GEM4 OCW Home > Summer Schools > Summer 2006: Infectious Disease
Summer 2006: Infectious Disease
The first GEM4 Summer School was held at MIT in Cambridge, Massachusetts in August, 2006, with a focus on the role of biomechanics in infectious disease. Enrollment included 48 students from around the world, with 23 faculty presenting lectures on a variety of topics from basic mechanics and biology to advanced concepts on how mechanics can influence or is reflected in infectious diseases. Classes were held all day, including a collection of intensive laboratory experiences on two afternoons. A high point was a reception at which the students presented posters of their own research and had a chance to sample the wide range of interests of their colleagues. Based on the comments received from participants after the Summer School, it was clear that this two-week session would have significant impact on their future research, and that many valuable ties were made, both with senior faculty and fellow students
Calendar
Lectures
Labs
Photographs
Calendar
| Day | Activities |
|---|---|
| 1 | Parallel Tutorial Session 1: Basic mechanics Parallel Tutorial Session 2: Introduction to physiology General Tutorial Session 1: Introduction to infectious diseases |
| 2 | Parallel Tutorial Session 3: Continuum and statistical
mechanics Parallel Tutorial Session 4: Introduction to molecular biology Parallel Tutorial Session 5: Introduction to the immune system Parallel Tutorial Session 6: Cell biology lab |
| 3 | Parallel Tutorial Session 7: Molecular mechanics Parallel Tutorial Session 8: Introduction to cell biology Laboratories in molecular and cell mechanics Tissue biomechanics and mechanobiology Cellular and tissue imaging with multi-photon excitation microscopy Fast fluorescence microrheology for quantitative studies of cytoskeletal mechanotransduction Magnetic trap microrheology |
| 4 | General Tutorial Session 3: Experimental methods Laboratories in molecular and cell mechanics Optical trap; DNA Optical trap; red blood cells MEMS; red blood cells Microfluidics; red blood cells |
| 5 | General Tutorial Session 4: Space, time, and energy landscapes
mechanobiology Laboratories in molecular and cell mechanics AFM/optical trap (hands-on) AFM; endothelial cells AFM; force spectroscopy |
| Over the weekend: Review problems, simple homework assignments Trainees prepare posters to illustrate their own related work, pose research questions |
|
| 6 | Session on connective tissue mechanics General discussion of dynamics of infectious diseases |
| 7 | Session on cell biomechanics Case studies on inflammation and mechanotransduction Poster session |
| 8 | General Session on molecular biomechanics Applications and Case Studies |
| 9 | Session on Computational Biomechanics Identification of force-generating element in kinesin motility Cytoskeleton dynamics simulation of the red blood cell Multi-scale cell modeling |
| 10 | Trainee presentations Summary and discussion |
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Lectures
This page contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.
| Day | Lectures |
|---|---|
| 1 |
Parallel Tutorial Session 1: Basic mechanics (PDF - 1 MB)# (student notes) Simple statistical mechanics for biological systems Foundations of continuum mechanics Parallel Tutorial Session 2: Introduction to physiology (PDF - 3.10 MB)# (student notes) General Tutorial Session 1: Introduction to infectious diseases (PDF)# (student notes) Human tuberculosis and malaria The inflammatory cascade (PDF 1) (PDF 2) Biosafety and laboratory preparedness (PDF - 1.8 MB) |
| 2 |
Parallel Tutorial Session 3: Continuum and statistical
mechanics (PDF)# (student notes) Simple statistical mechanics for biological systems Foundations of continuum mechanics; elastic and viscoelastic response Parallel Tutorial Session 4: Introduction to molecular biology (PDF - 4.2 MB)# (student notes) Basic concepts in molecular cell biology - the Central Dogma Control of gene expression Parallel Tutorial Session 5: Introduction to the immune system (PDF - 1.6 MB)# (student notes) The immune system of metazoans Parallel Tutorial Session 6: Cell biology lab Video show of cell structures, cell adhesion, cell growth and cell motion; laboratory demonstrations of cell culture; basics of light microscopy |
| 3 |
Parallel Tutorial Session 7: Molecular mechanics (PDF - 3.1 MB)# (student notes) Basic laws of thermodynamics, generalized force, nonequilibrium statistical mechanics of single molecules (PDF) The electron problem, classical ion dynamics, molecular dynamics situations Parallel Tutorial Session 8: Introduction to cell biology (PDF - 1.3 MB)# (student notes) The cytoskeleton and cell motility The biology of the red blood cell |
