Engineering topics

Peng, C. K.

Publications and source records attributed to Peng, C. K..

At least 37 records · Page 2

NASA NTRS1995

Statistical and linguistic features of DNA sequences

We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

Non-NASA Center↗

NASA NTRS1995

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

Non-NASA Center↗

NASA NTRS1995

Statistical properties of DNA sequences

We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

Non-NASA Center↗

NASA NTRS1995

Fractals in biology and medicine

Our purpose is to describe some recent progress in applying fractal concepts to systems of relevance to biology and medicine. We review several biological systems characterized by fractal geometry, with a particular focus on the long-range power-law correlations found recently in DNA sequences containing noncoding material. Furthermore, we discuss the finding that the exponent alpha quantifying these long-range correlations ("fractal complexity") is smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the normal heart is characterized by long-range "anticorrelations" which are absent in the diseased heart.

Review↗

NASA NTRS1995

Quantification of scaling exponents and crossover phenomena in nonstationary heartbeat time series

The healthy heartbeat is traditionally thought to be regulated according to the classical principle of homeostasis whereby physiologic systems operate to reduce variability and achieve an equilibrium-like state [Physiol. Rev. 9, 399-431 (1929)]. However, recent studies [Phys. Rev. Lett. 70, 1343-1346 (1993); Fractals in Biology and Medicine (Birkhauser-Verlag, Basel, 1994), pp. 55-65] reveal that under normal conditions, beat-to-beat fluctuations in heart rate display the kind of long-range correlations typically exhibited by dynamical systems far from equilibrium [Phys. Rev. Lett. 59, 381-384 (1987)]. In contrast, heart rate time series from patients with severe congestive heart failure show a breakdown of this long-range correlation behavior. We describe a new method--detrended fluctuation analysis (DFA)--for quantifying this correlation property in non-stationary physiological time series. Application of this technique shows evidence for a crossover phenomenon associated with a change in short and long-range scaling exponents. This method may be of use in distinguishing healthy from pathologic data sets based on differences in these scaling properties.

NASA Discipline Number 14-10↗

NASA NTRS1995

Fractal mechanisms and heart rate dynamics. Long-range correlations and their breakdown with disease

Under healthy conditions, the normal cardiac (sinus) interbeat interval fluctuates in a complex manner. Quantitative analysis using techniques adapted from statistical physics reveals the presence of long-range power-law correlations extending over thousands of heartbeats. This scale-invariant (fractal) behavior suggests that the regulatory system generating these fluctuations is operating far from equilibrium. In contrast, it is found that for subjects at high risk of sudden death (e.g., congestive heart failure patients), these long-range correlations break down. Application of fractal scaling analysis and related techniques provides new approaches to assessing cardiac risk and forecasting sudden cardiac death, as well as motivating development of novel physiologic models of systems that appear to be heterodynamic rather than homeostatic.

NASA Discipline Cardiopulmonary↗

NASA NTRS1994

Correlation approach to identify coding regions in DNA sequences

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

Non-NASA Center↗

NASA NTRS1994

Statistical mechanics in biology: how ubiquitous are long-range correlations?

The purpose of this opening talk is to describe examples of recent progress in applying statistical mechanics to biological systems. We first briefly review several biological systems, and then focus on the fractal features characterized by the long-range correlations found recently in DNA sequences containing non-coding material. We discuss the evidence supporting the finding that for sequences containing only coding regions, there are no long-range correlations. We also discuss the recent finding that the exponent alpha characterizing the long-range correlations increases with evolution, and we discuss two related models, the insertion model and the insertion-deletion model, that may account for the presence of long-range correlations. Finally, we summarize the analysis of long-term data on human heartbeats (up to 10(4) heart beats) that supports the possibility that the successive increments in the cardiac beat-to-beat intervals of healthy subjects display scale-invariant, long-range "anti-correlations" (a tendency to beat faster is balanced by a tendency to beat slower later on). In contrast, for a group of subjects with severe heart disease, long-range correlations vanish. This finding suggests that the classical theory of homeostasis, according to which stable physiological processes seek to maintain "constancy," should be extended to account for this type of dynamical, far from equilibrium, behavior.

