Dr. Alex Flamholz Profile

Dr. Alex Flamholz

Professor at Queensborough Community College

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Publications (23)

Proceedings Article | 11 September 2009 Paper

Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Todd Holden, G. Tremberger, E. Cheung, R. Subramaniam, N. Gadura, P. Schneider, R. Sullivan, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 7441, 74410R (2009) https://doi.org/10.1117/12.825827

KEYWORDS: Fractal analysis, Image information entropy, Proteins, Mars, Silver, Bacteria, Resistance, Statistical analysis, Calibration, Gamma radiation

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Proceedings Article | 4 September 2009 Paper

Multi-fractal property of perchlorate reductase gene sequences and DNA photonics application to UV fluorescence detection on Mars-like surfaces

George Tremberger, Eric Cheung, N. Gadura, Todd Holden, Raji Subramaniam, Regina Sullivan, Pat Schneider, Alex Flamholz, David Lieberman, Tak Cheung

Proceedings Volume 7441, 74410G (2009) https://doi.org/10.1117/12.825819

KEYWORDS: Fractal analysis, Image information entropy, Microorganisms, Ultraviolet radiation, Mars, Chemical analysis, Luminescence, DNA photonics, Proteins, Distance measurement

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The discovery of perchlorate on Mars raises the possibility of the existence of perchlorate reduction microbes on that planet. The perchlorate reductase gene sequence fractal dimensions of two Dechloromonas species were compared with five other sequences in the microbial dimethyl sulfoxide (DMSO) reductase family. A nucleotide sequence can be expressed as a numerical sequence where each nucleotide is assigned its proton number. The resulting numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. Analysis of the fractal dimensions for the DMSO reductase family supports phylogenetic analyses that show that the perchlorate reductase gene sequences are members of the same family. A sub-family with roughly the same nucleotide length emerges having the property that the gene fractal dimension is negatively correlated with the Shannon di-nucleotide entropy (R² ~ 0.95, N =5). The gene sequence fractal dimension is found to be positively correlated with the neighbor joining distances reported in a published protein phylogeny tree (R²~ 0.92, N = 5). The multi-fractal property associated with these genes shows that perchlorate reductase has lower dimensionality as compared to the relatively higher dimensionality DNA-break repair genes Rec-A and Rad-A observed in the Dechloromonas aromatica and Deinococcus radiodurans genomes. The studied perchlorate gene sequences show a higher Shannon di-nucleotide entropy (~3.97 bits) relative to Dechloromonas aromatica DNA repair sequences (~3.87 bits Rec-A, ~3.92 bits Rad-A), suggesting that there are fewer constraints on nucleotide variety in the perchorlate sequences . These observations thus allow for the existence of perchlorate reducing microbes on Mars now or in the past. Timeresolved UV fluorescence study near the emission bands of nucleotide sequences could be used for bio-detection on Mars-like surfaces and the results may further constrain the proposed conjectures.

Proceedings Article | 28 August 2008 Paper

Phaeodactylum tricornutum photosynthesis and Thalassiosira pseudonana bio-silica formation genes nucleotide fluctuations

Todd Holden, P. Marchese, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, M. Huerta, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970R (2008) https://doi.org/10.1117/12.794414

KEYWORDS: Fractal analysis, Photosynthesis, Proteins, Organisms, Calibration, Carbon, Satellite imaging, Satellites, Bioinformatics, Cadmium sulfide

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Proceedings Article | 28 August 2008 Paper

DNA sequence-based comparative studies between non-extremophile and extremophile organisms with implications in exobiology

Todd Holden, P. Marchese, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970Q (2008) https://doi.org/10.1117/12.801269

KEYWORDS: Fractal analysis, Organisms, Monte Carlo methods, Statistical analysis, Proteins, Image information entropy, Resistance, Biological research, Information science, Genetics

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Proceedings Article | 28 August 2008 Paper

Nucleotide fluctuation of RecA repair gene in Siberian permafrost Psychrobacter cryohalolentis K5

