Multi-Architecture Monte-Carlo (MC) Simulation of Soft Coarse-Grained Polymeric Materials: SOft coarse grained Monte-carlo Acceleration (SOMA)

Multi-component polymer systems are important for the development of new materials because of their ability to phase-separate or self-assemble into nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction with a soft, coarse-grained polymer model is an established technique to investigate these soft-matter systems. Here we present an im- plementation of this method: SOft coarse grained Monte-carlo Accelera- tion (SOMA). It is suitable to simulate large system sizes with up to billions of particles, yet versatile enough to study properties of different kinds of molecular architectures and interactions. We achieve efficiency of the simulations commissioning accelerators like GPUs on both workstations as well as supercomputers. The implementa- tion remains flexible and maintainable because of the implementation of the scientific programming language enhanced by OpenACC pragmas for the accelerators. We present implementation details and features of the program package, investigate the scalability of our implementation SOMA, and discuss two applications, which cover system sizes that are difficult to reach with other, common particle-based simulation methods

A Temperature and Abundance Retrieval Method for Exoplanet Atmospheres

We present a new method to retrieve molecular abundances and temperature profiles from exoplanet atmosphere photometry and spectroscopy. We run millions of 1D atmosphere models in order to cover the large range of allowed parameter space, and present error contours in the atmospheric properties, given the data. In order to run such a large number of models, we have developed a parametric pressure-temperature (P-T) profile coupled with line-by-line radiative transfer, hydrostatic equilibrium, and energy balance, along with prescriptions for non-equilibrium molecular composition and energy redistribution. We apply our temperature and abundance retrieval method to the atmospheres of two transiting exoplanets, HD 189733b and HD 209458b, which have the best available Spitzer and HST observations. For HD 189733b, we find efficient day-night redistribution of energy in the atmosphere, and molecular abundance constraints confirming the presence of H2O, CO, CH4, and CO2. For HD 209458b, we confirm and constrain the day-side thermal inversion in an average 1D temperature profile. We also report independent detections of H$_2$O, CO, CH$_4$ and CO$_2$ on the dayside of HD 209458b, based on six-channel Spitzer photometry. We report constraints for HD 189733b due to individual data sets separately; a few key observations are variable in different data sets at similar wavelengths. Moreover, a noticeably strong carbon dioxide absorption in one data set is significantly weaker in another. We must, therefore, acknowledge the strong possibility that the atmosphere is variable, both in its energy redistribution state and in the chemical abundances.Comment: 20 pages in emulateapj format, 11 figures. Final version, after proof correction

Graphene and Related Materials for the Internet of Bio-Nano Things

Internet of Bio-Nano Things (IoBNT) is a transformative communication framework, characterized by heterogeneous networks comprising both biological entities and artificial micro/nano-scale devices, so-called Bio-Nano Things (BNTs), interfaced with conventional communication networks for enabling innovative biomedical and environmental applications. Realizing the potential of IoBNT requires the development of new and unconventional communication technologies, such as molecular communications, as well as the corresponding transceivers, bio-cyber interfacing technologies connecting the biochemical domain of IoBNT to the electromagnetic domain of conventional networks, and miniaturized energy harvesting and storage components for the continuous power supply to BNTs. Graphene and related materials (GRMs) exhibit exceptional electrical, optical, biochemical, and mechanical properties, rendering them ideal candidates for addressing the challenges posed by IoBNT. This perspective article highlights recent advancements in GRM-based device technologies that are promising for implementing the core components of IoBNT. By identifying the unique opportunities afforded by GRMs and aligning them with the practical challenges associated with IoBNT, particularly in the materials domain, our aim is to accelerate the transition of envisaged IoBNT applications from theoretical concepts to practical implementations, while also uncovering new application areas for GRMs

Phase gate and readout with an atom/molecule hybrid platform

We suggest a combined atomic/molecular system for quantum computation, which takes advantage of highly developed techniques to control atoms and recent experimental progress in manipulation of ultracold molecules. We show that two atoms of different species in a given site, {\it e.g.}, in an optical lattice, could be used for qubit encoding, initialization and readout, with one atom carrying the qubit, the other enabling a gate. In particular, we describe how a two-qubit phase gate can be realized by transferring a pair of atoms into the ground rovibrational state of a polar molecule with a large dipole moment, and allowing two molecules to interact via their dipole-dipole interaction. We also discuss how the reverse process of coherently transferring a molecule into a pair of atoms could be used as a readout tool for molecular quantum computers

The physics of extreme sensitivity in whispering gallery mode optical biosensors

Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and nonspecific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, λ_R, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored