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Freed, Karl F.

Publications and source records attributed to Freed, Karl F..

Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water"

Best et al . claim that we provide no convincing basis to assert that a discrepancy remains between FRET and SAXS results on the dimensions of disordered proteins under physiological conditions. We maintain that a clear discrepancy is apparent in our and other recent publications, including results shown in the Best et al . comment. A plausible origin is fluorophore interactions in FRET experiments.

Riback, Joshua A. (ORCID:0000000215164484)↗

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward Molecular Engineering of Polymer Glasses

Glass formation has been central to fabrication technologies since the dawn of civilization. Glasses not only encompass window panes, the insulation in our homes, the optical fibers supplying our cable TV, and vessels for eating and drinking, but they also include a vast array of ‘‘plastic’’ polymeric materials. Glasses find applications in high technology (e.g., producing microelectronic materials, etc., amorphous semiconductors), and recent advances have created ‘‘plastic metallic glasses’’ that are promising for fabricating everyday structural materials. Many commercially relevant systems, such as microemulsions and colloidal suspensions, have complex molecular structures and thus solidify by glass formation. Despite the importance of understanding the fundamental nature of glass formation for the synthesis of new materials, a predictive molecular theory has been lacking. Much of our understanding of glass formation derives from the analysis of experimental data, a process that has uncovered a number of interesting universal behaviors, namely, relations between properties that are independent of molecular details. However, these empirically derived relations and their limitations remain to be understood on the basis of theories, and, more importantly, there is strong need for theories of the explicit variation with molecular system to enable the rational design and tailoring of new materials. We have recently developed the generalized entropy theory, the only analytic, theory that enables describing the dependence of the properties of glass-formation on monomer molecular structures. These properties include the two central quantities of glass formation, the glass transition temperature and the glass fragility parameter, material dependent properties that govern how a material may be processed (e.g., by extrusion, ink jet, molding, etc.) Our recent works, which are further described below, extend the studies of glass formation in polymer systems to test the theory by directly comparing between the predictions of our generalized entropy theory with experiment and with simulations and to expand the vistas of the theory to describe a wider range of important systems (e.g. glass formation in binary blends and systems with specific interactions) and phenomena that are describable by the generalized entropy theory. In addition, we have addressed longstanding fundamental problems associated with the validity of the Adam-Gibbs theory, one of the underpinnings of the general entropy theory. Theoretical advances to enable describing the properties of glass-formation over a wider class of important polymeric systems, included semi-flexible systems, the more general situation of specific interactions, and more. Our recent work removes the simplest approximation uses the simplest model in which the interaction is approximated by a single, monomer average. Thus, the theory has been extended to allow some variations of the energy parameters between the atoms within the monomers. The theory has also been extended to include all the contributions from chain semi-flexibility. Both projects are extremely difficult, but the payback is that the process of solving the problems developed strong theoretical skills in Dr. Xu, who has recently begun a postdoc position at ORNL. The theory has also been extended to describe glass formation in partially miscible blends, with good general agreement with experiment. Again, the development of the theory presented an extremely difficult problem, but the payback is the development of a theory for a very important class of systems. Another project provides an extremely simple approximation for certain properties of glass formation in polymer melts and should make the theory more accessible to everyone.

36 MATERIALS SCIENCE↗

Image method for induced surface charge from many-body system of dielectric spheres

Charged dielectric spheres embedded in a dielectric medium provide the simplest model for many-body systems of polarizable ions and charged colloidal particles. We provide a multiple scattering formulation for the total electrostatic energy for such systems and demonstrate that the polarization energy can be rapidly evaluated by an image method that generalizes the image methods for conducting spheres. Furthermore, individual contributions to the total electrostatic energy are ordered according to the number of polarized surfaces involved, and each additional surface polarization reduces the energy by a factor of $(a/R)^3ϵ$, where $a$ is the sphere radius, $R$ the average inter-sphere separation, and $ϵ$ the relevant dielectric mismatch at the interface. Explicit expressions are provided for both the energy and the forces acting on individual spheres, which can be readily implemented in Monte Carlo and molecular dynamics simulations of polarizable charged spheres, thereby avoiding costly computational techniques that introduce a surface charge distribution that requires numerical solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A theory of interactions between polarizable dielectric spheres

Surface charging or polarization can strongly affect the nature of interactions between charged dielectric objects, particularly when sharp dielectric discontinuities are involved. The perturbative theory presented here efficiently accounts for this effect by introducing a generalized image method that enables the rapid evaluation of the electrostatic energies and forces that arise in many-body systems. The theory is validated by comparison to full numerical solutions. The importance of polarizability is then examined in the context of clusters of dielectric spheres, as well as a periodic crystal of charged dielectric spheres arranged into an NaCl-type lattice.

