Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents.

We develop a Stockmayer fluid model that accounts for the dielectric responses of polar solvents (water, MeOH, EtOH, acetone, 1-propanol, DMSO, and DMF) and NaCl solutions. These solvent molecules are represented by Lennard-Jones (LJ) spheres with permanent dipole moments and the ions by charged LJ spheres. The simulated dielectric constants of these liquids are comparable to experimental values, including the substantial decrease in the dielectric constant of water upon the addition of NaCl. Moreover, the simulations predict an increase in the dielectric constant when considering the influence of ion translations in addition to the orientation of permanent dipoles.

Computational Pipeline for Glomerular Segmentation and Association of the Quantified Regions with Prognosis of Kidney Function in IgA Nephropathy.

The histopathological findings of the glomeruli from whole slide images (WSIs) of a renal biopsy play an important role in diagnosing and grading kidney disease. This study aimed to develop an automated computational pipeline to detect glomeruli and to segment the histopathological regions inside of the glomerulus in a WSI. In order to assess the significance of this pipeline, we conducted a multivariate regression analysis to determine whether the quantified regions were associated with the prognosis of kidney function in 46 cases of immunoglobulin A nephropathy (IgAN). The developed pipelines showed a mean intersection over union (IoU) of 0.670 and 0.693 for five classes (i.e., background, Bowman's space, glomerular tuft, crescentic, and sclerotic regions) against the WSI of its facility, and 0.678 and 0.609 against the WSI of the external facility. The multivariate analysis revealed that the predicted sclerotic regions, even those that were predicted by the external model, had a significant negative impact on the slope of the estimated glomerular filtration rate after biopsy. This is the first study to demonstrate that the quantified sclerotic regions that are predicted by an automated computational pipeline for the segmentation of the histopathological glomerular components on WSIs impact the prognosis of kidney function in patients with IgAN.

Solvation Energy of Ions in a Stockmayer Fluid.

We calculate the solvation energy of monovalent and divalent ions in various liquids with coarse-grained molecular dynamics simulations. Our theory treats the solvent as a Stockmayer fluid, which accounts for the intrinsic dipole moment of molecules and the rotational dynamics of the dipoles. Despite the simplicity of the model, we obtain qualitative agreement between the simulations and experimental data for the free energy and enthalpy of ion solvation, which indicates that the primary contribution to the solvation energy arises mainly from the first and possibly second solvation shells near the ions. Our results suggest that a Stockmayer fluid can serve as a reference model that enables direct comparison between theory and experiment and may be invoked to scale up electrostatic interactions from the atomic to the molecular length scale.

Minor taxa in human skin microbiome contribute to the personal identification.

The human skin microbiome can vary over time, and inter-individual variability of the microbiome is greater than the temporal variability within an individual. The skin microbiome has become a useful tool to identify individuals, and one type of personal identification using the skin microbiome has been reported in a community of less than 20 individuals. However, identification of individuals based on the skin microbiome has shown low accuracy in communities larger than 80 individuals. Here, we developed a new approach for personal identification, which considers that minor taxa are one of the important factors for distinguishing between individuals. We originally established a human skin microbiome for 66 samples from 11 individuals over two years (33 samples each year). Our method could classify individuals with 85% accuracy beyond a one-year sampling period. Moreover, we applied our method to 837 publicly available skin microbiome samples from 89 individuals and succeeded in identifying individuals with 78% accuracy. In short, our results investigate that (i) our new personal identification method worked well with two different communities (our data: 11 individuals; public data: 89 individuals) using the skin microbiome, (ii) defining the personal skin microbiome requires samples from several time points, (iii) inclusion of minor skin taxa strongly contributes to the effectiveness of personal identification.

Effects of Dielectric Inhomogeneity and Electrostatic Correlation on the Solvation Energy of Ions in Liquids.

Electrolytes often involve the spatially varying dielectric response of liquids and electrostatic correlation. Nevertheless, the complexity of their synergistic effects complicates our understanding of ion solvation and often limits theoretical approaches. Thus, we develop a Ginzburg-Landau-like (GL) theory that simultaneously considers these two features. We derive the modified Born solvation energy of ions, which accounts for the effect of saturated dipoles near the ions on the solvation energy, which is in good agreement with experimental data for different ionic charges and even for some selected liquid mixtures. Moreover, we consider the phase diagram of a mixture of polyelectrolyte and uncharged polymer and that of a mixture of ionic liquid and uncharged polymer. The GL theory encompasses the results of the previous mean-field theories, accounting for fluctuations of the electrostatic potentials and hence serves as a simple alternative approach to dielectrically inhomogeneous media.

Solvation Energy of Ions in Polymers: Effects of Chain Length and Connectivity on Saturated Dipoles near Ions.

