Sunil Dehipawala

Fiber optic based heart-rate and pulse pressure shape monitor

Macro-bending fiber optic based heart-rate and pulse pressure shape monitors have been fabricated and tested for non-invasive measurement. Study of fiber bending loss and its stability and variations are very important especially for sensor designs based on optical fiber bending. Wavelengths from 1300 nm to 1550 nm have been used with fabrication based on multimode fiber, single mode fiber, and photonic crystal fiber. The smallest studied curvature would demand the use of single mode standard fibers. The collected data series show high quality suitable for random series analysis. Fractal property of optically measured pulse pressure data has been observed to correlate with physical activity. Correlation to EKG signal suggests that the fabricated monitors are capable of measuring the differential time delays at wrist and leg locations. The difference in time delay could be used to formulate a velocity parameter for diagnostics. The pulse shape information collected by the fiber sensor provides additional parameters for the analysis of the fractal nature of the heart. The application to real time measurement of blood vessel stiffness with this optical non-invasive fiber sensor is discussed.

Optical diffusion property of cerumen from ear canal and correlation to metal content measured by synchrotron x-ray absorption

Human (and other mammals) would secrete cerumen (ear wax) to protect the skin of the ear canal against pathogens and insects. The studies of biodiversity of pathogen in human include intestine microbe colony, belly button microbe colony, etc. Metals such as zinc and iron are essentials to bio-molecular pathways and would be related to the underlying pathogen vitality. This project studies the biodiversity of cerumen via its metal content and aims to develop an optical probe for metal content characterization. The optical diffusion mean free path and absorption of human cerumen samples dissolved in solvent have been measured in standard transmission measurements. EXFAS and XANES have been measured at Brookhaven Synchrotron Light Source for the determination of metal contents, presumably embedded within microbes/insects/skin cells. The results show that a calibration procedure can be used to correlate the optical diffusion parameters to the metal content, thus expanding the diagnostic of cerumen in the study of human pathogen biodiversity without the regular use of a synchrotron light source. Although biodiversity measurements would not be seriously affected by dead microbes and absorption based method would do well, the scattering mean free path method would have potential to further study the cell based scattering centers (dead or live) via the information embedded in the speckle pattern in the deep-Fresnel zone.

Single mode and sub-cellular fiber probes for cell scattering and density variation measurements

Cell density is an important parameter in the question of bio-variation and the studying of cell scattering could be a viable tool. The development of spatially resolved optical fiber probe would enable the characterization of optical scattering from cells within a colony. Single mode fiber probe would be budget friendly as compared to a 50-nm sub-cellular fiber probe. This project develops a calibration procedure to correlate the optical scattering measured by a single mode fiber probe to that of a 50-nm sub-cellular fiber probe in the context of cell density variation. The Fourier transform of intensity angular transmission would give correlation information in the Efield in the spatial coordinate. Monte Carlo simulation could be used to constrain the input intensity function spatial content resembling microscopy. The use of a 50-nm sub-cellular fiber probe for detailed study of biological samples would give sub-micron scale length information.

Assessment of high-school engineering education outreach program employing project-based learning in astronomy and bio-optics within a college setting

A college outreach engineering education program designed for high school students was implemented in a community college using the three principles of K-12 engineering education, namely, product design, science knowledge, and mindset development. The means of transforming a science question into a design driven one was illustrated using examples and projects from the fields of astronomy and bio-optics. The relevant scientific principles were presented by introducing various iterated designs in an interactive learning environment. A high school level research component using astronomy and bio-optics-related public data was also implemented to enrich the students’ exposure to numerical processing techniques accessible in Microsoft Excel. Examples including solar events driven by magnetic field topology, cosmological images generated by IllustrisTNG Project, muon flux data, Killer T-cell motion, and wound assay cell migration are used in the teaching of iterated designs. A Path Diagram assessment model based on a LISREL computation scheme with learning intent and engineering mindset as latent variables was used to gauge the effectiveness of an implementation, the results of which would be used in the subsequent semester’s implementation of the research component. The materials developed in a College Now course, where high school students take a research course at a community college, would be readily adaptable to other four-year college programs. The possible future incorporation of an introductory engineering course for high school student education, using the MIT low-cost

Comparison of structural properties of iron nano-particles prepared by sol-gel method and spin coating technique

100 muon detector and Fermi Lab QuarkNet muon scintillation detector, is discussed.

Bioinformatics of CYP2E1 CpG intron methylation sites and application to HAR1-RELN sequence analysis

Small scale magnets have very high technological importance today. We synthesized thin film magnets containing iron and nickel oxides using sol-gel and spin coating methods. Structural properties of iron particles were investigated using Mossbauer spectroscopy, X-ray absorption spectroscopy including Extended X-ray Absorption Spectroscopy. The variation in oxidation state and other structural parameters were deduced. It appears the oxidation state of iron particles prepared by sol-gel method is very stable up to annealing temperatures of 600° C. The iron particles prepared by spin coating method exist in two different chemical environments with slightly different oxidation states.

