The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon
Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. 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 in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and
2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal
dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the
observed fractal dimensions (R2~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression
analysis decreases the R2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation
activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77
bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their
high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription
factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and
VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R2 ~ 0.997 for N =3.
The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to
sequences VNG7114 and VNG2184.
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.
Diatom bioactivity has been reported to be responsible for about 20% of carbon fixation globally and together
with other photosynthetic organisms, the bioactivity can be monitored via satellite ocean imaging. The bioinformatics
embedded in the nucleotide fluctuations of photosynthesis and bio-silicate genes in diatoms were
studied. The recently reported phosphoenolpyruvate carboxylase PEPC1 and PEPC2 C4-like photosynthesis
genes in Phaeodactylum tricornutum were found to have similar fractal dimensions of about 2.01. In
comparison, the green alga Chlamydomonas reinhardtii PEPC1 and PEPC2 genes have fractal dimensions of
about 2.05. The PEPC CpG dinucleotide content is 8% in P. tricornutum and 10% in C. reinhardtii. Further
comparison of the cell wall protein gene showed that the VSP1 gene sequence in C. reinhardtii has a fractal
dimension of 2.03 and the bio-silica formation silaffin gene in Thalassiosira pseudonana has a fractal dimension
of 2.01. The phosphoenolpyruvate carboxylase PPC1 and PPC2 in T. pseudonana were found to have fractal
dimensions and CpG dinucleotide content similar to that of P. tricornutum. The fractal dimension of the dnaB
replication helicase gene is about 1.98 for both diatoms as well as for the alga Heterosigma akashiwo. In
comparison, the E. coli dnaB gene has a fractal dimension of about 2.03. Given that high fractal dimension and
CpG dinucleotide content sequences have been associated with the presence of selective pressures, the relatively
low fractal dimension gene sequences of the two unique properties of Earth-bound diatoms (photosynthesis and
bio-silica cell wall) suggests the potential for the development of high fractal dimension sequences for adaptation
in harsh environments.
KEYWORDS: Fractal analysis, Organisms, Monte Carlo methods, Statistical analysis, Proteins, Image information entropy, Resistance, Biological research, Information science, Genetics
We have characterized function related DNA sequences of various organisms using informatics techniques,
including fractal dimension calculation, nucleotide and multi-nucleotide statistics, and sequence fluctuation
analysis. Our analysis shows trends which differentiate extremophile from non-extremophile organisms, which
could be reproduced in extraterrestrial life. Among the systems studied are radiation repair genes, genes involved
in thermal shocks, and genes involved in drug resistance. We also evaluate sequence level changes that have
occurred during short term evolution (several thousand generations) under extreme conditions.
A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton
number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution
and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the RecA
repair gene of Psychrobacter cryohalolentis K5, Psychrobacter arcticus 273-4, and Psychrobacter sp. PRwf-1.
The fractal dimension was found to correlate with the gene's operating temperature with the highest fractal
dimension associated with P. cryohalolentis K5 living at the low temperatures found in Siberian permafrost.
The CpG dinucleotide content was found to be about 5% for the three species of Psychrobacters, which is
substantially lower than that of Deinococcus radiodurans at about 12%. The average nucleotide pair-wise free
energy was found to be lowest for Psychrobacter sp. PRwf-1, the species with the lowest fractal dimension of
the three, consistent with the recent finding that Psychrobacter sp. PRw-f1 has a temperature growth maximum
of 15-20°C higher than P. arcticus 273-4 and P. cryohaloentis K5. The results suggest that microbial vitality in
extreme environments is associated with fractal dimension as well as high CpG dinucleotide content, while the
average nucleotide pair-wise free energy is related to the operating environment. Evidence that extreme
temperature operation would impose constraints measurable by Shannon entropy is also discussed. A
quantitative estimate of an entropy-based measure having the characteristics of a mechanical pressure shows that
the Psychrobacter RecA sequence experiences lower pressure than that of the human HAR1 sequence.
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.
