy eigenstructure becomes quite complicated and intractable from quantum models. To cope with the problem, a highly simplified energy eigenstructure (so-called ``pseudo-eigenstructure") of a condensed matter is constructed using a reduced-order method, where quantum models are replaced by typical solid-state models. The details of the approach are given and the method is applied to make kinetic predictions in various solid-state phenomena: the thermal expansion of silver, the magnetization of iron, and the continuous/discontinuous phase separation and ordering in binary alloys where a pseudo-eigenstructure is constructed using atomic/spin coupled oscillators or a mean-field approximation. In each application, the reliability of the approach is confirmed and the time-evolution processes are tracked from different initial states under varying conditions (including interactions with a heat reservoir and external magnetic field) using the SEAQT equation of motion derived for each specific application. Specifically, the SEAQT framework with a pseudo-eigenstructure successfully predicts: (i) lattice relaxations in any temperature range while accounting explicitly for anharmonic effects, (ii) low-temperature spin relaxations with fundamental descriptions of non-equilibrium temperature and magnetic field strength, and (iii) continuous and discontinuous mechanisms as well as concurrent ordering and phase separation mechanisms during the decomposition of solid-solutions. Ph. D. Many engineering materials have physical and chemical properties that change with time. The tendency of materials to change is quantified by the field of thermodynamics. The first and second laws of thermodynamics establish conditions under which a material has no tendency to change; these conditions are called equilibrium states. When a material is not in an equilibrium state, it is able to change spontaneously. Classical thermodynamics reliably identifies whether a material is susceptible to change, but it is incapable of predicting how change will take place or how fast it will occur. These are kinetic questions that fall outside the purview of thermodynamics. A relatively new theoretical treatment developed by Hatsopoulos, Gyftopoulos, Beretta and others over the past forty years extends classical thermodynamics into the kinetic realm. This framework, called steepest-entropy-ascent quantum thermodynamics (SEAQT), combines the tools of thermodynamics with quantum mechanics through a postulated equation of motion. Solving the equation of motion provides a kinetic description of the path a material will take as it changes from a non-equilibrium state to stable equilibrium. To date, the SEAQT framework has been applied primarily to systems of gases. In this dissertation, solid-state models are employed to extend the SEAQT approach to solid materials. The SEAQT framework is used to predict the thermal expansion of silver, the magnetization of iron, and the kinetics of atomic clustering and ordering in binary solid-solutions as a function of time or temperature. The model makes it possible to predict a unique kinetic path from any arbitrary, non-equilibrium, initial state to a stable equilibrium state. In each application, the approach is tested against experimental data. In addition to reproducing the qualitative kinetic trends in the cases considered, the SEAQT framework shows promise for modeling the behavior of materials far from equilibrium.

The kinetics of ordering and concurrent ordering and clustering is analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. A simplified energy eigenstructure, or pseudo-eigenstructure, is constructed from a static concentration wave method to describe the configuration-dependent energy for atomic ordering and clustering in a binary alloy. This pseudo-eigenstructure is used in conjunction with an equation of motion that follows steepest entropy ascent to calculate the kinetic path that leads to ordering and clustering in a series of hypothetical alloys. By adjusting the thermodynamic solution parameters, it is demonstrated that the model can predict the stable equilibrium state as well as the unique thermodynamic path and kinetics of continuous/discontinuous ordering and concurrent processes of simultaneous ordering and phase separation., Comment: 10 pages

Disruption of wild type acceptor site by the single nucleotide variants (c.853-2Aâ >â G) predicted from in silico programs. (PDF 184Â kb)

Creation of the new splice acceptor site by the three base insertion (NM_001204.6:c.1277-10_1277-9insGGG) predicted from in silico programs. (PDF 218Â kb)

Disruption of wild type acceptor site by the single nucleotide variants (c.853-2Aâ >â G) predicted from in silico programs. (PDF 184Â kb)

Possible pathogenic variants found in the intron of BMPR2 in family 4. A rare three base insertion (GGG) at 10 bases upstream from exon 10 creates identical sequences around the canonical splicing site (ACAGGG). By the insertion, an out-of-frame protein could be translated due to the new splice acceptor site. (PDF 411Â kb)

Summary of mapping statistics. (PDF 22Â kb)

Large deletion found in the patient in family 8. (a) The large deletion was supported by depth of coverage and discordant paired-end reads. (b) The length of the deletion was approximately 6.5 kilobases and spanned the entire region of exon 3. Breakpoints of the large heterozygous deletion were located in the Alu repeat sequences, which were supported by read depths and paired-end reads spanning the long region. (PDF 529Â kb)

Possible pathogenic variants found in the intron of BMPR2 in family 4. A rare three base insertion (GGG) at 10 bases upstream from exon 10 creates identical sequences around the canonical splicing site (ACAGGG). By the insertion, an out-of-frame protein could be translated due to the new splice acceptor site. (PDF 411Â kb)

Creation of the new splice acceptor site by the three base insertion (NM_001204.6:c.1277-10_1277-9insGGG) predicted from in silico programs. (PDF 218Â kb)

Padi2 and Padi4 are expressed in the spleens of wild-type mice. (a–e) Immunofluorescence staining (×40) shows that Padi2 is expressed ubiquitously in the spleen. Spleens were probed with anti-Padi2 (green fluorescent signal) and cell surface markers (red fluorescence signal; a, CD3; b, B220; c, Gr-1; d, CD56; e, F4/80). The nuclei were stained with DAPI (blue fluorescence signal). The arrows indicate the colocalization of Padi2 and each cell surface marker. (f–k) Immunofluorescence staining (×40) shows that Padi4 was expressed in splenocytes. The spleens were probed with anti-Padi4 (green fluorescence signal), and cell surface markers (red fluorescence signal; f, CD3; g, B220; h, Gr-1; i, CD56; j, F4/80). Nuclei were stained with DAPI (blue fluorescence signal). (K) Immunofluorescence staining (left, ×40; right, ×280) shows that Padi4 was localized in both the nuclei and cytoplasm of macrophages, which expressed F4/80. (PDF 286 KB)

Padi2 and Padi4 expression in NK1.1+ cells. mRNA levels were determined by real-time TaqMan RT-PCR using NK1.1+ cells as a reference for GAPDH normalization. Padi2 and Padi4 mRNA expressions were not different between wild-type collagen-induced arthritis (CIA) (n = 10) and control (n = 8) mice spleens. (PDF 209 KB)

Cytokine mRNA expression in CD11b + macrophages in the spleen. CD11b + wild-type (n = 19) and Padi4−/− CIA mice (n = 17) were used for 10 days from the day after booster injection. The cells were analyzed by real-time TaqMan RT-PCR for mRNA levels of (a) tumor necrosis factor alpha (TNF-α), (b) CSF-2, (c) IL-1β, (d) IL-6, and (e) IL-10. *P

Generation of a Padi4−/− mouse. (a) Genomic structure of A Padi4−/− mouse. A 5837-bp fragment containing exon 1 and intron 1 of Padi4 was inserted to the targeting vector. We constructed the targeting vector to replace exon 1 and intron 1, including the transcription initiation site, using mouse PGK-1 promoter and the neomycin-resistance gene. We confirmed the knockout condition by Southern blotting (b) and RT-PCR (c). (d) Distributions of immune cells in the spleen of wild-type (n = 3) and Padi4−/− (n = 3) mice were analyzed by FACS. (e) Hematoxylin and eosin (HE) staining of Padi4-expressed tissues from the wild-type (WT) mouse, Padi4+/− (Heterozygote) mouse, and Padi4−/− (KO) mouse. (PDF 458 KB)