Digital Commons Network^™

Protein Family Classification Using Structural And Sequence Information, Jennifer A. Smith

Jennifer A. Smith

Protein family classification usually relies on sequence information (as in the case of hidden Markov models and position-specific scoring matrices) or on structural information where some sort of average positional error between the atomic locations is used. The positional error method requires that the structure of all the proteins to be classified is known. Sequence methods have the advantage that a much larger number of proteins can be classified (since far more sequences are know than structures). However, sequence methods discard a large amount of useful information contained in the structures of the subset of proteins in the family for …

Rna Gene Finding With Biased Mutation Operators, Jennifer A. Smith

Jennifer A. Smith

The use of genetic algorithms for non-coding RNA gene finding has previously been investigated and found to be a potentially viable method for accelerating covariance-model-based database search relative to full dynamic-programming methods. The mutation operators in previous work chose new alignment insertion and deletion locations uniformly over the length of the model consensus sequence. Since the covariance models are estimated from multiple known members of a non-coding RNA family, information is available as to the likelihood of insertions or deletions at the individual model positions. This information is implicit in the state-transition parameters of the estimated covariance models. In the …

Searching For Protein Classification Features, Jennifer A. Smith

Jennifer A. Smith

A genetic algorithm is used to search for a set of classification features for a protein superfamily which is as unique as possible to the superfamily. These features may then be used for very fast classification of a query sequence into a protein superfamily. The features are based on windows onto modified consensus sequences of multiple aligned members of a training set for the protein superfamily. The efficacy of the method is demonstrated using receiver operating characteristic (ROC) values and the performance of resulting algorithm is compared with other database search algorithms.

Accelerated Non-Coding Rna Searches With Covariance Model Approximations, Jennifer A. Smith

Jennifer A. Smith

Covariance models (CMs) are a very sensitive tool for finding non-coding RNA (ncRNA) genes in DNA sequence data. However, CMs are extremely slow. One reason why CMs are so slow is that they allow all possible combinations of insertions and deletions relative to the consensus model even though the vast majority of these are never seen in practice. In this paper we examine reduction in the number of states in covariance models. A simplified CM with reduced states which can be scored much faster is introduced. A comparison of the results of a full CM versus a reduced-state model found …

Truncated Profile Hidden Markov Models, Jennifer A. Smith

Jennifer A. Smith

The profile hidden Markov model (HMM) is a powerful method for remote homolog database search. However, evaluating the score of each database sequence against a profile HMM is computationally demanding. The computation time required for score evaluation is proportional to the number of states in the profile HMM. This paper examines whether the number of states can be truncated without reducing the ability of the HMM to find proteins containing members of a protein domain family. A genetic algorithm (GA) is presented which finds a good truncation of the HMM states. The results of using truncation on searches of the …

A Genetic Algorithms Approach To Non-Coding Rna Gene Searches, Jennifer A. Smith

Jennifer A. Smith

A genetic algorithm is proposed as an alternative to the traditional linear programming method for scoring covariance models in non-coding RNA (ncRNA) gene searches. The standard method is guaranteed to find the best score, but it is too slow for general use. The observation that most of the search space investigated by the linear programming method does not even remotely resemble any observed sequence in real sequence data can be used to motivate the use of genetic algorithms (GAs) to quickly reject regions of the search space. A search space with many local minima makes gradient decent an unattractive alternative. …

An Asynchronous Gals Interface With Applications, Jennifer A. Smith

Jennifer A. Smith

A low-latency asynchronous interface for use in globally-asynchronous locally-synchronous (GALS) integrated circuits is presented. The interface is compact and does not alter the local clocks of the interfaced local clock domains in any way (unlike many existing GALS interfaces). Two applications of the interface to GALS systems are shown. The first is a single-chip shared-memory multiprocessor for generic supercomputing use. The second is an application-specific coprocessor for hardware acceleration of the Smith-Waterman algorithm. This is a bioinformatics algorithm used for sequence alignment (similarity searching) between DNA or amino acid (protein) sequences and sequence databases such as the recently completed human …

