6 research outputs found
OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining
The âbottom-upâ 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 ârecipesâ 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 alcoholâwater 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 (PÂ(BA)) and 2-hydroxyethyl acrylate
(PÂ(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 PÂ(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 PÂ(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 alcoholâwater mixtures
Water Structure and Mobility in Acrylamide Copolymer Glycohydrogels With Galactose and Siloxane Pendant Groups
Glycohydrogels containing 2â˛âacrylamidoethylâβâdâgalactopyranoside and varying levels of N,NⲠmethylene bisacrylamide and 3âacrylamidopropyltris(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 waterâpolymer 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 waterâpolymer binding and decreases waterâwater 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 alcoholâwater 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 polyÂ(<i>n</i>-butyl acrylate) (PBA), polyÂ(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 waterâwater
hydrogen bonds and the acceleration of hydrogen bond dynamics
OpenMSCG: A Software Tool for Bottom-up Coarse-graining
The âbottom-upâ approach to coarse-graining â for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes â 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 ârecipesâ for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications