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Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV aborption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. The software is available at http://bioinformatics.bc.edu/clotelab/RNAentropy.

The excitation of surface plasmons in magnetic nano-structures can strongly influence their magneto-optical properties. Here, we use photoemission electron microscopy to map the spatial distribution of the electric near-field on a nano-patterned magnetic surface that supports plasmon polaritons. By using different photon energies and polarization states of the incident light we reveal that the electric near-field is either concentrated in spots forming a hexagonal lattice with the same symmetry as the Ni nano-pattern or in stripes oriented along the $\Gamma$-K direction of the lattice and perpendicular to the polarization direction. We show that the polarization-dependent near-field enhancement on the patterned surface is directly correlated to both the excitation of surface plasmon polaritons on the patterned surface as well as the enhancement of the polar magneto-optical Kerr effect.

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 figures

Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure, or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. The web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0, Comment: 16 pages, 3 figures. Accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0 Accepted for publication in Nucleic Acid Research

Plasmonic antennas integrated on silicon devices have large and yet unexplored potential for controlling and routing light signals. Here, we present theoretical calculations of a hybrid silicon-metallic system in which a single gold nanoantenna embedded in a single-mode silicon waveguide acts as a resonance-driven filter. As a consequence of scattering and interference, when the resonance condition of the antenna is met, the transmission drops by 85% in the resonant frequency band. Firstly, we study analytically the interaction between the propagating mode and the antenna by including radiative corrections to the scattering process and the polarization of the waveguide walls. Secondly, we find the configuration of maximum interaction and numerically simulate a realistic nanoantenna in a silicon waveguide. The numerical calculations show a large suppression of transmission and three times more scattering than absorption, consequent with the analytical model. The system we propose can be easily fabricated by standard silicon and plasmonic lithographic methods, making it promising as real component in future optoelectronic circuits., Comment: 10 pages, 5 figures