Molecular dynamics simulation of thermoresponsive polymers under solvent flow: Topology files.

Molecular Dynamics SImulation of Thermoreactive Polymers in a Directed Flow: Topology Files Scott D. Hopkins and Estela Blaisten-Barojas Department of Computational and Data Sciences, George Mason University, Fairfax, Virginia, USA November 17, 2025 Abstract: Under initially laminar flow conditions of a liquid solution with very low concentration of linear polymers, it has been conjectured that elastic turbulence develops if polymers experience a structural change from elongated to ball-like compact structures. In this work, non-equilibrium molecular dynamics (MD) simulations were performed to establish the counteracting structural phase changes that two thermoreactive polymers, poly(N-isopropylacrylamide) (PNIPAM) and poly(N,N-diethylacrylamide) (PDEA), undergo when immersed in flowing water and glycerol solvents at their lower critical solution temperature (LCST) or above. Results indicate that under laminar flow conditions, an estimated minimum liquid flow velocity of approximately 1.1 m/s in water, 0.4 m/s in a mixed 50:50 glycerol:water solution, and 0.2 m/s in pure glycerol is required to counteract the phase change from globule-to-coil. Oligomers of these polymers transition from a globule into an extended configuration within 200 ns at the LCST. Eliminating the flowing conditions at the LCST, the flow-elongated oligomers return to their globule native phase. Analysis of the flow field at the sub-nanometer level was performed, along with an evaluation of the structural and energetic properties before and after oligomer extension. Contents: Supplementary Information of “Thermoresponsive polymers under solvent flow through molecular dynamics,” by S. D. Hopkins and E. Blaisten-Barojas, https://doi.org/10.1021/acs.jpcb.5c07833 File is named :SI_Hopkins_Blaisten_11-16-2025.pdf . GROMACS topology file of the oligomer 30-PNIPAM named: topology_30-PNIPAM.itp GROMACS topology file of the oligomer 30-PNIPAM named: topology_30-PDEA.itp Zipped files containing a custom python code to generate an initial syndiotactic oligomer structure, for either 30-PNIPAM or 30-PDEA: PNIPAM_PDEA_oligomer-builder.zip