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

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

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

Effective elastic thickness in the Central Andes. Correlation to orogenic deformation styles and lower crust high-gravity anomaly

Global studies have assessed the importance of elastic thickness (Te) on orogenic evolution, showing that the style and nature of upper crustal shortening are influenced by the inherited lithospheric strength. Thus, pioneer works have identified that the upper crustal deformation style in the easternmost sector of the Central Andes in South America are related to the elastic thickness (Te). There, the thick-skinned and pure-shear style of Santa Bárbara system was initially related to the existence of low Te values. In contrast, the thin-skinned and simple-shear style of deformation in the Subandean system involves high Te values. However, more recent Te studies in the Central Andes present conflicting results which lead to question this straightforward relation. Results from these studies show a strong dependence on the applied methodology hampering the general understanding of the lithospheric thermo-mechanical state of the Central Andes. To contribute to this issue, we perform a high-resolution Te map, using forward modeling by solving flexural equation of infinite plate model in two dimensions. To achieve this, the crust-mantle interface was calculated using a high-resolution gravity anomaly dataset which combines satellite and terrestrial data, and an average density contrast. Additionally, the gravity anomaly and the foreland basin depth in the Central Andes were best predicted by considering that lower crustal rocks fill the space deflected downward in the plate model. The obtained Te values show an inverse correlation with previous heat flow studies, and a strong spatial correlation with the styles and mechanisms of deformation in the easternmost sector of the Central Andes. In the Santa Bárbara system Te values less than 10 km predominate, whereas in the Subandean system high Te values were observed. Such high values correlate with the orogenic curvature and with an shallower gravity Moho zone, which breaks the regional trend of the Central Andes. This shallower gravity Moho is linked to a high-gravity anomaly located in the east part of the Eastern Cordillera and Subandean system. These results are also correlated with a high-velocity zone in the upper mantle previously found by receiver functions studies. This correlation could indicate changes in the properties of the lower crustal rocks that justify the shallower gravity Moho zone and explain in part the highest Te values.Fil: Garcia, Hector Pedro Antonio. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gianni, Guido Martin. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lupari, Marianela Nadia. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Sanchez, Marcos Ariel. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Soler, Santiago Rubén. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ruiz, Francisco. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; ArgentinaFil: Lince Klinger, Federico Gustavo. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Geofísico Sismológico Volponi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

NRF2 and primary cilia: An emerging partnership

When not dividing, many cell types target their centrosome to the plasma membrane, where it nucleates assembly of a primary cilium, an antenna-like signaling structure consisting of nine concentric microtubule pairs surrounded by membrane. Primary cilia play important pathophysiological roles in many tissues, their dysfunction being associated with cancer and ciliopathies, a diverse group of congenital human diseases. Several recent studies have unveiled functional connections between primary cilia and NRF2 (nuclear factor erythroid 2-related factor 2), the master transcription factor orchestrating cytoprotective responses to oxidative and other cellular stresses. These NRF2-cilia relationships are reciprocal: primary cilia, by promoting autophagy, downregulate NRF2 activity. In turn, NRF2 transcriptionally regulates genes involved in ciliogenesis and Hedgehog (Hh) signaling, a cilia-dependent pathway with major roles in embryogenesis, stem cell function and tumorigenesis. Nevertheless, while we found that NRF2 stimulates ciliogenesis and Hh signaling, a more recent study reported that NRF2 negatively affects these processes. Herein, we review the available evidence linking NRF2 to primary cilia, suggest possible explanations to reconcile seemingly contradictory data, and discuss what the emerging interplay between primary cilia and NRF2 may mean for human health and disease.This work was funded by European Regional Development Fund (ERDF/FEDER)-cofunded grants from the Spanish Ministry of Economy and Competitiveness (MINECO) to F.R.G.G. (SAF2015-66568-R and RYC2013-14887). A.M.H. was supported by a FEDER-cofunded predoctoral contract from the Community of Madrid governmen

Interface inductive currents and carrier injection in hybrid perovskite single crystals

nterfaces between the absorbing perovskite and transporting layers are gaining attention as the key locus that governs solar cell operation and long term performance. The interplay of ionic and electronic processes, along with the asymmetrical architecture of any solar cell, makes the interpretation of electrical measurements always inconclusive. A strategy to progress in relating electric responses, operating mechanisms, and device architecture relies upon simplifying the probing structure. Macroscopic CH3NH3PbBr3 single crystals with symmetrical contacts are tested by means of long-time current transient and impedance spectroscopy. It is observed that interfaces govern carrier injection to (and extraction from) perovskite layers through an inductive (negative capacitance) mechanism with a response time in the range of ∼1–1001–100 s under dark conditions and inert atmosphere. Current transient exhibits a slow recovering after the occurrence of an undershoot, signaling a complex carrier dynamics which involves changes in surface state occupancy

On Managing Knowledge for MAPE-K Loops in Self-Adaptive Robotics Using a Graph-Based Runtime Model

Service robotics involves the design of robots that work in a dynamic and very open environment, usually shared with people. In this scenario, it is very difficult for decision-making processes to be completely closed at design time, and it is necessary to define a certain variability that will be closed at runtime. MAPE-K (Monitor–Analyze–Plan–Execute over a shared Knowledge) loops are a very popular scheme to address this real-time self-adaptation. As stated in their own definition, they include monitoring, analysis, planning, and execution modules, which interact through a knowledge model. As the problems to be solved by the robot can be very complex, it may be necessary for several MAPE loops to coexist simultaneously in the robotic software architecture endowed in the robot. The loops will then need to be coordinated, for which they can use the knowledge model, a representation that will include information about the environment and the robot, but also about the actions being executed. This paper describes the use of a graph-based representation, the Deep State Representation (DSR), as the knowledge component of the MAPE-K scheme applied in robotics. The DSR manages perceptions and actions, and allows for inter- and intra-coordination of MAPE-K loops. The graph is updated at runtime, representing symbolic and geometric information. The scheme has been successfully applied in a retail intralogistics scenario, where a pallet truck robot has to manage roll containers for satisfying requests from human pickers working in the warehousePartial funding for open access charge: Universidad de Málaga. This work has been partially developed within SA3IR (an experiment funded by EU H2020 ESMERA Project under Grant Agreement 780265), the project RTI2018-099522-B-C4X, funded by the Gobierno de España and FEDER funds, and the B1-2021_26 project, funded by the University of Málaga

Effect of the polymer structure on the viscoelastic and interfacial healing behaviour of poly(urea-urethane) networks containing aromatic disulphides

The macroscopic interfacial healing behaviour in a series of urea-urethane networks as function of the hydrogen bonds and disulphides content is presented. The polymers were prepared with different crosslinking densities but with the same amount of dynamic covalent bonds (disulphide linkages). Tensile and fracture measurements were adopted to evaluate the degree of recovery of the mechanical properties after damage. Healing kinetics and healing efficiencies were quantitatively determined as a function of network composition, healing temperature and contact time. Finally, the recovery of mechanical properties was correlated with the viscoelastic response of the networks through rheological measurements and time-temperature superposition principle (TTS). The application of the TTS approach on both fracture healing and DMTA and subsequent mathematical descriptive model led to a better understanding of the influence of polymer architecture and that of the amount of reversible groups on the healing process