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7.88J Protein Folding Problem (MIT) 7.88J Protein Folding Problem (MIT)

Description

This course focuses on the mechanisms by which the amino acid sequence of polypeptide chains (proteins), determine their three-dimensional conformation. Topics in this course include sequence determinants of secondary structure, the folding of newly synthesized polypeptide chains within cells, folding intermediates aggregation and competing off-pathway reactions, and the unfolding and refolding of proteins in vitro. Additional topics covered are the role of helper proteins such as chaperonins and isomerases, protein recovery problems in the biotechnology industry, and diseases found associated with protein folding defects. This course focuses on the mechanisms by which the amino acid sequence of polypeptide chains (proteins), determine their three-dimensional conformation. Topics in this course include sequence determinants of secondary structure, the folding of newly synthesized polypeptide chains within cells, folding intermediates aggregation and competing off-pathway reactions, and the unfolding and refolding of proteins in vitro. Additional topics covered are the role of helper proteins such as chaperonins and isomerases, protein recovery problems in the biotechnology industry, and diseases found associated with protein folding defects.

Subjects

amino acid sequence | amino acid sequence | polypeptide chains | polypeptide chains | sequence determinants | sequence determinants | folding | folding | synthesized polypeptide chains within cells | synthesized polypeptide chains within cells | unfolding and refolding of proteins in vitro | unfolding and refolding of proteins in vitro | folding intermediates aggregation | folding intermediates aggregation | competing off-pathway reactions | competing off-pathway reactions | chaperonins | chaperonins | isomerases | isomerases | helper proteins | helper proteins | protein recovery problems | protein recovery problems | biotechnology industry | biotechnology industry | protein folding defects | protein folding defects | 3-D conformation | 3-D conformation | globular proteins | globular proteins | fibrous proteins | fibrous proteins | kinetics | kinetics | in vitro refolding | in vitro refolding | pathways | pathways | in vivo folding | in vivo folding | synthesized proteins | synthesized proteins | aggregation | aggregation | protein misfolding | protein misfolding | human disease | human disease | protein folding | protein folding | genome sequences | genome sequences | 7.88 | 7.88 | 5.48 | 5.48 | 7.24 | 7.24 | 10.543 | 10.543

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7.88J Protein Folding Problem (MIT)

Description

This course focuses on the mechanisms by which the amino acid sequence of polypeptide chains (proteins), determine their three-dimensional conformation. Topics in this course include sequence determinants of secondary structure, the folding of newly synthesized polypeptide chains within cells, folding intermediates aggregation and competing off-pathway reactions, and the unfolding and refolding of proteins in vitro. Additional topics covered are the role of helper proteins such as chaperonins and isomerases, protein recovery problems in the biotechnology industry, and diseases found associated with protein folding defects.

Subjects

amino acid sequence | polypeptide chains | sequence determinants | folding | synthesized polypeptide chains within cells | unfolding and refolding of proteins in vitro | folding intermediates aggregation | competing off-pathway reactions | chaperonins | isomerases | helper proteins | protein recovery problems | biotechnology industry | protein folding defects | 3-D conformation | globular proteins | fibrous proteins | kinetics | in vitro refolding | pathways | in vivo folding | synthesized proteins | aggregation | protein misfolding | human disease | protein folding | genome sequences | 7.88 | 5.48 | 7.24 | 10.543

License

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7.88J Protein Folding and Human Disease (MIT) 7.88J Protein Folding and Human Disease (MIT)

Description

This course covers amino acid sequence control of protein folding, misfolding, amyloid polymerization and aggregation. Readings and discussions address topics such as chaperone structure and function, folding and assembly of fibrous proteins, and pathologies associated with protein misfolding and aggregation in Alzheimer's, Parkinson's, Huntington's and other protein deposition diseases. Students are required to write and present a research paper. This course covers amino acid sequence control of protein folding, misfolding, amyloid polymerization and aggregation. Readings and discussions address topics such as chaperone structure and function, folding and assembly of fibrous proteins, and pathologies associated with protein misfolding and aggregation in Alzheimer's, Parkinson's, Huntington's and other protein deposition diseases. Students are required to write and present a research paper.

