OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining

The “bottom-up” approach to coarse-graining, for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes, is an important approach in computational chemistry, biophysics, and materials science. As one example, the Multiscale Coarse-Graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure, such as MS-CG modeling, is particularly valuable. Here, we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (EDCG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS, and NAMD. OpenMSCG is modularized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications

OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining

The “bottom-up” approach to coarse-graining, for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes, is an important approach in computational chemistry, biophysics, and materials science. As one example, the Multiscale Coarse-Graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure, such as MS-CG modeling, is particularly valuable. Here, we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (EDCG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS, and NAMD. OpenMSCG is modularized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications

Effect of Chain Flexibility and Interlayer Interactions on the Local Dynamics of Layered Polymer Systems

Layered polymeric systems are widely used in membrane separation applications; chain mobility in these layered systems is a key consideration in the design of the membranes. The transport properties of membrane polymers can be significantly altered by the perturbations in chain dynamics induced by the presence of an interface and also by the topological properties of the polymers constituting the layered systems. In this work, we use molecular dynamics (MD) simulations to determine the effects of polymer backbone flexibility and interlayer interactions on the glass transition and chain dynamics of polymer layers in the layered systems. We observed that the onset of glass transition of the entire layered system is governed by the stiffer polymer layer and is independent of the type of interactions between the layers. However, the interlayer interactions govern the strength of the glass transition of the entire layered system. Polymer mobility, on the other hand, exhibits a strong dependence on both the chain flexibility and the interlayer interactions. In systems with attractive interactions between the layers, the fully flexible polymer chains at the interface have a lower mobility than those in the bulk region of the layer; the behavior differs from that of rigid polymers, which have a higher mobility at the interface compared to that in the bulk. On the other hand, when the interactions between the layers are repulsive, each layer acts as a free-standing film with chains in both the layers exhibiting higher mobility at the interface

Molecular Origins of Dynamic Coupling between Water and Hydrated Polyacrylate Gels

Energy efficient separation of dilute alcohol–water mixtures is a critical consideration in commercialization of biofuels; pervaporation is an attractive separation technique for this purpose. Knowledge of the mechanism of solvent mobility inside polymeric membranes is of great interest for designing pervaporation-based separation processes. Recently, we employed molecular simulations to study water structure in three polyacrylate gels composed of homopolymers and copolymers of <i>n</i>-butyl acrylate (P­(BA)) and 2-hydroxyethyl acrylate (P­(HEA)). In this work, water and ethanol dynamics were studied using simulations in two systems: polyacrylate gels swollen to equilibrium and gels with low water content. Solvent dynamics show a concentration-dependent behavior in the gels. For gels swollen to equilibrium, both water and ethanol exhibit the highest mobility in the P­(HEA) gel due to the larger degree of swelling of the system, while for gels with a low solvent content, they show the lowest mobility in the P­(HEA) gel due to hydrogen bonding between solvent and polymer. Solvent dynamics in gels with low solvent content was characterized by determining solvent diffusivity, rotational relaxation time, and Van Hove autocorrelation function. The dynamics of water molecules is strongly coupled with polymer dynamics due to hydrogen-bonding interactions, while ethanol does not show such strong coupling due to a smaller degree of interaction with the polymer. Ethanol mobility instead follows the trend in the density and glass transition temperature of the polymer. Our results suggest that dynamic coupling between solvent and polymer can be exploited as a mechanism for separating dilute alcohol–water mixtures

Water Structure and Mobility in Acrylamide Copolymer Glycohydrogels With Galactose and Siloxane Pendant Groups

Glycohydrogels containing 2′‐acrylamidoethyl‐β‐d‐galactopyranoside and varying levels of N,N′ methylene bisacrylamide and 3‐acrylamidopropyltris(trimethylsiloxy)silane were synthesized to determine the effects of crosslinker and amphipathic balance on equilibrium water content (EWC), bound water population, and hydrogen bonding dynamics at the water–polymer interface. Analogous dimethylacrylamide hydrogels were synthesized for comparison with a system containing lower hydrogen bonding propensity. An approach combining experiment (proton nuclear magnetic resonance, thermogravimetric analysis, differential scanning calorimetry, and dynamic vapor sorption analysis) and molecular dynamics simulations was employed to examine the relationship between bulk hydrogel properties, molecular water mobility, and hydrogen bonding characteristics. It was found that copolymer composition (hydrophobic content) and crosslink concentration in high water content glycohydrogels affect EWC, and by extension, structural water population. The organization of water at the polymer interface is greatly impacted by the surrounding environment, where hindered molecular water mobility promotes water–polymer binding and decreases water–water clustering

Structure and Hydrogen Bonding of Water in Polyacrylate Gels: Effects of Polymer Hydrophilicity and Water Concentration

The ability to tune the hydrophilicity of polyacrylate copolymers by altering their composition makes these materials attractive candidates for membranes used to separate alcohol–water mixtures. The separation behavior of these polyacrylate membranes is governed by a complex interplay of factors such as water and alcohol concentrations, water structure in the membrane, polymer hydrophilicity, and temperature. We use molecular dynamics simulations to investigate the effect of polymer hydrophilicity and water concentration on the structure and dynamics of water molecules in the polymer matrix. Samples of poly­(<i>n</i>-butyl acrylate) (PBA), poly­(2-hydroxyethyl acrylate) (PHEA), and a 50/50 copolymer of BA and HEA were synthesized in laboratory, and their properties were measured. Model structures of these systems were validated by comparing the simulated values of their volumetric properties with the experimental values. Molecular simulations of polyacrylate gels swollen in water and ethanol mixtures showed that water exhibits very different affinities toward the different (carbonyl, alkoxy, and hydroxyl) functional groups of the polymers. Water molecules are well dispersed in the system at low concentrations and predominantly form hydrogen bonds with the polymer. However, water forms large clusters at high concentrations along with the predominant formation of water–water hydrogen bonds and the acceleration of hydrogen bond dynamics

OpenMSCG: A Software Tool for Bottom-up Coarse-graining

The “bottom-up” approach to coarse-graining – for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes – is an important approach in computational chemistry, biophysics, and materials science. As one example, the multiscale coarse-graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure such as MS-CG modeling is particularly valuable. Here we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (ED-CG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS and NAMD. OpenMSCG is modulized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications