Related papers: Shape optimization of metastable states
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
The development of active metasurface systems, such as lasing metasurfaces, requires the optimization of multiple modes at the absorption and lasing wavelength bands, including their quality factor, mode profile and angular dispersion.…
In this paper, we propose a model reduction method for solving multiscale elliptic PDEs with random coefficients in the multiquery setting using an optimization approach. The optimization approach enables us to construct a set of localized…
The expectation-maximization (EM) algorithm is a well-known iterative method for computing maximum likelihood estimates from incomplete data. Despite its numerous advantages, a main drawback of the EM algorithm is its frequently observed…
Particle-based shape modeling (PSM) is a popular approach to automatically quantify shape variability in populations of anatomies. The PSM family of methods employs optimization to automatically populate a dense set of corresponding…
Variational optimization of orbitals in time-independent density functional calculations of excited electronic states presents a significant challenge, as excited states typically correspond to saddle points on the electronic energy…
This paper discusses level set-based structural optimization. Level set-based structural optimization is a method used to determine an optimal configuration for minimizing an objective functional by updating level set functions…
This paper addresses optimal design problems governed by multi-state stationary diffusion equations, aiming at the simultaneous optimization of the domain shape and the distribution of two isotropic materials in prescribed proportions.…
A metastable state, characterized by a low degree of mass localization is identified using Density Functional Theory. This free energy minimum, located through the proper evaluation of the competing terms in the free energy functional, is…
The development of enhanced sampling methods has greatly extended the scope of atomistic simulations, allowing long-time phenomena to be studied with accessible computational resources. Many such methods rely on the identification of an…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
This paper is devoted to the analysis of multiphase shape optimization problems, which can formally be written as $\min\Big\{{g}(F_1(\Omega_1),\dots,F_h(\Omega_h))+ m\vert\,\bigcup_{i=1}^h\Omega_i\vert :\ \Omega_i\subset D,\ \Omega_i\cap…
We propose a method for approximating solutions to optimization problems involving the global stability properties of parameter-dependent continuous-time autonomous dynamical systems. The method relies on an approximation of the…
Physically motivated stochastic dynamics are often used to sample from high-dimensional distributions. However such dynamics often get stuck in specific regions of their state space and mix very slowly to the desired stationary state. This…
Molecular dynamics simulations have become essential in many areas of atomistic modelling from drug discovery to materials science. They provide critical atomic-level insights into key dynamical events experiments cannot easily capture.…
Since shape optimization methods have been proven useful for identifying interfaces in models governed by partial differential equations, we show how shape optimization techniques can also be applied to an interface identification problem…
The stochastic motions of a diffusing particle contain information concerning the particle's interactions with binding partners and with its local environment. However, accurate determination of the underlying diffusive properties, beyond…
Localized molecular orbitals are often used for the analysis of chemical bonds, but they can also serve to efficiently and comprehensibly compute linear response properties. While conventional canonical molecular orbitals provide an…
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…
In this article we consider an optimization problem where the objective function is evaluated at the fixed-point of a contraction mapping parameterized by a control variable, and optimization takes place over this control variable. Since…