Quantum simulation of enzyme catalysis

Separating the dynamics of variables that evolve on different timescales is a common assumption in exploring complex systems, and a great deal of progress has been made in understanding chemical systems by treating independently the fast processes of an activated chemical species from the slower processes that proceed activation. Protein motion underlies all biocatalytic reactions, and understanding the nature of this motion is central to understanding how enzymes catalyze reactions with such specificity and such rate enhancement. This understanding is challenged by evidence of breakdowns in the separability of timescales of dynamics in the active site form motions of the solvating protein. Quantum simulation methods that bridge these timescales by simultaneously evolving quantum and classical degrees of freedom provide an important method on which to explore this breakdown. In the following dissertation, three problems of enzyme catalysis are explored through quantum simulation.

Geometric elasticity for graphics, simulation, and computation

We develop new algorithms which combine the rigorous theory of mathematical elasticity with the geometric underpinnings and computational attractiveness of modern tools in geometry processing. We develop a simple elastic energy based on the Biot strain measure, which improves on state-of-the-art methods in geometry processing. We use this energy within a constrained optimization problem to, for the first time, provide surface parameterization tools which guarantee injectivity and bounded distortion, are user-directable, and which scale to large meshes. With the help of some new generalizations in the computation of matrix functions and their derivative, we extend our methods to a large class of hyperelastic stored energy functions quadratic in piecewise analytic strain measures, including the Hencky (logarithmic) strain, opening up a wide range of possibilities for robust and efficient nonlinear elastic simulation and geometry processing by elastic analogy.

On the solution of first excursion problems by simulation with applications to probabilistic seismic performance assessment

In a probabilistic assessment of the performance of structures subjected to uncertain environmental loads such as earthquakes, an important problem is to determine the probability that the structural response exceeds some specified limits within a given duration of interest. This problem is known as the first excursion problem, and it has been a challenging problem in the theory of stochastic dynamics and reliability analysis. In spite of the enormous amount of attention the problem has received, there is no procedure available for its general solution, especially for engineering problems of interest where the complexity of the system is large and the failure probability is small.

The application of simulation methods to solving the first excursion problem is investigated in this dissertation, with the objective of assessing the probabilistic performance of structures subjected to uncertain earthquake excitations modeled by stochastic processes. From a simulation perspective, the major difficulty in the first excursion problem comes from the large number of uncertain parameters often encountered in the stochastic description of the excitation. Existing simulation tools are examined, with special regard to their applicability in problems with a large number of uncertain parameters. Two efficient simulation methods are developed to solve the first excursion problem. The first method is developed specifically for linear dynamical systems, and it is found to be extremely efficient compared to existing techniques. The second method is more robust to the type of problem, and it is applicable to general dynamical systems. It is efficient for estimating small failure probabilities because the computational effort grows at a much slower rate with decreasing failure probability than standard Monte Carlo simulation. The simulation methods are applied to assess the probabilistic performance of structures subjected to uncertain earthquake excitation. Failure analysis is also carried out using the samples generated during simulation, which provide insight into the probable scenarios that will occur given that a structure fails.

Temporal characteristic simulation for stimulated emission depletion microscopy

The imaging technology of stimulated emission depletion (STED) utilizes the nonlinearity relationship between the fluorescence saturation and the excited state stimulated depletion. It implements three-dimensional (3D) imaging and breaks the diffraction barrier of far-field light microscopy by restricting fluorescent molecules at a sub-diffraction spot. In order to improve the resolution which attained by this technology, the computer simulation on temporal behavior of population probabilities of the sample was made in this paper, and the optimized parameters such as intensity, duration and delay time of the STED pulse were given.

Dynamic rupture simulation integrated with earthquake observations

Dynamic rupture simulations are unique in their contributions to the study of earthquake physics. The current rapid development of dynamic rupture simulations poses several new questions: Do the simulations reflect the real world? Do the simulations have predictive power? Which one should we believe when the simulations disagree? This thesis illustrates how integration with observations can help address these questions and reduce the effects of non-uniqueness of both dynamic rupture simulations and kinematic inversion problems. Dynamic rupture simulations with observational constraints can effectively identify non-physical features inferred from observations. Moreover, the integrative technique can also provide more physical insights into the mechanisms of earthquakes. This thesis demonstrates two examples of such kinds of integration: dynamic rupture simulations of the M_w 9.0 2011 Tohoku-Oki earthquake and of earthquake ruptures in damaged fault zones:

(1) We develop simulations of the Tohoku-Oki earthquake based on a variety of observations and minimum assumptions of model parameters. The simulations provide realistic estimations of stress drop and fracture energy of the region and explain the physical mechanisms of high-frequency radiation in the deep region. We also find that the overridding subduction wedge contributes significantly to the up-dip rupture propagation and large final slip in the shallow region. Such findings are also applicable to other megathrust earthquakes.

(2) Damaged fault zones are usually found around natural faults, but their effects on earthquake ruptures have been largely unknown. We simulate earthquake ruptures in damaged fault zones with material properties constrained by seismic and geological observations. We show that reflected waves in fault zones are effective at generating pulse-like ruptures and head waves tend to accelerate and decelerate rupture speeds. These mechanisms are robust in natural fault zones with large attenuation and off-fault plasticity. Moreover, earthquakes in damaged fault zones can propagate at super-Rayleigh speeds that are unstable in homogeneous media. Supershear transitions in fault zones do not require large fault stresses. In the end, we present observations in the Big Bear region, where variability of rupture speeds of small earthquakes correlates with the laterally variable materials in a damaged fault zone.

Direct simulation of quantum dynamics in complex systems

Accurate simulation of quantum dynamics in complex systems poses a fundamental theoretical challenge with immediate application to problems in biological catalysis, charge transfer, and solar energy conversion. The varied length- and timescales that characterize these kinds of processes necessitate development of novel simulation methodology that can both accurately evolve the coupled quantum and classical degrees of freedom and also be easily applicable to large, complex systems. In the following dissertation, the problems of quantum dynamics in complex systems are explored through direct simulation using path-integral methods as well as application of state-of-the-art analytical rate theories.