Non-NASA Center↗

NASA NTRS1994

Mosaic organization of DNA nucleotides

Long-range power-law correlations have been reported recently for DNA sequences containing noncoding regions. We address the question of whether such correlations may be a trivial consequence of the known mosaic structure ("patchiness") of DNA. We analyze two classes of controls consisting of patchy nucleotide sequences generated by different algorithms--one without and one with long-range power-law correlations. Although both types of sequences are highly heterogenous, they are quantitatively distinguishable by an alternative fluctuation analysis method that differentiates local patchiness from long-range correlations. Application of this analysis to selected DNA sequences demonstrates that patchiness is not sufficient to account for long-range correlation properties.

NASA Discipline Number 14-10↗

NASA NTRS1992

Fractal landscape analysis of DNA walks

By mapping nucleotide sequences onto a "DNA walk", we uncovered remarkably long-range power law correlations [Nature 356 (1992) 168] that imply a new scale invariant property of DNA. We found such long-range correlations in intron-containing genes and in non-transcribed regulatory DNA sequences, but not in cDNA sequences or intron-less genes. In this paper, we present more explicit evidences to support our findings.

NASA Program Space Physiology and Countermeasures↗

NASA NTRS1992

Long-range correlations in nucleotide sequences

DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'. We then use the mapping to provide a quantitative measure of the correlation between nucleotides over long distances along the DNA chain. Thus we uncover in the nucleotide sequence a remarkably long-range power law correlation that implies a new scale-invariant property of DNA. We find such long-range correlations in intron-containing genes and in nontranscribed regulatory DNA sequences, but not in complementary DNA sequences or intron-less genes.

NASA Discipline Cardiopulmonary↗

NASA NTRS1990

Analysis of energy states in modulation doped multiquantum well heterostructures

A precise and effective numerical procedure to model the band diagram of modulation doped multiquantum well heterostructures is presented. This method is based on a self-consistent iterative solution of the Schroedinger equation and the Poisson equation. It can be used rather easily in any arbitrary modulation-doped structure. In addition to confined energy subbands, the unconfined states can be calculated as well. Examples on realistic device structures are given to demonstrate capabilities of this procedure. The numerical results are in good agreement with experiments. With the aid of this method the transitions involving both the confined and unconfined conduction subbands in a modulation doped AlGaAs/GaAs superlattice, and in a strained layer InGaAs/GaAs superlattice are identified. These results represent the first observation of unconfined transitions in modulation doped multiquantum well structures.

Ji, G.↗

NASA NTRS1988

Contact regrowth technique for low-resistance nonalloyed contacts to the hot-electron transistor

A novel contact regrowth technique for the formation of extremely low nonalloyed ohmic contacts is reported. The successful demonstration of this technique is reported on an InGaAs/InAlAs hot-electron transistor device. For the investigated InGaAs-based structure, the regrown contacting scheme reported includes an In(0.53)Ga(0.47)As layer, an InAs/GaAs strained-layer superlattice, and an InAs cap, all heavily doped n type with Si. A very low specific contact resistance of 1.8 x 10 to the -7th ohm sq cm to the base layer is obtained. The higher current densities achieved in the transistor characteristics are in close agreement with calculations, and a contact model is presented explaining the poor results of conventional nonalloyed contacts.

Peng, C. K.↗

NASA NTRS1988

Extremely low resistance nonalloyed ohmic contacts on GaAs using InAs/InGaAs and InAs/GaAs strained-layer superlattices

Employing a structure consisting of n(+)-InAs/InGaAs and InAs/GaAs strained-layer superlattices (SLSs) grown by molecular beam epitaxy on GaAs films, nonalloyed contact resistances less than 8.5 x 10 to the -8th ohm sq cm have been obtained. Self-consistent simulations show that these extremely small nonalloyed contact resistances are due to the suppression of the depletion depth in the GaAs channel and tunneling through the SLS layer. Similar structures on InGaAs channels have led to nonalloyed specific contact resistances of about 1.5 x 10 to the -8th ohm sq cm. These results represent the smallest figures reported for these important material systems.

