In the burgeoning field of proteins, the effective analysis of intricate protein data remains a formidable challenge, necessitating advanced computational tools for data processing, feature extraction, and interpretation. This study introduces ProteinFlow, an innovative framework designed to revolutionize feature engineering in protein data analysis. ProteinFlow stands out by offering enhanced efficiency in data collection and preprocessing, along with advanced capabilities in feature extraction, directly addressing the complexities inherent in multidimensional protein data sets.
View Article and Find Full Text PDFWith the explosive growth of protein-related data, we are confronted with a critical scientific inquiry: How can we effectively retrieve, compare, and profoundly comprehend these protein structures to maximize the utilization of such data resources? PS-GO, a parametric protein search engine, has been specifically designed and developed to maximize the utilization of the rapidly growing volume of protein-related data. This innovative tool addresses the critical need for effective retrieval, comparison, and deep understanding of protein structures. By integrating computational biology, bioinformatics, and data science, PS-GO is capable of managing large-scale data and accurately predicting and comparing protein structures and functions.
View Article and Find Full Text PDFFront Bioeng Biotechnol
July 2023
In the field of bioinformatics and computational biology, protein structure modelling and analysis is a crucial aspect. However, most existing tools require a high degree of technical expertise and lack a user-friendly interface. To address this problem, we developed a protein workstation called PROFASA.
View Article and Find Full Text PDFA fundamental question regarding light scattering is how whiteness, generated from multiple scattering, can be obtained from thin layers of materials. This challenge arises from the phenomenon of optical crowding, whereby, for scatterers packed with filling fractions higher than ~30%, reflectance is drastically reduced due to near-field coupling between the scatterers. Here we show that the extreme birefringence of isoxanthopterin nanospheres overcomes optical crowding effects, enabling multiple scattering and brilliant whiteness from ultra-thin chromatophore cells in shrimp.
View Article and Find Full Text PDFMany animals undergo changes in functional colors during development, requiring the replacement of integument or pigment cells. A classic example of defensive color switching is found in hatchling lizards, which use conspicuous tail colors to deflect predator attacks away from vital organs. These tail colors usually fade to concealing colors during ontogeny.
View Article and Find Full Text PDFMany oceanic prey animals use transparent bodies to avoid detection. However, conspicuous eye pigments, required for vision, compromise the organisms' ability to remain unseen. We report the discovery of a reflector overlying the eye pigments in larval decapod crustaceans and show how it is tuned to render the organisms inconspicuous against the background.
View Article and Find Full Text PDFUnderstanding exciton-exciton interaction in multiply excited nanocrystals is crucial to their utilization as functional materials. Yet, for lead halide perovskite nanocrystals, which are promising candidates for nanocrystal-based technologies, numerous contradicting values have been reported for the strength and sign of their exciton-exciton interaction. In this work, we unambiguously determine the biexciton binding energy in single cesium lead halide perovskite nanocrystals at room temperature.
View Article and Find Full Text PDFMultiply excited states in semiconductor quantum dots feature intriguing physics and play a crucial role in nanocrystal-based technologies. While photoluminescence provides a natural probe to investigate these states, room-temperature single-particle spectroscopy of their emission has proved elusive due to the temporal and spectral overlap with emission from the singly excited and charged states. Here, we introduce biexciton heralded spectroscopy enabled by a single-photon avalanche diode array based spectrometer.
View Article and Find Full Text PDFRecent studies of optical reflectors as part of the vision apparatus in the eyes of decapod crustaceans revealed assemblies of nanoscale spherulites - spherical core-shell nanoparticles with radial birefringence. Simulations performed on the system highlighted the advantages of optical anisotropy in enhancing the functionality of these structures. So far, calculations of the nanoparticle optical properties have relied on refractive indices obtained using ab-initio calculations.
View Article and Find Full Text PDFProteins mediate and perform various fundamental functions of life. This versatility of protein function is an attribute of its 3D structure. In recent years, our understanding of protein 3D structure has been complemented with advances in computational and mathematical tools for protein modelling and protein design.
View Article and Find Full Text PDFProteins mediate many essential processes of life to a degree of functional precision unmatched by any synthetic device. While engineered proteins are currently used in biotech, food, biomedicine, and material technology-based industries, the true potential of proteins is practically untapped. The emerging field of in silico protein design is predicted to provide the next quantum leap in the biotech industry.
View Article and Find Full Text PDFReflective assemblies of high refractive index organic crystals are used to produce striking optical phenomena in organisms based on light reflection and scattering. In aquatic animals, organic crystal-based reflectors are used both for image-formation and to increase photon capture. Here we report the characterization of a poorly-documented reflector in the eye of the shrimp L.
