scholarly journals Unveiling Temporal Nonlinear Structure–Rheology Relationships under Dynamic Shearing

Polymers ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 1189 ◽  
Author(s):  
Johnny Ching-Wei Lee ◽  
Lionel Porcar ◽  
Simon A. Rogers
Keyword(s):  
3D Structure ◽  
Uniaxial Extension ◽  
Soft Materials ◽  
Equilibrium Structure ◽  
Nonlinear Structure ◽  
Natural Approach ◽  
Viscoelastic Parameters ◽  
3D Space ◽  
Nonlinear Viscoelastic ◽  
Dynamic Shearing

Understanding how microscopic rearrangements manifest in macroscopic flow responses is one of the central goals of nonlinear rheological studies. Using the sequence-of-physical-processes framework, we present a natural 3D structure–rheology space that temporally correlates the structural and nonlinear viscoelastic parameters. Exploiting the rheo-small-angle neutron scattering (rheo-SANS) techniques, we demonstrate the use of the framework with a model system of polymer-like micelles (PLMs), where we unveil a sequence of microscopic events that micelles experience under dynamic shearing across a range of frequencies. The least-aligned state of the PLMs is observed to migrate from the total strain extreme toward zero strain with increasing frequency. Our proposed 3D space is generic, and can be equally applied to other soft materials under any sort of deformation, such as startup shear or uniaxial extension. This work therefore provides a natural approach for researchers to study complex out-of-equilibrium structure–rheology relationships of soft materials.

scholarly journals CoeViz 2: Protein Graphs Derived From Amino Acid Covariance

2021 ◽  
Vol 1 ◽  
Author(s):  
Daniel Corcoran ◽  
Nicholas Maltbie ◽  
Shivchander Sudalairaj ◽  
Frazier N. Baker ◽  
Joseph Hirschfeld ◽  
...  
Keyword(s):  
Metal Binding ◽  
Large Scale ◽  
Pearson Correlation ◽  
3D Structure ◽  
Covariance Analysis ◽  
Web Based ◽  
Functional Sites ◽  
3D Space ◽  
Chi Squared ◽  
Molecular Functions

Proteins by and large carry out their molecular functions in a folded state when residues, distant in sequence, assemble together in 3D space to bind a ligand, catalyze a reaction, form a channel, or exert another concerted macromolecular interaction. It has been long recognized that covariance of amino acids between distant positions within a protein sequence allows for the inference of long range contacts to facilitate 3D structure modeling. In this work, we investigated whether covariance analysis may reveal residues involved in the same molecular function. Building upon our previous work, CoeViz, we have conducted a large scale covariance analysis among 7,595 non-redundant proteins with resolved 3D structures to assess 1) whether the residues with the same function coevolve, 2) which covariance metric captures such couplings better, and 3) how different molecular functions compare in this context. We found that the chi-squared metric is the most informative for the identification of coevolving functional sites, followed by the Pearson correlation-based, whereas mutual information is the least informative. Of the seven categories of the most common natural ligands, including coenzyme A, dinucleotide, DNA/RNA, heme, metal, nucleoside, and sugar, the trace metal binding residues display the most prominent coupling, followed by the sugar binding sites. We also developed a web-based tool, CoeViz 2, that enables the interactive visualization of covarying residues as cliques from a larger protein graph. CoeViz 2 is publicly available at https://research.cchmc.org/CoevLab/.

A Method of Structure Comparison Using Spatial Topological Patterns

2005 ◽  
Vol 277-279 ◽  
pp. 272-277
Author(s):  
Sung Hee Park ◽  
Keun Ho Ryu
Keyword(s):  
Spatial Data ◽  
Similarity Search ◽  
3D Structure ◽  
Structural Similarity ◽  
Query Protein ◽  
Data Types ◽  
Structure Comparison ◽  
3D Space ◽  
Structure Databases ◽  
Computationally Expensive

The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approach, the geometry of secondary structure elements in 3D space is represented by spatial data types and is indexed using Rtrees. Topological patterns are discovered by spatial topology relations based on the Rtree index join. An algorithm for a similarity search compares topological patterns of a query protein with those of proteins in structure databases by the intersection frequency of SSEs. Our experimental results show that the execution time of our method is three times faster than the generally known method DALITE. Our method can generate small candidate sets for more accurate alignment tools such as DALI and SSAP.

