Abstract:
The multi-protein β-barrel assembly machine (BAM) of Escherichia coli is responsible for the folding and insertion of β-barrel containing integral outer membrane proteins (OMPs) into the bacterial outer membrane. An essential component of this complex is the BamA protein, which binds unfolded β-barrel precursors via the five polypeptide transport-associated (POTRA) domains in its N-terminus. The C-terminus of BamA contains a β-barrel domain, which tethers BamA to the outer membrane and is also thought to be involved in OMP insertion. Here we mutagenize BamA using linker scanning mutagenesis and demonstrate that all five POTRA domains are essential for BamA protein function in our experimental system. Furthermore, we generate a homology based model of the BamA β-barrel and test our model using insertion mutagenesis, deletion analysis and immunofluorescence to identify β-strands, periplasmic turns and extracellular loops. We show that the surface-exposed loops of the BamA β-barrel are essential.

Abstract:
The steady state values of the viscosity and the intrinsic ionic-conductivity of quenched melts are computed, in terms of independently measurable quantities. The frequency dependence of the ac dielectric response is estimated. The discrepancy between the corresponding characteristic relaxation times is only apparent; it does not imply distinct mechanisms, but stems from the intrinsic barrier distribution for $\alpha$-relaxation in supercooled fluids and glasses. This type of intrinsic ``decoupling'' is argued not to exceed four orders in magnitude, for known glassformers. We explain the origin of the discrepancy between the stretching exponent $\beta$, as extracted from $\epsilon(\omega)$ and the dielectric modulus data. The actual width of the barrier distribution always grows with lowering the temperature. The contrary is an artifact of the large contribution of the dc-conductivity component to the modulus data. The methodology allows one to single out other contributions to the conductivity, as in ``superionic'' liquids or when charge carriers are delocalized, implying that in those systems, charge transfer does not require structural reconfiguration.

Abstract:
Melting is analyzed dynamically as a problem of localization at a liquid-solid interface. A Lindemann-like criterion of melting is derived in terms of particular vibrational amplitudes, which turn out to equal a universal quotient (about one-tenth) of the molecular spacing, at the interface. The near universality of the Lindemann ratio apparently arises owing to strongly overdamped dynamics near melting, and despite the anharmonic interactions' being system-specific. A similar criterion is derived for structural displacements in the bulk of the {\em solid}, in particular the premelted layer; the criterion is no longer strictly universal, but still depends only on the harmonic properties of the solid. We further compute the dependence of the magnitude of the elemental molecular translations, in deeply supercooled fluids, on the temperature and the high frequency elastic constants. We show explicitly that the surface tension between distinct liquid states, near the glass transition of a supercooled liquid, is nearly evenly split between entropic and energetic contributions.

Abstract:
The random first-order transition (RFOT) theory of the structural glass transition is reviewed in a pedagogical fashion. The rigidity that emerges in crystals and glassy liquids is of the same fundamental origin. In both cases, it corresponds with a breaking of the translational symmetry; analogies with freezing transitions in spin systems can also be made. The common aspect of these seemingly distinct phenomena is a spontaneous emergence of the molecular field, a venerable and well-understood concept. In crucial distinction from periodic crystallisation, the free energy landscape of a glassy liquid is vastly degenerate, which gives rise to new length and time scales while rendering the emergence of rigidity gradual. We obviate the standard notion that to be mechanically stable a structure must be essentially unique; instead, we show that bulk degeneracy is perfectly allowed but should not exceed a certain value. The present microscopic description thus explains both crystallisation and the emergence of the landscape regime followed by vitrification in a unified, thermodynamics-rooted fashion. The article contains a self-contained exposition of the basics of the classical density functional theory and liquid theory, which are subsequently used to quantitatively estimate, without using adjustable parameters, the key attributes of glassy liquids, viz., the relaxation barriers, glass transition temperature, and cooperativity size. These results are then used to quantitatively discuss many diverse glassy phenomena, including: the intrinsic connection between the excess liquid entropy and relaxation rates, the non-Arrhenius temperature dependence of $\alpha$-relaxation, the dynamic heterogeneity, ... (see Comments for the remainder of Abstract.)

Abstract:
We formulate a minimal ansatz for local stress distribution in a solid that includes the possibility of strongly anharmonic short-length motions. We discover a broken-symmetry metastable phase that exhibits an aperiodic, frozen-in stress distribution. This aperiodic metastable phase is characterized by many distinct, nearly degenerate configurations. The activated transitions between the configurations are mapped onto the dynamics of a long range classical Heisenberg model with 6-component spins and anisotropic couplings. We argue the metastable phase corresponds to a deeply supercooled non-polymeric, non-metallic liquid, and further establish an order parameter for the glass-to-crystal transition. The spin model itself exhibits a continuous range of behaviors between two limits corresponding to frozen-in shear and uniform compression/dilation respectively. The two regimes are separated by a continuous transition controlled by the anisotropy in the spin-spin interaction, which is directly related to the Poisson ratio $\sigma$ of the material. The latter ratio and the ultra-violet cutoff of the theory determine the liquid configurational entropy. Our results suggest that liquid's fragility depends on the Poisson ratio in a non-monotonic way. The present ansatz provides a microscopic framework for computing the configurational entropy and relaxational spectrum of specific substances.

