相关论文: A Central Partition of Molecular Conformational Sp…
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…
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…
A combinatorial model of molecular conformational space that was previously developped (J. Gabarro-Arpa, Comp. Biol. and Chem. 27, (2003) 153-159), had the drawback that structures could not be properly embedded beacause it lacked explicit…
In previous works it was shown that protein 3D-conformations could be encoded into discrete sequences called dominance partition sequences (DPS), that generated a linear partition of molecular conformational space into regions of molecular…
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…
In many areas of applied geometric/numeric computational mathematics, including geo-mapping, computer vision, computer graphics, finite element analysis, medical imaging, geometric design, and solid modeling, one has to compute incidences,…
This article describes a geometric partitioning software that can be used for quick computation of data partitions on many-core HPC machines. It is most suited for dynamic applications with load distributions that vary with time.…
Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…
For each positive integer $n$, let $G_n$ be the graph of integer partitions of $n$, where two partitions are adjacent if one is obtained from the other by an elementary transfer of a cell in the Ferrers diagram, followed by reordering.…
We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
Graph-based signal processing techniques have become essential for handling data in non-Euclidean spaces. However, there is a growing awareness that these graph models might need to be expanded into `higher-order' domains to effectively…
A method is proposed for the characterisation of the entropy of cellular structures, based on the compactivity concept for granular packings. Hamiltonian-like volume functions are constructed both in two and in three dimensions, enabling…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…
In this paper we propose a novel algorithm to combine two or more cellular complexes, providing a minimal fragmentation of the cells of the resulting complex. We introduce here the idea of arrangement generated by a collection of cellular…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
This paper proposes a concise coding of the cells of n-dimensional finite regular grids. It induces a simple, generic and efficient framework for implementing classical digital topology data structures and algorithms. Discrete subsets of…
Current distributed data fabrics lack a rigorous mathematical foundation, often relying on ad-hoc architectures that struggle with consistency, lineage, and scale. We propose a mathematical framework for data fabrics, unifying heterogeneous…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…