Strongly charged polyelectrolytes (PEs) demonstrate complex solution behavior as a function of chain length, concentrations, and ionic strength. The viscosity behavior is important to understand and is a core quantity for many applications, but aspects remain a challenge. Molecular dynamics simulations using implicit solvent coarse-grained (CG) models successfully reproduce structure, but are often inappropriate for calculating viscosities. To address the need for CG models which reproduce viscoelastic properties of one of the most studied PEs, sodium polystyrene sulfonate (NaPSS), we report our recent efforts in using Bayesian optimization to develop CG models of NaPSS which capture both polymer structure and dynamics in aqueous solutions with explicit solvent. We demonstrate that our explicit solvent CG NaPSS model with the ML-BOP water model [Chan et al. Nat Commun 10, 379 (2019)] quantitatively reproduces NaPSS chain statistics and solution structure. The new explicit solvent CG model is benchmarked against diffusivities from atomistic simulations and experimental specific viscosities for short chains. We also show that our Bayesian-optimized CG model is transferable to larger chain lengths across a range of concentrations. Overall, this work provides a machine-learned model to probe the structural, dynamic, and rheological properties of polyelectrolytes such as NaPSS and aids in the design of novel, strongly charged polymers with tunable structural and viscoelastic properties.
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http://dx.doi.org/10.1140/epje/s10189-023-00355-x | DOI Listing |
Molecules
November 2024
ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne 3000, Australia.
Xanthione is a sulfated polycyclic aromatic hydrocarbon which exhibits unique anti-Kasha properties and substantial sensitivity to its medium. Due to this sensitivity however, this makes xanthione-based systems very difficult to simulate. Further, xanthione's is understood to be come more photostable in the presence of a highly polar medium, however whether these photophysical properties could be taken advantage of for certain applications remains to be seen.
View Article and Find Full Text PDFJ Chem Inf Model
December 2024
Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland.
The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Multiscale Modeling of Fluid Materials, Department of Engineering Physics and Computation, TUM School of Engineering and Design, Technical University of Munich, Munich, Germany.
Machine learning (ML) potentials are a powerful tool in molecular modeling, enabling ab initio accuracy for comparably small computational costs. Nevertheless, all-atom simulations employing best-performing graph neural network architectures are still too expensive for applications requiring extensive sampling, such as free energy computations. Implicit solvent models could provide the necessary speed-up due to reduced degrees of freedom and faster dynamics.
View Article and Find Full Text PDFBlood Adv
December 2024
University of Illinois at Urbana Champaign, Urbana, Illinois, United States.
Formation of the extrinsic complex (EC) on cell surfaces is the event that triggers the coagulation cascade. Tissue factor (TF) and factor VIIa (FVIIa) form the EC together with factor X (FX) on phosphatidylserine-containing membranes, leading to FX activation by TF:FVIIa. This lipid dependence has made experimental characterization of the EC structure challenging.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
Accurate calculation of solvation energies has long fascinated researchers, but complex interactions within bulk water molecules pose significant challenges. Currently, molecular solvation energy calculations are mostly based on implicit solvent approximations in which the solvent molecules are treated as continuum dielectric media. However, the implicit solvent approach is not ideal because it lacks certain real solvation effects, such as that of the first solvation shell, etc.
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