Subjects

protein folding | protein folding | misfolding | misfolding | aggregation | aggregation | protein structures | protein structures | folding intermediates | folding intermediates | off-pathway aggregation | off-pathway aggregation | amyloid formation | amyloid formation | Key chaperones | Key chaperones | chaperonins | chaperonins | human protein deposition diseases | human protein deposition diseases | Alzheimer’s disease | Alzheimer’s disease | Parkinson’s disease | Parkinson’s disease | Huntington’s disease | Huntington’s disease | amyloids | amyloids | prions | prions | amino acid sequence | amino acid sequence | amyloid polymerization | amyloid polymerization | chaperone structure and function | chaperone structure and function | folding and assembly of fibrous proteins | folding and assembly of fibrous proteins

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18.966 Geometry of Manifolds (MIT) 18.966 Geometry of Manifolds (MIT)

Description

This is a second-semester graduate course on the geometry of manifolds. The main emphasis is on the geometry of symplectic manifolds, but the material also includes long digressions into complex geometry and the geometry of 4-manifolds, with special emphasis on topological considerations. This is a second-semester graduate course on the geometry of manifolds. The main emphasis is on the geometry of symplectic manifolds, but the material also includes long digressions into complex geometry and the geometry of 4-manifolds, with special emphasis on topological considerations.

Subjects

Differential forms | Differential forms | Lie groups | Lie groups | DeRham | DeRham | Riemannian manifolds | Riemannian manifolds | curvature | curvature | Hodge | Hodge | Hodge theory | Hodge theory | manifolds | manifolds | Riemannian geometry | Riemannian geometry | holonomy | holonomy | symplectic geometry | symplectic geometry | complex geometry | complex geometry | Hodge-Kahler theory | Hodge-Kahler theory | smooth manifold topology | smooth manifold topology

License

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18.117 Topics in Several Complex Variables (MIT) 18.117 Topics in Several Complex Variables (MIT)

Description

This course covers harmonic theory on complex manifolds, the Hodge decomposition theorem, the Hard Lefschetz theorem, and Vanishing theorems. Some results and tools on deformation and uniformization of complex manifolds are also discussed. This course covers harmonic theory on complex manifolds, the Hodge decomposition theorem, the Hard Lefschetz theorem, and Vanishing theorems. Some results and tools on deformation and uniformization of complex manifolds are also discussed.

Subjects

Harmonic theory | Harmonic theory | complex manifolds | complex manifolds | Hodge decomposition theorem | Hodge decomposition theorem | Hard Lefschetz theorem | Hard Lefschetz theorem | Vanishing theorems | Vanishing theorems | deformation of complex manifolds | deformation of complex manifolds | uniformization of complex manifolds | uniformization of complex manifolds

License

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6.849 Geometric Folding Algorithms: Linkages, Origami, Polyhedra (MIT) 6.849 Geometric Folding Algorithms: Linkages, Origami, Polyhedra (MIT)

Description

Includes audio/video content: AV lectures. This course focuses on the algorithms for analyzing and designing geometric foldings. Topics include reconfiguration of foldable structures, linkages made from one-dimensional rods connected by hinges, folding two-dimensional paper (origami), and unfolding and folding three-dimensional polyhedra. Applications to architecture, robotics, manufacturing, and biology are also covered in this course. Acknowledgments Thanks to videographers Martin Demaine and Jayson Lynch. Includes audio/video content: AV lectures. This course focuses on the algorithms for analyzing and designing geometric foldings. Topics include reconfiguration of foldable structures, linkages made from one-dimensional rods connected by hinges, folding two-dimensional paper (origami), and unfolding and folding three-dimensional polyhedra. Applications to architecture, robotics, manufacturing, and biology are also covered in this course. Acknowledgments Thanks to videographers Martin Demaine and Jayson Lynch.

Subjects

origami | origami | geometry | geometry | algorithm | algorithm | folding | folding | linkage | linkage | polyhedra | polyhedra | seam | seam | crease pattern | crease pattern | universal molecule | universal molecule | box pleating | box pleating | triangulation | triangulation | vertex | vertex | edge | edge | curved crease | curved crease | rigidity | rigidity | tensegrity | tensegrity | hinged dissection | hinged dissection | unfolding | unfolding | gluing | gluing | platonic solid | platonic solid | refolding | refolding | sculpture | sculpture | paper | paper | 3D chain | 3D chain | design | design

License

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7.343 Protein Folding, Misfolding and Human Disease (MIT) 7.343 Protein Folding, Misfolding and Human Disease (MIT)

