Related papers: Unassigned distance geometry and the Buckminsterfu…
The morphology of Bucky onions is investigated by {\it ab initio} calculations using Yang's new $O(N)$ method. It is found that for large single shell fullerenes with $I_h$ symmetry, the spherical morphology has the lower energy than that…
Using a systematic search algorithm we identify several types of point defects in the boron fullerene with 80 atoms. All these point defect leave the cage structure intact. In addition the cage structure is also very stable with respect to…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
One-dimensional NMR spectroscopy is one of the most widely used techniques for the characterization of organic compounds and natural products. For molecules with up to 36 non-hydrogen atoms, the number of possible structures has been…
Machine-learning models based on a point-cloud representation of a physical object are ubiquitous in scientific applications and particularly well-suited to the atomic-scale description of molecules and materials. Among the many different…
A fullerene graph can be embedded in a piecewise linear 2-manifold with each non-hexagonal carbon ring corresponding to a cone vertex. Adjacent two or three such vertices can be combined as a cluster cut out from a parent cone round a…
A linear-complexity algorithm for computing the Wasserstein-1 distance on non-uniform meshes is proposed. This work extends the fast Sinkhorn algorithms from [Q. Liao et al., Commun. Math. Sci., 20(2022)] and [Q. Liao et al., J. Sci.…
The present work is a generalisation of the dynamical screening factor presented in [1] to consider an atom located at an arbitrary position within the fullerene. A more elaborated investigation into the case where the atom is located at…
We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to…
Finding an optimal match between two different crystal structures underpins many important materials science problems, including describing solid-solid phase transitions, developing models for interface and grain boundary structures. In…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
Besides buckminsterfullerene (C60), other fullerenes and their derivatives may also reside in space. In this work, we study the formation and photo-dissociation processes of astronomically relevant fullerene/anthracene (C14H10) cluster…
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined…
An algorithm is developed for structure identification of amorphous carbonaceous nanomaterials with a joint x-ray and neutron diffraction data analysis, using the data on the chemical composition of the sample from other diagnostics. The…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
We study the electronic states of giant single-shell and the recently discovered nested multi-shell carbon fullerenes within the tight-binding approximation. We use two different approaches, one based on iterations and the other on…
Small cationic fullerene fragments, produced by electron impact ionization of C60, were mass-selected and accumulated in cryogenic Ne matrixes. Optical absorption spectroscopy of these fragments with up to 18 carbon atoms revealed linear…
The most fundamental model of a molecule is a cloud of unordered atoms, even without chemical bonds that can depend on thresholds for distances and angles. The strongest equivalence between clouds of atoms is rigid motion, which is a…
This is an investigation on the dynamical screening of an atom confined within a fullerene of finite width. The two surfaces of the fullerene lead to the presence of two surface plasmon eigenmodes. It is shown that, in the vicinity of these…
Buckminsterfullerene, C$_{60}$, has not only a beautiful truncated icosahedral (soccerball) shape, but simple H\"uckel calculations predict a three-fold degenerate lowest unoccupied molecular orbital (LUMO) which can accomodate up to six…