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The first step in drug discovery is finding drug molecule moieties with medicinal activity against specific targets. Therefore, it is crucial to investigate the interaction between drug-target proteins and small chemical molecules. However,…

Predicting relaxed atomic structures of chemically complex materials remains a major computational challenge, particularly for high-entropy systems where traditional first-principles methods become prohibitively expensive. We introduce the…

The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…

Gradient pattern analysis (GPA) is a well-established technique for measuring gradient bilateral asymmetries of a square numerical lattice. This paper introduces an improved version of GPA designed for galaxy morphometry. We show the…

The layered graphene systems exhibit the rich and unique excitation spectra arising from the electron-electron Coulomb interactions. The generalized tight-binding model is developed to cover the planar/buckled/cylindrical structures,…

The first-principles band theory paradigm has been a key player not only in the process of discovering new classes of topologically interesting materials, but also for identifying salient characteristics of topological states, enabling…

A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule…

The wave function and binding energy for shallow donors in GaAs are calculated within the tight binding (TB) approach, for supercells containing up to two million atoms. The resulting solutions, coupled with a scaling law, allow…

Graphene nanoflakes (GNFs) exhibit rich magnetic behaviors arising from two primary mechanisms: geometry frustration in non-Kekul\'e structures and electron delocalization-driven aromatic stabilization in Kekul\'e-type systems. Herein, we…

Generating molecular graphs with desired chemical properties driven by deep graph generative models provides a very promising way to accelerate drug discovery process. Such graph generative models usually consist of two steps: learning…

Accurate prediction of drug-target binding affinity accelerates drug discovery by prioritizing compounds for experimental validation. Current methods face three limitations: sequence-based approaches discard spatial geometric constraints,…

There is a perceived dichotomy between structure-based and descriptor-based molecular representations used for predictive chemistry tasks. Here, we study the performance, generalizability, and interpretability of the recently proposed…

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Based on the postulates of quantum mechanics, we introduce a hierarchy of representations which meet…

We numerically study thermodynamic and structural properties of the one-component Gaussian core model (GCM) at very high densities. The solid-fluid phase boundary is carefully determined. We find that the density dependence of both the…

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

Grain Boundary (GB) deformation mechanisms such as Sliding (GBS) and Opening (GBO) are prevalent in alloys at high homologous temperatures but are hard to capture quantitatively. We propose an automated procedure to quantify 3D GB…

Community detection is the task of clustering objects based on their pairwise relationships. Most of the model-based community detection methods, such as the stochastic block model and its variants, are designed for networks with binary…

We introduce a theory of chemical bond with a corpuscular picture of electrons. It employs a minimal set of localized electron wave packets with 'floating and breathing' degrees of freedom and the spin-coupling of non-orthogonal…

Charge transfer among individual atoms in a molecule is the key concept in the modern electronic theory of chemical bonding. In this work, we defined an atomic region between two atoms by Slater orbital exponents of valence electrons and…

With increasing interest in the use of glassy carbon (GC) for a wide variety of application areas, the need for developing fundamental understanding of its mechanical properties has come to the forefront. Further, recent theoretical and…