scholarly journals Latent 3D Volume for Joint Depth Estimation and Semantic Segmentation from a Single Image

Sensors ◽  
2020 ◽  
Vol 20 (20) ◽  
pp. 5765 ◽  
Author(s):  
Seiya Ito ◽  
Naoshi Kaneko ◽  
Kazuhiko Sumi
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Semantic Segmentation ◽  
Depth Estimation ◽  
Image Features ◽  
Feature Representation ◽  
Single Image ◽  
Feature Vectors ◽  
3D Space ◽  
3D Volume

This paper proposes a novel 3D representation, namely, a latent 3D volume, for joint depth estimation and semantic segmentation. Most previous studies encoded an input scene (typically given as a 2D image) into a set of feature vectors arranged over a 2D plane. However, considering the real world is three-dimensional, this 2D arrangement reduces one dimension and may limit the capacity of feature representation. In contrast, we examine the idea of arranging the feature vectors in 3D space rather than in a 2D plane. We refer to this 3D volumetric arrangement as a latent 3D volume. We will show that the latent 3D volume is beneficial to the tasks of depth estimation and semantic segmentation because these tasks require an understanding of the 3D structure of the scene. Our network first constructs an initial 3D volume using image features and then generates latent 3D volume by passing the initial 3D volume through several 3D convolutional layers. We apply depth regression and semantic segmentation by projecting the latent 3D volume onto a 2D plane. The evaluation results show that our method outperforms previous approaches on the NYU Depth v2 dataset.

scholarly journals Computational Design and Analysis of a Magic Snake

2020 ◽  
Vol 12 (5) ◽  
Author(s):  
Zilong Li ◽  
Songming Hou ◽  
Thomas C. Bishop
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Computational Design ◽  
Space Curve ◽  
One Dimensional ◽  
3D Structures ◽  
Multi Scale ◽  
3D Space ◽  
Slender Bodies ◽  
Self Similar

Abstract The Magic Snake (Rubik’s Snake) is a toy that was invented decades ago. It draws much less attention than Rubik’s Cube, which was invented by the same professor, Erno Rubik. The number of configurations of a Magic Snake, determined by the number of discrete rotations about the elementary wedges in a typical snake, is far less than the possible configurations of a typical cube. However, a cube has only a single three-dimensional (3D) structure while the number of sterically allowed 3D conformations of the snake is unknown. Here, we demonstrate how to represent a Magic Snake as a one-dimensional (1D) sequence that can be converted into a 3D structure. We then provide two strategies for designing Magic Snakes to have specified 3D structures. The first enables the folding of a Magic Snake onto any 3D space curve. The second introduces the idea of “embedding” to expand an existing Magic Snake into a longer, more complex, self-similar Magic Snake. Collectively, these ideas allow us to rapidly list and then compute all possible 3D conformations of a Magic Snake. They also form the basis for multidimensional, multi-scale representations of chain-like structures and other slender bodies including certain types of robots, polymers, proteins, and DNA.

scholarly journals Shape Morphable Hydrogel/Elastomer Bilayer for Implanted Retinal Electronics

Micromachines ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 392 ◽  
Author(s):  
Muru Zhou ◽  
Do Hyun Kang ◽  
Jinsang Kim ◽  
James D. Weiland
Keyword(s):  
Rational Design ◽  
3D Structure ◽  
Electrode Array ◽  
Soft Materials ◽  
Bilayer Film ◽  
Wide Field ◽  
Pdms Layer ◽  
Electrode Arrays ◽  
Shape Transformation ◽  
Design Guideline

Direct fabrication of a three-dimensional (3D) structure using soft materials has been challenging. The hybrid bilayer is a promising approach to address this challenge because of its programable shape-transformation ability when responding to various stimuli. The goals of this study are to experimentally and theoretically establish a rational design principle of a hydrogel/elastomer bilayer system and further optimize the programed 3D structures that can serve as substrates for multi-electrode arrays. The hydrogel/elastomer bilayer consists of a hygroscopic polyacrylamide (PAAm) layer cofacially laminated with a water-insensitive polydimethylsiloxane (PDMS) layer. The asymmetric volume change in the PAAm hydrogel can bend the bilayer into a curvature. We manipulate the initial monomer concentrations of the pre-gel solutions of PAAm to experimentally and theoretically investigate the effect of intrinsic mechanical properties of the hydrogel on the resulting curvature. By using the obtained results as a design guideline, we demonstrated stimuli-responsive transformation of a PAAm/PDMS flower-shaped bilayer from a flat bilayer film to a curved 3D structure that can serve as a substrate for a wide-field retinal electrode array.