Bioinformatics comparison of sulfate-reducing metabolism nucleotide sequences

The CYP2E1 CpG methylation sites in the first intron (site +626 to +742 from the starting ATG) as reported in a 2015 epigenetics psychiatry study were analyzed from a bioinformatics perspective. The studied sequences for human, monkey, dog and cow showed a high correlation (R-sq > 0.99) between CpG content and mononucleotide entropy. A comparably high correlation (R-sq > 0.95) was also found between the first exon sequences and mononucleotide entropy. These findings lend support to the hypothesis that CpG content is proportional to nucleotide availability when the latter quantity is computed as information entropy. To probe the nature of CpG sites in HAR1, a comparative study was conducted using the known promoter methylation regions in RELN and EGFR sequences. The observed high correlation (R-sq = 0.999) suggests that the eight CpG sites in HAR1 may function as human-specific gene expression controller sites since the equivalent chimp sequence has no CpG sites. A general scheme using randomly selected CpG methylation sites that precede the starting ATG codon is discussed with regard to fractal dimension modeling. Furthermore, an analysis of the studied RELN homolog CDS sequences for human, bovine, mouse and rat showed a high correlation of dinucleotide entropy with free energy (R > 0.9), consistent with the high correlation (R > 0.9) observed in a similar analysis of the studied pro-BDNF homolog CDS sequences for human, chimp, mouse and rat.

Characterization of nano-sized iron particle layers spin coated on glass substrate

The sulfate-reducing bacteria can be traced back to 3.5 billion years ago. The thermodynamics details of the sulfur cycle have been well documented. A recent sulfate-reducing bacteria report (Robator, Jungbluth, et al , 2015 Jan, Front. Microbiol) with Genbank nucleotide data has been analyzed in terms of the sulfite reductase (dsrAB) via fractal dimension and entropy values. Comparison to oil field sulfate-reducing sequences was included. The AUCG translational mass fractal dimension versus ATCG transcriptional mass fractal dimension for the low temperature dsrB and dsrA sequences reported in Reference Thirteen shows correlation R-sq ~ 0.79 , with a probably of about 3% in simulation. A recent report of using Cystathionine gamma-lyase sequence to produce CdS quantum dot in a biological method, where the sulfur is reduced just like in the H2S production process, was included for comparison. The AUCG mass fractal dimension versus ATCG mass fractal dimension for the Cystathionine gamma-lyase sequences was found to have R-sq of 0.72, similar to the low temperature dissimilatory sulfite reductase dsr group with 3% probability, in contrary to the oil field group having R-sq ~ 0.94, a high probable outcome in the simulation. The other two simulation histograms, namely, fractal dimension versus entropy R-sq outcome values, and di-nucleotide entropy versus mono-nucleotide entropy R-sq outcome values are also discussed in the data analysis focusing on low probability outcomes.

Complexity of genetic sequences modified by horizontal gene transfer and degraded-DNA uptake

Nanometer scale iron particles have a variety of technological applications. They are vastly utilized in optical and microwave devices. Thin films with varying compositions of iron (III) nitrate and ethylene glycol were deposited on glass substrate using a spin coating technique. The thicknesses of the films were controlled by the spin rate. Precursor films on the substrate were then annealed to different temperatures ranging from 200°C to 600°C for 1-3 hours in air. The microstructures of iron particles in films prepared under different conditions were investigated using X-ray Absorption spectroscopy and Mossbauer spectroscopy. The main absorption edge peak position and pre-edge energy position were identical in samples with different numbers of layers, but prepared under similar conditions. This indicates that there was no change in the charge state of the iron regardless of the number of layers. However the intensity of the pre-edge feature decreases as the number of layers increases, which shows a decrease of Fe-O compounds as the number of layers increases. Mossbauer spectrum of these iron particles contains only quadrupole doublets. The absence of six-linespectrum confirms the nano-size nature of the particles.

The bioinformatics of nucleotide sequence coding for proteins requiring metal coenzymes and proteins embedded with metals

Horizontal gene transfer has been a major vehicle for efficient transfer of genetic materials among living species and could be one of the sources for noncoding DNA incorporation into a genome. Our previous study of lnc- RNA sequence complexity in terms of fractal dimension and information entropy shows a tight regulation among the studied genes in numerous diseases. The role of sequence complexity in horizontal transferred genes was investigated with Mealybug in symbiotic relation with a 139K genome microbe and Deinococcus radiodurans as examples. The fractal dimension and entropy showed correlation R-sq of 0.82 (N = 6) for the studied Deinococcus radiodurans sequences. For comparison the Deinococcus radiodurans oxidative stress tolerant catalase and superoxide dismutase genes under extracellular dGMP growth condition showed R-sq ~ 0.42 (N = 6); and the studied arsenate reductase horizontal transferred genes for toxicity survival in several microorganisms showed no correlation. Simulation results showed that R-sq < 0.4 would be improbable at less than one percent chance, suggestive of additional selection pressure when compared to the R-sq ~ 0.29 (N = 21) in the studied transferred genes in Mealybug. The mild correlation of R-sq ~ 0.5 for fractal dimension versus transcription level in the studied Deinococcus radiodurans sequences upon extracellular dGMP growth condition would suggest that lower fractal dimension with less electron density fluctuation favors higher transcription level.