Cell scattering produces a speckle pattern, while imaging produces a contrast pattern. This family of fluctuation signals can be studied by analysis techniques such as correlation and fractal dimension. Human breast cell (normal and cancerous) samples were investigated using laser speckle and imaging microscopy. Image data from tetraploid human cell motion and quorum sensing biofilm growth were studied as well, and we found that the signal fluctuations could be interpreted as gene expression fluctuations occurring during inter-cell communication. We have mapped nucleotide sequences as images and studied the fluctuation. We showed that the fractal dimension and correlation can be used for the description of bio-information from the DNA (nanometer) scale to the tissue (millimeter) level. Fluctuations of the HAR1 nucleotide sequence and IRF-6 single-mutation cases in the van der Woude syndrome were discussed. Sub-cell structures such as the 40S ribosome, GroEL, and lysozyme, were shown to carry texture fractal dimension information in their images consistent with their biological states. Clinical applications to X-ray mammography and Parkinson disease MRI data were discussed.
The absorption effect of the back surface boundary of a diffuse layer was studied via laser generated reflection speckle pattern. The spatial speckle intensity provided by a laser beam was measured. The speckle data were analyzed in terms of fractal dimension (computed by NIH ImageJ software via the box counting fractal method) and weak localization theory based on Mie scattering. Bar code imaging was modeled as binary absorption contrast and scanning resolution in millimeter range was achieved for diffusive layers up to thirty transport mean free path thick. Samples included alumina, porous glass and chicken tissue. Computer simulation was used to study the effect of speckle spatial distribution and observed fractal dimension differences were ascribed to variance controlled speckle sizes. Fractal dimension suppressions were observed in samples that had thickness dimensions around ten transport mean free path. Computer simulation suggested a maximum fractal dimension of about 2 and that subtracting information could lower fractal dimension. The fractal dimension was shown to be sensitive to sample thickness up to about fifteen transport mean free paths, and embedded objects which modified 20% or more of the effective thickness was shown to be detectable. The box counting fractal method was supplemented with the Higuchi data series fractal method and application to architectural distortion mammograms was demonstrated. The use of fractals in diffusive analysis would provide a simple language for a dialog between optics experts and mammography radiologists, facilitating the applications of laser diagnostics in tissues.
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.
The shape of an exoplanet lightcurve is usually obtained by averaging the noise over multiple datasets. Fractal
analysis has been demonstrated to be an effective tool for the detection of exoplanet transits using lightcurves
summed over all wavelengths sensitive to the detector (G. Tremberger, Jr et. al, 2006 Proc SPIE Vol 6265). The
detection of spectral features would depend on the extent to which the signal was buried in the noise. Different
noise sources would have different fractal characteristics. Also, the signal strength could be discontinuous in
time depending on the exoplanet's local atmospheric environment. Such a discontinuity is unlikely to be
detected with time integrated data. The lightcurve noise and shape information were characterized with fractal
dimension analysis of a noise buried time series signal. Computer simulation revealed that when the noise is
three times that of the signal, the fractal algorithm could detect the signal at about the 87% confidence level.
Application to noise buried time series datasets (HD 209458b lightcurve, HD149026b lightcurve) detected
discontinuities consistent with the results obtained by averaging datasets. Extension to individual wavelength
lightcurves would establish a detection limit for the existence of spectral features at wavelengths important for
exoplanet study. Other applications such as pre-implantation genetic screening spectroscopy and spatially varied
aneuploidy bio-data could use the same analysis principle as well.
Images of packaged raw chicken purchased in neighborhood supermarkets were captured via a digital camera in laboratory and home settings. Each image contained the surface reflectivity information of the chicken tissue. The camera's red, green and blue light signals fluctuated and each spectral signal exhibited a random series across the surface. The Higuchi method, where the length of each increment in time (or spatial) lag is plotted against the lag, was used to explore the fractal property of the random series. (Higuchi, T., "Approach to an irregular time series on the basis of fractal theory", Physica D, vol 31, 277-283, 1988). The fractal calculation algorithm was calibrated with the Weierstrass function. The standard deviation and fractal dimension were shown to correlate with the time duration that a package was left at room temperature within a 24-hour period. Comparison to packaged beef results suggested that the time dependence could be due microbial spoilage. The fractal dimension results in this study were consistent with those obtained from yeast cell, mammalian cell and bacterial cell studies. This analysis method can be used to detect the re-refrigeration of a "left-out" package of chicken. The extension to public health issues such as consumer shopping is also discussed.