Covariance Searches For Ncrna Gene Finding, Jennifer A. Smith

Jennifer A. Smith

The use of covariance models for non-coding RNA gene finding is extremely powerful and also extremely computationally demanding. A major reason for the high computational burden of this algorithm is that the search proceeds through every possible start position in the database and every possible sequence length between zero and a user-defined maximum length at every one of these start positions. Furthermore, for every start position and sequence length, all possible combinations of insertions and deletions leading to the given sequence length are searched. It has been previously shown that a large portion of this search space is nowhere near …

The Mechanism Of Electroforming Of Metal Oxide Memristive Switches, Jianhua Yang, Feng Miao, Matthew Pickett, Douglas Ohlberg, Duncan Stewart, Chun Ning Lau, R Stanley Williams

Jianhua Yang

Aln Contour-Mode Resonators For Narrow-Band Filters Above 3 Ghz, Matteo Rinaldi, Chiara Zuniga, Chengjie Zuo, Gianluca Piazza

Matteo Rinaldi

This paper reports on the design and experimental verification of a new class of thin-film (250 nm) Super High Frequency (SHF) laterally-vibrating piezoelectric microelectromechanical (MEMS) resonators suitable for the fabrication of narrow-band MEMS filters operating at frequencies above 3 GHz. The device dimensions have been opportunely scaled both in the lateral and vertical dimensions in order to excite a contour-extensional mode of vibration in nano features of an ultra-thin (250 nm) Aluminum Nitride (AlN) film. In this first demonstration two-port resonators vibrating up to 4.5 GHz were fabricated on the same die and attained electromechanical coupling, kt2, in excess of …

Electric Energy Sector In Egypt: A Review, Dr. Adel A. Elbaset

Dr. Adel A. Elbaset

No abstract provided.

Gravimetric Chemical Sensor Based On The Direct Integration Of Swnts On Aln Contour-Mode Mems Resonators, Matteo Rinaldi, Chiara Zuniga, Nipun Sinha, Marzie Taheri, Samuel M. Khamis, Alan T. Johnson, Gianluca Piazza

Nipun Sinha

This paper reports on the first demonstration of a gravimetric chemical sensor based on direct integration of Single Wall Carbon Nanotubes (SWNTs) grown by Chemical Vapor Deposition (CVD) on AlN Contour-Mode MicroElectroMechanical (MEMS) resonators. In this first prototype the ability of SWNTs to readily adsorb volatile organic chemicals has been combined with the capability of AlN Contour-Mode MEMS resonator to provide for different levels of sensitivity due to separate frequencies of operation on the same die. Two devices with resonance frequencies of 287 MHz and 442 MHz have been exposed to different concentrations of DMMP in the range from 80 …

Multi-Frequency Pierce Oscillators Based On Piezoelectric Aln Contour-Mode Mems Resonators, Chengjie Zuo, Nipun Sinha, Jan Van Der Spiegel, Gianluca Piazza

Nipun Sinha

This paper reports on the first demonstration of multi-frequency (176, 222, 307, and 482 MHz) oscillators based on piezoelectric AlN contour-mode MEMS resonators. All the oscillators show phase noise values between –88 and –68 dBc/Hz at 1 kHz offset and phase noise floors as low as –160 dBc/Hz at 1 MHz offset. The same Pierce circuit design is employed to sustain oscillations at the 4 different frequencies, while the oscillator core consumes at most 10 mW. The AlN resonators are currently wirebonded to the integrated circuit realized in the AMIS 0.5 μm 5 V CMOS process. This work constitutes a …

Steady State Analysis Of Unified Power Flow Controllers, Omar H. Abdalla, Mohamed A. E. Ghazy, Lotfy M. Lotfy, Nermeen A. M. Hassan

Omar H. Abdalla

The paper presents a tutorial review of the basic operation, control functions and steady state performance of a Unified Power Flow Controller (UPFC). A typical circuit arrangement of a UPFC is given and principles of controlling active and reactive powers are described. The main functions of UPFC are analyzed; including voltage regulation, series reactive compensation, phase compensation, and combined actions. A simplified two-bus power system is considered to demonstrate the main effects of the UPFC. Studies and results are presented to show the wide range capabilities of the UPFC in controlling transmission active and reactive powers simultaneously and/or independently.