Description

This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. The instructor for this course, Dr. Kosinski-Collins, is a member of the HHMI Education Group. Maintenance of the complex three-dimensional structure adopted by a protein in the cell is vital for function. Oftentimes, as a consequence of environmental stress, genetic mutation, and/or infection, the folded structure of a protein gets altered and multiple proteins stick and fall out of solution in a process known as aggregation. In many protein aggregation diseases, incorrectly folded proteins self-associate, for This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. The instructor for this course, Dr. Kosinski-Collins, is a member of the HHMI Education Group. Maintenance of the complex three-dimensional structure adopted by a protein in the cell is vital for function. Oftentimes, as a consequence of environmental stress, genetic mutation, and/or infection, the folded structure of a protein gets altered and multiple proteins stick and fall out of solution in a process known as aggregation. In many protein aggregation diseases, incorrectly folded proteins self-associate, for

Subjects

protein folding | protein folding | misfolded proteins | misfolded proteins | Mad Cow | Mad Cow | Creutzfedt-Jakob Disease | Creutzfedt-Jakob Disease | Alzheimer's Disease | Alzheimer's Disease | Huntington's Disease | Huntington's Disease | protein aggregation | protein aggregation | self-associate | self-associate | cell death | cell death | dementia | dementia | prions | prions | bovine spongiform encephalopathy | bovine spongiform encephalopathy | kuru | kuru | scrapie | scrapie | protein structure | protein structure | amyloid protein | amyloid protein | amyloidosis | amyloidosis | polyglutamine repeats | polyglutamine repeats | fibrils | fibrils

License

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18.965 Geometry of Manifolds (MIT) 18.965 Geometry of Manifolds (MIT)

Description

Geometry of Manifolds analyzes topics such as the differentiable manifolds and vector fields and forms. It also makes an introduction to Lie groups, the de Rham theorem, and Riemannian manifolds. Geometry of Manifolds analyzes topics such as the differentiable manifolds and vector fields and forms. It also makes an introduction to Lie groups, the de Rham theorem, and Riemannian manifolds.

Subjects

Differentiable manifolds | Differentiable manifolds | vector fields forms | vector fields forms | Lie groups | Lie groups | DeRham theorem | DeRham theorem | Riemannian manifolds | Riemannian manifolds

License

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TALAT Lecture 3706: Bending and Folding

Description

This lecture describes the fundamentals of bending and folding aluminium sheet; it also describes different methods in design of folding tools. Background in production engineering and sheet metal forming and familiarity with the subject matter covered in TALAT This lectures 3701- 3705 is assumed.

Subjects

aluminium | aluminum | european aluminium association | EAA | Training in Aluminium Application Technologies | training | metallurgy | technology | lecture | machining | forming | forging | sheet | folding | fold geometries | drawn parts | bending | springback | bending line geometries | counter pressure | springback angle | yield stress | pre-straining | failure mechanism | tearing | pre-folding | pre-bending punches | bending forces | final folding | corematerials | ukoer

License

http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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TALAT Lecture 3706: Bending and Folding

Description

This lecture describes the fundamentals of bending and folding aluminium sheet; it also describes different methods in design of folding tools. Background in production engineering and sheet metal forming and familiarity with the subject matter covered in TALAT This lectures 3701- 3705 is assumed.

Subjects

aluminium | aluminum | european aluminium association | eaa | talat | training in aluminium application technologies | training | metallurgy | technology | lecture | machining | forming | forging | sheet | folding | fold geometries | drawn parts | bending | springback | bending line geometries | counter pressure | springback angle | yield stress | pre-straining | failure mechanism | tearing | pre-folding | pre-bending punches | bending forces | final folding | corematerials | ukoer | Engineering | H000

License

Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales Attribution-Noncommercial-Share Alike 2.0 UK: England & Wales http://creativecommons.org/licenses/by-nc-sa/2.0/uk/ http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

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7.88J Protein Folding and Human Disease (MIT)

Description

This course covers amino acid sequence control of protein folding, misfolding, amyloid polymerization and aggregation. Readings and discussions address topics such as chaperone structure and function, folding and assembly of fibrous proteins, and pathologies associated with protein misfolding and aggregation in Alzheimer's, Parkinson's, Huntington's and other protein deposition diseases. Students are required to write and present a research paper.

Subjects

protein folding | misfolding | aggregation | protein structures | folding intermediates | off-pathway aggregation | amyloid formation | Key chaperones | chaperonins | human protein deposition diseases | ?s disease | amyloids | prions | amino acid sequence | amyloid polymerization | chaperone structure and function | folding and assembly of fibrous proteins

License

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18.966 Geometry of Manifolds (MIT)

Description

This is a second-semester graduate course on the geometry of manifolds. The main emphasis is on the geometry of symplectic manifolds, but the material also includes long digressions into complex geometry and the geometry of 4-manifolds, with special emphasis on topological considerations.