We illustrate the effects of chain connectivity on the solvation energy of ions immersed in polymer liquids by developing a new coarse-grained molecular dynamics simulation. Our theory accounts for the dielectric response of the polymers through the connection of dipolar, monomeric units with nonlinear springs. In stark contrast to the standard Born solvation energy of ions, our results depend substantially on the chain length of the polymers. We also demonstrate the marked difference in the solvation energies of the ions immersed in non-polymeric particle mixtures, single-component polymers, polymer blends, and block copolymers. Thus, we suggest that the chain architecture of polymers is a key factor in ion solvation, whereas this feature is often inadequately considered in main theory and simulation literature. Our results are consistent with those predicted by previous coarse-grained mean-field theories when the dipole moment of the polymer compositions is relatively small. However, we also demonstrate that the strong ion-dipole and dipole-dipole interactions cause the chain-like association of the monomeric units, resulting in a qualitative discrepancy between the mean-field theory and simulation. Such a strong electrostatic correlation may reverse the dependence of the chain length on the solvation energy of the ions in the polymers.

A new lattice Monte Carlo simulation for dielectric saturation in ion-containing liquids.

We develop a new, rapid method for the lattice Monte Carlo simulation of ion-containing liquids that accounts for the effects of the reorganization of solvent dipoles under external electrostatic fields. Our results are in reasonable agreement with the analytical solutions to the dielectric continuum theory of Booth for single ions, ion pairs, and ionic cross-links. We also illustrate the substantial disparity between the dielectric functions for like and unlike charges on the nanometer scale. Our simulation rationalizes the experimental data for the dependence of the bulk dielectric value of water on ion concentrations in terms of saturated dipoles near ions.

Synergistic effects of ion pairs on the dielectric properties of diblock copolymer melts.

We study the solvation of ion pairs in diblock copolymer melts. Our theory accounts for the size of the ions, the permanent dipole moment and the molecular polarizability of the monomers, the Kuhn length, the compressibility of the liquid mixtures, and the degrees of polymerization. We demonstrate that the electrostatic field near an ion pair causes marked, synergistic effects on the volume fractions of the two blocks and hence the dielectric function. In particular, we illustrate the oscillatory behavior of the dielectric function near an ion pair and the disparity of the dielectric functions between like and unlike charges. These results depend significantly on the chain length and Kuhn length of the diblock copolymers on the nanometer scale.

Ion solvation in polymer blends and block copolymer melts: effects of chain length and connectivity on the reorganization of dipoles.

We studied the thermodynamic properties of ion solvation in polymer blends and block copolymer melts and developed a dipolar self-consistent field theory for polymer mixtures. Our theory accounts for the chain connectivity of polymerized monomers, the compressibility of the liquid mixtures under electrostriction, the permanent and induced dipole moments of monomers, and the resultant dielectric contrast among species. In our coarse-grained model, dipoles are attached to the monomers and allowed to rotate freely in response to electrostatic fields. We demonstrate that a strong electrostatic field near an ion reorganizes dipolar monomers, resulting in nonmonotonic changes in the volume fraction profile and the dielectric function of the polymers with respect to those of simple liquid mixtures. For the parameter sets used, the spatial variations near an ion can be in the range of 1 nm or larger, producing significant differences in the solvation energy among simple liquid mixtures, polymer blends, and block copolymers. The solvation energy of an ion depends substantially on the chain length in block copolymers; thus, our theory predicts the preferential solvation of ions arising from differences in chain length.

Thermodynamics of Salt-Doped Block Copolymers.

We provide a perspective on the thermodynamics of salt-doped block copolymer electrolytes consisting of ion-conducting and inert blocks, taking poly(ethylene oxide)-b-polystyrene and lithium salts as an example. We focus on the origin for enhanced immiscibility between the constituent blocks upon addition of lithium salts and discuss issues from selected experiments and from our recent self-consistent field study.

First-Order Disordered-to-Lamellar Phase Transition in Lithium Salt-Doped Block Copolymers.

We study the microphase separation of block copolymer electrolytes containing lithium salts. Taking poly(ethylene oxide)-b-polystyrene (PEO-b-PS) as an example, we show that in the presence of lithium salts the disordered-to-lamellar phase transition becomes first-order even at the level of mean-field theory, with a moderate range of temperature in which both the disordered and lamellar phases coexist, and different salt concentration in the coexisting phases. The coexistence arises from the different partitioning of the salt ions between the disordered phase and the lamellar phase, driven primarily by the solvation energy of anions. A striking consequence of the coexistence is that heating a lamellar phase into the coexistence region leads to increased order in the remaining lamellar phase.

Ion solvation in liquid mixtures: effects of solvent reorganization.

Using field-theoretic techniques, we study the solvation of salt ions in liquid mixtures, accounting for the permanent and induced dipole moments, as well as the molecular volume of the species. With no adjustable parameters, we predict solvation energies in both single-component liquids and binary liquid mixtures that are in excellent agreement with experimental data. Our study shows that the solvation energy of an ion is largely determined by the local response of the permanent and induced dipoles, as well as the local solvent composition in the case of mixtures, and does not simply correlate with the bulk dielectric constant. In particular, we show that, in a binary mixture, it is possible for the component with the lower bulk dielectric constant but larger molecular polarizability to be enriched near the ion.

Thermodynamics of ion-containing polymer blends and block copolymers.