Optimal Design Of Wind-Pv-Diesel-Battery System Using Genetic Algorithm, Dr. Adel A. Elbaset

Dr. Adel A. Elbaset

The optimization of diesel generators (DGs) and renewable energy sources have to be done within a cost benefit, high reliability and environmentally friendly framework. Most of optimization method just consider only from economical point of view. This paper presents complete optimization method involving of cost, reliability and pollutant emission into optimization process. The reliability level is analyzed using basic probabilistic concept in order to find loss of load probability (LOLP). This value is then used to determine the customer damage cost due to electricity interruption. Meanwhile, CO2 emission as an indicator of pollution is calculated to determine the annual emission …

Integration Of Aln Micromechanical Contour-Mode Technology Filters With Three-Finger Dual Beam Aln Mems Switches, Nipun Sinha, Rashed Mahameed, Chengjie Zuo, Gianluca Piazza

Nipun Sinha

In this paper, we present the first demonstration of the monolithic integration of Aluminum Nitride (AlN) micromechanical contour mode technology filters with dual-beam actuated MEMS AlN switches. This integration has lead to the development of the first prototype of a fully-integrated all-mechanical switchable filter. Integration has been demonstrated by using AlN contour-mode MEMS filters at two center frequencies, i.e. 98.7 and 279.9 MHz. The micromechanical switch design used here is a novel three-finger dual-beam topology that improves the isolation and insertion loss of the switch by decreasing the parasitic coupling between the DC and RF signals over a previous AlN …

Body-Biased Complementary Logic Implemented Using Aln Piezoelectric Mems Switches, Nipun Sinha, Timothy S. Jones, Zhijun Guo, Gianluca Piazza

Nipun Sinha

This paper reports on the first implementation of low voltage complementary logic (< 1.5 V) by using body-biased aluminum nitride (AlN) piezoelectric MEMS switches. For the first time, by using opposite body biases the same mechanical switch has been made to operate as both an n-type and p-type (complementary) device. Body-biasing also gives the ability to precisely tune the threshold voltage of a switch. The AlN MEMS switches have shown extremely small subthreshold slopes and threshold voltages as low as 0.8 mV/dec and 30 mV, respectively. Furthermore, this work presents a fully mechanical body-biased inverter formed by two AlN MEMS switches operating at 100 Hz with a ± 1.5 V voltage swing.

Software Engineering Education At Carnegie Mellon University: One University; Programs Taught In Two Places, Ray Bareiss, Mel Rosso-Llopart

Ray Bareiss

Teaching Software Engineering to professional master’s students is a challenging endeavor, and arguably for the past 20 years, Carnegie Mellon University has been quite successful. Although CMU teaches Software Engineering at sites world-wide and uses different pedagogies, the goal of the curriculum -- to produce world-class software engineers -- remains constant. This paper will discuss two of the most mature versions of Carnegie Mellon’s Software Engineering program -- the main campus program and its “daughter program” at the Silicon Valley Campus. We discuss the programs with respect to the dimensions of curriculum, how students work and learn, how faculty teach, …

Developing Software Engineering Leaders At Carnegie Mellon Silicon Valley, Ray Bareiss, Todd Sedano

Ray Bareiss

The Carnegie Mellon’s Silicon Valley Campus offers a master’s degree in Software Engineering, with technical and development management tracks, targeted at working software professionals in Silicon Valley. We believe the program to be unique in that it is entirely team-based and project-centered. Students learn by doing as they are coached just in time by faculty in the context of their work on authentic projects, and they are evaluated based on what they produce. In response to our interactions with an industry characterized by innovation and short project development timelines, the program evolved from one focused on “high ceremony” processes to …

Multi-Agent Modeling And Analysis For Space Situation Awareness, Genshe Chen, Erik P. Blasch, Huimin Chen, Khanh Pham

Huimin Chen

No abstract provided.

Ultra Thin Aln Piezoelectric Nano-Actuators, Nipun Sinha, Graham E. Wabiszewski, Rashed Mahameed, Valery V. Felmetsger, Shawn M. Tanner, Robert W. Carpick, Gianluca Piazza

Nipun Sinha

This paper reports the first implementation of ultra thin (100 nm) Aluminum Nitride (AlN) piezoelectric layers for the fabrication of vertically deflecting nano-actuators. An average piezoelectric coefficient (d31~ 1.9 pC/N) that is comparable to its microscale counterpart has been demonstrated in nanoscale thin AlN films. Vertical deflections as large as 40 nm have been obtained in 18 μm long and 350 nm thick cantilever beams under bimorph actuation with 2 V. Furthermore, in-plane stress and stress gradients have been simultaneously controlled. Leakage current lower than 2 nA/cm2 at 1 V has been recorded and an average relative dielectric constant of …