Subjects

Differential forms | Lie groups | DeRham | Riemannian manifolds | curvature | Hodge | Hodge theory | manifolds | Riemannian geometry | holonomy | symplectic geometry | complex geometry | Hodge-Kahler theory | smooth manifold topology

License

Content within individual OCW courses is (c) by the individual authors unless otherwise noted. MIT OpenCourseWare materials are licensed by the Massachusetts Institute of Technology under a Creative Commons License (Attribution-NonCommercial-ShareAlike). For further information see https://ocw.mit.edu/terms/index.htm

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18.117 Topics in Several Complex Variables (MIT)

Description

This course covers harmonic theory on complex manifolds, the Hodge decomposition theorem, the Hard Lefschetz theorem, and Vanishing theorems. Some results and tools on deformation and uniformization of complex manifolds are also discussed.

Subjects

Harmonic theory | complex manifolds | Hodge decomposition theorem | Hard Lefschetz theorem | Vanishing theorems | deformation of complex manifolds | uniformization of complex manifolds

License

Content within individual OCW courses is (c) by the individual authors unless otherwise noted. MIT OpenCourseWare materials are licensed by the Massachusetts Institute of Technology under a Creative Commons License (Attribution-NonCommercial-ShareAlike). For further information see https://ocw.mit.edu/terms/index.htm

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6.849 Geometric Folding Algorithms: Linkages, Origami, Polyhedra (MIT)

Description

This course focuses on the algorithms for analyzing and designing geometric foldings. Topics include reconfiguration of foldable structures, linkages made from one-dimensional rods connected by hinges, folding two-dimensional paper (origami), and unfolding and folding three-dimensional polyhedra. Applications to architecture, robotics, manufacturing, and biology are also covered in this course. Acknowledgments Thanks to videographers Martin Demaine and Jayson Lynch.

Subjects

origami | geometry | algorithm | folding | linkage | polyhedra | seam | crease pattern | universal molecule | box pleating | triangulation | vertex | edge | curved crease | rigidity | tensegrity | hinged dissection | unfolding | gluing | platonic solid | refolding | sculpture | paper | 3D chain | design

License

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6.895 Computational Biology: Genomes, Networks, Evolution (MIT) 6.895 Computational Biology: Genomes, Networks, Evolution (MIT)

Description

This course focuses on the algorithmic and machine learning foundations of computational biology, combining theory with practice. We study the principles of algorithm design for biological datasets, and analyze influential problems and techniques. We use these to analyze real datasets from large-scale studies in genomics and proteomics. The topics covered include:Genomes: Biological Sequence Analysis, Hidden Markov Models, Gene Finding, RNA Folding, Sequence Alignment, Genome Assembly.Networks: Gene Expression Analysis, Regulatory Motifs, Graph Algorithms, Scale-free Networks, Network Motifs, Network Evolution.Evolution: Comparative Genomics, Phylogenetics, Genome Duplication, Genome Rearrangements, Evolutionary Theory, Rapid Evolution. This course focuses on the algorithmic and machine learning foundations of computational biology, combining theory with practice. We study the principles of algorithm design for biological datasets, and analyze influential problems and techniques. We use these to analyze real datasets from large-scale studies in genomics and proteomics. The topics covered include:Genomes: Biological Sequence Analysis, Hidden Markov Models, Gene Finding, RNA Folding, Sequence Alignment, Genome Assembly.Networks: Gene Expression Analysis, Regulatory Motifs, Graph Algorithms, Scale-free Networks, Network Motifs, Network Evolution.Evolution: Comparative Genomics, Phylogenetics, Genome Duplication, Genome Rearrangements, Evolutionary Theory, Rapid Evolution.