View Article and Find Full Text PDFExcitons in colloidal semiconductor nanoplatelets (NPLs) are weakly confined in the lateral dimensions. This results in significantly smaller Auger rates and, consequently, larger biexciton quantum yields, when compared to spherical quantum dots (QDs). Here we report a study of the temperature dependence of the biexciton Auger rate in individual CdSe/CdS core-shell NPLs, through the measurement of time-gated second-order photon correlations in the photoluminescence.
View Article and Find Full Text PDFSpectacular natural optical phenomena are produced by highly reflective assemblies of organic crystals. Here we show how the tapetum reflector in a shrimp eye is constructed from arrays of spherical isoxanthopterin nanoparticles and relate the particle properties to their optical function. The nanoparticles are composed of single-crystal isoxanthopterin nanoplates arranged in concentric lamellae around a hollow core.
View Article and Find Full Text PDFSpherulites are birefringent structures with spherical symmetry, typically observed in crystallized polymers. We compute the band structure of opals made of close-packed assemblies of highly birefringent spherulites. We demonstrate that spherulitic birefringence of constituent spheres does not affect the symmetries of an opal, yet significantly affects the dispersion of eigenmodes, leading to new pseudogaps in sections of the band structure and, consequently, enhanced reflectivity.
View Article and Find Full Text PDFAnimals use photonic structures in their eyes to form images, enhance sensitivity and provide camouflage. A recent exciting discovery shows that the eyes of some larval mantis shrimp possess photonic crystals that function as color filters to detect bioluminescence.
View Article and Find Full Text PDFProtein engineering and synthetic biology stand to benefit immensely from recent advances in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on individual parameters of a query protein, with output scores/metrics unique to each parameter. In reality, proteins feature multiple "parts"/functions and modification of a protein aimed at altering a given part, typically has collateral impact on other protein parts.
View Article and Find Full Text PDFContinuous monitoring of bacterial growth in aqueous media is a crucial process in academic research as well as in the biotechnology industry. Bacterial growth is usually monitored by measuring the optical density of bacteria in liquid media, using benchtop spectrophotometers. Due to the large form factor of the existing spectrophotometers, they cannot be used for live monitoring of the bacteria inside bacterial incubation chambers.
View Article and Find Full Text PDFSupercontinuum generation using photonic crystal fibers is a useful technique to generate light spanning a broad wavelength range, using femtosecond laser pulses. For some applications, one may desire higher power density at specific wavelengths. Increasing the pump power results primarily in further broadening of the output spectrum and is not particularly useful for this purpose.
View Article and Find Full Text PDFHigh precision measurements of optical beam shifts are important in various fields including sensing, atomic force microscopy, and measuring beam shifts at interfaces. Sub-micron shifts are generally measured by indirect techniques such as weak measurements. We demonstrate a straightforward and robust measurement scheme for the shift, based on a scanning quadrant photodiode (QPD) that is biased using a low noise electronic circuit.
View Article and Find Full Text PDFMetasurfaces with sub-wavelength features are useful in modulating the phase, amplitude or polarization of electromagnetic fields. While several applications are reported for light manipulation and control, the sharp phase changes would be useful in enhancing the beam shifts at reflection from a metasurface. In designed periodic patterns on metal film, at surface plasmon resonance, we demonstrate Goos-Hanchen shift of the order of 70 times the incident wavelength and the angular shifts of several hundred microradians.
View Article and Find Full Text PDFPlasmonic quasicrystals (PlQCs), by integrating the properties of quasicrystals (rotational symmetry and long range ordering but lack translational symmetry) and surface plasmon polariton mediated effects, offer several advantages over plasmonic crystals (PlCs). For example, in PlQCs one could have broadband, polarization independent response. However, large area patterning by electron beam lithography requires precise lattice coordinates as well as a practical way to design the structures for specific spectral response.
View Article and Find Full Text PDFMagnetic field control of light is among the most intriguing methods for modulation of light intensity and polarization on sub-nanosecond timescales. The implementation in nanostructured hybrid materials provides a remarkable increase of magneto-optical effects. However, so far only the enhancement of already known effects has been demonstrated in such materials.
View Article and Find Full Text PDFWe present the first calculation of the Goos-Hänchen shifts in the context of the nonlinear generation of fields. We specifically concentrate on shifts of second harmonic generated at metallic surfaces. At metallic surfaces the second harmonic primarily arises from discontinuities of the field at surfaces which not only result in large harmonic generation but also in significant Goos-Hänchen shifts of the generated second harmonic.
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