Developing Software Engineering Leaders At Carnegie Mellon Silicon Valley, Ray Bareiss, Todd Sedano

Todd Sedano

The Carnegie Mellon’s Silicon Valley Campus offers a master’s degree in Software Engineering, with technical and development management tracks, targeted at working software professionals in Silicon Valley. We believe the program to be unique in that it is entirely team-based and project-centered. Students learn by doing as they are coached just in time by faculty in the context of their work on authentic projects, and they are evaluated based on what they produce. In response to our interactions with an industry characterized by innovation and short project development timelines, the program evolved from one focused on “high ceremony” processes to …

Building A Business On Open Source Software, Tony Wasserman

Tony Wasserman

For many years, free and open source software was exclusively associated with the research community, in contrast to the closed source products developed by commercial software vendors. Over the past decade, there has been a vast increase in the availability of open source software, growing from such projects as Linux and Apache. Open source software is being widely adopted in industry, which has led to numerous business opportunities for entrepreneurs and vendors. This activity is having a disruptive effect on the software industry that has affected even the largest software vendors. This paper describes the emergence of open source business, …

Vlsi Implementation Of High Resolution High Speed Low Latency Pipeline Floating Point Adder/Subtractor For Fft Applications, Rozita Teymourzadeh, Burhan Yeop Majlis, Mok Vh, Masuri Othman

Dr. Rozita Teymourzadeh, CEng.

The Development Of Humans – A Study Including Languages, Cultures, Religions And Genetics, Dr. Erik Dahlquist, Dr. Allan Dahlquist

Dr. Erik Dahlquist

The book covers the development of culture, religion, language and genetics of the human population since prehistory. Four main cultures have spread around the globe: 1) Monosyllabic language people with ancestor cult 2) Austroasiatic people with sun worshipping and megalit graves. Counting with 20 as the base 3) Uralic speaking people with kings from the sky, and strong city states. Moon and mother godess. Don´t differentiate between male and female, he and she. 4) Inflectual language speaking people with sky gods and cattles. Indoeuropeans. Often endings differentiating he and she. Shows how original cultures are refelected in todays society.

Throughput And Delay In Wireless Sensor Networks Using Directional Antennas, Hong-Ning Dai

Hong-Ning Dai

Most of studies only consider that wireless sensor networks are equipped with only omni-directional antennas, which can cause high collisions. It is shown that the per node throughput in such networks is decreased with the increased number of nodes. Thus, the transmission with multiple short-range hops is preferred to reduce the interference. However, other studies show that the transmission delay increases with the increased number of hops.

In this paper, we consider using directional antennas in wireless sensor networks. We have found that using directional antennas not only can increase the throughput capacity but also can decrease the delay by …

Constraint Handling Using Tournament Selection: Abductive Inference In Partly Deterministic Bayesian Network, Severino F. Galan, Ole J. Mengshoel

Ole J Mengshoel

Constraints occur in many application areas of interest to evolutionary computation. The area considered here is Bayesian networks (BNs), which is a probability-based method for representing and reasoning with uncertain knowledge. This work deals with constraints in BNs and investigates how tournament selection can be adapted to better process such constraints in the context of abductive inference. Abductive inference in BNs consists of finding the most probable explanation given some evidence. Since exact abductive inference is NP-hard, several approximate approaches to this inference task have been developed. One of them applies evolutionary techniques in order to find optimal or close-to-optimal …

Methods For Probabilistic Fault Diagnosis: An Electrical Power System Case Study, Brian Ricks, Ole J. Mengshoel

Ole J Mengshoel

Health management systems that more accurately and quickly diagnose faults that may occur in different technical systems on-board a vehicle will play a key role in the success of future NASA missions. We discuss in this paper the diagnosis of abrupt continuous (or parametric) faults within the context of probabilistic graphical models, more specifically Bayesian networks that are compiled to arithmetic circuits. This paper extends our previous research, within the same probabilistic setting, on diagnosis of abrupt discrete faults. Our approach and diagnostic algorithm ProDiagnose are domain-independent; however we use an electrical power system testbed called ADAPT as a case …