George Tremberger, T. Holden, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, P. Marchese, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970U (2008) https://doi.org/10.1117/12.794390

KEYWORDS: Fractal analysis, Image information entropy, Astrobiology, Calibration, Proteins, Genetics, Chemical analysis, Microorganisms, Thermodynamics, Biology

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Proceedings Article | 28 August 2008 Paper

Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology

Todd Holden, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, P. Marchese, O. Hiciano, H. Yao, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970V (2008) https://doi.org/10.1117/12.794398

KEYWORDS: Fractal analysis, Mars, Pathology, Chemical analysis, Proteins, Biological research, Environmental sensing, Bioinformatics, Calibration, Astrobiology

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Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface, could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could exist in extremely cold conditions (such as that which existed on early Mars) where demands on gene activity are low. In addition, the comparative study of the Methanococcoides burtonii cold shock domain sequence has provided further support for the correlation between multitasking capacity and fractal dimension.

Proceedings Article | 30 October 2007 Paper

Intensity fluctuation analysis of cell scattering/imaging with clinical application

Raji Subramaniam, R. Sullivan, P. Schneider, T. Holden, G. Tremberger, E. Cheung, A. Flamholz, D. Lieberman, T. Cheung, F. Garcia, N. Bewry, N. Pennie

Proceedings Volume 6796, 67960N (2007) https://doi.org/10.1117/12.778063

KEYWORDS: Fractal analysis, Breast, Biological research, Video, Speckle pattern, Mammography, Magnetic resonance imaging, Microscopes, Speckle, Microscopy

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Proceedings Article | 15 October 2007 Paper

Imaging through diffusive layers using speckle pattern fractal analysis and application to embedded object detection in tissues

George Tremberger, A. Flamholz, E. Cheung, R. Sullivan, R. Subramaniam, P. Schneider, G. Brathwaite, J. Boteju, P. Marchese, D. Lieberman, T. Cheung, Todd Holden

Proceedings Volume 6771, 677117 (2007) https://doi.org/10.1117/12.732302

KEYWORDS: Fractal analysis, Speckle pattern, Speckle, Tissues, Computer simulations, Mammography, Binary data, Absorption, Glasses, Architectural distortion

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Proceedings Article | 1 October 2007 Paper

ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes

Todd Holden, R. Subramaniam, R. Sullivan, E. Cheung, C. Schneider, G. Tremberger, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 6694, 669417 (2007) https://doi.org/10.1117/12.732283

KEYWORDS: Fractal analysis, Gamma radiation, Statistical analysis, Proteins, Monte Carlo methods, Calibration, Analytical research, Biological research, Computer simulations, Brain

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The radiation resistance-repair genes in Deinococcus radiodurans (DR) and E-coli were analyzed in terms of the A, T, C, G nucleotide fluctuations. The studied genes were Rec-A, Rec-Q, and the unique DR PprA gene. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis. Fractal analysis using the Higuchi method gave a fractal dimension increase of the Deinococcus radiodurans genes as compared to E-coli, which is comparable to the enhancement observed in the human HAR1 region (HAR1F gene) over that of the chimpanzee. Near neighbor fluctuation was also studied via the Black-Scholes model where the increment sequence was treated as a random walk series. The Deinococcus radiodurans radiation gene standard deviations were consistently higher than that of the E-coli deviations, and agree with the fractal analysis results. The sequence stacking interaction was studied using the published nucleotide-pair melting free energy values and Deinococcus radiodurans radiation genes were shown to possess larger negative free energies. The high sensitivity of the fractal dimension as a biomarker was tested with correlation analysis of the gamma ray dose versus fractal dimension, and the R square values were found to be above 0.9 (N=5). When compared with other nucleotide sequences such as the rRNA sequences, HAR1 and its chimpanzee counterpart, the higher fluctuation (correlated randomness) and larger negative free energy of a DR radiation gene suggested that a radiation resistance-repair sequence exhibited higher complexity. As the HAR1 nucleotide sequence complexity and its transcription activity of co-expressing cortex protein reelin supported a positive selection event in humans, a similar inference of positive selection of coding genes could be drawn for Deinococcus radiodurans when compared to E-coli. The origin of such a positive selection would be consistent with that of a Martian environment.