Breast cancer cells and normal cells were grown on glass substrates and investigated via laser generated
speckles. The optical speckle pattern of a layer was investigated via angular correlation and fractal dimension
analysis. A porous silicate slab with various water contents was used as calibration. The angular correlation and
its associated Fourier transform results were consistent with the property of the cells. The speckle intensity data
can be treated as a random series and the Higuchi method was used to explore the fractal property of the random
series. The fractal dimension results differentiated the cancer cells (fractal dimension about 1.5) from the normal
cells (fractal dimension about 1.8). The Fourier transformed series showed fractal dimension results consistent
with cell functions. A composite of breast cancer/normal cell matrix was built with cancer cell layers embedded
within normal cell layers. The optical speckle pattern of a composite was investigated and computer modeling
was used to extract the embedded cancer cell fractal dimension information. The measurement of the efficacy of
a drug was simulated with the monitoring of the effect of added chemicals in the growth media. Laboratory
optical speckle pattern monitoring of the effect of added chemicals was discussed. The extension for early
cancer detection in mammography was also discussed and an example of the application of the anisotropic
spatial variation of the fractal dimension via the Higuchi fractal method was presented.
Exoplanet transit time series photometric data usually contain noise levels that are comparable to the transit
signal jumps. The analysis that assumes Gaussian noise and extensive
data averaging calibrated to a reference
star has been the traditionally used algorithm. This paper studied the fractal property of the time series and
found that the fractal dimension changes for time series data that contain transits. The Higuchi fractal method,
where the length of the increment in various time lags is plotted against the lags, was used in this study.
(Higuchi, T., "Approach to an irregular time series on the basis of fractal theory", Physica D, vol 31, 277-283,
1988). The fractal algorithm was calibrated with the Weierstrass function. Simulations using Gaussian noise
suggested that a transit jump signal at about 1-sigma noise level would produce changes in fractal dimension,
while non-Gaussian noise simulations suggested a higher transit jump signal. The fractal algorithm was applied
to data collected on HD 209458 as well as on published data. The transit caused a fractal dimension change of
about 0.06. An over-exposed CCD dataset with much noise was also analyzed and a fractal dimension change of
about 0.02 was obtained. The result suggests that fractal dimension analysis, without the assumption of error
normality, is an alternative method for identifying transits in time series photometric data.
Steady state laser light propagation in diffuse media such as biological cells generally provide bulk parameter information, such as the mean free path and absorption, via the transmission profile. The accompanying optical speckle can be analyzed as a random spatial data series and its fractal dimension can be used to further classify biological media that show similar mean free path and absorption properties, such as those obtained from a single population. A population of yeast cells can be separated into different portions by centrifuge, and microscope analysis can be used to provide the population statistics. Fractal analysis of the speckle suggests that lower fractal dimension is associated with higher cell packing density. The spatial intensity correlation revealed that the higher cell packing gives rise to higher refractive index. A calibration sample system that behaves similar as the yeast samples in fractal dimension, spatial intensity correlation and diffusion was selected. Porous silicate slabs with different refractive index values controlled by water content were used for system calibration. The porous glass as well as the yeast random spatial data series fractal dimension was found to depend on the imaging resolution. The fractal method was also applied to fission yeast single cell fluorescent data as well as aging yeast optical data; and consistency was demonstrated. It is concluded that fractal analysis can be a high sensitivity tool for relative comparison of cell structure but that additional diffusion measurements are necessary for determining the optimal image resolution. Practical application to dental plaque bio-film and cam-pill endoscope images was also demonstrated.
