Related papers: Inferring a Cell Structure on the Space of Cyclooc…
It is known that the $k$-faces of the permutohedron $\Pi_n$ are labeled by (all possible) linearly ordered partitions of the set $[n]=\{1,...,n\}$ into $(n-k)$ non-empty parts. The incidence relation corresponds to the refinement: a face…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
The classic Voronoi cells can be generalized to a higher-order version by considering the cells of points for which a given $k$-element subset of the set of sites consists of the $k$ closest sites. We study the structure of the $k$-order…
Rearrangement of atoms due to broken translational symmetries at the surface of SrTiO$_3$ is scarcely debatable in the present day scenario. Actual concern demands to unveil the true structure and precise mechanism responsible for atomic…
We report the structure of transient fluctuations in the liquid phase of a two-dimensional system that exhibits several ordered phases with different symmetries. The density-temperature phase diagram of the system studied, composed of…
Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…
Cell shape has long been used to discern cell phenotypes and states, but the underlying premise has not been quantitatively tested. Here, we show that a single cell image can be used to discriminate its migration behavior by analyzing a…
The electronic structures and properties of 2-oxazolidinone and the related compound cycloserine (CS) have been investigated using core and valence photoelectron spectroscopy and theoretical calculations. Isomerization of the central…
Biologically inspired pressure actuated cellular structures can alter their shape through pressure variations. Previous work introduced a computational framework for pressure actuated cellular structures which was limited to two cell rows…
Cellular systems are observed everywhere in nature, from crystal domains in metals, soap froth and cucumber cells to the network of cosmological voids. Surprisingly, despite their disparate scale and origin all cellular systems follow…
The c(6x2) is a reconstruction of the SrTiO3(001) surface that is formed between 1050-1100oC in oxidizing annealing conditions. This work proposes a model for the atomic structure for the c(6x2) obtained through a combination of results…
Modeling the electronic and optical properties of organic semiconductors remains a challenge for theory, despite the remarkable progress achieved in the last three decades. The complexity of these systems, including structural (dis)order…
There has been considerable controversy regarding the structure of TiBe$_{12}$, which is variously reported as hexagonal and tetragonal. Lattice dynamics simulations based on density functional theory show the tetragonal phase space group…
Whereas it is easy to reduce the translational symmetry of a molecular system by using, e.g., Jacobi coordinates the situation is much more involved for the rotational symmetry. In this paper we address the latter problem using {\it…
Communicating cells can coordinate their gene expressions to form spatial patterns. 'Secrete-and-sense cells' secrete and sense the same molecule to do so and are ubiquitous. Here we address why and how these cells, from disordered…
Organoids are in vitro cellular collectives from which brain-like, or gut-like, or kidney-like structures emerge. To make quantitative predictions regarding the morphology and rheology of a cellular collective in its initial stages of…
A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
There is a high degree of compartmentalization in the living cell where various compartments sustain different chemical reactions and transport reactants among themselves. It is exactly such situation that is investigated. The main…
Molecular dynamics (MD) simulations of equilibrium structures and flows of polar water, nonpolar argon and methane, and mixtures of water and methane confined by single - walled carbon nanotubes (SWCNTs) with different rectangular cross…