Ordering Transition in Salt-Doped Diblock Copolymers

Lithium salt-doped block copolymers offer promise for applications as solid electrolytes in lithium ion batteries. Control of the conductivity and mechanical properties of these materials for membrane applications relies critically on the ability to predict and manipulate their microphase separation temperature. Past attempts to predict the so-called “order–disorder transition temperature” of copolymer electrolytes have relied on approximate treatments of electrostatic interactions. In this work, we introduce a coarse-grained simulation model that treats Coulomb interactions explicitly, and we use it to investigate the ordering transition of charged block copolymers. The order–disorder transition temperature is determined from the ordering free energy, which we calculate with a high level of precision using a density-of-states approach. Our calculations allow us to discern a delicate competition between two physical effects: ion association, which raises the transition temperature, and solvent dilution, which lowers the transition temperature. In the intermediate salt concentration regime, our results predict that the order–disorder transition temperature increases with salt content, in agreement with available experimental data

Coarse-Grained Ions for Nucleic Acid Modeling

We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. <i>Phys. Chem. B</i>, <i>116</i>, 8383–93 (2012)] that maximizes the information retained in a coarse-grained model. We describe the local distribution of ions in the vicinity of a recently published coarse-grained DNA model and demonstrate a dependence of persistence length on ionic strength that differs from that predicted by Odijk–Skolnick–Fixman theory. Consistent with experimental observations, we show that spermidine induces DNA condensation whereas magnesium and sodium do not. This model can be used alongside any coarse-grained DNA model that has explicit charges and an accurate reproduction of the excluded volume of dsDNA

Dynamics and Deformation Response of Rod-Containing Nanocomposites

Theoretical and computational studies of polymer nanocomposites have largely focused on spherical inclusions in a polymer matrix. In order to address the influence of particle shape on nanocomposite behavior, extensive Monte Carlo and molecular dynamics simulations are used to examine the structure and deformation behavior of a model polymer upon addition of rods of varying aspect ratios. It is found that, at constant temperature, nanorod length does not meaningfully affect the elastic properties of composites but does affect postyield properties, such as the strain hardening modulus. In contrast, at constant <i>T</i>/<i>T</i>_g, several trends with additive length arise. Examination of the polymer bond autocorrelation function during deformation reveals that longer, dispersed rods induce a broadening of the relaxation spectrum. Nanocomposites show longer bond orientation relaxation times than the pure polymer during all stages of deformation. For the truly nanoscale additives used in this study, polymer mobility is found to be only a weak function of distance to the nearest nanorod so long as the additives did not aggregate

Efficient Free Energy Calculation of Biomolecules from Diffusion-Biased Molecular Dynamics

Recently proposed metadynamics techniques offer an effective means for improving sampling in simulations of complex systems, including polymers and biological macromolecules. One of the drawbacks of such methods has been the absence of well-defined or effective convergence criteria. A solution to this problem is considered here in which an optimal ensemble is introduced to minimize the travel time across the entire order parameter range of interest. The usefulness of the proposed approach is illustrated in the context of two systems consisting of biological molecules dissolved in water. The results presented in this work indicate that the proposed method is considerably faster than other existing algorithms for the study of these systems, and that the corresponding free energy that emerges from the simulations converges to the exact result

Topological Effects in Isolated Poly[<i>n</i>]catenanes: Molecular Dynamics Simulations and Rouse Mode Analysis

Poly­[<i>n</i>]­catenanes are mechanically interlocked polymers consisting of interlocking ring molecules. Over the years, researchers have speculated that the permanent topological interactions within the poly­[<i>n</i>]­catenane backbone could lead to unique dynamical behaviors. To investigate these unusual polymers, molecular dynamics simulations of isolated poly­[<i>n</i>]­catenanes have been conducted, along with a Rouse mode analysis. Owing to the mechanical bonds within the molecule, the dynamics of poly­[<i>n</i>]­catenanes at short length scales are significantly slowed and the distribution of relaxation times is broadened; these same behaviors have been observed in melts of linear polymers and are associated with entanglement. Despite these entanglement-like effects, at large length scales poly­[<i>n</i>]­catenanes do not relax much slower than isolated linear polymers and are less strongly impacted by increased segmental stiffness

Mechanical Response of DNA–Nanoparticle Crystals to Controlled Deformation

The self-assembly of DNA-conjugated nanoparticles represents a promising avenue toward the design of engineered hierarchical materials. By using DNA to encode nanoscale interactions, macroscale crystals can be formed with mechanical properties that can, at least in principle, be tuned. Here we present <i>in silico</i> evidence that the mechanical response of these assemblies can indeed be controlled, and that subtle modifications of the linking DNA sequences can change the Young’s modulus from 97 kPa to 2.1 MPa. We rely on a detailed molecular model to quantify the energetics of DNA–nanoparticle assembly and demonstrate that the mechanical response is governed by entropic, rather than enthalpic, contributions and that the response of the entire network can be estimated from the elastic properties of an individual nanoparticle. The results here provide a first step toward the mechanical characterization of DNA–nanoparticle assemblies, and suggest the possibility of mechanical metamaterials constructed using DNA

Secondary Structure of Rat and Human Amylin across Force Fields

<div><p>The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.</p></div

Free Energy of Defects in Ordered Assemblies of Block Copolymer Domains

We investigate commonly occurring defects in block copolymer thin films assembled on chemically nanopatterned substrates and predict their probability of occurrence by computing their free energies. A theoretically informed 3D coarse grain model is used to describe the system. These defects become increasingly unstable as the strength of interactions between the copolymer and the patterned substrate increases and when partial defects occur close to the top surface of the film. The results presented here reveal an extraordinarily large thermodynamic driving force for the elimination of defects. When the characteristics of the substrate are commensurate with the morphology of the block copolymer, the probability of creating a defect is extremely small and well below the specifications of the semiconductor industry for fabrication of features having characteristic dimensions on the scale of tens of nanometers. We also investigate how the occurrence of defect changes when imperfections arise in the underlying patterns and find that, while defects continue to be remarkably unstable, stretched patterns are more permissive than compressed patterns

Liquid Crystal-Based Emulsions for Synthesis of Spherical and Non-Spherical Particles with Chemical Patches

We report the use of liquid crystal (LC)-in-water emulsions for the synthesis of either spherical or non-spherical particles with chemically distinct domains located at the poles of the particles. The approach involves the localization of solid colloids at topological defects that form predictably at surfaces of water-dispersed LC droplets. By polymerizing the LC droplets displaying the colloids at their surface defects, we demonstrate formation of both spherical and, upon extraction of the mesogen, anisotropic composite particles with colloids located at either one or both of the poles. Because the colloids protrude from the surfaces of the particles, they also define organized, chemical patches with functionality controlled by the colloid surface

Helmholtz free energy in kT versus β_RMSD for rat and human amylin.

<p>The β_RMSD is correlated with the number of residues in a β-hairpin. The results for rIAPP are shown using solid lines, while the results for hIAPP are given in dashed lines. The Helmholtz free energy is shown for Amberff99sb*-ILDN with TIP3P (black), Amberff03w with TIP4P2005 (red), and CHARMM22* with TIP4P (blue).</p