Related papers: Recognizing Local and Global Structural Motifs at …

Molecular dynamics simulations demand an unprecedented combination of accuracy and scalability to tackle grand challenges in catalysis and materials design. To bridge this gap, we present AlphaNet, a local-frame-based equivariant model that…

Scanning probe experiments such as scanning tunneling microscopy (STM) and atomic force microscopy (AFM) on strongly correlated electronic systems often reveal complex pattern formation on multiple length scales. By studying the universal…

Attention mechanisms are developing into a viable alternative to convolutional layers as elementary building block of NNs. Their main advantage is that they are not restricted to capture local dependencies in the input, but can draw…

Anticipating the low energy arrangements of atoms in space is an indispensable scientific task. Modern stochastic approaches to searching for these configurations depend on the optimisation of structures to nearby local minima in the energy…

Atomistic structures of materials offer valuable insights into their functionality. Determining these structures remains a fundamental challenge in materials science, especially for systems with defects. While both experimental and…

Machine-learning models in chemistry - when based on descriptors of atoms embedded within molecules - face essential challenges in transferring the quality of predictions of local electronic structures and their associated properties across…

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes…

We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic…

We develop a new method to locally cluster curves and discover functional motifs, i.e.~typical ``shapes'' that may recur several times along and across the curves capturing important local characteristics. In order to identify these shared…

Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…

In the age of social computing, finding interesting network patterns or motifs is significant and critical for various areas such as decision intelligence, intrusion detection, medical diagnosis, social network analysis, fake news…

This article presents a novel method for causal discovery with generalized structural equation models suited for analyzing diverse types of outcomes, including discrete, continuous, and mixed data. Causal discovery often faces challenges…

A routine crystallography technique, crystal structure analysis, is rarely performed in computational condensed matter research. The lack of methods to identify and characterize crystal structures reliably in particle simulation data…

Studying the topology of so-called real networks, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that networks are…

Recently, the core-periphery (CP) structure of networks as one type of meso-scale structure has received attention. The CP structure is composed of a dense core and a sparse connected periphery. In this paper, we propose an algorithm to…

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…

Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and…

The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that…

We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…

Data coding as a building block of several image processing algorithms has been received great attention recently. Indeed, the importance of the locality assumption in coding approaches is studied in numerous works and several methods are…