相关论文: Graph theoretical approach to evaluate molecular i…
Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…
We present a method based on graph theory for evaluation of the inelastic propensity rules for molecules exhibiting complete destructive quantum interference in their elastic transmission. The method uses an extended adjacency matrix…
We find that energy surfaces of more than two atoms or molecules interacting via dipole-dipole po- tentials generically possess conical intersections (CIs). Typically only few atoms participate strongly in such an intersection. For the…
We consider a simple model for the assembly of chiral molecules in two dimensions driven by maximization of the contact area. We derive a macroscopic model described by a parameter taking nine possible values corresponding to the possible…
Molecular crystals possess a highly complex crystallographic landscape which in many cases results in the experimental observation of multiple crystal structures for the same compound. Accurate results can often be obtained for such systems…
The Glauber theory description of particle- and nucleus-crystal Coulomb interactions at high-energy is developed. The allowance for the lattice thermal vibrations is shown to produce strong absorption effect which is of prime importance for…
New interlayer intermolecular potential model was proposed and it represented ``ABAB'' staking of graphite. Hydrogen atom sputtering on graphite surface was investigated using molecular dynamics simulation. In the initial short time period,…
We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…
We extend previous work on injectivity in chemical reaction networks to general interaction networks. Matrix- and graph-theoretic conditions for injectivity of these systems are presented. A particular signed, directed, labelled, bipartite…
Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides…
Multiparticle systems on complicated metric graphs might have many applications in physics, biology and social life. But the corresponding science still does not exist. Here we start it with simplest examples where there is quadratic…
Very often it is an implied paradigm of molecular magnetism that magnetic molecules in a crystal interact so weakly that measurements of dc magnetic observables reflect ensemble properties of single molecules. But the number of cases where…
In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality…
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…
There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very…
A macroscopic theory for the molecular or Casimir interaction of dielectric materials with arbitrarily shaped surfaces is developed. The interaction is generated by the quantum and thermal fluctuations of the electromagnetic field which…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
We present a hierarchical neural message passing architecture for learning on molecular graphs. Our model takes in two complementary graph representations: the raw molecular graph representation and its associated junction tree, where nodes…
The interaction energy between a water molecule and graphitic structured clusters terminated by hydrogen atoms is analyzed by ab initio methods and decomposed into electrostatic, induction, Pauli repulsion, and correlation energy…
Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems.…