Applications of Principal Component Analysis (PCA) in Materials Science

Shenai, Prathamesh M.; Xu, Zhiping; Zhao, Yang

doi:10.5772/37523

Cited by 7 publications

(4 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In previous sections, we observed that both the FLD and TMD regions approach the central core of the protein, in those proteins that have at least one such domain. The conformational changes were studied identifying global collective motions, which are most relevant to the activity of the protein by using essential dynamics [34].…”

Section: Resultsmentioning

confidence: 99%

Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region

et al. 2019

View full text Add to dashboard Cite

Members of the Bcl-2 protein family regulate apoptosis through interactions with several proteins. A critical intrinsically disordered region (IDR) present in some members of the Bcl-2 family is essential for their function. Also, the structural and conformational plasticity of disordered regions is essential for the regulation of the Bcl-2 protein’s activity. Further, some proteins of the family contain transmembrane-helical regions, which anchor them into organelle membranes. Bcl-2, the archetypical member of the family, is characterized by an IDR labeled as a flexible loop domain (FLD) and a transmembrane domain (TMD). Another member of this family is the Bcl-2A1 protein, containing a TMD but lacking the FLD. To our knowledge, this is the first report which characterizes the individual and simultaneous dynamical contributions of FLD and TMD in Bcl-2 and Bcl-2A1 using molecular dynamics simulations (MDS). We examined the conformational spaces of Bcl-2, Bcl-2A1, and two artificial constructs lacking the TMD (Bcl-2ΔTM and Bcl-2A1ΔTM). As the results show, FLD and TMD stabilized each protein independently when they are present. When they coincided, such as in Bcl-2, an additive stabilizing effect is observed. This information is crucial for understanding the structural mechanisms of interaction in the Bcl-2 family.

show abstract

Section: Resultsmentioning

confidence: 99%

Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Principal Component Analysis. PCA is a dimensionality reduction technique that has been used widely and successfully across various engineering and science disciplines [37][38][39][40] and is implemented in most scientific computing platforms (e.g. Matlab, R, Python, etc.).…”

Section: Methodsmentioning

confidence: 99%

Mapping the global design space of nanophotonic components using machine learning pattern recognition

Melati¹,

Grinberg²,

Dezfouli³

et al. 2018

Preprint

View full text Add to dashboard Cite

These authors contributed equally to this work. AbstractNanophotonics finds ever broadening applications requiring complex component designs with a large number of parameters to be simultaneously optimized. Recent methodologies employing optimization algorithms commonly focus on a single design objective, provide isolated designs, and do not describe how the design parameters influence the device behaviour. Here we propose and demonstrate a machinelearning-based approach to map and characterize the multi-parameter design space of nanophotonic components. Pattern recognition is used to reveal the relationship between an initial sparse set of optimized designs through a significant reduction in the number of characterizing parameters. This defines a design sub-space of lower dimensionality that can be mapped faster by orders of magnitude than the original design space. As a result, multiple performance criteria are clearly visualized, revealing the interplay of the design parameters, highlighting performance and structural limitations, and inspiring new design ideas. This global perspective on high-dimensional design problems represents a major shift in how modern nanophotonic design is approached and provides a powerful tool to explore complexity in next-generation devices.

show abstract

“…PCA has vital application in the field of material science, were PCA was used to study of SWNTs (Single-walled Carbon Nano Tubes) on coarse grained simulations and atomistic fine grained simulation. In PCA was implemented to identify the dynamic factors [6]. The prevalence patient to reach vision centers in rural area was found using factor analysis.…”

Section: Introductionmentioning

confidence: 99%

Data Preprocessing for Quality Analysis of Contact Lens Material in Ophthalmology using Factor Analysis

Sumitra¹,

Sheshasaayee²

2016

IJERT

View full text Add to dashboard Cite

This paper focuses on Factor analysis performed on contact lens material. The Factor Analysis on the contact lens material and interpretation are the central steps in this research process. The extracted contact lens data are comprehended and interpreted to trigger the research. Analysis based on a wide range of variables can be tedious and time consuming. The contact lens materials such as RGP, Soft and Hybrid are considered as the source of dataset for factor analysis. Principle Component Analysis is the method adopted to do Factor Analysis. From the result it is found, out of 10 parameters 5 parameters are considered to be the key parameters for identifying the quality contact lens material in the field of ophthalmology.

show abstract

Applications of Principal Component Analysis (PCA) in Materials Science

Cited by 7 publications

References 31 publications

Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region

Exploring the Conformational Space of Bcl-2 Protein Variants: Dynamic Contributions of the Flexible Loop Domain and Transmembrane Region

Mapping the global design space of nanophotonic components using machine learning pattern recognition

Data Preprocessing for Quality Analysis of Contact Lens Material in Ophthalmology using Factor Analysis

Contact Info

Product

Resources

About