Subjects

Genomes: Biological sequence analysis | Genomes: Biological sequence analysis | hidden Markov models | hidden Markov models | gene finding | gene finding | RNA folding | RNA folding | sequence alignment | sequence alignment | genome assembly | genome assembly | Networks: Gene expression analysis | Networks: Gene expression analysis | regulatory motifs | regulatory motifs | graph algorithms | graph algorithms | scale-free networks | scale-free networks | network motifs | network motifs | network evolution | network evolution | Evolution: Comparative genomics | Evolution: Comparative genomics | phylogenetics | phylogenetics | genome duplication | genome duplication | genome rearrangements | genome rearrangements | evolutionary theory | evolutionary theory | rapid evolution | rapid evolution

License

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18.950 Differential Geometry (MIT) 18.950 Differential Geometry (MIT)

Description

This course is an introduction to differential geometry of curves and surfaces in three dimensional Euclidean space. First and second fundamental forms, Gaussian and mean curvature, parallel transport, geodesics, Gauss-Bonnet theorem, complete surfaces, minimal surfaces and Bernstein's theorem are among the main topics studied. This course is an introduction to differential geometry of curves and surfaces in three dimensional Euclidean space. First and second fundamental forms, Gaussian and mean curvature, parallel transport, geodesics, Gauss-Bonnet theorem, complete surfaces, minimal surfaces and Bernstein's theorem are among the main topics studied.

Subjects

Metrics | Metrics | Lie bracket | Lie bracket | connections | connections | geodesics | geodesics | tensors | tensors | intrinsic and extrinsic curvature | intrinsic and extrinsic curvature | defined manifolds using coordinate charts | defined manifolds using coordinate charts | Curves and surfaces in three dimensions | Curves and surfaces in three dimensions | Gauss-Bonnet theorem for surfaces | Gauss-Bonnet theorem for surfaces | general relativity | general relativity

License

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18.385 Nonlinear Dynamics and Chaos (MIT) 18.385 Nonlinear Dynamics and Chaos (MIT)

Description

Nonlinear dynamics with applications. Intuitive approach with emphasis on geometric thinking, computational and analytical methods. Extensive use of demonstration software. Topics: Bifurcations. Phase plane. Nonlinear coupled oscillators in biology and physics. Perturbation, averaging theory. Parametric resonances, Floquet theory. Relaxation oscillations. Hysterises. Phase locking. Chaos: Lorenz model, iterated mappings, period doubling, renormalization. Fractals. Hamiltonian systems, area preserving maps; KAM theory.Technical RequirementsMATLAB® software is required to run the .m files found on this course site.MATLAB® is a trademark of The MathWorks, Inc. Nonlinear dynamics with applications. Intuitive approach with emphasis on geometric thinking, computational and analytical methods. Extensive use of demonstration software. Topics: Bifurcations. Phase plane. Nonlinear coupled oscillators in biology and physics. Perturbation, averaging theory. Parametric resonances, Floquet theory. Relaxation oscillations. Hysterises. Phase locking. Chaos: Lorenz model, iterated mappings, period doubling, renormalization. Fractals. Hamiltonian systems, area preserving maps; KAM theory.Technical RequirementsMATLAB® software is required to run the .m files found on this course site.MATLAB® is a trademark of The MathWorks, Inc.

Subjects

Phase plane | Phase plane | limit cycles | limit cycles | Poincare-Bendixson theory | Poincare-Bendixson theory | Time-dependent systems | Time-dependent systems | Floquet theory | Floquet theory | Poincare maps | Poincare maps | averaging | averaging | Stability of equilibria | Stability of equilibria | near-equilibrium dynamics | near-equilibrium dynamics | Center manifolds | Center manifolds | elementary bifurcations | elementary bifurcations | normal forms | normal forms | chaos | chaos

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18.101 Analysis II (MIT) 18.101 Analysis II (MIT)

Description

This course continues from Analysis I (18.100B), in the direction of manifolds and global analysis. The first half of the course covers multivariable calculus. The rest of the course covers the theory of differential forms in n-dimensional vector spaces and manifolds. This course continues from Analysis I (18.100B), in the direction of manifolds and global analysis. The first half of the course covers multivariable calculus. The rest of the course covers the theory of differential forms in n-dimensional vector spaces and manifolds.

Subjects

Differentiable maps | Differentiable maps | inverse and implicit function theorems | inverse and implicit function theorems | n-dimensional Riemann integral | n-dimensional Riemann integral | change of variables in multiple integrals | change of variables in multiple integrals | manifolds | manifolds | differential forms | differential forms | and n-dimensional version of Stokes' theorem. | and n-dimensional version of Stokes' theorem. | n-dimensional version of Stokes' theorem | n-dimensional version of Stokes' theorem

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13.472J Computational Geometry (MIT) 13.472J Computational Geometry (MIT)

