The structure specificity of alpha-chymotrypsin. I. Polypeptides as substrates. II. N-acylated peptide esters as substrates. III. Some reactive esters of N-acylated amino acids as substrates

The structural specificity of α-chymotrypsin for polypeptides and denatured proteins has been examined. The primary specificity of the enzyme for these natural substrates is shown to closely correspond to that observed for model substrates. A pattern of secondary specificity is proposed.

A series of N-acetylated peptide esters of varying length have been evaluated as substrates of α-chymotrypsin. The results are interpreted in terms of proposed specificity theories.

The α-chymotrypsin-catalyzed hydrolyses of a number of N-acetylated dipeptide methyl esters were studied. The results are interpreted in terms of the available specificity theories and are compared with results obtained in the study of polypeptide substrates. The importance of non-productive binding in determining the kinetic parameters of these substrates is discussed. A partial model of the locus of the active site which interacts with the R’₁CONH- group of a substrate of the form R’₁CONHCHR₂COR’₃ is proposed.

Finally, some reactive esters of N-acetylated amino acids have been evaluated as substrates of α-chymotrypsin. Their reactivity and stereo-chemical behavior are discussed in terms of the specificity theories available. The importance of a binding interaction between the carboxyl function of the substrate and the enzyme is suggested by the results obtained.

Applications of plasticity theory to selected problems in soil mechanics

Two topics in plane strain perfect plasticity are studied using the method of characteristics. The first is the steady-state indentation of an infinite medium by either a rigid wedge having a triangular cross section or a smooth plate inclined to the direction of motion. Solutions are exact and results include deformation patterns and forces of resistance; the latter are also applicable for the case of incipient failure. Experiments on sharp wedges in clay, where forces and deformations are recorded, showed a good agreement with the mechanism of cutting assumed by the theory; on the other hand the indentation process for blunt wedges transforms into that of compression with a rigid part of clay moving with the wedge. Finite element solutions, for a bilinear material model, were obtained to establish a correspondence between the response of the plane strain wedge and its axi-symmetric counterpart, the cone. Results of the study afford a better understanding of the process of indentation of soils by penetrometers and piles as well as the mechanism of failure of deep foundations (piles and anchor plates).

The second topic concerns the plane strain steady-state free rolling of a rigid roller on clays. The problem is solved approximately for small loads by getting the exact solution of two problems that encompass the one of interest; the first is a steady-state with a geometry that approximates the one of the roller and the second is an instantaneous solution of the rolling process but is not a steady-state. Deformations and rolling resistance are derived. When compared with existing empirical formulae the latter was found to agree closely.

Understanding Micro- and Macro-Mechanics of Soil Liquefaction: A Necessary Step for Field-Scale Assessment

Liquefaction is a devastating instability associated with saturated, loose, and cohesionless soils. It poses a significant risk to distributed infrastructure systems that are vital for the security, economy, safety, health, and welfare of societies. In order to make our cities resilient to the effects of liquefaction, it is important to be able to identify areas that are most susceptible. Some of the prevalent methodologies employed to identify susceptible areas include conventional slope stability analysis and the use of so-called liquefaction charts. However, these methodologies have some limitations, which motivate our research objectives. In this dissertation, we investigate the mechanics of origin of liquefaction in a laboratory test using grain-scale simulations, which helps (i) understand why certain soils liquefy under certain conditions, and (ii) identify a necessary precursor for onset of flow liquefaction. Furthermore, we investigate the mechanics of liquefaction charts using a continuum plasticity model; this can help in modeling the surface hazards of liquefaction following an earthquake. Finally, we also investigate the microscopic definition of soil shear wave velocity, a soil property that is used as an index to quantify liquefaction resistance of soil. We show that anisotropy in fabric, or grain arrangement can be correlated with anisotropy in shear wave velocity. This has the potential to quantify the effects of sample disturbance when a soil specimen is extracted from the field. In conclusion, by developing a more fundamental understanding of soil liquefaction, this dissertation takes necessary steps for a more physical assessment of liquefaction susceptibility at the field-scale.