Parallel genetic algorithm and parallel simulated annealing algorithm for the closest string problem

In this paper, we design genetic algorithm and simulated annealing algorithm and their parallel versions to solve the Closest String problem. Our implementation and experiments show usefulness of the parallel GA and SA algorithms

PVM algorithms for some problems in bioinformatics

We design and analyze implementation aspects of a PVM version of the well known Smith-Waterman algorithm, and then we consider other problems important for bioinformatics, such as finding longest common substring, finding repeated substrings and finding palindromes

Modeling of Exoplanet Atmospheres

Spectrally characterizing exoplanet atmospheres will be one of the fastest moving astronomical disciplines in the years to come. Especially the upcoming James Webb Space Telescope (JWST) will provide spectral measurements from the near- to mid-infrared of unprecedented precision. With other next generation instruments on the horizon, it is crucial to possess the tools necessary for interpretating observations. To this end I wrote the petitCODE, which solves for the self-consistent atmospheric structures of exoplanets, assuming chemical and radiative-convective equilibrium. The code includes scattering, and models clouds. The code outputs the planet’s observable emission and transmission spectra. In addition, I constructed a spectral retrieval code, which derives the full posterior probability distribution of atmospheric parameters from observations. I used petitCODE to systematically study the atmospheres of hot jupiters and found, e.g., that their structures depend strongly on the type of their host stars. Moreover, I found that C/O ratios around unity can lead to atmospheric inversions. Next, I produced synthetic observations of prime exoplanet targets for JWST, and studied how well we will be able to distinguish various atmospheric scenarios. Finally, I verified the implementation of my retrieval code using mock JWST observations

Visualization 1.mp4

The evolution of phase over time (ground truth, wrapped, 2D unwrapped and 3D unwrapped) is demonstrated in the video (Visualization 1)

visualization 2.mp4

The changes of cell morphology over time during the detachment process

Sequential and parallel algorithms for sequence analysis problems in bioinformatics

The study of biological and genetic information, mostly DNA data, is an extremely important subject which can provide critical information in many areas, such as understanding human diseases or discovering new drugs. A huge number of computing algorithms are developed and available now to help with the study of these, and in order to solve these problems more efficiently and accurately, much attention has been paid in recent decades to developing new and better algorithms. [continues] </p

Media 1: Real-time 3D and 4D Fourier domain Doppler optical coherence tomography based on dual graphics processing units

Originally published in Biomedical Optics Express on 01 September 2012 (boe-3-9-2162

Efficient H₂ Evolution Coupled with Oxidative Refining of Alcohols via A Hierarchically Porous Nickel Bifunctional Electrocatalyst

Water electrolysis to produce H₂ and O₂ with renewable energy input has been generally viewed as an attractive route to meet future global energy demands. However, the sluggish O₂ evolution reaction usually requires high overpotential and may yield reactive oxygen species (ROS) that can degrade the electrolyzer membrane and hence shorten the device lifetime. In addition, the potential gas crossover may result in an explosive H₂/O₂ mixture and hence safety risks. To address these issues, we herein report a general electrolysis strategy for the simultaneous H₂ production and alcohol oxidative upgrading (e.g., benzyl alcohol, 4-nitrobenzyl alcohol, 4-methylbenzyl alcohol, ethanol, and 5-hydroxymethylfurfural), in which the thermodynamics of the latter is much easier than that of water oxidation. A facile and environmentally friendly template-free electrodeposition was used to obtain a 3D hierarchically porous nickel-based electrocatalyst (hp-Ni) for such an integrated electrolysis, requiring a voltage of ∼220 mV smaller than that of water splitting to achieve 50 mA cm^–2 together with robust stability, high Faradaic efficiencies, and no formation of ROS, as well as production of valuable products at both the cathode (H₂) and anode (alcohol oxidation products). More importantly, we demonstrated that these diverse alcohol oxidations over hp-Ni exhibited similar onset potentials which were largely determined by the desirable oxidation potential of hp-Ni, irrespective of the different intrinsic thermodynamics of these alcohol oxidation reactions. This result provides a new direction for the rational design of heterogeneous transition-metal-based electrocatalysts with lower oxidation potential for more highly efficient electrocatalytic alcohol oxidation

A General Strategy for Decoupled Hydrogen Production from Water Splitting by Integrating Oxidative Biomass Valorization

Conventional water electrolyzers produce H₂ and O₂ simultaneously, such that additional gas separation steps are needed to prevent H₂/O₂ mixing. The sluggish anodic O₂ evolution reaction (OER) always results in low overall energy conversion efficiency and the product of OER, O₂, is not of significant value. In addition, the potential formation of reactive oxygen species (ROS) may lead to degradation of cell membranes and thus premature device failure. Herein we report a general concept of integrating oxidative biomass upgrading reactions with decoupled H₂ generation from water splitting. Five representative biomass substrates, ethanol, benzyl alcohol, furfural, furfuryl alcohol, and 5-hydroxymethylfurfural (HMF), were selected for oxidative upgrading catalyzed by a hierarchically porous Ni₃S₂/Ni foam bifunctional electrocatalyst (Ni₃S₂/NF). All the five organics can be oxidized to value-added liquid products at much lower overpotentials than that of OER. In particular, the electrocatalytic oxidation of HMF to the value-added 2,5-furandicarboxylic acid (FDCA) was further studied in detail. Benefiting from the more favorable thermodynamics of HMF oxidation than that of OER, the cell voltage for integrated H₂ production and HMF oxidation was significantly reduced by ∼200 mV relative to pure water splitting to achieve 100 mA cm^–2, while the oxidation product (FDCA) at the anode was much more valuable than O₂. When utilized as electrocatalysts for both cathode and anode, Ni₃S₂/NF demonstrated outstanding durability and nearly unity Faradaic efficiencies for both H₂ and FDCA production. Overall, such an integration of oxidative biomass valorization and HER via earth-abundant electrocatalysts not only avoids the generation of explosive H₂/O₂ mixture and ROS, but also yields products of high value at both electrodes with lower voltage input, maximizing the energy conversion efficiency