Description

Topics in surface modeling: b-splines, non-uniform rational b-splines, physically based deformable surfaces, sweeps and generalized cylinders, offsets, blending and filleting surfaces. Non-linear solvers and intersection problems. Solid modeling: constructive solid geometry, boundary representation, non-manifold and mixed-dimension boundary representation models, octrees. Robustness of geometric computations. Interval methods. Finite and boundary element discretization methods for continuum mechanics problems. Scientific visualization. Variational geometry. Tolerances. Inspection methods. Feature representation and recognition. Shape interrogation for design, analysis, and manufacturing. Involves analytical and programming assignments. Topics in surface modeling: b-splines, non-uniform rational b-splines, physically based deformable surfaces, sweeps and generalized cylinders, offsets, blending and filleting surfaces. Non-linear solvers and intersection problems. Solid modeling: constructive solid geometry, boundary representation, non-manifold and mixed-dimension boundary representation models, octrees. Robustness of geometric computations. Interval methods. Finite and boundary element discretization methods for continuum mechanics problems. Scientific visualization. Variational geometry. Tolerances. Inspection methods. Feature representation and recognition. Shape interrogation for design, analysis, and manufacturing. Involves analytical and programming assignments.

Subjects

surface modeling | surface modeling | b-splines | b-splines | deformable surfaces | deformable surfaces | generalized cylinders | generalized cylinders | offsets | offsets | filleting surfaces | filleting surfaces | Non-linear solvers and intersection problems | Non-linear solvers and intersection problems | Solid modeling | Solid modeling | boundary representation | boundary representation | non-manifold and mixed-dimension boundary representation models | non-manifold and mixed-dimension boundary representation models | octrees | octrees | Interval methods | Interval methods | discretization methods | discretization methods | Scientific visualization | Scientific visualization | Variational geometry | Variational geometry | Tolerances | Tolerances | Inspection methods | Inspection methods | Shape interrogation | Shape interrogation | 2.158J | 2.158J | 1.128J | 1.128J | 16.940J | 16.940J | 13.472 | 13.472 | 2.158 | 2.158 | 1.128 | 1.128 | 16.940 | 16.940

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8.592 Statistical Physics in Biology (MIT) 8.592 Statistical Physics in Biology (MIT)

Description

Statistical Physics in Biology is a survey of problems at the interface of statistical physics and modern biology. Topics include: bioinformatic methods for extracting information content of DNA; gene finding, sequence comparison, and phylogenetic trees; physical interactions responsible for structure of biopolymers; DNA double helix, secondary structure of RNA, and elements of protein folding; Considerations of force, motion, and packaging; protein motors, membranes. We also look at collective behavior of biological elements, cellular networks, neural networks, and evolution.Technical RequirementsAny number of biological sequence comparison software tools can be used to import the .fna files found on this course site. Statistical Physics in Biology is a survey of problems at the interface of statistical physics and modern biology. Topics include: bioinformatic methods for extracting information content of DNA; gene finding, sequence comparison, and phylogenetic trees; physical interactions responsible for structure of biopolymers; DNA double helix, secondary structure of RNA, and elements of protein folding; Considerations of force, motion, and packaging; protein motors, membranes. We also look at collective behavior of biological elements, cellular networks, neural networks, and evolution.Technical RequirementsAny number of biological sequence comparison software tools can be used to import the .fna files found on this course site.

Subjects

Bioinformatics | Bioinformatics | DNA | DNA | gene finding | gene finding | sequence comparison | sequence comparison | phylogenetic trees | phylogenetic trees | biopolymers | biopolymers | DNA double helix | DNA double helix | secondary structure of RNA | secondary structure of RNA | protein folding | protein folding | protein motors | membranes | protein motors | membranes | cellular networks | cellular networks | neural networks | neural networks | evolution | evolution | statistical physics | statistical physics | molecular biology | molecular biology | deoxyribonucleic acid | deoxyribonucleic acid | genes | genes | genetics | genetics | gene sequencing | gene sequencing | phylogenetics | phylogenetics | double helix | double helix | RNA | RNA | ribonucleic acid | ribonucleic acid | force | force | motion | motion | packaging | packaging | protein motors | protein motors | membranes | membranes | biochemistry | biochemistry | genome | genome | optimization | optimization | partitioning | partitioning | pattern recognition | pattern recognition | collective behavior | collective behavior

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2.782J Design of Medical Devices and Implants (MIT) 2.782J Design of Medical Devices and Implants (MIT)

