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Projects in 2000–2001

Applied Biosystems: Modeling of TaqMan Reactions for DNA/RNA Quantifications Using PCR (polymerase chain reaction)

Lesley Ward

Polymerase chain reaction amplification, or PCR, is a powerful and widely used technique for producing large quantities of a given DNA (or RNA) species from a small initial amount in a biological sample. The initial sample could contain as little as a single copy of the DNA molecule. Roughly speaking, PCR works by separating the two strands of the double helix, and using each strand as the template for a new double helix. So each cycle of PCR doubles the quantity of the given DNA species present (the PCR product).

A recent application is quantitative PCR: the use of PCR to determine how much of a given DNA species there was in the initial sample. The underlying idea is that because of the exponential increase of the PCR product, there is a linear relationship between (i) the time (number of PCR cycles) taken to accumulate a certain fixed threshold quantity of PCR product, and (ii) the logarithm of the initial amount of DNA present.

In practice, the accumulation of PCR product is monitored using fluorescent probe molecules called TaqMan molecules. The TaqMan molecule alternatively binds to and is cleaved from the DNA when PCR amplification is occurring. It fluoresces (under ultraviolet light) when it cleaves from the DNA. As more DNA molecules are produced, the fluorescence increases.

The number (usually fractional) of cycles after which the fluorescence passes a given threshold value is denoted by CT. Currently, CT values are determined empirically; one can identify the cycle before and the cycle just after the threshold value was reached, and simply interpolate between them to calculate the fractional cycle number CT that corresponds to the threshold value. This is where our clinic project comes in.

We would like to determine CT values more precisely, taking advantage of the fact that the plots obtained by graphing increase in fluorescence against cycle number have a characteristic shape.

This project has three main goals. 1. Mathematically model TaqMan detection of PCR amplification; 2. Refine model by applying real data from Applied Biosystems instruments; and 3. Develop algorithm for automatic calculation of CT values.


  • Tae Jenson
  • Justin Lyon
  • Cameron McLeman
  • Bryan Tysinger

Etec Systems, An Applied Materials Company: Statistics of Error Budget for Laser Lithography Systems

Michael Moody

The motivation for the project arises from the manner in which the performance of semiconductor equipment used for the manufacture of integrated circuit (IC) devices is tested and specified. Typically, one defines the critical parameters associated with the output of such equipment and devises tests to verify that the system meets a specified set of criteria. For example, one such parameter could be the repeatability of the rate at which an etcher removes material, and the specification could be that the standard deviation of the etch rate is less than 1%.


  • Neville Khambatta
  • Marco Latini
  • Ian Schempp
  • Jennifer Wetmore

Fair, Isaac, and Company, Inc.: Preference Analysis of E-Commerce Webs

Darryl Yong

The purpose of this project is to design a decision framework to translate consumer preferences and tradeoffs into a model that makes smart and rapid choices about product offerings. Students will be given a particular website (to be determined) that offers products to consumers; they will attempt to improve its usefulness and value to customers with utility-based prediction/decision models. For instance, many sites use simple “knockout rules” to find products a consumer wants. Sites that make use of consumer preferences should be able to make offers that are very responsive to consumer needs and that are an improvement on models that use “collaborative filtering techniques” to detect patterns of pooled individuals but do not elicit the notion of preferences or utility.


  • Natan Bershtel
  • John Chou
  • Claire Launay
  • John Lu

Space Systems/Loral: Optimization of Orbit-Raising Using Ion Propulsion

Andrew J. Bernoff

Space Systems/Loral is one of the world leaders in the design, building, launching, and management of weather and communications satellite. Because the cost of raising propellant into orbit is roughly $10,000 per kilogram, determining the optimal launch parameters for getting a satellite into orbit efficiently may ultimately save millions of dollars.

At present Space Systems/Loral's electric orbit raising (EOR) algorithm which is used to determine trajectories for optimal propellant usage is, unwieldy, unreliable, and difficult to use. It consists of numerical routines that arrive at a solution, but does so in a ponderous fashion. It may also produce solutions that are local minimum but not globally optimal.

This clinic would concentrate on improving the efficiency and reliability of the EOR, goals include 1. Reduce processing time; 2. Implement a more efficient ODE solver (at present the routine uses fourth-order Runge Kutta); 3. Improve the optimization routine; and 4. Develop methods for accessing if a locally optimal solution is globally optimal


  • Kylie Bryant
  • Matt Gedigian
  • Tyson MacDonald
  • Jay Trautman
  • Alex Wilkins