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The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
Analysis of emission lines in gaseous nebulae yields direct measures of physical conditions and chemical abundances and is the cornerstone of nebular astrophysics. Although the physical problem is conceptually simple, its practical…
Diffusion behaviors of heterogeneous materials are of paramount importance in many engineering problems. Numerical models that take into account the internal structure of such materials are robust but computationally very expensive. This…
Wide variety of engineering design tasks can be formulated as constrained optimization problems where the shape and topology of the domain are optimized to reduce costs while satisfying certain constraints. Several mathematical approaches…
In this thesis, a computational framework for microstructural modelling of transverse behaviour of heterogeneous materials is presented. The context of this research is part of the broad and active field of Computational Micromechanics,…
This paper presents a density-based topology optimization method for designing 3D thin-walled structures with adaptive meshing. Uniform wall thickness is achieved by simultaneously constraining the minimum and maximum feature sizes using…
Accurate prediction of protein active-site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a…
Consensus-based optimization (CBO) is a versatile multi-particle optimization method for performing nonconvex and nonsmooth global optimizations in high dimensions. Proofs of global convergence in probability have been achieved for a broad…
Chemical accuracy serves as an important metric for assessing the effectiveness of the numerical method in Kohn--Sham density functional theory. It is found that to achieve chemical accuracy, not only the Kohn--Sham wavefunctions but also…
Credibility building activities in computational research include verification and validation, reproducibility and replication, and uncertainty quantification. Though orthogonal to each other, they are related. This paper presents…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Calculations of the lowest valence {\pi}* as well as the 3s and higher energy 3p{\sigma} Rydberg excited states of the CO2 molecule are carried out using density functionals with variational optimization of the orbitals, an approach…
This work presents a robust design optimization approach for a char combustion process in a limited-data setting, where simulations of the fluid-solid coupled system are computationally expensive. We integrate a polynomial dimensional…
Recent progress in learning-based image compression has demonstrated that end-to-end optimization can substantially outperform traditional codecs by jointly learning compact latent representations and probabilistic entropy models. However,…
Design-space dimensionality reduction is essential to mitigate the cost of high-fidelity simulation-based optimization, especially when dealing with high-dimensional geometric parameterizations. Traditional linear techniques, such as…
An automated framework is presented for the numerical solution of optimal control problems with PDEs as constraints, in both the stationary and instationary settings. The associated code can solve both linear and non-linear problems, and…
We study the large-scale behavior of a small-strain lattice model for a network composed of elastoplastic springs with random material properties. We formulate the model as an evolutionary rate independent system (ERIS). In an earlier work…
Efficient Matlab codes in 2D and 3D have been proposed recently to assemble finite element matrices. In this paper we present simple, compact and efficient vectorized algorithms, which are variants of these codes, in arbitrary dimension,…
Finite element simulations have been used to solve various partial differential equations (PDEs) that model physical, chemical, and biological phenomena. The resulting discretized solutions to PDEs often do not satisfy requisite physical…
A new numerical code, based upon a mixed FEM-Runge-Kutta method, is used for the analysis and design of plane 2-D smart structures. The code is applied to the study of arbitrarily shaped PEM plates, based on a weak formulation of their…