Description

This design course targets the solution of clinical problems by use of implants and other medical devices. Topics include the systematic use of cell-matrix control volumes; the role of stress analysis in the design process; anatomic fit, shape and size of implants; selection of biomaterials; instrumentation for surgical implantation procedures; preclinical testing for safety and efficacy, including risk/benefit ratio assessment evaluation of clinical performance and design of clinical trials. Student project materials are drawn from orthopedic devices, soft tissue implants, artificial organs, and dental implants. This design course targets the solution of clinical problems by use of implants and other medical devices. Topics include the systematic use of cell-matrix control volumes; the role of stress analysis in the design process; anatomic fit, shape and size of implants; selection of biomaterials; instrumentation for surgical implantation procedures; preclinical testing for safety and efficacy, including risk/benefit ratio assessment evaluation of clinical performance and design of clinical trials. Student project materials are drawn from orthopedic devices, soft tissue implants, artificial organs, and dental implants.

Subjects

2.782 | 2.782 | 3.961 | 3.961 | 20.451 | 20.451 | HST.524 | HST.524 | clinical problems | clinical problems | implants | implants | medical devices | medical devices | cell-matrix control volumes | cell-matrix control volumes | stress analysis | stress analysis | anatomic fit | anatomic fit | biomaterials | biomaterials | surgical implantation procedures | surgical implantation procedures | Preclinical testing | Preclinical testing | risk/benefit ratio assessment | risk/benefit ratio assessment | clinical performance | clinical performance | clinical trials | clinical trials | orthopedic devices | orthopedic devices | soft tissue implants | soft tissue implants | artificial organs | artificial organs | dental implants | dental implants | stent | stent | prosthesis | prosthesis | scaffold | scaffold | bio-implant | bio-implant | scar | scar | genetics | genetics | skin | skin | nerve | nerve | bone | bone | tooth | tooth | joint | joint | FDA | FDA | FDA approval | FDA approval | cartilage | cartilage | ACL | ACL | health | health | regulation | regulation | healthcare | healthcare | medicine | medicine | bioengineering | bioengineering

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2.158J Computational Geometry (MIT) 2.158J Computational Geometry (MIT)

Description

Topics in surface modeling: b-splines, non-uniform rational b-splines, physically based deformable surfaces, sweeps and generalized cylinders, offsets, blending and filleting surfaces. Non-linear solvers and intersection problems. Solid modeling: constructive solid geometry, boundary representation, non-manifold and mixed-dimension boundary representation models, octrees. Robustness of geometric computations. Interval methods. Finite and boundary element discretization methods for continuum mechanics problems. Scientific visualization. Variational geometry. Tolerances. Inspection methods. Feature representation and recognition. Shape interrogation for design, analysis, and manufacturing. Involves analytical and programming assignments. This course was originally offered in Course 13 (Depar Topics in surface modeling: b-splines, non-uniform rational b-splines, physically based deformable surfaces, sweeps and generalized cylinders, offsets, blending and filleting surfaces. Non-linear solvers and intersection problems. Solid modeling: constructive solid geometry, boundary representation, non-manifold and mixed-dimension boundary representation models, octrees. Robustness of geometric computations. Interval methods. Finite and boundary element discretization methods for continuum mechanics problems. Scientific visualization. Variational geometry. Tolerances. Inspection methods. Feature representation and recognition. Shape interrogation for design, analysis, and manufacturing. Involves analytical and programming assignments. This course was originally offered in Course 13 (Depar

Subjects

surface modeling | surface modeling | b-splines | b-splines | deformable surfaces | deformable surfaces | generalized cylinders | generalized cylinders | offsets | offsets | filleting surfaces | filleting surfaces | Non-linear solvers and intersection problems | Non-linear solvers and intersection problems | Solid modeling | Solid modeling | boundary representation | boundary representation | non-manifold and mixed-dimension boundary representation models | non-manifold and mixed-dimension boundary representation models | octrees | octrees | Interval methods | Interval methods | discretization methods | discretization methods | Scientific visualization | Scientific visualization | Variational geometry | Variational geometry | Tolerances | Tolerances | Inspection methods | Inspection methods | Shape interrogation | Shape interrogation | 13.472J | 13.472J | 13.472 | 13.472 | 2.158 | 2.158 | 1.128 | 1.128 | 16.940 | 16.940

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5.08J Biological Chemistry II (MIT) 5.08J Biological Chemistry II (MIT)

Description

This course deals with a more advanced treatment of the biochemical mechanisms that underlie biological processes. Emphasis will be given to the experimental methods used to unravel how these processes fit into the cellular context as well as the coordinated regulation of these processes. Topics include macromolecular machines for energy and force transduction, regulation of biosynthetic and degradative pathways, and the structure and function of nucleic acids. This course deals with a more advanced treatment of the biochemical mechanisms that underlie biological processes. Emphasis will be given to the experimental methods used to unravel how these processes fit into the cellular context as well as the coordinated regulation of these processes. Topics include macromolecular machines for energy and force transduction, regulation of biosynthetic and degradative pathways, and the structure and function of nucleic acids.

