Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis.

In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37 °C) and moderate cold (10 °C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis

Molecular Dynamics Simulation of Solvent-Polymer Interdiffusion. I. Fickian diffusion

The interdiffusion of a solvent into a polymer melt has been studied using large scale molecular dynamics and Monte Carlo simulation techniques. The solvent concentration profile and weight gain by the polymer have been measured as a function of time. The weight gain is found to scale as t^{1/2}, which is expected for Fickian type of diffusion. The concentration profiles are fit very well assuming Fick's second law with a constant diffusivity. The diffusivity found from fitting Fick's second law is found to be independent of time and equal to the self diffusion constant in the dilute solvent limit. We separately calculated the diffusivity as a function of concentration using the Darken equation and found that the diffusivity is essentially constant for the concentration range relevant for interdiffusion.Comment: 17 pages and 7 figure

Scattering of a proton with the Li4 cluster: non-adiabatic molecular dynamics description based on time-dependent density-functional theory

We have employed non-adiabatic molecular dynamics based on time-dependent density-functional theory to characterize the scattering behaviour of a proton with the Li$_4$ cluster. This technique assumes a classical approximation for the nuclei, effectively coupled to the quantum electronic system. This time-dependent theoretical framework accounts, by construction, for possible charge transfer and ionization processes, as well as electronic excitations, which may play a role in the non-adiabatic regime. We have varied the incidence angles in order to analyze the possible reaction patterns. The initial proton kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects. For all the incidence angles considered the proton is scattered away, except in one interesting case in which one of the Lithium atoms captures it, forming a LiH molecule. This theoretical formalism proves to be a powerful, effective and predictive tool for the analysis of non-adiabatic processes at the nanoscale.Comment: 18 pages, 4 figure

Temperature Dependence of Low-Lying Electronic Excitations of LaMnO_3

We report on the optical properties of undoped single crystal LaMnO_3, the parent compound of the colossal magneto-resistive manganites. Near-Normal incidence reflectance measurements are reported in the frequency range of 20-50,000 cm-1 and in the temperature range 10-300 K. The optical conductivity, s_1(w), is derived by performing a Kramers-Kronig analysis of the reflectance data. The far-infrared spectrum of s_1(w) displays the infrared active optical phonons. We observe a shift of several of the phonon to high frequencies as the temperature is lowered through the Neel temperature of the sample (T_N = 137 K). The high-frequency s_1(w) is characterized by the onset of absorption near 1.5 eV. This energy has been identified as the threshold for optical transitions across the Jahn-Teller split e_g levels. The spectral weight of this feature increases in the low-temperature state. This implies a transfer of spectral weight from the UV to the visible associated with the paramagnetic to antiferromagnetic state. We discuss the results in terms of the double exchange processes that affect the optical processes in this magnetic material.Comment: 7 pages, 5 figure