Size and shape of excluded volume polymers confined between parallel plates

Unravel-engineer-design: a three-pronged approach to advance ionomer performance at interfaces in proton exchange membrane fuel cells

Proton exchange membrane fuel cells (PEMFCs), which use hydrogen as fuel, present an eco-friendly alternative to internal combustion engines (ICEs) for powering low-to-heavy-duty vehicles and various devices. Despite their promise, PEMFCs must meet strict cost, performance, and durability standards to reach their full potential. A key challenge lies in optimizing the electrode, where a thin ionomer layer is responsible for proton conduction and binding catalyst particles to the electrode. Enhancing ion transport within these sub-μm thick films is critical to improving the oxygen reduction reaction (ORR) at the cathodes of PEMFCs. For the past 15 years, our research has targeted this limitation through a comprehensive "Unravel - Engineer - Design" approach. We first unraveled the behavior of ionomers, gaining deeper insights into both the average and distributed proton conduction properties within sub-μm thick films and at interfaces that mimic catalyst binder layers. Next, we engineered ionomer-substrate interfaces to gain control over interfacial makeup and boost proton conductivity, essential for PEMFC efficiency. Finally, we designed novel nature-derived or nature-inspired, fluorine-free ionomers to tackle the ion transport limitations seen in state-of-the-art ionomers under thin-film confinement. Some of these ionomers even pave the way to address cost and sustainability challenges in PEMFC materials. This feature article highlights our contributions and their importance in advancing PEMFCs and other sustainable energy conversion and storage technologies.

Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome

The chromosome of a bacterium consists of a mega-base pair-long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike eukaryotic chromosomes, it lacks a nuclear membrane and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modelling the chromosome simply as a circular polymer decorated with closed side loops in a cylindrical confining volume has been shown to already recapture some of the salient properties observed experimentally. Here we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.

Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement

In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.

Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome

The chromosome of a bacterium consists of a mega-base pair long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike in eukaryotes, it lacks a nuclear membrane, and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modeling the chromosome simply as a circular polymer decorated with closed side-loops in a cylindrical confining volume, has been shown to already recapture some of the salient properties observed experimentally. Here, we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.

Correlation anisotropy and stiffness of DNA molecules confined in nanochannels

The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function ⟨C(s)⟩_⊥ in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels. At moderate-to-weak confinement, the negative ⟨C(s)⟩_⊥ correlations imply a preference of DNA segments for transverse looping. The inclination for looping can explain a reduction of stiffness as well as the enhanced knotting of confined DNA relative to that detected earlier in bulk at some channel sizes. Furthermore, it is shown that the orientational persistence length P_or fails to convey the apparent stiffness of DNA molecules in channels. Instead, correlation lengths P_∥ and P_⊥ in the axial and transverse directions, respectively, encompass the channel-induced modifications of DNA stiffness.

Dimensional reduction of duplex DNA under confinement to nanofluidic slits

There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.