Ultrafast dynamics of electron-phonon coupling in a metal

In the past decade, the advent of time-resolved spectroscopic tools has provided a new ground to explore fundamental interactions in solids and to disentangle degrees of freedom whose coupling leads to broad structures in the frequency domain. Time- and angle-resolved photoemission spectroscopy (tr-ARPES) has been utilized to directly study the relaxation dynamics of a metal in the presence of electron-phonon coupling. The effect of photo-excitations on the real and imaginary part of the self-energy as well as the time scale associated with different recombination processes are discussed. In contrast to a theoretical model, the phonon energy does not set a clear scale governing quasiparticle dynamics, which is also different from the results observed in a superconducting material. These results point to the need for a more complete theoretical framework to understand electron-phonon interaction in a photo-excited state.Comment: 4 figure

Detecting distant homologs using phylogenetic tree-based HMMs

It is often desired to identify further homologs of a family of biological sequences from the ever-growing sequence databases. Profile hidden Markov models excel at capturing the common statistical features of a group of biological sequences. With these common features, we can search the biological database and find new homologous sequences. Most general profile hidden Markov model methods, however, treat the evolutionary relationships between the sequences in a homologous group in an ad-hoc manner. We hereby introduce a method to incorporate phylogenetic information directly into hidden Markov models, and demonstrate that the resulting model performs better than most of the current multiple sequence-based methods for finding distant homologs. Proteins 2003;52:446–453. © 2003 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34977/1/10373_ftp.pd

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

<p>Abstract</p> <p>Background</p> <p>Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations.</p> <p>Results</p> <p>We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively estimating the evolutionary process. Using two large datasets, we show that qualitative changes in site-specific substitution properties over time occurred significantly. To test whether this unaccounted qualitative variation can lead to an erroneous phylogenetic tree, we analyzed a concatenation of mitochondrial proteins in which Cnidaria and Porifera were erroneously grouped. The progressive removal of the sites with the most heterogeneous CAT profiles across clades led to the recovery of the monophyly of Eumetazoa (Cnidaria+Bilateria), suggesting that this heterogeneity can negatively influence phylogenetic inference.</p> <p>Conclusion</p> <p>The time-heterogeneity of the amino-acid replacement process is therefore an important evolutionary aspect that should be incorporated in future models of sequence change.</p

Friction Reduction by Laser Irradiation for a Friction System Using Bearing Steel and Aluminum Alloy in Engine Oil

Aluminum alloy sliding components are widely used in internal combustion engines. However, aluminum easily adheres to the countersurface, resulting in high friction. Hence, laser irradiation was used to oxidize the aluminum surface and promote tribofilm formation using molybdenum dithiocarbamate and zinc dialkyldithiophosphate (ZnDTP). This study investigated laser irradiation to reduce friction between steel balls and aluminum disks in fully formulated engine oil. Laser scanning was used to create 100-μm-pitch concentric circles on the disks. The friction behavior was classified into two modes: no friction reduction (mode-I, μ: 0.09–0.12) and friction reduction after the high-friction period (mode-II, μ: 0.06–0.09). Friction mode transition occurred when the laser energy density exceeded the critical value (Ec). Energy-dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy showed that, for mode-I, aluminum adhered to the ball, and no sulfur-containing tribofilm formed. For mode-II, the ZnDTP-derived phosphate film formed on the disk suppressed aluminum adhesion, and a sulfur-containing tribofilm formed on the ball. Micro-Vickers tests and X-ray diffraction showed that an amorphous/nanocrystalline structure formed in the unirradiated area owing to heat diffusion under high-energy-density laser irradiation (&gt;Ec). Results suggest that metallographic structural change in the unirradiated area promotes ZnDTP reactions, causing the mode transition