| 4 |
General Tutorial Session 3: Experimental methods (PDF - 3.1 MB)# (student notes) Optical tweezers and single-molecule fluorescence methods AFM imaging and force spectroscopy Home-built teaching AFM and optical traps Single and multiple particle tracking methods, magnetic trap (PDF) 3D microscopy -- deconvolution, confocal, 2-photon (PDF) Micropipette aspiration, other microfluidic methods MEMS-based tools (PDF) |
| 5 |
General Tutorial Session 5: Space, time, and energy landscapes
mechanobiology (PDF - 1.4 MB)# (student notes) 1) Molecular forces: basic interactions (steric, electrostatic, van der Waals, hydrogen bond, hydrophobic); macromolecular surface forces (electrostatic double layer, DL VO, surface tension); kT as a ruler of molecular forces; self-assembly as a result of competing molecular forces 2) Thermal forces and Brownian motion: random walk picture; meaning of the Central Limit Theorem; diffusion vs. Langevin equation descriptions; diffusion coefficient and fluctuation-dissipation theorem (PDF) 3) Reaction kinetics: Michaelis-Menten kinetics; Arrhenius relation; binding energy/affinity; classical equilibrium picture vs. stochastic picture of rate processes; cooperativity 4) Biological relevance in the context of cell migration, sensing and force generation |
| 6 |
Session on connective tissue mechanics (PDF)# (student notes) Elastic and viscoelastic response of connective tissues Review of basic mechanics Poroelasticity; Darcy's Law; hydraulic permeability Tissue mechanics and case studies in human health Arthritis and joint regeneration Tendon, ligament, cartilage, bone Atherosclerosis General discussion of dynamics of infectious diseases (PDF - 1.4 MB)# (student notes) Beyond single organism, discuss infection mechanisms and epidemiology/population dynamics |
| 7 |
Session on cell biomechanics (PDF - 1.3 MB)# (student notes) Cell membrane mechanics Cytoskeletal structure and motility Time dependent responses, CSK mechanics Cell adhesion, receptor-ligand interaction, focal adhesions Measurement of cell adhesive forces and kinetics Microrheology (Mason and Weitz method) Generalized Stokes-Einstein relationship (GSER) Nonequilibrium dynamics; evidence for a glassy domain Case studies on inflammation and mechanotransduction (PDF - 1.7 MB)# (student notes) Mechanotransduction Malaria Asthma T-cells and immunology from a statistical mechanics perspective |
| 8 |
General Session on molecular biomechanics (PDF - 4.3 MB)# (student notes) Brief introduction to molecular biomechanics Polymer chains, statistics of random walks, persistence length, Boltzmann distribution, freely jointed chain, worm-like chain model (PDF) Protein conformational dynamics, the role of force in protein-protein interactions Motor molecules and protein nanomachines Motility at the macromolecular level, polymerization forces Applications and Case Studies (PDF)# (student notes) Case studies on molecular biomechanics and its linkage to infectious diseases How to decipher the pathogenic processes driven by micro-organisms at the molecular, cellular, and tissue levels Molecular biomechanics issues in viral replication and viral packaging Molecular pathways in infectious diseases Molecular aspects in therapeutics and vaccine design |
| 9 |
Session on Computational Biomechanics (PDF - 1 MB)# (student notes)
Cytoskeleton dynamics simulation of the red blood cell (PDF - 8.9 MB)
Multi-scale cell modeling |
| 10 | Trainee presentations Summary and discussion |
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Labs
This page contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.
| Lab# | Topics |
|---|---|
| 1 | Tissue biomechanics and mechanobiology (PDF) |
| 2 | Cellular and tissue imaging with multiphoton excitation microscopy (PDF) |
| 3 | Fast fluorescence microrheology for quantitative studies of cytoskeletal mechanotransduction (PDF) |
| 4 | Magnetic trap microrheology (PDF) |
| 5 | Optical trapping and single molecule fluorescence (PDF) |
| 6 | Optical tweezers: membrane and cell (PDF) |
| 7 | Advanced instrumentation in the teaching lab (PDF) |
| 8 | Atomic force microscopy imaging of cells (PDF) |
| 9 | Molecular force spectroscopy on living cells (PDF) |
| 10 | BioMEMS force sensor (PDF) |
| 11 | Microfluidics (PDF) |
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2006 Summer School Group Photos
Click a photo below to see a larger version.