Simulating 3D Cloud Shape Based on Computer Vision and Particle System

2012 ◽  
Vol 182-183 ◽  
pp. 819-822 ◽  
Author(s):  
Lin Gong
Keyword(s):  
Computer Vision ◽  
Computer Graphics ◽  
Natural Environment ◽  
Particle System ◽  
3D Structure ◽  
Realistic Simulation ◽  
Structure Information ◽  
Efficient Approach ◽  
3D Space ◽  
Computer Vision Technology

Clouds are an important part of natural environment. The realistic simulation of cloud is a challenging topic in computer graphics. This paper proposes a simple, efficient approach based on computer vision and particle system to model various 3D clouds. This method use computer vision technology to extract 3D structure information of clouds from images, then using particles technology to fill the 3D space and render the cloud. This method is suitable to model all kinds of clouds, such as stratus, cumulus, cirrus etc. It is an improvement over earlier systems that modeled only one type of cloud.

Continuous molecular fields and the concept of molecular co-fields in structure–activity studies

2019 ◽  
Vol 11 (20) ◽  
pp. 2701-2713
Author(s):  
Igor I Baskin ◽  
Nelly I Zhokhova
Keyword(s):  
Molecular Design ◽  
3D Structure ◽  
Biological Targets ◽  
3D Space ◽  
Structure Of Molecules ◽  
Structure Activity ◽  
Activity Models ◽  
Molecular Fields ◽  
Physical Fields ◽  
Continuous Molecular Fields

The analysis of information on the spatial structure of molecules and the physical fields of their interactions with biological targets is extremely important for solving various problems in drug discovery. This mini-review article surveys the main features of the continuous molecular fields approach and its use for analyzing structure–activity relationships in 3D space, building 3D quantitative structure–activity models and conducting similarity based virtual screening. Particular attention is paid to the consideration of the concept of molecular co-fields and their use for the interpretation of 3D structure–activity models. The principles of molecular design based on the overlapping and the similarity of molecular fields with corresponding co-fields are formulated.

NONLINEAR MODEL OF A FABRIC WARP AND WEFT

2006 ◽  
Vol 09 (01n02) ◽  
pp. 99-120 ◽  
Author(s):  
PASCAL BRUNIAUX ◽  
CYRIL NGO NGOC
Keyword(s):  
Dynamic Behavior ◽  
3D Structure ◽  
Three Dimensional ◽  
Geometrical Model ◽  
Nonlinear Phenomena ◽  
Initial State ◽  
Numerical Resolution ◽  
3D Space ◽  
Proposed Model ◽  
Nodal Model

This study aims to develop a realistic mathematical model of fabric. In contrast to other studies on fabric modeling as a deformable surface, the model described in this article takes into account the geometry of the object. Moreover, it integrates the nonlinear phenomena of the dynamic behavior of material. As input parameters, the weaving data that define the 3D structure of the object and the mechanical properties of the yarn that express its dynamics are used. Thus, the fabric model is composed of a geometrical model of fabric (structure) on which a model of yarn (material characterization) is added. This hypothesis may be reasonable since a fabric shows the result of a three-dimensional assembly of yarns judiciously disposed. Since these yarns interact dynamically: the main difficulty consists of defining the yarn model. In our case, it is composed of various nonlinear functions representing the dynamic behavior of yarn. In order to characterize the flexibility of material, the weight, the elasticity and any other mechanical characteristics defining the relation between the strain and the stretching out of the shape should be taken into account. Firstly, several works dealing with realistic mathematical models of fabric are described. A taxonomic classification is achieved in order to position our study (in comparison to the scientific community). Secondly, the model of the fabric is described. A geometrical model of the object is presented. It allows one to dimension the object in a 3D space and then to position it at its initial state. Subsequently, a nodal model of yarns is described, step by step, in order to demonstrate the separability of the various dynamic behaviors. These nodal links make it simple to integrate the proposed model in the global geometrical model. Thus, the methods of numerical resolution used to simulate the complete model of the fabric are exposed. One method is selected and used in order to improve the performances of the fabric simulator and to obtain better stability. Several simulations illustrate the quality of the results obtained.

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