Related papers: Graph theoretical approach to evaluate molecular i…

We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…

The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on…

Chemical graphs are simple undirected connected graphs, where vertices represent atoms in a molecule and edges represent chemical bonds. A degree-based topological index is a molecular descriptor used to study specific physicochemical…

We investigate the Casimir-Polder interaction between two atoms one of which is excited. We show that the perturbation theory results in divergence of integrals for the interaction between an excited atom and a media of dilute gas. We…

This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…

The Casimir and Casimir-Polder interactions are investigated in a stack of equally spaced graphene layers. The optical response of the individual graphene is taken into account using gauge invariant components of the polarization tensor…

One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…

We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions…

Connected networks are a fundamental structure of neurobiology. Understanding these networks will help us elucidate the neural mechanisms of computation. Mathematically speaking these networks are `graphs' - structures containing objects…

The chordal ring (CR) graphs are a well-known family of graphs used to model some interconnection networks for computer systems in which all nodes are in a cycle. Generalizing the CR graphs, in this paper, we introduce the families of…

In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…

Diagrammatic techniques are well-known in the calculation of dispersion interactions between atoms or molecules. The multipolar coupling scheme combined with Feynman ordered diagrams significantly reduces the number of graphs compared to…

Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are…

Applying machine learning to molecules is challenging because of their natural representation as graphs rather than vectors.Several architectures have been recently proposed for deep learning from molecular graphs, but they suffer from…

In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…

Finding the common structural features of two molecules is a fundamental task in cheminformatics. Most drugs are small molecules, which can naturally be interpreted as graphs. Hence, the task is formalized as maximum common subgraph…

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…

Tiered graph autoencoders provide the architecture and mechanisms for learning tiered latent representations and latent spaces for molecular graphs that explicitly represent and utilize groups (e.g., functional groups). This enables the…