Astronomy is among the most popular courses that students select to fulfill their college science requirement at Queensborough Community College, New York City. Recent advances in photonics now enable us to observe celestial objects from exoplanets to ultra deep space galaxies that are 13 billion light years away. These results are regularly reported in the popular press such as the New York Times and “Sky & Telescope” magazine. We upgraded our astronomy course to keep pace with these advances in optics and photonics. The laboratory hands-on exercises include observations in our observatory using a telescope with digital camera and CCD; spectrum analysis with grating; Java photonics simulation delivered over the Internet; the use of virtual instruments in optics and photonics written with Labview. Advanced techniques such as interferometry are also included as demonstrations in the laboratory. Light is described light as an electromagnetic wave to avoid confusion with the dictionary description. As a result of these teaching designs, the students gain a clearer understanding of the optics and photonics basis of the astronomy instrumentation reported in popular articles.
Cell parameters such as size and density may provide crucial information on issues such as aging and cancer. Measurement of these parameters in bulk, in a cells natural environment are therefore important. For bulk samples light diffusion measurements using transmission spatial profiles and correlation function analysis provide information on the mean free path, absorption and refractive index. Speckle fractal analysis can also provide cell structure information. For cells in suspension forward scattering is used to provide size information via the Mie theory for spherical objects. Two types of live yeast cells were measured in bulk and in suspension at various densities. The bulk samples were compacted by centrifuge into fractions whose mass and volume was measured. The parameter values obtained by optical diffusion were used to infer the density and size variations. The measurement detected density variation of about 10% for yeast grown under normal conditions. The size variation is also about 10% but it contained more uncertainty due to the constant density assumption used in the Mie theory for spherical objects. High resolution optical microscopy confirmed the cell size and showed that it followed a lognormal distribution. The density variation resulted mainly from size differences with a smaller contribution from mass structure such as protein. The results indicate that diffusion measurement is consistent with density measurement and could possibly be used as a cell density probe in clinical applications.
Chicken tissue acts as a turbid medium in optical wavelength. Optical characterization data of fresh chicken dark and white meat were studied using the theory of light diffusion. The gaussian-like transmission profile was used to determine the transport mean free path and absorption. The refractive index, a fundamental parameter, was extracted via transmission correlation function analysis without using index-matching fluid. The variation in refractive index also produced various small shifts in the oscillatory feature of the intensity spatial correlation function at distance shorter than the transport mean free path. The optical system was calibrated with porous silicate slabs containing different water contents and also with a solid alumina slab. The result suggested that the selective scattering/absorption of myoglobin and mitochondria in the dark tissues is consistent with the transmission data. The refractive index was similar for dark and white tissues at the He-Ne wavelength and suggested that the index could serve as a marker for quality control. Application to chicken lunchmeat samples revealed that higher protein and lower carbohydrate would shift the correlation toward smaller distance. The pure fat refractive index was different from that of the meat tissue. Application of refractive index as a fat marker is also discussed
Short-range speckle correlation techniques were used to measure the refractive index of turbid biological media. The refractive index depends on the cell content, which is about 80% water and 15% protein. The variation in water or protein content produced various small shifts in the oscillatory features of the speckle intensity spatial correlation function for correlation distances shorter than the transport mean free path. Optical diffusion profiles in transmission, and long range speckle intensity correlation techniques were used to measure the transport mean free path. The optical system was calibrated with a porous silicate slab, and live yeast was the biological system studied. It is found that the techniques employed could serve as markers for the cell's water and protein contents. Consistent results were also found for chicken tissue and a combined yeast sample. Extension to abnormal cell detection, and the application to in-situ refractive index mapping are also discussed.
This paper discusses the resolution capabilities of proximity x-ray lithography (PXRL) system. Exposure characteristics of features designed at 150 nm pitch size: 75 nm dense lines with 1:1 duty ratio, 2D features at 1:1 and 1:2 duty ratios and isolated lines have been studied. Aerial image simulations were compared to the experimental data. Verification of the aerial image model has been accomplished by measurements of exposure windows of 100 nm and 125 nm nested lines. The PXRL aerial image parameter, equivalent penumbra blur, has been determined from the experimental data. Contributions from the synchrotron radiation x-ray source, stepper and the chemically amplified resist to the degradation of the aerial image have been evaluated. Patterning capability of PXRL at 75 nm feature size is compared to projection optics using the optical k1 factor as a common figure of merit. To facilitate the comparison, optical imagin was at pattern sizes currently manufacturable by the mainstream optical tools while the PXRL imaging was at 75 nm pattern size. Requirements for a PXRL system of manufacturing VLSI at 70 nm minimum feature sizes with the critical dimension control better than 10 percent are also discussed.
