During July 10-28, 2006 , Mississippi State University, Starkville will be the host of the Institute for Mathematics and its Applications (IMA) summer graduate program in mathematics. The course will concentrate on Topology and its Applications.

This program is open to graduate students from IMA Participating Institutions. Students are nominated by their department head. Participating institution department heads nominate graduate students from their institution by an e-mail to visit@ima.umn.edu with the students' names and e-mail addresses.

Those students may then register by filling out the application form. Places are guaranteed for two graduate students from each participating institution, with additional students accommodated as space allows.

**Course Description:**

In a number of diverse areas, topological issues have begun to surface. In molecular biology, for example, the geometric features of the surface of a molecule have been shown to influence certain protein docking processes. Knot theory is becoming increasingly important in the study of DNA. Computer scientists encounter topological problems in attempts to reconstruct surfaces from sampled data. Topology in phase space can help overcome the inherent sensitivity in longtime simulations of dynamical systems. During the three-week meeting in the period July 9-29, 2006, there will be three week-long courses in the following areas:

- Week 1: Applications to Dynamical Systems
- Week 2: Topological Approximation and Surface Reconstruction
- Week 3: Applications to Molecular Biology

Below are the Lecturers and the description for each course.

**Applications to Dynamical Systems (Week 1): **Konstantin Mischaikow, Georgia Institute of Technology

We will discuss computational homology and its use in the study of nonlinear dynamical systems. The lectures will survey five topics:

(1) Algorithms for computing the homology of spaces.

(2) The use of homology in investigating and classifying nonlinear systems based on the patterns observed in experiments or numerical simulations.

(3) Algorithms for computing the homology of maps.

(4) Conley index theory and associated algorithms.

(5) Computer assisted proofs in dynamics.

The associated projects will involve the application of these tools to specific problems.

**Topological Approximation and Surface (Week 2) Reconstruction: **Gunnar Carlsson, Stanford University

High dimensional data is now being generated at a very rapid rate in many different disciplines. Further, the data is frequently noisy, and is not equipped with any theoretical model. Rather, the data analysis needs to be used to discover the model. Since there is frequently no model, and therefore no preferred coordinate system, it is important to study those properties which don't change under continuous coordinate changes, which are called topological. The goal of this course is to provide an introduction to a recently developed computational version of algebraic topology, called persistent homology, which allows one to infer topological properties of geometric objects from "point clouds" sampled from them. We will introduce algebraic topology itself, the theory of persistent homology, software which permits its computation, and demonstrate how it is used in several real world examples.

**Applications to Molecular Biology (Week 3): **John Harer, Duke University

- Protein surface and docking geometry

- Intro to protein structure

- Constructing the interface surface

- Flattening

- Docked structure characterization

- Elevation

- Extended persistence

- Docking predition

- Topology for Point Clouds

- /alpha - /beta witness complexes

- Local homology and manifold recognition

- Stratified spaces and intersection homology

- Persistence for intersection homology

- Segmentation of Medical Image Data - Watershed algorithm

- Adding persistence

- Deformable Models

- Testing the algorithms on a variety of datasets

**Schedule**

The typical day's schedule will consist of two lectures in the morning, one after lunch, and informal problem sessions in the late afternoon as shown below.

9:00—10:00 lecture

10:00—10:30 break

10:30—11:30 lecture

11:30—1:30 lunch

1:30 until ? computer demos/problem sessions

Organizer is also trying to work out some Saturday excursions. Perhaps a day trip to Memphis one weekend, and a canoe trip in Noxubee wildlife refuge another. More details to follow.

**Lecture room:** **Swalm Hall, Room 140**. Please meet here 9:00 Monday morning

**Dorm info:** single rooms, shared bathroom at **Cresswell Hall**

**Abstracts, reading materials, etc.** will be posted as it is received.

**Gunnar Carlsson** (Stanford University)

kleintwo.pdf mississippitwo.pdf

**Vin de Silva** (Pomona College)

VdS_CUC_colloq06.pdf

**John Harer** (Duke University)

Morse.pdf PL-Morse_Theory.pdf Persistence.pdf extended.pdf 2d-Morse.pdf

3d_Morse_Conference_version.pdf Alpha_and_persistence.pdf interface.pdf Interfaces.pdf

PersTop.pdf vineyards_socg06.pdf Vor_Del_old.pdf elevation-final-journal.ps elevation-final-journal.pdf segmentation.pdf kettlebell.pdf

**Kevin P. Knudson** (Mississippi State University)

morse.pdf

**Konstantin Mischaikow** (Georgia Tech/Rutgers) and **William Kalies** (Florida Atlantic University)

7/10/2006 Morning Slides: pdf

7/10/2006 Afternoon Slides: pdf

Paper: pdf