Spring 2017

PHY 380 Introduction to Computational Physics

Introduction to Open Source Physics and Java.
Simulating Particle Motion.
Oscillatory Systems.
Few-Body Problems: The Motion of the Planets.
The Chaotic Motion of Dynamical Systems.
Random Walks and Chemical Reactions.
Molecular Dynamics Simulations of Many Particle Systems.
Normal Modes and Waves.
Electrodynamics.
Monte Carlo Simulation of Thermal Systems.
Quantum Systems.
Fractals. Self-organized Critical Phenomena. Neural Networks.

 

Textbook: H. Gould, J. Tobochnik, and W. Christian, "Computer Simulation
Methods, Applications to Physical Systems" third edition

The lecture notes and homework for this course are available through Course Site

 

Fall 2016

 

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamilton's Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

PHY 372/472 Cellular Physics of Membranes and the Cytoskeleton

 

Instructors:

Prof. Aurelia Honerkamp-Smith

Prof. Dimitrios Vavylonis

Department of Physics  

 

The filaments and motor proteins of the cytoskeleton organize into networks that provide cells with shape, generate mechanical forces and movement by polymerization and motor-based sliding. The plasma membrane is a fluid surface which is responsive to environmental and biochemical signals. It defines the boundaries of the cell, internal compartments, and organelles. Changes of cell shape and intracellular organization require coordination of the cytoskeleton and membranes. This course is an introduction to the physical principles relevant to this organization, which spans several orders of magnitude in length and time.

 

Spring 2016

 

PHY 442 Statistical Mechanics

 

Physics and Probability

Entropy and Thermodynamics

Canonical Ensemble

Grand Canonical Ensemble

Statistical Physics of Bosons and Fermions

Phase Transitions

Continuus Phase Transitions

 

Textbook: Leonard M. Sander, "Equilibrium Statistical Physics", 2013 

 

 

Fall 2015

 

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

PHY 372/472 Dynamics of the Cytoskeleton: Physical Principles and Self-Organization

 

The filaments and motor proteins of the cytoskeleton organize into networks that provide cells with shape, generate mechanical forces and movement by polymerization and motor-based sliding, and regulate intracellular transport. This course is an introduction to the physical principles relevant to this organization that spans several orders of magnitude in length and time, including diffusion, transport, polymerization, nonlinear dynamical aspects, bistable and oscillatory behavior, feedback mechanisms, pattern formation, and mechanical forces

 

 

Spring 2014

PHY 13: General Physics II

 

Syllabus

Physics 13 is the second half of introductory physics, primarily for biological science and earth and environmental science students. Subjects include electricity and magnetism, light, quantum mechanics, atoms, and the nucleus. Prerequisites: PHY 10/11, and MATH 21/31/51.

 

Lecture notes and other course related information is available at Course Site.

 

Fall 2013

 

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

PHY 398/498 Dynamics of the Cytoskeleton: Physical Principles and Self-Organization

 

The filaments and motor proteins of the cytoskeleton organize into networks that provide cells with shape, generate mechanical forces and movement by polymerization and motor-based sliding, and regulate intracellular transport. This course is an introduction to the physical principles relevant to this organization that spans several orders of magnitude in length and time, including diffusion, transport, polymerization, nonlinear dynamical aspects, bistable and oscillatory behavior, feedback mechanisms, pattern formation, and mechanical forces

 

 

Spring 2013

PHY 13: General Physics II

 

Syllabus

Physics 13 is the second half of introductory physics, primarily for biological science and earth and environmental science students. Subjects include electricity and magnetism, light, quantum mechanics, atoms, and the nucleus. Prerequisites: PHY 10/11, and MATH 21/31/51.

 

Lecture notes and other course related information is available at Course Site.

 

 

Fall 2012 

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

 

Spring 2012

PHY 13: General Physics II

 

Syllabus

Physics 13 is the second half of introductory physics, primarily for biological science and earth and environmental science students. Subjects include electricity and magnetism, light, quantum mechanics, atoms, and the nucleus. Prerequisites: PHY 10/11, and MATH 21/31/51.

 

Lecture notes and other course related information is available at Course Site.

 

 

Fall 2011 

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

 

Spring 2011

PHY 13: General Physics II

 

Syllabus

 

Physics 13 is the second half of introductory physics, primarily for biological science and earth and environmental science students. Subjects include electricity and magnetism, light, quantum mechanics, atoms, and the nucleus. Prerequisites: PHY 10/11, and MATH 21/31/51.

 

Lecture notes and other course related information is available at Course Site.

 

 

Fall 2010 

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

 

Spring 2010

PHY 13: General Physics II

 

Syllabus

 

Physics 13 is the second half of introductory physics, primarily for biological science and earth and environmental science students. Subjects include electricity and magnetism, light, quantum mechanics, atoms, and the nucleus. Prerequisites: PHY 10/11, and MATH 21/31/51.

 

Lecture notes and other course related information is available at Course Site.

 

Fall 2009

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998

 

 

Spring 2009

PHY 398/BIOS 398 Physical Concepts in Cell Biology

 

Dimitrios Vavylonis (main instructor)
Department of Physics

 

James Gunton
Department of Physics

 

Lynne Cassimeris
Biological Sciences

 

An interdisciplinary course for undergraduate and graduate students in biology, bio-engineering, chemical and mechanical engineering, chemistry, and physics. The course addresses the biophysical principles of structure formation in the cell, emphasizing the role of the polymers of the cellís cytoskeleton is establishing patterns within cells.

 

The course was supported by the Biosystems Dynamics Summer Institute

 

Fall 2008

PHY 420 Mechanics

 

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

Rigid Bodies

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

 

Spring 2008

PHY 380 Introduction to Computational Physics (click here)

Introduction to Open Source Physics and Java.
Simulating Particle Motion.
Oscillatory Systems.
Few-Body Problems: The Motion of the Planets.
The Chaotic Motion of Dynamical Systems.
Random Walks and Chemical Reactions.
Molecular Dynamics Simulations of Many Particle Systems.
Normal Modes and Waves.
Electrodynamics.
Monte Carlo Simulation of Thermal Systems.
Quantum Systems.
Fractals. Self-organized Critical Phenomena. Neural Networks.

 

Textbook: H. Gould, J. Tobochnik, and W. Christian, ``Computer Simulation
Methods, Applications to Physical Systems'' third edition, Pearson, 2007

 

 

Fall 2007

PHY 420 Mechanics (click here)

Lagrangian Mechanics

Scattering and Linear Oscillations

Hamiltons' Equations of Motion

Canonical Transformations

The Hamilton-Jacobi Method

Perturbation Theory

Nonlinear Dynamics and Chaos

Rigid Bodies

 

Textbook: Josť and Saletan, "Classical Dynamics: A Contemporary Approach", Cambridge University Press, 1998 

 

Spring 2007

PHY 372 Physical Concepts and Modeling in Cell Biology

 

Modern biological research is becoming more quantitative. Advances in experimental methods allow us to study with extreme detail processes within the basic unit of life, the cell, all the way down to the level of molecules. We can watch DNA, proteins and lipids assemble into elaborate dynamic structures such as chromosomes, organelles, membranes, and filaments within living cells. A major challenge in modern science is to (1) find ways to extract quantitative information from such experiments, and (2) use this information to formulate predictive models which capture the essence of the underlying mechanisms. The course is an introduction to recent research in this area.

 

 

Fall 2006

PHY 011 Introductory Physics I

Recitation Instructor