Magnetic-field control of near-field radiative heat transfer and the realization of highly tunable hyperbolic thermal emitters

We present a comprehensive theoretical study of the magnetic field dependence of the near-field radiative heat transfer (NFRHT) between two parallel plates. We show that when the plates are made of doped semiconductors, the near-field thermal radiation can be severely affected by the application of a static magnetic field. We find that irrespective of its direction, the presence of a magnetic field reduces the radiative heat conductance, and dramatic reductions up to 700% can be found with fields of about 6 T at room temperature. We show that this striking behavior is due to the fact that the magnetic field radically changes the nature of the NFRHT. The field not only affects the electromagnetic surface waves (both plasmons and phonon polaritons) that normally dominate the near-field radiation in doped semiconductors, but it also induces hyperbolic modes that progressively dominate the heat transfer as the field increases. In particular, we show that when the field is perpendicular to the plates, the semiconductors become ideal hyperbolic near-field emitters. More importantly, by changing the magnetic field, the system can be continuously tuned from a situation where the surface waves dominate the heat transfer to a situation where hyperbolic modes completely govern the near-field thermal radiation. We show that this high tunability can be achieved with accessible magnetic fields and very common materials like n-doped InSb or Si. Our study paves the way for an active control of NFRHT and it opens the possibility to study unique hyperbolic thermal emitters without the need to resort to complicated metamaterials.Comment: 21 pages, 10 figure

RNA inverse folding and synthetic design

Thesis advisor: Welkin E. JohnsonThesis advisor: Peter G. CloteSynthetic biology currently is a rapidly emerging discipline, where innovative and interdisciplinary work has led to promising results. Synthetic design of RNA requires novel methods to study and analyze known functional molecules, as well as to generate design candidates that have a high likelihood of being functional. This thesis is primarily focused on the development of novel algorithms for the design of synthetic RNAs. Previous strategies, such as RNAinverse, NUPACK-DESIGN, etc. use heuristic methods, such as adaptive walk, ensemble defect optimization (a form of simulated annealing), genetic algorithms, etc. to generate sequences that minimize specific measures (probability of the target structure, ensemble defect). In contrast, our approach is to generate a large number of sequences whose minimum free energy structure is identical to the target design structure, and subsequently filter with respect to different criteria in order to select the most promising candidates for biochemical validation. In addition, our software must be made accessible and user-friendly, thus allowing researchers from different backgrounds to use our software in their work. Therefore, the work presented in this thesis concerns three areas: Create a potent, versatile and user friendly RNA inverse folding algorithm suitable for the specific requirements of each project, implement tools to analyze the properties that differentiate known functional RNA structures, and use these methods for synthetic design of de-novo functional RNA molecules.Thesis (PhD) — Boston College, 2016.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Biology

Complete RNA inverse folding: computational design of functional hammerhead ribozymes

Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.Comment: 17 pages, 2 tables, 7 figures, final version to appear in Nucleic Acids Researc

RNAiFold2T: Constraint Programming design of thermo-IRES switches

Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allow- ing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent transla- tion efficiency is approximately 50% greater at 42?C than 30?C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements. Availability: RNAiFold2T is publicly available as as part of the new re- lease RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http: //bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C++ and uses OR-Tools CP search engine.Comment: 24 pages, 5 figures, Intelligent Systems for Molecular Biology (ISMB 2016), to appear in journal Bioinformatics 201

Structural, photoluminescent properties and Judd-Ofelt analysis of Eu3+-activated CaF2 nanocubes

Eu3+-doped CaF2 nanocubes with variable europium concentration, [Eu3+] = 0, 0.6, 1.3, 1.7, 2.2 and 5.4 mol%, have been synthesized by a direct precipitation route. It has been found that, within this concentration range, the nanoparticles present the fluoride-type crystalline structure and the characteristic cubic shape of CaF2 crystals. The nanoparticle size follows a log-normal distribution with a mean value decreasing with the Eu3+ content. Rietveld refinement has been performed to calculate the lattice parameter and crystallite size. Eu3+ concentration affects both parameters giving rise to an increase in the lattice parameter and a reduction of crystallite size. The luminescent properties of Eu3+ ions in these nanostructures have been investigated under CW and pulsed excitation. A Judd-Ofelt analysis, as function of the Eu3+ content, has been performed to determine the transition probabilities, radiative lifetimes and branching ratios of the 5D0 emitting level. It was found that and Judd-Ofelt intensity parameters are dependent on the doping level, showing an evolution that indicates a decrease in the Eu3+ site local symmetry with increasing Eu3+ concentration. Finally, it has been observed that the characteristic luminescence decay time of the 5D0 manifold is reduced with increasing Eu3+ concentration. This effect is partially due to an increase of radiative transition probability, associated with a reduction in the local symmetry of the lanthanide ions, and also to the occurrence of concentration quenching effectsThis work has been partially supported by Ministerio de Economía y Competitividad and Ministerio de Ciencia, Innovación y Universidades under projects MAT2016-75716-2-2-R and RTI2018- 101020-B-I00

Breeding and scientific advances in the fight against Dutch elm disease - will they allow the use of elms in forest restoration?

