Mechanisms of Mechanical Behavior of Filled Rubber by Coarse-Grained Molecular Dynamics Simulations

2020 ◽  
Vol 48 (2) ◽  
pp. 78-106 ◽  
Author(s):  
Takashi Kojima ◽  
Masataka Koishi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Reinforcement Effect ◽  
Stress Softening ◽  
Filled Rubber ◽  
Dynamics Simulations ◽  
Polymer Density

ABSTRACT: We reproduced mechanical behaviors, such as the reinforcement effect, hysteresis, and stress softening, of filled rubber under cyclic deformations using coarse-grained molecular dynamics simulations. We measured polymer density distribution in the nonload equilibrium state and conformational changes in polymer chains during deformation for dispersed and aggregated filler structures. We found that the polymer–filler attractive interactions increase the polymer density in the vicinity of fillers and decrease the polymer density in the other regions. The polymer bonds that connect polymer particles away from fillers are extended when the polymer density decreases. This alteration increases the modulus of the polymer phase, and the reinforcement effect appears. For aggregated filler structures, the polymer chains interacting with adjacent fillers act as a bridge between these fillers and increase the modulus, especially when the strain is low. To test the mechanisms of hysteresis and stress softening, we measured the changes in the polymer paths. A polymer path is the minimal path of polymer networks between two fillers; in other words, it is the “bridge” that connects two fillers. We found that the polymer paths increase in length, especially during primary loading, because of polymer adsorption/desorption on the filler surface to adjust the change of filler positions. It was also found that the influence of the filler structure diminishes in the first loading. During subsequent unloading, a long path does not become a short path again but will be folded even though the filler distance reduces. Hence, the change in the polymer paths in the second cycle is smaller than that in the first cycle because the polymer path is just unfolded. We confirmed the hysteresis and stress-softening result from these conformational changes. In this article, we also discuss the recovery mechanism for stress softening and the history dependence.

Molecular dynamics simulation of thermo-mechanical behaviour of elastomer cross-linked via multifunctional zwitterions

2019 ◽  
Vol 21 (38) ◽  
pp. 21615-21625 ◽  
Author(s):  
Naveed Athir ◽  
Ling Shi ◽  
Sayyed Asim Ali Shah ◽  
Zhiyu Zhang ◽  
Jue Cheng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Mechanical Behaviour ◽  
Mechanical Response ◽  
Polymer Chains ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Dynamics Simulations

Coarse-grained (CG) molecular dynamics simulations have been employed to study the thermo-mechanical response of a physically cross-linked network composed of zwitterionic moieties and fully flexible elastomeric polymer chains.

scholarly journals Analysis on Microstructure–Property Linkages of Filled Rubber Using Machine Learning and Molecular Dynamics Simulations

Polymers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 2683
Author(s):  
Takashi Kojima ◽  
Takashi Washio ◽  
Satoshi Hara ◽  
Masataka Koishi ◽  
Naoya Amino
Keyword(s):  
Machine Learning ◽  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Stress ◽  
Classification Model ◽  
Machine Learning Techniques ◽  
Coarse Grained ◽  
Filled Rubber ◽  
Dynamics Simulations

A better understanding of the microstructure–property relationship can be achieved by sampling and analyzing a microstructure leading to a desired material property. During the simulation of filled rubber, this approach includes extracting common aggregates from a complex filler morphology consisting of hundreds of filler particles. However, a method for extracting a core structure that determines the rubber mechanical properties has not been established yet. In this study, we analyzed complex filler morphologies that generated extremely high stress using two machine learning techniques. First, filler morphology was quantified by persistent homology and then vectorized using persistence image as the input data. After that, a binary classification model involving logistic regression analysis was developed by training a dataset consisting of the vectorized morphology and stress-based class. The filler aggregates contributing to the desired mechanical properties were extracted based on the trained regression coefficients. Second, a convolutional neural network was employed to establish a classification model by training a dataset containing the imaged filler morphology and class. The aggregates strongly contributing to stress generation were extracted by a kernel. The aggregates extracted by both models were compared, and their shapes and distributions producing high stress levels were discussed. Finally, we confirmed the effects of the extracted aggregates on the mechanical property, namely the validity of the proposed method for extracting stress-contributing fillers, by performing coarse-grained molecular dynamics simulations.

scholarly journals Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways

2017 ◽  
Vol 114 (38) ◽  
pp. E7959-E7968 ◽  
Author(s):  
Wen-Ting Chu ◽  
Xiakun Chu ◽  
Jin Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Change ◽  
Conformational Changes ◽  
Coarse Grained ◽  
Binding Mechanism ◽  
Induced Fit ◽  
C Subunit ◽  
Dynamics Simulations ◽  
Substrate Inhibitor

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations forapoPKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

Coarse-Grained Molecular Modeling of Composite Interfaces

2005 ◽  
Vol 502 ◽  
pp. 39-44
Author(s):  
Vincent B.C. Tan ◽  
M. Deng ◽  
Tong Earn Tay
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Ab Initio Molecular Dynamics ◽  
Attractive Potential ◽  
Dynamics Simulations ◽  
Computational Resources ◽  
Nonlinear Elastic

The interface of fiber and matrix strongly influences the performance and strength of fiber-reinforced composite materials. Due to the limitations of continuum mechanics at the nanometer length scale, atomistic level computer simulation has started to play an important role in the understanding of such interfacial systems. Our study focuses on a typical crosslinked interfacial system of glass-epoxy composite with the presence of silanes. To explore the mechanical properties of the interfacial network system, Coarse-grained Molecular Dynamics is used. Currently it is not possible to study mechanical properties of interfacial systems purely through ab initio molecular dynamics simulations because of the huge computational resources required. Although pure atomistic classical molecular dynamics simulations have been used to study systems comprising billions of atoms, classical MD simulation do not take into account the effects of crosslinking of molecular chains. A new force field, which combines the Lennard-Jones potential and a finiteextensible nonlinear elastic attractive potential, is proposed and incorporated in a bead-spring model to simulate glass/epoxy interfacial system with the crosslinked structure of silanes. The finite-extensible nonlinear elastic attractive potential is included to control the motion and breakage of polymer chains. Interfacial adhesion and mechanical properties were studied through the simulation of mechanically separating the interfacial system.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

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