Proceedings Article | 19 September 2007 Paper

Fractal analysis of noise buried time series signals with applications to exoplanet spectroscopy and bio-data

George Tremberger, T. Holden, E. Cheung, A. Flamholz, P. Marchese, H. Yao, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 6693, 66931D (2007) https://doi.org/10.1117/12.732987

KEYWORDS: Fractal analysis, Interference (communication), Exoplanets, Signal detection, Stars, Spectroscopy, Computer simulations, Calibration, Detection and tracking algorithms, Genetics

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Proceedings Article | 23 October 2006 Paper

The statistical and fractal properties of surface reflectivity of raw chicken tissue with application to public health safety

Raji Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, E. Cheung, G. Tremberger, P. Wong, D. Lieberman, T. Cheung, F. Garcia, N. Bewry, A. Yee

Proceedings Volume 6381, 63810H (2006) https://doi.org/10.1117/12.686285

KEYWORDS: Fractal analysis, Natural surfaces, Tissues, Breast, Reflectivity, Cameras, Microscopes, Yeast, Safety, Calibration

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Proceedings Article | 17 October 2006 Paper

Optical speckle angular correlation and fractal property of a composite of cancer/normal cell layers with application for laboratory monitoring of drug efficacy

Regina Sullivan, R. Subramaniam, P. Schneider, A. Flamholz, G. Tremberger, E. Cheung, S. Rotenberg, P. Wong, D. Lieberman, T. Cheung, Rafael Perez

Proceedings Volume 6386, 63860B (2006) https://doi.org/10.1117/12.686241

KEYWORDS: Fractal analysis, Speckle, Breast, Mammography, Cancer, Microscopes, Composites, Speckle pattern, Diffusion, Calibration

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Proceedings Article | 15 June 2006 Paper

Fractal characteristics of exoplanet transit time series data

George Tremberger, H. Yao, A. Flamholz, E. Cheung, P. Marchese, D. Cotten, D. Lieberman, T. Cheung

Proceedings Volume 6265, 62653V (2006) https://doi.org/10.1117/12.672206

KEYWORDS: Fractal analysis, Stars, Interference (communication), Signal detection, Calibration, Exoplanets, Error analysis, Charge-coupled devices, Telescopes, Planets

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Proceedings Article | 1 March 2006 Paper

Fractal analysis of yeast cell optical speckle

A. Flamholz, P. Schneider, R. Subramaniam, P. Wong, D. Lieberman, T. Cheung, J. Burgos, K. Leon, J. Romero

Proceedings Volume 6084, 60840R (2006) https://doi.org/10.1117/12.646399

KEYWORDS: Fractal analysis, Yeast, Speckle, Diffusion, Refractive index, Image resolution, Calibration, Endoscopes, Absorption, Geometrical optics

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Proceedings Article | 9 December 2004 Paper

Teaching of optics and photonics in a college astronomy course

George Tremberger, Alex Flamholz, Paul Marchese, David Lieberman, Tak Cheung

Proceedings Volume 5578, (2004) https://doi.org/10.1117/12.567455

KEYWORDS: Photonics, Java, Astronomy, Space telescopes, Telescopes, Astronomical imaging, Venus, Galactic astronomy, LabVIEW, Sun

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Proceedings Article | 9 December 2004 Paper

Examination of yeast cell parameters using light diffusion

Patricia Schneider, Alex Flamholz, Peter Wong, David Lieberman, Tak Cheung, Harriet Itoka, Troy Minott, Janie Quizhpi, Jacquelin Rodriguez

Proceedings Volume 5578, (2004) https://doi.org/10.1117/12.567406

KEYWORDS: Yeast, Speckle, Fractal analysis, Diffusion, Mie scattering, Refractive index, Scattering, Microscopy, Light scattering, Diamond