Revisión de los avances científicos y de producción de planta con fin de evaluar el potencial en la recuperación del olmo común

Influence of climate variables on resin yield and secretory structures in tapped Pinus pinaster Ait. in central Spain

The role of climate and soil water availability on resin yield was evaluated. Resin yield increased with temperature, radiation and evapotranspiration values. Resin yield and axial canal size were correlated with water deficit in spring. Above a certain threshold of cumulated water deficit, summer rainfall favored resin yield. Stand density and soil quality affected the relations between climate and resin yield

Learning Criteria and Evaluation Metrics for Textual Transfer between Non-Parallel Corpora

We consider the problem of automatically generating textual paraphrases with modified attributes or stylistic properties, focusing on the setting without parallel data (Hu et al., 2017; Shen et al., 2017). This setting poses challenges for learning and evaluation. We show that the metric of post-transfer classification accuracy is insufficient on its own, and propose additional metrics based on semantic content preservation and fluency. For reliable evaluation, all three metric categories must be taken into account. We contribute new loss functions and training strategies to address the new metrics. Semantic preservation is addressed by adding a cyclic consistency loss and a loss based on paraphrase pairs, while fluency is improved by integrating losses based on style-specific language models. Automatic and manual evaluation show large improvements over the baseline method of Shen et al. (2017). Our hope is that these losses and metrics can be general and useful tools for a range of textual transfer settings without parallel corpora

Reversible Formation of Gold Halides in Single‐Crystal Hybrid‐Perovskite/Au Interface upon Biasing and Effect on Electronic Carrier Injection

Solar cells, light emitting diodes, and X‐ray detectors based on perovskite materials often incorporate gold electrodes, either in direct or indirect contact with the perovskite compound. Chemical interactions between active layers and contacts deteriorate the operation and induce degradation, being the identification of the chemical nature of such interfacial structures an open question. Chemical reactivity of gold in contact with the perovskite semiconductor leads to reversible formation of oxidized gold halide species and explains the generation of halide vacancies in the vicinity of the interface. Electrical biasing induces contact reaction and produces modifications of the current level by favoring the ability of perovskite/Au interfaces to inject electronic carriers. The current injection increment does not depend on the halogen source used, either extrinsically by iodine vapor sublimation of Au electrodes, or intrinsically by bias‐driven migration of bromide ions. In addition, the formation of a dipole‐like structure at the reacted electrode that lowers the potential barrier for electronic carriers is confirmed. These findings highlight adequate selection of the external contacts and suggest the need for a deeper understanding of contact reactivity as it dominates the operation characteristics, rather than being governed by the bulk transport properties of the charge carriers, either electronic or ionic

Genetic variation and heritability estimates of Ulmus minor and Ulmus pumila hybrids for budburst, growth and tolerance to Ophiostoma novo-ulmi

Seedlings obtained by crossing Ulmus minor and U. minor × U. pumila clones were assessed for flowering, bark beetle damage, vegetative budburst, height growth and resistance to Ophiostoma novo-ulmi. Ramets and open pollinated seedlings obtained from the parent trees were assessed for the same traits. Most progenies had similar traits to their parents, but some presented heterosis in annual growth or resistance to O. novo-ulmi. Leaf wilting was significantly lower in progenies with U. minor × U. pumila rather than U. minor as female parent (21.5 and 30.6%, respectively; P<0.05). Resistance to O. novoulmi increased significantly as a function of increased amounts of U. pumila germplasm from the female parent, suggesting that resistance to Dutch elm disease is primarily transmitted from the mother. Budburst occurred earlier in seedlings with low rather than high growth rates (P=0.0007) and percentage of wilting was negatively related to early budburst (P<0.0001). Other phenotypic relations included percentage of flowering trees and annual height growth (rp=0.44; P=0.0042), percentage of flowering trees and vegetative budburst (rp=-0.53; P=0.0004) and percentage of beetle-affected trees and annual height growth (rp=0.60; P<0.0001). Heritability estimates obtained from the regression and variance components methods ranged from 0.06 ± 0.04 to 0.64 ± 0.18, 0.10 ± 0.05 to 0.69 ± 0.17, and 0.13 ± 0.32 to 0.71 ± 0.22 for budburst, growth and tolerance to O. novo-ulmi, respectively. Broad- and narrowsense heritability values were higher when estimated 60 days post inoculation (dpi) than 15, 30 or 120 dpi. Heritability estimates and genetic gains reported indicate a high degree of additive genetic control and show the effectiveness of selection for Dutch elm disease resistance and rapid tree growth