Related papers: Global Structure Search for Molecules on Surfaces:…
Molecular geometry prediction of flexible molecules, or conformer search, is a long-standing challenge in computational chemistry. This task is of great importance for predicting structure-activity relationships for a wide variety of…
Recent advancements in the synthesis of anisotropic macromolecules and nanoparticles have spurred an immense interest in theoretical and computational studies of self-assembly. The cornerstone of such studies is the role of shape in…
The dominant paradigm in computational materials discovery relies on heavily parameterized deep architectures, including message-passing graph networks and equivariant models, that require millions of DFT-labeled training structures and…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
We have developed a general Bayesian algorithm for determining the coordinates of points in a three-dimensional space. The algorithm takes as input a set of probabilistic constraints on the coordinates of the points, and an a priori…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
We introduce a continuous global optimization method to the field of surface reconstruction from discrete noisy cloud of points with weak information on orientation. The proposed method uses an energy functional combining flux-based…
Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state-of-the-art tools. Visualizing the structure of complex…
Differentiable simulation is a promising toolkit for fast gradient-based policy optimization and system identification. However, existing approaches to differentiable simulation have largely tackled scenarios where obtaining smooth…
We introduce a computational method to optimize target physical properties in the full configuration space regarding atomic composition, chemical stoichiometry, and crystal structure. The approach combines the universal potential of the…
Local optimization of adsorption systems inherently involves different scales: within the substrate, within the molecule, and between molecule and substrate. In this work, we show how the explicit modeling of the different character of the…
Optimal design facilitates intelligent data collection. In this paper, we introduce a fully Bayesian design approach for spatial processes with complex covariance structures, like those typically exhibited in natural ecosystems. Coordinate…
A local optimization method based on Bayesian Gaussian Processes is developed and applied to atomic structures. The method is applied to a variety of systems including molecules, clusters, bulk materials, and molecules at surfaces. The…
Global optimization of crystal compositions is a significant yet computationally intensive method to identify stable structures within chemical space. The specific physical properties linked to a three-dimensional atomic arrangement make…
We present a real-space adaptive-coordinate method, which combines the advantages of the finite-difference approach with the accuracy and flexibility of the adaptive coordinate method. The discretized Kohn-Sham equations are written in…
The theoretical investigation of gas adsorption, storage, separation, diffusion and related transport processes in porous materials relies on a detailed knowledge of the potential energy surface of molecules in a stationary environment. In…
In this publication we introduce SAMPLE, a structure search approach for commensurate organic monolayers on inorganic substrates. Such monolayers often show rich polymorphism with diverse molecular arrangements in differently shaped unit…
Due to the growth of geo-tagged images, recent web and mobile applications provide search capabilities for images that are similar to a given query image and simultaneously within a given geographical area. In this paper, we focus on…
Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening methods. To approach chemical space exploration more…
Orientation mapping is a widely used technique for revealing the microstructure of a polycrystalline sample. The crystalline orientation at each point in the sample is determined by analysis of the diffraction pattern, a process known as…