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Proceedings Article | 19 November 2004 Paper

Optical diffusion property of chicken tissue

Patricia Schneider, Alex Flamholz, Peter Wong, David Lieberman, Tak Cheung, Harriet Itoka, Troy Minott, Janie Quizhpi, Jacquelin Rodriguez

Proceedings Volume 5587, (2004) https://doi.org/10.1117/12.571661

KEYWORDS: Refractive index, Tissues, Correlation function, Tissue optics, Diffusion, Fourier transforms, Proteins, Breast, Calibration, Water

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Proceedings Article | 2 August 2004 Paper

Speckle intensity correlation and optical diffusion profile in biological media

Alex Flamholz, Patricia Schneider, Peter Wong, David Lieberman, Tak Cheung, Harriet Itoka, Troy Minott, Janie Quizhpi, Jacquelin Rodriguez

Proceedings Volume 5531, (2004) https://doi.org/10.1117/12.558071

KEYWORDS: Refractive index, Correlation function, Yeast, Speckle, Proteins, Diffusion, Water, Fourier transforms, Calibration, Sensors

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Proceedings Article | 25 June 1999 Paper

Imaging capabilities of proximity x-ray lithography at 70-nm ground rules

Azalia Krasnoperova, Robert Rippstein, Alex Flamholz, Ernst Kratschmer, Shalom Wind, Cameron Brooks, Michael Lercel

Proceedings Volume 3676, (1999) https://doi.org/10.1117/12.351118

KEYWORDS: Photomasks, X-rays, Photoresist materials, Gold, Semiconducting wafers, Image quality, Lithography, Diffusion, X-ray imaging, X-ray lithography

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Proceedings Article | 5 June 1998 Paper

X ray fills the gap

Chet Wasik, G. Murphy, Alek Chen, Azalia Krasnoperova, Alex Flamholz, Daniel DeMay, Jeffrey Leavey, Steve Loh, Sue Chaloux, Alan Thomas, Sang Lee, Kenneth Giewont, Paul Agnello

Proceedings Volume 3331, (1998) https://doi.org/10.1117/12.309566

KEYWORDS: Photomasks, X-rays, Semiconducting wafers, Lithography, X-ray lithography, Etching, Photoresist processing, Logic, Capacitors, X-ray imaging

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Proceedings Article | 7 July 1997 Paper

Evaluation of the Defense Advanced Lithography Program (DALP) x-ray lithography aligner

Alek Chen, Alex Flamholz, Azalia Krasnoperova, Robert Rippstein, Ben Vampatella, George Gomba, Robert Fair, William Chu, V. Dimilia, J. Silverman, R. Amodeo, Dave Heald, P. Kochersperger, Carl Stahlhammer

Proceedings Volume 3048, (1997) https://doi.org/10.1117/12.275803

KEYWORDS: Semiconducting wafers, Photomasks, Optical alignment, X-rays, X-ray lithography, Lithography, Overlay metrology, Calibration, Error analysis, Sensors

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Proceedings Article | 24 June 1993 Paper

Mask-to-wafer alignment using x-ray-printed alignment marks in x-ray lithography

S. Liang, Alex Flamholz, John Conway

Proceedings Volume 1924, (1993) https://doi.org/10.1117/12.146512

KEYWORDS: Optical alignment, X-rays, Photomasks, X-ray lithography, Semiconducting wafers, Overlay metrology, X-ray optics, Wafer-level optics, Lithography, Oxides

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Proceedings Article | 24 June 1993 Paper

Fabrication of high-density SRAM chips using mix-and-match x-ray lithography

John Conway, C. Alcorn, D. Patel, James Ricker, R. Yandow, S. Liang, Alex Flamholz

Proceedings Volume 1924, (1993) https://doi.org/10.1117/12.146513

KEYWORDS: X-rays, X-ray lithography, X-ray optics, Semiconducting wafers, Metals, Photomasks, Lithography, Optical alignment, Very large scale integration, Etching

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Showing 5 of 23 publications

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