Design of a film surface roughness-minimizing molecular beam epitaxy

Molecular beam epitaxy of germanium was used along with kinetic Monte Carlo simulations to study time-varying processing parameters and their effect on surface morphology. Epitaxial Ge films were deposited on highly oriented Ge(001) substrates, with reflection high-energy electron diffraction as a real-time sensor. The Monte Carlo simulations were used to model the growth process, and physical parameters were determined during growth under time-varying flux. A reduced version of the simulations was generated, enabling the application on an optimization algorithm. Temperature profiles were then computed that minimize surface roughness subject to various experimental constraints. The final roughness after two layers of growth was reduced to 0.32, compared to 0.36 at the maximum growth temperature. The study presented here is an initial demonstration of a general approach that could also be used to optimize properties in other materials and deposition processes

Effective transition rates for epitaxial growth using fast modulation

Thin-film deposition is an industrially important process that is highly dependent on the processing conditions. Most films are grown under constant conditions, but a few studies show that modified properties may be obtained with periodic inputs. However, assessing the effects of modulation experimentally becomes impractical with increasing material complexity. Here we consider periodic conditions in which the period is short relative to the time scales of growth. We analyze a stochastic model of thin-film growth, computing effective transition rates associated with rapid periodic process parameters. Combinations of effective rates may exist that are not attainable under steady conditions, potentially enabling new film properties. An algorithm is presented to construct the periodic input for a desired set of effective transition rates. These ideas are demonstrated in three simple examples using kinetic Monte Carlo simulations of epitaxial growth

The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes

Phylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.
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A Computational Study of Cation−π Interactions vs Salt Bridges in Aqueous Media: Implications for Protein Engineering

A direct comparison of the energetic significance of a representative salt bridge vs a representative cation−π interaction in aqueous media and in a range of organic solvents is presented using ab initio electronic structures and the SM5.42R/HF solvation model of Cramer and Truhlar. The cation−π interaction shows a well depth of 5.5 kcal/mol in water, significantly larger than the 2.2 kcal/mol seen for the salt bridge. Consistent with this idea, a survey of the Protein Data Bank reveals that energetically significant cation−π interactions are rarely completely buried within proteins, but prefer to be exposed to solvent. These results suggest that engineering surface-exposed cation−π interactions could be a novel way to enhance protein stability

Preliminary basic performance analysis of the Cedar multiprocessor memory system

Some preliminary basic results on the performance of the Cedar multiprocessor memory system are presented. Empirical results are presented and used to calibrate a memory system simulator which is then used to discuss the scalability of the system

From ab initio quantum mechanics to molecular neurobiology: A cation-pi binding site in the nicotinic receptor

The nicotinic acetylcholine receptor is the prototype ligand-gated ion channel. A number of aromatic amino acids have been identified as contributing to the agonist binding site, suggesting that cation-pi interactions may be involved in binding the quaternary ammonium group of the agonist, acetylcholine. Here we show a compelling correlation between: (i) ab initio quantum mechanical predictions of cation-pi binding abilities and (ii) EC50 values for acetylcholine at the receptor for a series of tryptophan derivatives that were incorporated into the receptor by using the in vivo nonsense-suppression method for unnatural amino acid incorporation. Such a correlation is seen at one, and only one, of the aromatic residues-tryptophan-149 of the alpha subunit. This finding indicates that, on binding, the cationic, quaternary ammonium group of acetylcholine makes van der Waals contact with the indole side chain of alpha tryptophan-149, providing the most precise structural information to date on this receptor. Consistent with this model, a tethered quaternary ammonium group emanating from position alpha 149 produces a constitutively active receptor

Incidence and viral aetiologies of acute respiratory illnesses (ARIs) in the United States: a population-based study.

We conducted prospective, community-wide surveillance for acute respiratory illnesses (ARIs) in Rochester, NY and Marshfield, WI during a 3-month period in winter 2011. We estimated the incidence of ARIs in each community, tested for viruses, and determined the proportion of ARIs associated with healthcare visits. We used a rolling cross-sectional design to sample participants, conducted telephone interviews to assess ARI symptoms (defined as a current illness with feverishness or cough within the past 7 days), collected nasal/throat swabs to identify viruses, and extracted healthcare utilization from outpatient/inpatient records. Of 6492 individuals, 321 reported an ARI within 7 days (4·9% total, 5·7% in Rochester, 4·4% in Marshfield); swabs were collected from 208 subjects. The cumulative ARI incidence for the entire 3-month period was 52% in Rochester [95% confidence interval (CI) 42-63] and 35% in Marshfield (95% CI 28-42). A specific virus was identified in 39% of specimens: human coronavirus (13% of samples), rhinovirus (12%), RSV (7%), influenza virus (4%), human metapneumovirus (4%), and adenovirus (1%). Only 39/200 (20%) had a healthcare visit (2/9 individuals with influenza). ARI incidence was ~5% per week during winter

Measurement of the ΔS=-ΔQ Amplitude from K_(e3)^0 Decay

We have measured the time distribution of the π^+e^-ν and π^-e^+ν modes from initial K^0's in a spark-chamber experiment performed at the Bevatron. From 1079 events between 0.2 and 7 K_S^0 lifetime, we find ReX=-0.069±0.036, ImX=+0.108_(-0.074)^(+0.092). This result is consistent with X=0 (relative probability = 0.25), but more than 4 standard deviations from the existing world average, +0.14 -0.13i