Abstract:
Semiconductor glasses exhibit many unique optical and electronic anomalies. We have put forth a semi-phenomenological scenario (J. Chem. Phys. 132, 044508 (2010)) in which several of these anomalies arise from deep midgap electronic states residing on high-strain regions intrinsic to the activated transport above the glass transition. Here we demonstrate at the molecular level how this scenario is realized in an important class of semiconductor glasses, namely chalcogen and pnictogen containing alloys. Both the glass itself and the intrinsic electronic midgap states emerge as a result of the formation of a network composed of $\sigma$-bonded atomic $p$-orbitals that are only weakly hybridized. Despite a large number of weak bonds, these $pp\sigma$-networks are stable with respect to competing types of bonding, while exhibiting a high degree of structural degeneracy. The stability is rationalized with the help of a hereby proposed structural model, by which $pp\sigma$-networks are symmetry-broken and distorted versions of a high symmetry structure. The latter structure exhibits exact octahedral coordination and is fully covalently-bonded. The present approach provides a microscopic route to a fully consistent description of the electronic and structural excitations in vitreous semiconductors.

Abstract:
We propose a structural model that treats in a unified fashion both the atomic motions and electronic excitations in quenched melts of pnictide and chalcogenide semiconductors. In Part I (submitted to J. Chem. Phys.), we argued these quenched melts represent aperiodic $pp\sigma$-networks that are highly stable and, at the same time, structurally degenerate. These networks are characterized by a continuous range of coordination. Here we present a systematic way to classify these types of coordination in terms of discrete coordination defects in a parent structure defined on a simple cubic lattice. We identify the lowest energy coordination defects with the intrinsic midgap electronic states in semiconductor glasses, which were argued earlier to cause many of the unique optoelectronic anomalies in these materials. In addition, these coordination defects are mobile and correspond to the transition state configurations during the activated transport above the glass transition. The presence of the coordination defects may account for the puzzling discrepancy between the kinetic and thermodynamic fragility in chalcogenides. Finally, the proposed model recovers as limiting cases several popular types of bonding patterns proposed earlier, including: valence-alternation pairs, hypervalent configurations, and homopolar bonds in heteropolar compounds.

Abstract:
We show that the vibrational response of a glassy liquid at finite frequencies can be described by continuum mechanics despite the vast degeneracy of the vibrational ground state; standard continuum elasticity assumes a unique ground state. The effective elastic constants are determined by the bare elastic constants of individual free energy minima of the liquid, the magnitude of built-in stress, and temperature, analogously to how the dielectric response of a polar liquid is determined by the dipole moment of the constituent molecules and temperature. In contrast with the dielectric constant---which is enhanced by adding polar molecules to the system---the elastic constants are down-renormalized by the relaxation of the built-in stress. The renormalization flow of the elastic constants has three fixed points, two of which are trivial and correspond to the uniform liquid state and an infinitely compressible solid respectively. There is also a nontrivial fixed point at the Poisson ratio equal to 1/5, which corresponds to an isospin-like degeneracy between shear and uniform deformation. The present description predicts a discontinuous jump in the (finite frequency) shear modulus at the crossover from collisional to activated transport, consistent with the RFOT theory.

Abstract:
We explore several potential issues that have been raised over the years regarding the "entropic droplet" scenario of activated transport in liquids, due to Wolynes and coworkers, with the aim of clarifying the status of various approximations of the random first order transition theory (RFOT) of the structural glass transition. In doing so, we estimate the mismatch penalty between alternative aperiodic structures, above the glass transition; the penalty is equal to the typical magnitude of free energy fluctuations in the liquid. The resulting expressions for the activation barrier and the cooperativity length contain exclusively bulk, static properties; in their simplest form they contains only the bulk modulus and the configurational entropy per unit volume. The expressions are universal in that they do not depend explicitly on the molecular detail. The predicted values for the barrier and cooperativity length and, in particular, the temperature dependence of the barrier are in satisfactory agreement with observation. We thus confirm that the entropic droplet picture is indeed not only internally-consistent but is also fully constructive, consistent with the apparent success of its many quantitative predictions. A simple view of a glassy liquid as a locally metastable, degenerate pattern of frozen-in stress emerges in the present description. Finally, we derive testable relationships between the bulk modulus and several characteristics of glassy liquids and peculiarities in low-temperature glasses.

Abstract:
We argue that the intrinsic glassy degrees of freedom in amorphous solids giving rise to the thermal conductivity plateau and the ``boson peak'' in the heat capacity at moderately low temperatures are directly connected to those motions giving rise to the two-level like excitations seen at still lower temperatures. These degrees of freedom can be thought of as strongly anharmonic transitions between the local minima of the glassy energy landscape that are accompanied by ripplon-like domain wall motions of the glassy mosaic structure predicted to occur at $T_g$ by the random first order transition theory. The energy spectrum of the vibrations of the mosaic depends on the glass transition temperature, the Debye frequency and the molecular length scale. The resulting spectrum reproduces the experimental low temperature Boson peak. The ``non-universality'' of the thermal conductivity plateau depends on $k_B T_g/\hbar \omega_D$ and arises from calculable interactions with the phonons.