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
X-ray lithography has been used in mix and match mode with optical steppers to build test circuits in support of DRAM and Logic development at IBM's Advanced Semiconductor Technology Center, ASTC. Prior to building the test devices, hundreds of wafers were exposed using x-ray lithography to define the etch processes for critical levels and to help separate optical lithography, resist and etching effects. The demand for this type of support required IBM's Advanced Lithography Facility (ALF) to focus on a set of pilot line issues not previously faced by this emerging lithography. The challenges and solutions which resulted are discussed. This paper examines the requirements for the introduction of x-ray into pilot line use based on ALF's most recent experience and performance.
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
A state-of-the-art proximity x-ray lithography aligner was developed for the Defense Advanced Lithography Program (DALP) and installed in IBM's Advanced Lithography Facility (ALF) in 1995. This aligner was designed to satisfy the manufacturing requirements for 250 and 180 nm groundrule electronic devices, such as 256 Mbit and 1 Gbit DRAMs, while connected to synchrotron beamlines which use scanning beam systems for x- ray flux delivery. The aligner uses an innovative x-ray image sensor (XRIS) to align the mask by detecting its x-ray actinic image, and uses an off-axis alignment system, similar to the alignment system used in Micrascan-II, to align the wafer. As a result, the same wafer alignment marks can be used by either tool. This facilitates the mix and match between the x-ray aligner and Micrascan-II optical steppers. A stabilized helium environment is maintained from the beryllium window of the beamline to the exposure plane, including the gap between mask and wafer. The aligner can accept x-ray masks that conform to NIST standards, and has a maximum exposure field of 50 mm by 50 mm. The important lithography performance parameters, i.e., overlay, linewidth control and throughput, have been evaluated. The test methodologies and their results are presented in detail. Potential improvements of the system's performance will also be discussed.
X-ray lithography can be used to achieve deep sub-micron design groundrules. With X-ray, as with other lithographic systems, mix and match techniques are often used to achieve timely, cost effective implementation. This can, in some cases, reduce overlay accuracy and complicate mask and wafer layout. In this paper we will present methods which will facilitate the use of X-ray lithography in mix and match environments to simplify layout and improve overlay accuracy. An alignment scheme for 0.35 micron CMOS device fabrication and a method for printing alignment marks for the next X-ray level are described. In this scheme all the critical levels such as oxide isolation, polysilicon gate, contact, and first metallization levels are printed using X-ray lithography with the same X-ray stepper (Karl Suss XRS200/2). All other noncritical levels are printed optically. The initial wafer lot using this scheme has been successfully processed to the first metallization level. The X-ray stepper alignment system can compensate for the first order overlay components such as translation and rotation. This feature is very useful for compensating for certain mask difference and process induced distortion. However, mask magnification difference must be compensated otherwise. A linear regression method has been used to analyze the overlay data and the results are fed back to the stepper for correction. A 3-sigma overlay distribution +/- 180 nm has been achieved.
As part of the Defense Advanced Lithography Program (DALP), IBM has fabricated 0.35 micrometers high-density static random access memory (SRAM) chips with all critical levels being exposed using synchrotron X-ray lithography. X-ray exposures for the four critical levels (isolation, gate, contact holes, and metal 1) were performed at the Advanced Lithography Facility (ALF) at the IBM East Fishkill, New York site. Nonlithographic processing and noncritical level optical exposures were performed in the Very Large Scale Integration (VLSI) pilot line at the IBM Manassas, Virginia site. Extensive alignment and process latitude studies were conducted to determine the best operating points in preparation for the full product SRAM runs. Overlay error, dose and gap latitude, etch bias control, and electrical test results will be presented and compared to results obtained with optical lithography.
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