Related papers: Unassigned distance geometry and the Buckminsterfu…
Systematic efforts to synthesise fullerene containing LCs have produced a variety of successful model compounds. We present a simple molecular theory relating the self-organisation observed in these systems to their molecular structure. The…
In this work we intend to report on some results obtained by an analytical modelling of biomacromolecular structures as driven by the study of Steiner points and Steiner trees with an Euclidean definition of distance.
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
We investigate the formation of fullerene-like structures from hot Carbon gas using classical molecular dynamics, employing Brenner's potential. In particular we examine the influence of different annealing strategies on fullerene yield,…
Transformation of amorphous carbon clusters into fullerenes under high temperature is studied using molecular dynamics simulations at microsecond times. Based on the analysis of both structure and energy of the system, it is found that…
We present a method for reliably determining the lowest energy structure of an atomic cluster in an arbitrary model potential. The method is based on a genetic algorithm, which operates on a population of candidate structures to produce new…
Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state-of-the-art tools. Visualizing the structure of complex…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Molecular structures are always depicted as 2D printed form in scientific documents like journal papers and patents. However, these 2D depictions are not machine-readable. Due to a backlog of decades and an increasing amount of these…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
Single molecule X-ray scattering experiments with free electron lasers have opened a new route to the structure determination of biomolecules. Because typically only very few photons per scattering image are recorded and thus the…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
We study the motion of C60 fullerene molecules (buckyballs) and short-length carbon nanotubes on graphene nanoribbons. We demonstrate that the nanoribbon edge creates an effective potential that keeps the carbon structures on the surface.…
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly well-suited to determine the structure of molecules and materials in powdered form. Structure determination usually proceeds by finding the best match between experimentally…
Molecular emission is observed in a wide variety of astrophysical environments, yet a substantial fraction of spectral features detected at mm wavelengths remains unidentified. Identifying these features is essential for constraining the…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation…
This presentation starts with the regular polygons, of course, then with the Platonic and Archimedean solids. The latter ones are whose symmetry groups are transitive on the vertices, and in addition, whose faces are regular polygons (see…
Determining the structure and following the structural evolution of molecules undergoing chemical reactions is one of the key goals of ultrafast molecular physics and chemistry. Recently, Coulomb explosion imaging has emerged as a promising…
Although recovering an Euclidean distance matrix from noisy observations is a common problem in practice, how well this could be done remains largely unknown. To fill in this void, we study a simple distance matrix estimate based upon the…