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1. The UA?CG Workflow: High Performance Molecular Dynamics of Coarse-Grained Polymers

   https://doi.org/10.1109/PDP.2016.127  

   Ozog, David ; Malony, Allen D. ; Guenza, Marina ( February 2016 , Parallel, Distributed, and Network-Based Processing (DPD), 2016 24th Euromicro International Conference on)

   Our analytically based technique for coarse-graining (CG) polymer simulations dramatically improves spatial and temporal scaling while preserving thermodynamic quantities and bulk properties. The purpose of CG codes is to run more efficient molecular dynamics simulations, yet the research field generally lacks thorough analysis of how such codes scale with respect to full-atom representations. This paper conducts an in-depth performance study of highly realistic polymer melts on modern supercomputing systems. We also present a workflow that integrates our analytical solution for calculating CG forces with new high-performance techniques for mapping back and forth between the atomistic and CG descriptions in LAMMPS. The workflow benefits from the performance of CG, while maintaining full-atom accuracy. Our results show speedups up to 12x faster than atomistic simulations. 

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2. Energy Renormalization for Coarse‐Graining Polymers with Different Fragilities: Predictions from the Generalized Entropy Theory

   https://doi.org/10.1002/mats.201900051  

   Xu, Wen‐Sheng ; Xia, Wenjie ( January 2020 , Macromolecular Theory and Simulations)

   Bottom‐up prediction of physical performance of glass‐forming (GF) polymers via coarse‐grained (CG) modeling is challenging because these CG models normally experience significantly altered dynamics that strongly vary with temperature. Building upon the recently developed energy‐renormalization (ER) coarse‐graining method based on molecular dynamics simulations, generalized entropy theory (GET) is employed to theoretically investigate the influence of fundamental molecular parameters on CG modeling of polymers having different glass “fragilities” Taking a linear polymer melt as a model system within the GET framework, it is shown that the chain bending rigidity and cohesive interaction play critical roles in the glass formation of polymers and their CG analogs. To coarse‐grain polymers having a higher fragility index, it requires greater magnitudes of ER factor ε_CGto rescale the cohesive interaction strength under coarse‐graining and thus recover the atomistic relaxation dynamics over a wide temperature range. The GET further predicts that a higher degree of coarse‐graining generally requires greater magnitudes of ε_CGdue to the influence of loss of configuration entropys_con the dynamics. GET analyses herein theoretically demonstrate the efficacy of the ER method toward building a multiscale temperature transferable modeling framework for GF polymers, and confirm the importance of preservings_cin CG modeling of dynamics of soft materials.

    

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3. Combining simulations and experiments for the molecular engineering of multifunctional collagen mimetic peptide-based materials

   https://doi.org/10.1039/D0SM01562H  

   Hilderbrand, Amber M. ; Taylor, Phillip A. ; Stanzione, Francesca ; LaRue, Mark ; Guo, Chen ; Jayaraman, Arthi ; Kloxin, April M. ( February 2021 , Soft Matter)

   null (Ed.)

   Assembling peptides allow the creation of structurally complex materials, where amino acid selection influences resulting properties. We present a synergistic approach of experiments and simulations for examining the influence of natural and non-natural amino acid substitutions via incorporation of charged residues and a reactive handle on the thermal stability and assembly of multifunctional collagen mimetic peptides (CMPs). Experimentally, we observed inclusion of charged residues significantly decreased the melting temperature of CMP triple helices with further destabilization upon inclusion of the reactive handle. Atomistic simulations of a single CMP triple helix in explicit water showed increased residue-level and helical structural fluctuations caused by the inclusion of the reactive handle; however, these atomistic simulations cannot be used to predict changes in CMP melting transition. Coarse-grained (CG) simulations of CMPs at experimentally relevant solution conditions, showed, qualitatively, the same trends as experiments in CMP melting transition temperature with CMP design. These simulations show that when charged residues are included electrostatic repulsions significantly destabilize the CMP triple helix and that an additional inclusion of a reactive handle does not significantly change the melting transition. Based on findings from both experiments and simulations, the sequence design was refined for increased CMP triple helix thermal stability, and the reactive handle was utilized for the incorporation of the assembled CMPs within covalently crosslinked hydrogels. Overall, a unique approach was established for predicting stability of CMP triple helices for various sequences prior to synthesis, providing molecular insights for sequence design towards the creation of bulk nanostructured soft biomaterials. 

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4. Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

   https://doi.org/10.7717/peerj.4230  

   Hills, Jr ( January 2018 , PeerJ)

   Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems. 

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5. Insights into the thermomechanical and interfacial behaviors of polymer‐clay nanocomposites via coarse‐grained molecular dynamics simulations

   https://doi.org/10.1002/pc.28357  

   Nie, Wenjian ; Liao, Yangchao ; Ghazanfari, Sarah ; Wang, Yang ; Wang, Xingyu ; Huang, Ying ; Xia, Wenjie ( March 2024 , Polymer Composites)

   Polymer‐clay nanocomposites (PCNs) are commonly applied as multi‐functional structural materials with exceptional thermomechanical properties, while maintaining the characteristics of lightweight and optical clarity. In this study, building upon previously developed coarse‐grained (CG) models for nanoclay and poly (methyl methacrylate) (PMMA), we employ molecular dynamics (MD) simulations to systematically investigate the thermomechanical properties of PCNs when arranged in stacked configurations. Incorporating stacked clay nanofillers into a polymer matrix, we systematically conduct shear and tensile simulations to investigate the influences of variations in weight percentage, system temperature, and nanoclay size on the thermomechanical properties of PCNs at a fundamental level. The weight percentage of nanoclay in nanocomposites proves to have a significant influence on both the shear and Young's modulus (e.g., the addition of 10 Wt% nanoclay leads to an increase of 32.6% in the Young's modulus), with each exhibiting greater mechanical strength in the in‐plane direction compared to the out‐of‐plane direction, and the disparity between these two directions further widens with an increase in the weight percentage of nanoclay. Furthermore, the increase in the size of nanoclay contributes to an overall modulus enhancement in the composite while the growth reaches a saturation point after a certain threshold of about 10 nm. Our simulation results indicate that the overall dynamics of PMMA are suppressed due to the strong interactions between nanoclay and PMMA, where the confinement effect on local segmental dynamics of PMMA decays from the nanoclay‐polymer interface to the polymer matrix. Our findings provide valuable molecular‐level insights into microstructural and dynamical features of PCNs under deformation, emphasizing the pivotal role of clay‐polymer interface in influencing the thermomechanical properties of the composite materials.

   CG modeling is performed to explore the thermomechanical behavior of PCN.

   Effects of nanoclay weight percentage and size on modulus are studied.

   Interface leads to nanoconfinement effect onT_gand molecular stiffness.

   Correlations between molecular stiffness and modulus are identified.

   Simulations show spatial variation of dynamical heterogeneity.

    

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