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Spring 2019
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 2018
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: José and Saletan,
"Classical Dynamics: A Contemporary Approach", Cambridge University Press,
1998
PHY 382 Physics of Cells
Instructor: Dimitrios
Vavylonis
co-Instructor: Aurelia
Honerkamp-Smith
This course focuses on the physical principles underlying the organization
of living cells, which spans several orders of magnitude in length and time.
It provides an introduction to biological physics and relevant concepts of
soft-matter physics.
Textbook: Physical Biology of the Cell (Phillips, Kondev,
Theriot, Garcia, Second Edition, Garland Science, New York, 2012).
1. Introduction to physical biology
of the cell: numbers, length and time scales in biology.
2. Mechanical and chemical equilibrium. Two state systems and cooperativity.
Biopolymers and membranes. Electrostatics in solution.
3. Dynamics in the cell. Brownian motion. Rate equations and kinetics of
association and dissociation.
4. Cytoskeleton and molecular motors. Polymerization kinetics. Transport and
force generation.
5. Biological electricity. Pumps and channels. The Hodgkin-Huxley model.
6. Biological networks. Cell signaling. Biological pattern formation.
Spring 2018
PHY 442 Statistical Mechanics
Physics and Probability
Entropy and Thermodynamics
Canonical Ensemble
Grand Canonical Ensemble
Statistical Physics of
Bosons and Fermions
Phase Transitions
Textbooks:
Robert H. Swendsen, "An Introduction to
Statistical Mechanics and Thermodynamics," Oxford University Press, 2012
Leonard M. Sander,
"Equilibrium Statistical Physics", 2013
Fall 2017
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: José and Saletan,
"Classical Dynamics: A Contemporary Approach", Cambridge University Press,
1998
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: José 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: José 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: José 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: José 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: José 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: José 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: José 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 cell’s 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: José 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: José 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.
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