scholarly journals Machine learning-aided analysis for complex local structure of liquid crystal polymers

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hideo Doi ◽  
Kazuaki Z. Takahashi ◽  
Kenji Tagashira ◽  
Jun-ichi Fukuda ◽  
Takeshi Aoyagi

Abstract Elucidation of mesoscopic structures of molecular systems is of considerable scientific and technological interest for the development and optimization of advanced materials. Molecular dynamics simulations are a promising means of revealing macroscopic physical properties of materials from a microscopic viewpoint, but analysis of the resulting complex mesoscopic structures from microscopic information is a non-trivial and challenging task. In this study, a Machine Learning-aided Local Structure Analyzer (ML-LSA) is developed to classify the complex local mesoscopic structures of molecules that have not only simple atomistic group units but also rigid anisotropic functional groups such as mesogens. The proposed ML-LSA is applied to classifying the local structures of liquid crystal polymer (LCP) systems, which are of considerable scientific and technological interest because of their potential for sensors and soft actuators. A machine learning (ML) model is constructed from small, and thus computationally less costly, monodomain LCP trajectories. The ML model can distinguish nematic- and smectic-like monodomain structures with high accuracy. The ML-LSA is applied to large, complex quenched LCP structures, and the complex local structures are successfully classified as either nematic- or smectic-like. Furthermore, the results of the ML-LSA suggest the best order parameter for distinguishing the two mesogenic structures. Our ML model enables automatic and systematic analysis of the mesogenic structures without prior knowledge, and thus can overcome the difficulty of manually determining the specific order parameter required for the classification of complex structures.

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Emanuele Boattini ◽  
Susana Marín-Aguilar ◽  
Saheli Mitra ◽  
Giuseppe Foffi ◽  
Frank Smallenburg ◽  
...  

Abstract Few questions in condensed matter science have proven as difficult to unravel as the interplay between structure and dynamics in supercooled liquids. To explore this link, much research has been devoted to pinpointing local structures and order parameters that correlate strongly with dynamics. Here we use an unsupervised machine learning algorithm to identify structural heterogeneities in three archetypical glass formers—without using any dynamical information. In each system, the unsupervised machine learning approach autonomously designs a purely structural order parameter within a single snapshot. Comparing the structural order parameter with the dynamics, we find strong correlations with the dynamical heterogeneities. Moreover, the structural characteristics linked to slow particles disappear further away from the glass transition. Our results demonstrate the power of machine learning techniques to detect structural patterns even in disordered systems, and provide a new way forward for unraveling the structural origins of the slow dynamics of glassy materials.


2005 ◽  
Vol 03 (06) ◽  
pp. 1391-1409 ◽  
Author(s):  
LU-YONG WANG

Local structural information is supposed to be frequently encoded in local amino acid sequences. Previous research only indicated that some local structure positions have specific residue preferences in some particular local structures. However, correlated pairwise replacements for interacting residues in recurrent local structural motifs from unrelated proteins have not been studied systematically. We introduced a new method fusing statistical covariation analysis and local structure-based alignment. Systematic analysis of structure-based multiple alignments of recurrent local structures from unrelated proteins in representative subset of Protein Databank indicates that covarying residue pairs with statistical significance exist in local structural motifs, in particular β-turns and helix caps. These residue pairs are mostly linked through polar functional groups with direct or indirect hydrogen bonding. Hydrophobic interaction is also a major factor in constraining pairwise amino acid residue replacement in recurrent local structures. We also found correlated residue pairs that are not clearly linked with through-space interactions. The physical constrains underlying these covariations are less clear. Overall, covarying residue pairs with statistical significance exist in local structures from unrelated proteins. The existence of sequence covariations in local structural motifs from unrelated proteins indicates that many relics of local relations are still retained in the tertiary structures after protein folding. It supports the notion that some local structural information is encoded in local sequences and the local structural codes could play important roles in determining native state protein folding topology.


2013 ◽  
Vol 27 (06) ◽  
pp. 1350011 ◽  
Author(s):  
QING-HAI HAO ◽  
YU-WEI YOU ◽  
XIANG-SHAN KONG ◽  
C. S. LIU

The microscopic structure and dynamics of liquid Mg x Bi 1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg 3 Bi 2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.


2018 ◽  
Author(s):  
Kyle Hall ◽  
Zhengcai Zhang ◽  
Christian Burnham ◽  
Guang-Jun Guo ◽  
Sheelagh Carpendale ◽  
...  

<p>The broad scientific and technological importance of crystallization has led to significant research probing and rationalizing crystallization processes, particularly how nascent</p> <p>crystal phases appear. Previous work has generally neglected the possibility of the molecular-level dynamics of individual nuclei coupling to local structures (e.g., that of the nucleus and its</p> <p>surrounding environment). However, recent experimental work has conjectured that this can occur. Therefore, to address a deficiency in scientific understanding of crystallization, we have</p> <p>probed the nucleation of prototypical single and multi-component crystals (specifically, ice and mixed gas hydrates). Here, we establish that local structures can bias the evolution of nascent</p> <p>crystal phases on a nanosecond timescale by, for example, promoting the appearance or disappearance of specific crystal motifs, and thus reveal a new facet of crystallization behaviour.</p> <p>Analysis of the crystallization literature confirms that structural biases are likely present during crystallization processes beyond ice and gas hydrate formation. Moreover, we demonstrate that</p> <p>structurally-biased dynamics are a lens for understanding existing computational and experimental results while pointing to future opportunities.</p>


2018 ◽  
Author(s):  
Kyle Hall ◽  
Zhengcai Zhang ◽  
Christian Burnham ◽  
Guang-Jun Guo ◽  
Sheelagh Carpendale ◽  
...  

<p>The broad scientific and technological importance of crystallization has led to significant research probing and rationalizing crystallization processes, particularly how nascent</p> <p>crystal phases appear. Previous work has generally neglected the possibility of the molecular-level dynamics of individual nuclei coupling to local structures (e.g., that of the nucleus and its</p> <p>surrounding environment). However, recent experimental work has conjectured that this can occur. Therefore, to address a deficiency in scientific understanding of crystallization, we have</p> <p>probed the nucleation of prototypical single and multi-component crystals (specifically, ice and mixed gas hydrates). Here, we establish that local structures can bias the evolution of nascent</p> <p>crystal phases on a nanosecond timescale by, for example, promoting the appearance or disappearance of specific crystal motifs, and thus reveal a new facet of crystallization behaviour.</p> <p>Analysis of the crystallization literature confirms that structural biases are likely present during crystallization processes beyond ice and gas hydrate formation. Moreover, we demonstrate that</p> <p>structurally-biased dynamics are a lens for understanding existing computational and experimental results while pointing to future opportunities.</p>


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