GRAPH INVARIANTS AND THE TOPOLOGY OF RNA FOLDING

1994 ◽  
Vol 03 (03) ◽  
pp. 233-245 ◽  
Author(s):  
LOUIS H. KAUFFMAN ◽  
YURI MAGARSHAK
Keyword(s):  
Rna Folding ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Graph Embeddings ◽  
Graph Invariants ◽  
Vassiliev Invariants ◽  
Ambient Isotopy ◽  
Molecular Folding ◽  
General Method ◽  
Three Dimensional Space

A new general method is described for obtaining ambient isotopy or regular isotopy invariants of even valence rigid vertex graphs embedded in three-dimensional space. The paper concentrates on the case of 4-valent vertices and defines an RNA vertex in analogy to the structure of a folded molecule. Examples are given to show how these methods can discriminate graph embeddings that are indistinguishable via Vassiliev invariants. Applications to molecular folding are discussed.

scholarly journals Classification of book representations of K6

2017 ◽  
Vol 26 (12) ◽  
pp. 1750075
Author(s):  
Dana Rowland
Keyword(s):  
Complete Graph ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Crossing Number ◽  
Ambient Isotopy ◽  
Three Dimensional Space

A book representation of a graph is a particular way of embedding a graph in three-dimensional space so that the vertices lie on a circle and the edges are chords on disjoint topological disks. We describe a set of operations on book representations that preserves ambient isotopy, and apply these operations to [Formula: see text], the complete graph with six vertices. We prove there are exactly 59 distinct book representations for [Formula: see text], and we identify the number and type of knotted and linked cycles in each representation. We show that book representations of [Formula: see text] contain between one and seven links, and up to nine knotted cycles. Furthermore, all links and cycles in a book representation of [Formula: see text] have crossing number at most four.

scholarly journals General method to retrieve all effective acoustic properties of fully-anisotropic fluid materials in three dimensional space

2019 ◽  
Vol 125 (2) ◽  
pp. 025114 ◽  
Author(s):  
Arthur Terroir ◽  
Logan Schwan ◽  
Théo Cavalieri ◽  
Vicente Romero-García ◽  
Gwénaël Gabard ◽  
...  
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Acoustic Properties ◽  
Anisotropic Fluid ◽  
General Method ◽  
Three Dimensional Space

Extension of the Spatial PDI Model to Three Dimensions

1997 ◽  
Vol 84 (1) ◽  
pp. 176-178
Author(s):  
Frank O'Brien
Keyword(s):  
Population Density ◽  
Dimensional Space ◽  
Finite Lattice ◽  
Three Dimensional ◽  
Upper Bounds ◽  
Three Dimensions ◽  
Lower And Upper Bounds ◽  
Density Index ◽  
Three Dimensional Space

The author's population density index ( PDI) model is extended to three-dimensional distributions. A derived formula is presented that allows for the calculation of the lower and upper bounds of density in three-dimensional space for any finite lattice.

A Peptoid with Extended Shape in Water

2019 ◽  
Author(s):  
Jumpei Morimoto ◽  
Yasuhiro Fukuda ◽  
Takumu Watanabe ◽  
Daisuke Kuroda ◽  
Kouhei Tsumoto ◽  
...  
Keyword(s):  
Spectroscopic Analysis ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Biomolecular Recognition ◽  
Biological Application ◽  
New Class ◽  
Proteolytic Resistance ◽  
Pharmacokinetic Properties ◽  
Optically Pure ◽  
Three Dimensional Space

<div> <div> <div> <p>“Peptoids” was proposed, over decades ago, as a term describing analogs of peptides that exhibit better physicochemical and pharmacokinetic properties than peptides. Oligo-(N-substituted glycines) (oligo-NSG) was previously proposed as a peptoid due to its high proteolytic resistance and membrane permeability. However, oligo-NSG is conformationally flexible and is difficult to achieve a defined shape in water. This conformational flexibility is severely limiting biological application of oligo-NSG. Here, we propose oligo-(N-substituted alanines) (oligo-NSA) as a new peptoid that forms a defined shape in water. A synthetic method established in this study enabled the first isolation and conformational study of optically pure oligo-NSA. Computational simulations, crystallographic studies and spectroscopic analysis demonstrated the well-defined extended shape of oligo-NSA realized by backbone steric effects. The new class of peptoid achieves the constrained conformation without any assistance of N-substituents and serves as an ideal scaffold for displaying functional groups in well-defined three-dimensional space, which leads to effective biomolecular recognition. </p> </div> </div> </div>

scholarly journals Quantitative image analysis of microbial communities with BiofilmQ

2021 ◽  
Author(s):  
Raimo Hartmann ◽  
Hannah Jeckel ◽  
Eric Jelli ◽  
Praveen K. Singh ◽  
Sanika Vaidya ◽  
...  
Keyword(s):  
Image Analysis ◽  
Microbial Communities ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Quantitative Image Analysis ◽  
Space And Time ◽  
Quantitative Image ◽  
Three Dimensional Space

AbstractBiofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

scholarly journals How Can I Grab That?

i-com ◽  
2020 ◽  
Vol 19 (2) ◽  
pp. 67-85
Author(s):  
Matthias Weise ◽  
Raphael Zender ◽  
Ulrike Lucke
Keyword(s):  
Virtual Reality ◽  
User Experience ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Advantages And Disadvantages ◽  
Multiple Dimensions ◽  
Application Developers ◽  
Three Dimensional Space

AbstractThe selection and manipulation of objects in Virtual Reality face application developers with a substantial challenge as they need to ensure a seamless interaction in three-dimensional space. Assessing the advantages and disadvantages of selection and manipulation techniques in specific scenarios and regarding usability and user experience is a mandatory task to find suitable forms of interaction. In this article, we take a look at the most common issues arising in the interaction with objects in VR. We present a taxonomy allowing the classification of techniques regarding multiple dimensions. The issues are then associated with these dimensions. Furthermore, we analyze the results of a study comparing multiple selection techniques and present a tool allowing developers of VR applications to search for appropriate selection and manipulation techniques and to get scenario dependent suggestions based on the data of the executed study.

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