Qin, Jian↗

Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory

Standard Flory-Huggins (FH) theory is utilized to describe the enigmatic cosolvency and cononsolvency phenomena for systems of polymers dissolved in mixed solvents. In particular, phase boundaries (specifically upper critical solution temperature spinodals) are calculated for solutions of homopolymers B in pure solvents and in binary mixtures of small molecule liquids A and C. The miscibility (or immiscibility) patterns for the ternary systems are classified in terms of the FH binary interaction parameters (χ{sub αβ}) and the ratio r = ϕ{sub A}/ϕ{sub C} of the concentrations ϕ{sub A} and ϕ{sub C} of the two solvents. The trends in miscibility are compared to those observed for blends of random copolymers (A{sub x}C{sub 1−x}) with homopolymers (B) and to those deduced for A/B/C solutions of polymers B in liquid mixtures of small molecules A and C that associate into polymeric clusters (A{sub p}C{sub q}){sub i}, (i = 1, 2, …, ∞). Although the classic FH theory is able to explain cosolvency and cononsolvency phenomena, the theory does not include a consideration of the mutual association of the solvent molecules and the competitive association between the solvent molecules and the polymer. These interactions can be incorporated in refinements of the FH theory, and the present paper provides a foundation for such extensions for modeling the rich thermodynamics of polymers in mixed solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Communication: The simplified generalized entropy theory of glass-formation in polymer melts

While a wide range of non-trivial predictions of the generalized entropy theory (GET) of glass-formation in polymer melts agree with a large number of observed universal and non-universal properties of these glass-formers and even for the dependence of these properties on monomer molecular structure, the huge mathematical complexity of the theory precludes its extension to describe, for instance, the perplexing, complex behavior observed for technologically important polymer films with thickness below ∼100 nm and for which a fundamental molecular theory is lacking for the structural relaxation. The present communication describes a hugely simplified version of the theory, called the simplified generalized entropy theory (SGET) that provides one component necessary for devising a theory for the structural relaxation of thin polymer films and thereby supplements the first required ingredient, the recently developed Flory-Huggins level theory for the thermodynamic properties of thin polymer films, before the concluding third step of combining all the components into the SGET for thin polymer films. Comparisons between the predictions of the SGET and the full GET for the four characteristic temperatures of glass-formation provide good agreement for a highly non-trivial model system of polymer melts with chains of the structure of poly(n-α olefins) systems where the GET has produced good agreement with experiment. The comparisons consider values of the relative backbone and side group stiffnesses such that the glass transition temperature decreases as the amount of excess free volume diminishes, contrary to general expectations but in accord with observations for poly(n-alkyl methacrylates). Moreover, the SGET is sufficiently concise to enable its discussion in a standard course on statistical mechanics or polymer physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lattice cluster theory for dense, thin polymer films

While the application of the lattice cluster theory (LCT) to study the miscibility of polymer blends has greatly expanded our understanding of the monomer scale molecular details influencing miscibility, the corresponding theory for inhomogeneous systems has not yet emerged because of considerable technical difficulties and much greater complexity. Here, we present a general formulation enabling the extension of the LCT to describe the thermodynamic properties of dense, thin polymer films using a high dimension, high temperature expansion. Whereas the leading order of the LCT for bulk polymer systems is essentially simple Flory-Huggins theory, the highly non-trivial leading order inhomogeneous LCT (ILCT) for a film with L layers already involves the numerical solution of 3(L − 1) coupled, highly nonlinear equations for the various density profiles in the film. The new theory incorporates the essential “transport” constraints of Helfand and focuses on the strict imposition of excluded volume constraints, appropriate to dense polymer systems, rather than the maintenance of chain connectivity as appropriate for lower densities and as implemented in self-consistent theories of polymer adsorption at interfaces. The ILCT is illustrated by presenting examples of the computed profiles of the density, the parallel and perpendicular bonds, and the chain ends for free standing and supported films as a function of average film density, chain length, temperature, interaction with support, and chain stiffness. The results generally agree with expected general trends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Benchmarking all-atom simulations using hydrogen exchange

Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to assess their description of protein folding, yet the results remain difficult to validate experimentally. We apply a combination of hydrogen exchange, NMR, and other techniques to test the simulations with a resolution of single H-bonds. Several significant discrepancies between the simulations and experimental data were uncovered for regions of the energy surface outside of the native basin. This comparison yields suggestions for improving the force fields and provides a general method for experimentally validating folding simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