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We have performed molecular dynamics simulations on a glass-forming liquid consisting of a three-dimensional binary mixture of soft spheres. We show that a peak in the specific heat versus temperature can occur because a glassy system that shows no signs of aging progresses so slowly through the energy landscape that the minimum sampling time needed to obtain accurate thermodynamic averages exceeds the observation time. We develop a systematic technique to determine the equilibrium value of the specific heat and the minimum sampling time. Below the temperature of the specific heat peak, the minimum sampling time is orders of magnitude longer than the alpha relaxation time. We find that an equilibrium system that is not undergoing structural relaxation or aging has a frequency dependent specific heat that rises as the frequency decreases. The rise occurs at frequencies corresponding to periods that are long enough for the system to sample statistically independent energies. When the period is comparable to the minimum sampling time, the frequency dependent specific heat reaches a plateau. As a result, the specific heat has a frequency dependence at frequencies orders of magnitude lower than is implied by the inverse alpha relaxation time.

We present a novel view of the standard model of tunneling two level systems (TLS) to explain the puzzling universal value of a quantity, C ∼ 3 × 10 −4 , that characterizes phonon scattering in glasses below 1 K as reflected in thermal conductivity, ultrasonic attenuation, internal friction, and the change in sound velocity. Physical considerations lead to a broad distribution of phonon-TLS couplings that (1) exponentially renormalize tunneling matrix elements, and (2) reduce the TLS density of states through TLS-TLS interactions. We find good agreement between theory and experiment for a variety of individual glasses.

SUMMARY Post-translational modification of tubulin provides differential functions to microtubule networks. Here, we address the role of tubulin acetylation on the penetrative capacity of cells undergoing radial intercalation, which is the process by which cells move apically, insert between outer cells, and join an epithelium. There are opposing forces that regulate intercalation, namely, the restrictive forces of the epithelial barrier versus the penetrative forces of the intercalating cell. Positively and negatively modulating tubulin acetylation in intercalating cells alters the developmental timing such that cells with more acetylation penetrate faster. We find that intercalating cells preferentially penetrate higher-order vertices rather than the more prevalent tricellular vertices. Differential timing in the ability of cells to penetrate different vertices reveals that lower-order vertices represent more restrictive sites of insertion. We shift the accessibility of intercalating cells toward more restrictive junctions by increasing tubulin acetylation, and we provide a geometric-based mathematical model that describes our results.

We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming liquid consisting of a two component mixture of soft spheres in three dimensions. As the temperature is lowered (or as the density is increased), the generalized compressibility drops sharply at the glass transition, with the drop becoming more and more abrupt as the measurement time increases. At our longest measurement times, the drop occurs approximately at the mode coupling temperature TC . The drop in the linear generalized compressibility occurs at the same temperature as the peak in the specific heat. By examining the inherent structure energy as a function of temperature, we find that our results are consistent with the kinetic view of the glass transition in which the system falls out of equilibrium. We find no size dependence and no evidence for a second order phase transition though this does not exclude the possibility of a phase transition below the observed glass transition temperature. We discuss the relation between the linear generalized compressibility and the ordinary isothermal compressibility as well as the static structure factor.