We develop a theory for the thermodynamics of ion-containing polymer blends and diblock copolymers, taking polyethylene oxide (PEO), polystyrene and lithium salts as an example. We account for the tight binding of Li^{+} ions to the PEO, the preferential solvation energy of anions in the PEO domain, the translational entropy of anions, and the ion-pair equilibrium between EO-complexed Li^{+} and anion. Our theory is able to predict many features observed in experiments, particularly the systematic dependence in the effective χ parameter on the size of the anions. Furthermore, comparison with the observed linear dependence in the effective χ on salt concentration yields an upper limit for the binding constant of the ion pair.

Phase separation induced by ladder-like polymer-polymer complexation.

Polymer-polymer complexation in solvent is studied using an extension of the self-consistent field theory. The model polymers are capable of forming ladder-like duplex structures. The duplex formation occurs with an abrupt change of entropy, resulting in a first-order transition. Moreover, the complexation can be stabilized by solvent-polymer interactions, instead of the usual specific binding interactions. Various types of unconventional phase diagrams are predicted. For example, phase separation with decreasing χ-parameter between duplex polymer and solvent can be induced, leading to a lower critical solution temperature (LCST) behavior. Multiphase coexistence points at which two, three, or four phases coexist are also obtained. Under certain conditions a homogeneous phase becomes unstable when the polymer chain length is decreased, in contrast to the standard Flory-Huggins theory.

Conformation of a tethered polymer in a leaky nanocavity.

The conformation of an ideal polymer chain confined in a box with a D x D hole is studied by N-step random walk simulations. For a polymer chain tethered inside the box, three conformational states are observed when the chain length is increased. For short chains the polymer assumes "mushroom" configurations. Increasing the chain length leads to a state in which the polymer fills the box. When the chain is long enough, the polymer escapes from the box, assuring an overall random walk state. Probability distributions of the free end and end-to-end distance are used to characterize polymer conformations. The escape transition is determined by the disappearance of the bimodal feature in the end-to-end probability density function. A crossover of the free energy difference between the confined and escaped states signals an escape transition analogous to the coil-globule transition of a free ideal chain.

Self-consistent field theory of polymer-ionic molecule complexation.

A self-consistent field theory is developed for polymers that are capable of binding small ionic molecules (adsorbates). The polymer-ionic molecule association is described by Ising-like binding variables, C(i) ((a))(kDelta)(=0 or 1), whose average determines the number of adsorbed molecules, n(BI). Polymer gelation can occur through polymer-ionic molecule complexation in our model. For polymer-polymer cross-links through the ionic molecules, three types of solutions for n(BI) are obtained, depending on the equilibrium constant of single-ion binding. Spinodal lines calculated from the mean-field free energy exhibit closed-loop regions where the homogeneous phase becomes unstable. This phase instability is driven by the excluded-volume interaction due to the single occupancy of ion-binding sites on the polymers. Moreover, sol-gel transitions are examined using a critical degree of conversion. A gel phase is induced when the concentration of adsorbates is increased. At a higher concentration of the adsorbates, however, a re-entrance from a gel phase into a sol phase arises from the correlation between unoccupied and occupied ion-binding sites. The theory is applied to a model system, poly(vinyl alcohol) and borate ion in aqueous solution with sodium chloride. Good agreement between theory and experiment is obtained.

Orientational imaging of single molecules by using azimuthal and radial polarizations.

Three-dimensional molecular orientations of single fluorescence molecules in polymeric thin films were measured by focused azimuthally and radially polarized light, in which we found that the fluorescence intensity was dependent on the depth position of the molecule with respect to the film surface. We found that the fluorescence intensity for a molecule which is 80 nm deep in the film excited by radial polarization is appreciably larger when compared with the fluorescence intensity for a molecule which is also excited by radial polarization but which is closer to the polymer/air interface, a feature which leads to different fluorescence intensities, under excitation by radial polarization, for molecules with the same polar orientation but with different depths inside the film. We also found that the variation of fluorescence intensity from a molecule inside an 80 nm film in radial polarization is appreciably larger compared with one in azimuthal polarization. These findings were confirmed by comparing experiments using different thickness films with theoretically calculated electric field distributions.

Study of entropy-driven self-assembly of rigid macromolecules.

A simple model composed of two rigid macromolecules (adsorbents) immersed in a large number of small molecules (adsorbates) is used to study entropy-driven association processes. The surfaces of the adsorbents are capable of adsorbing the smaller adsorbates. The partition function of the model is obtained analytically. The probability of dimerization and the number of adsorbed molecules are shown to depend on the enthalpy and the entropy differences between the assembled and the disassembled states. Under certain conditions, dimerization of the macromolecules occurs with increasing temperature. This entropy-driven self-assembly is originated from an overall entropy gain due to the release of the adsorbed small molecules, leading to a large peak in the heat capacity due to the dimer formation. The desorption of the adsorbates induces a sharp change in the first-order derivative of the free energy, resulting in another large peak in the heat capacity. A temperature-induced re-entrance into the dimer state is also contained in the model.