Peng, C. K.↗

NASA NTRS1988

Extremely low nonalloyed and alloyed contact resistance using an InAs cap layer on InGaAs by molecular-beam epitaxy

Extremely low alloyed and nonalloyed ohmic contact resistances have been formed on n-type InAs/In(0.53)Ga(0.47)As/In(0.52)Al(0.48)As structures grown on InP(Fe) by molecular-beam epitaxy. To insure the accuracy of the small contact resistances measured, an extended transmission line model was used to extrapolate contact resistances from test patterns with multiple gap spacings varying from 1 to 20 microns. For a 150-A-thick InAs layer doped to 2 x 10 to the 18th/cu cm and a 0.1-micron-thick InGaAs layer doped to 1 x 10 to the 18th/cu cm, a specific contact resistance of 2.6 x 10 to the -8th ohm-asterisk sq cm was measured for the nonalloyed contact, while a resistance less than 1.7 x 10 to the -8th ohm-asterisk sq cm is reported for the alloyed contact. Conventional Au-Ge/Ni/Au was used for the ohmic metal contact and alloying was performed at 500 C for 50 s in flowing H2. Using a thermionic field emission model, the barrier height at the InAs/InGaAs interface was calculated to be 20 meV.

Peng, C. K.↗

NASA NTRS1987

Characterization of graded interface In(x)Ga(1-x)As/In(0.52)Al(0.48)As (x between 0.53 and 0.70) structures grown by molecular-beam epitaxy

Modulation-doped In(x)Ga(1-x)As/In(0.52)Al(0.48)As/InP structures were grown by molecular-beam epitaxy with x values between 53 and 70 percent. For pseudomorphic cases, graded instead of abrupt interfaces were used. Hall mobility and persistent photoconductivity measurements as a function of temperature were used to characterize samples with different structural parameters. Consistent trends in the variation of mobilities and two-dimensional carrier concentration, n(2D), under light and dark conditions have been observed and discussed in terms of applicable scattering mechanisms. The Hall mobilities are comparable to the best results obtained to date but with significantly higher n(2D) concentration.

Peng, C. K.↗

NASA NTRS1987

Pseudomorphic InGaAs/AlGaAs modulation-doped FET's with reduced low-frequency noise and thermally stable performance

A high-performance MODFET structure grown by MBE with the incorporation of a single quantum well In(0.15)Ga(0.85)As layer for the transport of two-dimensional electron gas has been critically examined for its thermal stability at 80 K and low-frequency noise form 0.01 to 10 to the 8th Hz. Experimental results indicate that the behavior of this device in both these respects is much superior when compared with the same behavior of conventional MODFETs. A maximum low-field carrier mobility of 29,000 sq cm/s at 80 K and an average carrier saturation velocity of 2 x 10 to the 7th cm/s at 300 K in a 1-micron gate device clearly indicate that the quality of the pseudomorphic quantum well (InGaAs) layer is either comparable or better than that of the usual GaAs buffer layer. The deep level spectra, obtained through photo-FET measurements, and the low-frequency noise spectra at different temperatures obtained for the new pseudomorphic and conventional MODFET's have clearly indicated that contributions from various deep levels present in the new structure are significantly reduced.

Liu, Shih-Ming↗

NASA NTRS1987

Microwave performance of InAlAs/InGaAs/InP MODFET's

Modulation-doped InAlAs/InGaAs/InP structures were grown by molecular beam epitaxy and fabricated into FETs with excellent RF gain performance. The intrinsic transconductance was about 400 mS/mm at 300 K. Current gain cutoff frequencies of up to 26.5 GHz were obtained in 1-micron gate devices. Extremely small S12 and large S21 led to a very large F(max) of 62 GHz. These results represent the best reported figures for 1-micron devices in this material system, and slightly better than those obtained in recently developed pseudomorphic modulation-doped field effect transistors.

Peng, C. K.↗