scholarly journals High-throughput prediction of stress–strain curves of thermoplastic elastomer model block copolymers by combining hierarchical simulation and deep learning

MRS Advances ◽  
2021 ◽  
Author(s):  
Takeshi Aoyagi

Abstract We achieved high-throughput prediction of the stress–strain (S–S) curves of thermoplastic elastomers by combining hierarchical simulation and deep learning. ABA triblock copolymer with a phase-separated structure was used as a thermoplastic elastomer model. The S–S curves of the ABA triblock copolymers were calculated from the hierarchical simulation of self-consistent field theory calculations and coarse-grained molecular dynamics simulations. Because such hierarchical simulations require considerable computational resources, we applied a deep learning technique to accelerate the prediction. Sets of phase-separated structures and the S–S curves obtained from the hierarchical simulation were used to train a 3D convolutional neural network. Using the trained network, we confirmed that the predicted S–S curves of the untrained structures accurately reproduced the simulation results. These results will enable us to design novel polymers and phase-separated structures with desired S–S curves by high-throughput screening of a wide variety of structures. Graphic abstract

RSC Advances ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 3233-3245 ◽  
Author(s):  
Amin Koochaki ◽  
Mohammad Reza Moghbeli ◽  
Sousa Javan Nikkhah ◽  
Alessandro Ianiro ◽  
Remco Tuinier

The self-assembly behaviour of dual-responsive block copolymers and their ability to solubilize the drug doxorubicin is demonstrated using molecular dynamics simulations, coarse-grained force field simulations and self-consistent field theory.


2019 ◽  
Author(s):  
Seoin Back ◽  
Junwoong Yoon ◽  
Nianhan Tian ◽  
Wen Zhong ◽  
Kevin Tran ◽  
...  

We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis.


Soft Matter ◽  
2019 ◽  
Vol 15 (5) ◽  
pp. 926-936 ◽  
Author(s):  
Katsumi Hagita ◽  
Keizo Akutagawa ◽  
Tetsuo Tominaga ◽  
Hiroshi Jinnai

To develop molecularly based interpretations of the two-dimensional scattering patterns (2DSPs) of phase-separated block copolymers (BCPs), we performed coarse-grained molecular dynamics simulations of ABA tri-BCPs under uniaxial stretching for block-fractions where the A-segment (glassy domain) is smaller than the B-segment (rubbery domain), and estimated the behaviour of their 2DSPs.


2019 ◽  
Author(s):  
Seoin Back ◽  
Junwoong Yoon ◽  
Nianhan Tian ◽  
Wen Zhong ◽  
Kevin Tran ◽  
...  

We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis.


2008 ◽  
Vol 36 (1) ◽  
pp. 27-32 ◽  
Author(s):  
Mark S.P. Sansom ◽  
Kathryn A. Scott ◽  
Peter J. Bond

An understanding of the interactions of membrane proteins with a lipid bilayer environment is central to relating their structure to their function and stability. A high-throughput approach to prediction of membrane protein interactions with a lipid bilayer based on coarse-grained Molecular Dynamics simulations is described. This method has been used to develop a database of CG simulations (coarse-grained simulations) of membrane proteins (http://sbcb.bioch.ox.ac.uk/cgdb). Comparison of CG simulations and AT simulations (atomistic simulations) of lactose permease reveals good agreement between the two methods in terms of predicted lipid headgroup contacts. Both CG and AT simulations predict considerable local bilayer deformation by the voltage sensor domain of the potassium channel KvAP.


2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Dongfang Xu ◽  
Guangpu Xue ◽  
Bangya Peng ◽  
Zanjie Feng ◽  
Hongling Lu ◽  
...  

Human coagulation factor XIIa (FXIIa) is a trypsin-like serine protease that is involved in pathologic thrombosis. As a potential target for designing safe anticoagulants, FXIIa has received a great deal of interest in recent years. In the present study, we employed virtual high-throughput screening of 500,064 compounds within Enamine database to acquire the most potential inhibitors of FXIIa. Subsequently, 18 compounds with significant binding energy (from -65.195 to -15.726 kcal/mol) were selected, and their ADMET properties were predicted to select representative inhibitors. Three compounds (Z1225120358, Z432246974, and Z146790068) exhibited excellent binding affinity and druggability. MD simulation for FXIIa-ligand complexes was carried out to reveal the stability and inhibition mechanism of these three compounds. Through the inhibition of activated factor XIIa assay, we tested the activity of five compounds Z1225120358, Z432246974, Z45287215, Z30974175, and Z146790068, with pIC50 values of 9.3∗10−7, 3.0∗10−5, 7.8∗10−7, 8.7∗10−7, and 1.3∗10−6 M, respectively; the AMDET properties of Z45287215 and Z30974175 show not well but have better inhibition activity. We also found that compounds Z1225120358, Z45287215, Z30974175, and Z146790068 could be more inhibition of FXIIa than Z432246974. Collectively, compounds Z1225120358, Z45287215, Z30974175, and Z146790068 were anticipated to be promising drug candidates for inhibition of FXIIa.


2020 ◽  
Vol 22 (29) ◽  
pp. 16760-16771 ◽  
Author(s):  
Jianxiang Shen ◽  
Xiangsong Lin ◽  
Jun Liu ◽  
Xue Li

Through coarse-grained MD simulations, the effects of nanoparticle properties, polymer–nanoparticle interactions, chain crosslinks and temperature on the stress–strain behavior and mechanical reinforcement of PNCs are comprehensively investigated.


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