Related papers: Inferring a Cell Structure on the Space of Cyclooc…
On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions characterized by the dominance relations between cartesian…
In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into…
Molecular Mechanics describes molecules as particle configurations interacting via classical potentials. These {\it configurational energies} usually consist of the sum of different phenomenological terms which are tailored to the…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We define and study a class of finite topological spaces, which model the cell structure of a space obtained by gluing finitely many Euclidean convex polyhedral cells along congruent faces. We call these finite topological spaces,…
The two pillars of Algebraic topology - Homology and homotopy theory rely on the availability of basic building blocks called cells. Cells take the form of simplexes, and have properties such as faces, sub-cells, convexity and…
We consider causal 3-dimensional triangulations with the topology of $S^2\times [0,1]$ or $D^2\times [0,1]$ where $S^2$ and $D^2$ are the two-dimensional sphere and disc, respectively. These triangulations consist of slices and we show that…
A novel crystalline structure of hybrid monolayer hexagonal boron nitride (BN) and graphene is predicted by means of the first-principles calculations. This material can be derived via boron or nitrogen atoms substituted by carbon atoms…
In a previous work arXiv:physics/0611108v2, it was shown that the volume spanned by a molecular system in its conformational space can be effectively bounded by a polyhedral cone, this cone is described by means of a simple combinatorial…
We propose a model of the functional architecture of curvature sensible cells in the visual cortex that associates curvature with scale. The feature space of orientation and position is naturally enhanced via its oriented prolongation,…
A ring-shaped carbon allotrope was recently synthesized for the first time, reinvigorating theoretical interest in this class of molecules. The dual $\pi$ structure of these molecules allows for the possibility of novel electronic…
It is well known that for many semilinear parabolic equations there is a global attractor which has a cell complex structure with finite dimensional cells. Additionally, many semilinear parabolic equations have equilibria with finite…
Topology is a central concept of mathematics, which allows us to distinguish two isolated rings with linked ones. In material science, researchers discovered topologically different carbon allotropes in a form of a cage, a tube, and a…
We use ab initio density functional calculations to study the formation and structural as well as thermal stability of cellular foam-like carbon nanostructures. These systems with a mixed $sp^2/sp^3$ bonding character may be viewed as…
The cyclotomic matrix is commonly used to arrange cyclotomic numbers in a convenient format. A natural question is whether the structure of the matrix can reflect properties of these numbers. In this article, we examine cyclotomic numbers…
We present a development of cellular cohomology in homotopy type theory. Cohomology associates to each space a sequence of abelian groups capturing part of its structure, and has the advantage over homotopy groups in that these abelian…
Simple cubic structure with one atom in the unit cell found in compressed calcium is contrintuitive with regards to traditional view on tendency of transition to densely packed structures on the increase of pressure. To understand this…
This article describes a natural piecewise Euclidean bi-simplicial cell structure for the space of $n$-element multisets in a fixed Euclidean rectangle. In particular, we highlight some connections with spaces of complex polynomials and…