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I present a strategy for unsupervised manifold learning on local atomic environments in molecular simulations based on simple rotation- and permutation-invariant three-body features. These features are highly descriptive, generalize to…
Particle-wall interactions play a crucially important role in various applications such as microfluidic devices for cell sorting, particle separation, entire class of hydrodynamic filtration and its derivatives, etc. Yet, accurate…
We present a new version of the Ogre open source Python package with the capability to perform structure prediction of epitaxial inorganic interfaces by lattice and surface matching. In the lattice matching step a scan over combinations of…
Smoothing and sharpening are two fundamental image processing operations. The latter is usually related to the former through the unsharp masking algorithm. In this paper, we develop a new type of filter which performs smoothing or…
Summary: Founded upon diffusion with damping, ITM Probe is an application for modeling information flow in protein interaction networks without prior restriction to the sub-network of interest. Given a context consisting of desired origins…
The implicit boundary integral method (IBIM) provides a framework to construct quadrature rules on regular lattices for integrals over irregular domain boundaries. This work provides a systematic error analysis for IBIMs on uniform…
We present an interval-based approach for parameter identification in structural static inverse problems. The proposed inverse formulation exploits the Interval Finite Element Method (IFEM) combined with adjoint-based optimization. The…
In this paper we propose an approach for solving systems of nonlinear equations without computing function derivatives. Motivated by the application area of tomographic absorption spectroscopy, which is a highly-nonlinear problem with…
Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key…
Regularized least-squares approaches have been successfully applied to linear system identification. Recent approaches use quadratic penalty terms on the unknown impulse response defined by stable spline kernels, which control model space…
In the past decade, variational implicit solvation models (VISM) have achieved great success in solvation energy predictions. However, all existing VISMs in literature lack the uniqueness of an energy minimizing solute-solvent interface and…
Rational design of interface passivators for perovskite solar cells is hindered by the entanglement of intrinsic molecular efficacy with extrinsic platform-dependent performance - a confounding factor that obscures true chemical advances.…
This paper describes a method for fast simplification of surface meshes. Whereas past methods focus on visual appearance, our goal is to solve equations on the surface. Hence, rather than approximate the extrinsic geometry, we construct a…
An algorithm for determining crystal structures from diffraction data is described which does not rely on the usual Fourier-space formulations of atomicity. The new algorithm implements atomicity constraints in real-space, as well as…
Chemistry plays an important role in the interstellar medium (ISM), regulating heating and cooling of the gas, and determining abundances of molecular species that trace gas properties in observations. Although solving the time-dependent…
We are interested in the challenging problem of modelling densities on Riemannian manifolds with a known symmetry group using normalising flows. This has many potential applications in physical sciences such as molecular dynamics and…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
We present an imaging technique that allows the recovery of the transparency profile of wavelength-scale objects with deep subwavelength resolution based on far-field intensity measurements. The approach, interscale mixing microscopy (IMM),…
This paper describes an interdisciplinary approach to geometry modeling of geospatial boundaries. The objective is to extract surfaces from irregular spatial patterns using differential geometry and obtain coherent directional predictions…