Subjects

biochemistry | biochemistry | biological chemistry | biological chemistry | Rasmol | Rasmol | Deep Viewer | Deep Viewer | CHIME | CHIME | BLAST | BLAST | PDB | PDB | macromolecular machines | macromolecular machines | protein folding | protein folding | protein degradation | protein degradation | fatty acid synthases | fatty acid synthases | polyketide synthases | polyketide synthases | non-ribosomal polypeptide synthases | non-ribosomal polypeptide synthases | metal homeostasis | metal homeostasis | biochemical mechanisms | biochemical mechanisms | biochemical pathways | biochemical pathways | macromolecular interactions | macromolecular interactions | ribosome | ribosome | mRNA | mRNA | metabolic networking | metabolic networking | 5.08 | 5.08 | 7.08 | 7.08

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6.096 Algorithms for Computational Biology (MIT) 6.096 Algorithms for Computational Biology (MIT)

Description

This course is offered to undergraduates and addresses several algorithmic challenges in computational biology. The principles of algorithmic design for biological datasets are studied and existing algorithms analyzed for application to real datasets. Topics covered include: biological sequence analysis, gene identification, regulatory motif discovery, genome assembly, genome duplication and rearrangements, evolutionary theory, clustering algorithms, and scale-free networks. This course is offered to undergraduates and addresses several algorithmic challenges in computational biology. The principles of algorithmic design for biological datasets are studied and existing algorithms analyzed for application to real datasets. Topics covered include: biological sequence analysis, gene identification, regulatory motif discovery, genome assembly, genome duplication and rearrangements, evolutionary theory, clustering algorithms, and scale-free networks.

Subjects

biological sequence analysis | biological sequence analysis | gene finding | gene finding | motif discovery | motif discovery | RNA folding | RNA folding | global and local sequence alignment | global and local sequence alignment | genome assembly | genome assembly | comparative genomics | comparative genomics | genome duplication | genome duplication | genome rearrangements | genome rearrangements | evolutionary theory | evolutionary theory | gene expression | gene expression | clustering algorithms | clustering algorithms | scale-free networks | scale-free networks | machine learning applications | machine learning applications

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6.881 Representation and Modeling for Image Analysis (MIT) 6.881 Representation and Modeling for Image Analysis (MIT)

Description

Most algorithms in computer vision and image analysis can be understood in terms of two important components: a representation and a modeling/estimation algorithm. The representation defines what information is important about the objects and is used to describe them. The modeling techniques extract the information from images to instantiate the representation for the particular objects present in the scene. In this seminar, we will discuss popular representations (such as contours, level sets, deformation fields) and useful methods that allow us to extract and manipulate image information, including manifold fitting, markov random fields, expectation maximization, clustering and others. For each concept -- a new representation or an estimation algorithm -- a lecture on the mathematical f Most algorithms in computer vision and image analysis can be understood in terms of two important components: a representation and a modeling/estimation algorithm. The representation defines what information is important about the objects and is used to describe them. The modeling techniques extract the information from images to instantiate the representation for the particular objects present in the scene. In this seminar, we will discuss popular representations (such as contours, level sets, deformation fields) and useful methods that allow us to extract and manipulate image information, including manifold fitting, markov random fields, expectation maximization, clustering and others. For each concept -- a new representation or an estimation algorithm -- a lecture on the mathematical f

Subjects

computer vision | computer vision | image analysis | image analysis | representation algorithm | representation algorithm | modeling | modeling | estimation algorithm | estimation algorithm | information | information | objects | objects | modeling techniques | modeling techniques | images | images | representations | representations | contours | contours | level sets | level sets | deformation fields | deformation fields | image information | image information | manifold fitting | manifold fitting | markov random fields | markov random fields | expectation maximization | expectation maximization | clustering | clustering | mathematical foundations | mathematical foundations | medical and biological imaging | medical and biological imaging

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