Abstract:
Effective and efficient multiscale modeling is essential to advance both the science and synthesis in a wide array of fields such as physics, chemistry, materials science, biology, biotechnology and pharmacology. This study investigates the efficacy and potential of using genetic algorithms for multiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry.
The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2–9 orders-of-magnitude increase in real-time dynamics simulations taking 4–7 orders-of-magnitude less CPU time.
The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry
simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene—two common building-blocks in organic chemistry—indicate that MOGAs produce high-quality semiempirical methods that (1) are stable to small perturbations, (2) yield accurate configuration energies on untested and critical excited states, and
(3) yield ab initio quality excited-state dynamics. The proposed method enables simulations of more complex systems to realistic multi-picosecond timescales, well beyond previous attempts or expectation of human experts, and 2–3 orders-of-magnitude reduction in computational cost.
While the two applications use simple evolutionary operators, in order to tackle more complex systems, their scalability and limitations have to be investigated. The second part of the thesis addresses some of the challenges involved with a successful design of genetic algorithms and genetic programming for multiscale modeling. The first issue addressed is the scalability of genetic programming, where facetwise models are built to assess the population size required by GP to ensure adequate supply of raw building blocks and also to ensure accurate decision-making between competing building blocks.
This study also presents a design of competent genetic programming, where traditional fixed recombination operators are replaced by building and sampling probabilistic models of promising candidate programs. The proposed scalable GP, called extended compact GP (eCGP), combines the ideas from extended compact genetic algorithm (eCGA) and probabilistic incremental program evolution (PIPE) and adaptively identifies, propagates and exchanges important subsolutions of a search problem. Results show that eCGP scales cubically with problem size on both GP-easy and GP-hard problems.
Finally, facetwise models are developed to explore limitations of scalability of MOGAs, where the scalability of multiobjective algorithms in reliably maintaining Pareto-optimal solutions is addressed. The results show that even when the building blocks are accurately identified, massive multimodality of the search problems can easily overwhelm the nicher (diversity preserving operator) and lead to exponential scale-up. Facetwise models are developed, which incorporate the combined effects of model accuracy, decision making, and sub-structure supply, as well as the effect of niching on the population sizing, to predict a limit on the growth rate of a maximum number of sub-structures that can compete in the two objectives to circumvent the failure of the niching method. The results show that if the number of competing building blocks between multiple objectives is less than the proposed limit, multiobjective GAs scale-up polynomially with the problem size on boundedly-difficult problems.
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Abstract:
Excited-state photodynamics is important in numerous varieties of important materials applications (e.g., liquid crystal display, light emitting diode), pharmaceuticals, and chemical manufacturing processing. We study the effectiveness of multiobjective genetic and evolutionary algorithms in multiscaling excited-state direct photodynamics via rapid reparameterization of semiempirical methods. Using a very limited set of ab initio and experimental data, semiempirical parameters are reoptimized to provide globally accurate potential energy surfaces, thereby eliminating the need for expensive ab initio dynamics simulations. Through reoptimization, excited-state energetics are predicted accurately via semiempirical methods, while retaining accurate ground-state predictions. In our initial study of small photo-excited molecules, our results show that the multiobjective evolutionary algorithm consistently yields solutions that are significantly better – up to 384% lower error in the energy and 87% lower error in the energy-gradient – than those reported previously. As verified with direct quantum dynamical calculations, multiple high-quality parameter sets obtained via genetic algorithms show near-ideal behavior on critical and untested excited-state geometries. The results demonstrate that the reparameterization via evolutionary algorithms is a promising way to extend direct dynamics simulations of photochemistry to multi-picosecond time scales and to larger molecules, with promise in more application beyond simple molecular chemistry.
Abstract:
This paper studies the effectiveness of multiobjective genetic and evolutionary algorithms in multiscaling excited state direct dynamics in photochemistry via rapid reparameterization of semiempirical methods. Using a very limited set of ab initio and experimental data, semiempirical parameters are reoptimized to provide globally accurate potential energy surfaces, thereby eliminating the need for a full-fledged ab initio dynamics simulations, which is very expensive. Through reoptimization of the semiempirical methods, excited-state energetics are predicted accurately, while retaining accurate ground-state predictions. The results show that the multiobjective evolutionary algorithm consistently yields solutions that are significantly better—up to 230% lower in error in energy and 86.5% lower in error in energy-gradient—than those reported in literature. Multiple high-quality parameter sets are obtained that are verified with quantum dynamical calculations, which show near-ideal behavior on critical and untested excited state geometries. The results demonstrate that the reparameterization strategy via evolutionary algorithms is a promising way to extend direct dynamics simulations of photochemistry to multi-picosecond time scales.
Abstract: