Biomedical Engineering < Columbia Engineering Academic Catalog (2024)

BMCHE4500BIOL TRANSPORT ＆ RATE PROCESS. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (CHEMUN2443) and (APMAE2101)
Corequisites: BIOLUN2005
Convective and diffusive movement and reaction of molecules in biological systems. Kinetics of hom*ogeneous and hetergeneous reactions in biological environments. Mechanisms and models of transport across membranes. Convective diffusion with and without chemical reaction. Diffusion in restricted spaces. Irreversible thermodynamic approaches to transport and reaction in biological systems

BMCHE4810ARTIFICAL ORGANS. 3.00 points.

Lect: 3.

Analysis and design of replacements for the heart, kidneys, and lungs. Specification amd realization of structures for artificial organ systems

BMEBW4020Computational neuroscience: circuits in the brain. 3 points.

Lect: 3.

Prerequisites: (ELENE3801) or (BIOLUN3004)

The biophysics of computation: modeling biological neurons, the Hodgkin-Huxley neuron, modeling channel conductances and synapses as memristive systems, bursting neurons and central pattern generators, I/O equivalence and spiking neuron models. Information representation and neural encoding: stimulus representation with time encoding machines, the geometry of time encoding, encoding with neural circuits with feedback, population time encoding machines. Dendritic computation: elements of spike processing and neural computation, synaptic plasticity and learning algorithms, unsupervised learning and spike time-dependent plasticity, basic dendritic integration. Projects in MATLAB.

BMEEE4030NEURAL CONTROL ENGINEERING. 3.00 points.

Lect: 3.

Prerequisites: (ELENE3801) ELENE3801
Topics include basic cell biophysics, active conductance and the Hodgkin-Huxley model, simple neuron models, ion channel models and synaptic models, statistical models of spike generation, Wilson-Cowan model of cortex, large-scale electrohysiological recording methods, sensorimotor integration and optimal state estimation, operant conditioning of neural activity, nonlinear modelling of neural systems, sensory systems: visual pathway and somatosensory pathway, neural encoding model; spike triggered average (STA) and spike triggered covariance (STC) analysis, neuronal response to electrical micro-stimulation, DBS for Parkinson's disease treatment, motor neural prostheses, and sensory neural prostheses

BMEEE4400Wavelet applications in biomedical image and signal processing. 3 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (APMAE2101) or (APMAE3101) or equivalent.

An introduction to methods of wavelet analysis and processing techniques for the quantification of biomedical images and signals. Topics include: frames and overcomplete representations, multiresolution algorithms for denoising and image restoration, multiscale texture segmentation and classification methods for computer aided diagnosis.

BMEEE4740BIOINSTRUMENTATION. 3.00 points.

Lect: 1. Lab: 3.

Prerequisites: (ELENE1201) and (COMSW1005)
Hands-on experience designing, building, and testing the various components of a benchtop cardiac pacemaker. Design instrumentation to measure biomedical signals as well as to actuate living tissues. Transducers, signal conditioning electronics, data acquisition boards, the Arduino microprocessor, and data acquisition and processing using MATLAB will be covered. Various devices will be discussed throughout the course, with laboratory work focusing on building an emulated version of a cardiac pacemaker

BMENELab-to-market: commercializing biomedical innovations. 0 points.

Not offered during 2023-2024 academic year.

BMENE2300BIOMECHANICS TRACK. 0.00 points.

BMENE2400BIOSIGNAL ＆ BIOMED IMAG TRACK. 0.00 points.

BMENE2500CELLULAR ＆ TISSUE ENGIN TRACK. 0.00 points.

BMENE3010BIOMEDICAL ENGINEERING I. 3.00 points.

Lect: 3.

Prerequisites: (BIOLUN2005) and (BIOLUN2006) or with instructor's permission
Corequisites: BMENE3810,BMENE4001
Various concepts within the field of biomedical engineering, foundational knowledge of engineering methodology applied to biological and/or medical problems through modules in biomechanics, biomaterials, and cell ＆ tissue engineering

BMENE3020BIOMEDICAL ENGINEERING II. 3.00 points.

Lect: 3.

Prerequisites: (BIOLUN2005) and (BIOLUN2006) or with instructor's permission.
Corequisites: BMENE3820,BMENE4002
Various concepts within the field of biomedical engineering, foundational knowledge of engineering methodology applied to biological and/or medical problems through modules in biomechanics, bioinstrumentation, and biomedical imaging

BMENE3150THE CELL AS A MACHINE. 3.00 points.

Cells as complex micron-sized machines, basic physical aspects of cell components (diffusion, mechanics, electrostatics, hydrophobicity), energy transduction (motors, transporters, chaperones, synthesis complexes), basic cell functions. Biophysical principles, feedback controls for robust cell function, adaptation to environmental perturbations

BMENE3320FLUID BIOMECHANICS. 3.00 points.

BMENE3500BIOL TRANSPORT ＆ RATE PROCESS. 3.00 points.

BMENE3810BIOMEDICAL ENGINEERING LAB I. 3.00 points.

Lab: 4.

Fundamental considerations of wave mechanics; design philosophies; reliability and risk concepts; basics of fluid mechanics; design of structures subjected to blast; elements of seismic design; elements of fire design; flood considerations; advanced analysis in support of structural design

BMENE3820BIOMEDICAL ENGINEERING LAB II. 3.00 points.

Lab: 4.

Biomedical experimental design and hypothesis testing. Statistical analysis of experimental measurements. Analysis of experimental measurements. Analysis of variance, post hoc testing. Fluid shear and cell adhesion, neuro-electrophysiology, soft tissue biomechanics, biomecial imaging and ultrasound, characterization of excitable tissues, microfluidics

BMENE3830BIOMEDICAL ENGINEERING LAB III. 3.00 points.

BMENE3899Research Training. 0.00 points.

Research training course. Recommended in preparation for laboratory related research

BMENE3910BIOMEDICAL ENGINEERING DESIGN. 4.00 points.

Lect: 1. Lab: 3.

A two-semester design sequence to be taken in the senior year. Elements of the design process, with specific applications to biomedical engineering: concept formulation, systems synthesis, design analysis, optimization, biocompatibility, impact on patient health and comfort, health care costs, regulatory issues, and medical ethics. Selection and execution of a project involving the design of an actual engineering device or system. Introduction to entrepreneurship, biomedical start-ups, and venture capital. Semester I: statistical analysis of detection/classification systems (receiver operation characteristic analysis, logistic regression), development of design prototype, need, approach, benefits and competition analysis. Semester II: spiral develop process and testing, iteration and refinement of the initial design/prototype and business plan development. A lab fee of $100 each is collected

BMENE3920BIOMEDICAL ENGIN DESIGN II. 4.00 points.

Lect: 1. Lab: 3.

A two-semester design sequence to be taken in the senior year. Elements of the design process, with specific applications to biomedical engineering: concept formulation, systems synthesis, design analysis, optimization, biocompatibility, impact on patient health and comfort, health care costs, regulatory issues, and medical ethics. Selection and execution of a project involving the design of an actual engineering device or system. Introduction to entrepreneurship, biomedical start-ups, and venture capital. Semester I: statistical analysis of detection/classification systems (receiver operation characteristic analysis, logistic regression), development of design prototype, need, approach, benefits and competition analysis. Semester II: spiral develop process and testing, iteration and refinement of the initial design/prototype and business plan development. A lab fee of $100 each is collected

BMENE3998PROJECTS IN BIOMEDICAL ENGIN. 1.00-3.00 points.

Hours to be arranged.

Independent projects involving experimental, theoretical, computational, or engineering design work. May be repeated, but no more than 3 points of this or any other projects or research course may be counted toward the technical elective degree requirements as engineering technical electives

BMENE3999UNDERGRADUATE FIELDWORK. 1.00-2.00 points.

Prerequisites: Obtained internship and approval from faculty advisor. BMEN undergraduate students only.
May be repeated for credit, but no more than 3 total points may be used toward the 128-credit degree requirement. Only for BMEN undergraduate students who include relevant off-campus work experience as part of their approved program of study. Final report and letter of evaluation required. Fieldwork credits may not count toward any major core, technical, elective, and non-technical requirements. May not be taken for pass/fail credit or audited

BMENE4000SPECIAL TOPICS IN BIOMEDICAL ENGINEERING. 3.00 points.

Lect: 3.

Current topics in biomedical engineering. Subject matter will vary by year

BMENE4001QUANTITATIVE PHYSIOLOGY I. 3.00 points.

Lect: 3.

Prerequisites: (BIOLUN2005) and (BIOLUN2006)
Corequisites: BMENE3010,BMENE3810
Physiological systems at the cellular and molecular level are examined in a highly quantitative context. Topics include chemical kinetics, molecular binding and enzymatic processes, molecular motors, biological membranes, and muscles

BMENE4002QUANT PHYSIOLOGY II:ORGAN SYST. 3.00 points.

Lect: 3.

Prerequisites: (BIOLUN2005) and (BIOLUN2006)
Corequisites: BMENE3020,BMENE3820
Students are introduced to a quantitative, engineering approach to cellular biology and mammalian physiology. Beginning with biological issues related to the cell, the course progresses to considerations of the major physiological systems of the human body (nervous, circulatory, respiratory, renal)

BMENE4050ELECTROPHYS OF HUM MEMORY * NAVIGATION. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: Instructor's permission.
Human memory, including working, episodic, and procedural memory. Electrophysiology of cognition, noninvasive and invasive recordings. Neural basis of spatial navigation, with links to spatial and episodic memory. Computational models of memory, brain stimulation, lesion studies

BMENE4100BMakE – Biomedical Device Design ＆ Fabrication. 3.00 points.

Hands-on course. Covers medical device design to develop basic fabrication skills. Includes central project theme, i.e., through individual modules, students create different components of a biomedical device. First offering focuses on creation of a device pertinent for COVID-19: a mechanical ventilator. The mechanical ventilator combines physics (fluid dynamics, pressure-flow relationships) with fabrication, (bio)materials, sensing, signal acquisition and processing, and controls. As a highly advanced, life-supporting device, its functional aspects can be decomposed into modules of this course to create a benchtop ventilator

BMENE4110BIOSTATISTICS FOR ENGINEERS. 4.00 points.

Lect: 3.

Prerequisites: (MATHUN1202) and (APMAE2101) MATH V1202 and APMAE2101
Fundamental concepts of probability and statistics applied to biology and medicine. Probability distributions, hypothesis testing and inference, summarizing data and testing for trends. Signal detection theory and the receiver operator characteristic. Lectures accompanied by data analysis assignments using MATLAB as well as discussion of case studies in biomedicine

BMENE4150THE CELL AS A MACHINE. 3.00 points.

Lect: 3.

Prerequisites: (MATHUN1101) or MATH V1101 or equivalent
Corequisites: One semester of BIOL C2005 or BIOCC3501, and one semester of PHYSC1401 or equivalent
Cells as complex micron-sized machines, basic physical aspects of cell components (diffusion, mechanics, electrostatics, hydrophobicity), energy transduction (motors, transporters, chaperones, synthesis complexes), basic cell functions. Biophysical principles, feedback controls for robust cell function, adaptation to environmental perturbations

BMENE4210DRIVING FORCES OF BIOLOGICAL SYSTEMS. 4.00 points.

Lect: 4.

Prerequisites: (CHEMUN1404) and (MATHUN1202)
Corequisites: BIOLUN2005
Introduction to the statistical mechanics and thermodynamics of biological systems, with a focus on connecting microscopic molecular properties to macroscopic states. Both classical and statistical thermodynamics will be applied to biological systems; phase equilibria, chemical reactions, and colligative properties. Topics in modern biology, macromolecular behavior in solutions and interfaces, protein-ligand binding, and the hydrophobic effect

BMENE4300SOLID BIOMECHANICS. 3.00 points.

BMENE4302BIOMECHANICS OF MUSCULOSKELETAL SOFT TIS. 3.00 points.

Lect.: 3.

Prerequisites: (ENMEE3113) or equivalent. Restricted to seniors and graduate students.
Biomechanics of orthopaedic soft tissues (cartilage, tendon, ligament, meniscus, etc.). Basic and advanced viscoelasticity applied to the muscoskeletal system. Topics include mechanical properties, applied viscoelasticity theory, and biology of orthopaedic soft tissues

BMENE4305CARDIAC MECHANICS. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (BMENE4310) and (BMENE4320) or equivalents.
Cardiac anatomy, passive myocardial constitutive properties, electrical activation, ventricular-vascular coupling, invasive and noninvasive measures of regional and global function, models for predicting ventricular wall stress. Alterations in muscle properties and ventricular function resulting from myocardial infarction, heart failure, and felt ventricular assist

BMENE4310SOLID BIOMECHANICS. 3.00 points.

Lect.: 3.

Prerequisites: (ENMEE3105) and (ENMEE3113) and
Applications of continuum mechanics to the understanding of various biological tissues properties. The structure, function, and mechanical properties of various tissues in biolgical systems, such as blood vessels, muscle, skin, brain tissue, bone, tendon, cartilage, ligaments, etc. are examined. The establishment of basic governing mechanical principles and constitutive relations for each tissue. Experimental determination of various tissue properties. Medical and clinical implications of tissue mechanical behavior

BMENE4320FLUID BIOMECHANICS. 3.00 points.

Prerequisites: (APMAE2101) and (ENMEE3105) and (MECEE4100) APMAE2101, ENMEE3105, and MECEE4100.
The principles of continuum mechanics as applied to biological fluid flows and transport. Continuum formulations of basic conservation laws, Navier-Stokes equations, mechanics of arterial and venous blood flow, blood rheology and non-Newtonian properties, flow and transport in the microcirculation, oxygen diffusion, capillary filtration

BMENE4330Cellular Bioengineering ＆ Therapeutics. 3.00 points.

Explores cutting-edge field of cellular bioengineering and applications of cell therapies. Comprehensive understanding of the principles, techniques, and ethical considerations involved in cells for medical applications studied

BMENE4340BIOMECHANICS OF CELLS. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (BMENE3320) and (BMENE4300) or equivalents.
Survey of experiments and theoretical analyses of the mechanical behavior of individual living nonmuscle cells. Emphasis on quantitative analytic description using continuum mechanics and molecular level theory from the standpoint of statistical mechanics and mechanical models. Mechanics of erythrocytes, leukocytes, endothelial cells, and fibroblasts; models of aggregation, adhesion, locomotion, amoeba motility, cell division and morphogenesis; molecular level models of actin, myosin, microtubules, and intermediate filaments and relation to mechanical properties of cells and cytoskeleton. Alternative models of cytoskeletal mechanics, foam theory, tensegrity. Analysis of experimental techniques including micropipette studies, optical and magnetic cytometry, and nanoindentation

BMENE4350Biomechanics of Developmental Biology. 3.00 points.

Biophysical mechanisms of tissue organization during embryonic development: conservation laws, reaction-diffusion, finite elasticity, and fluid mechanics are reviewed and applied to a broad range of topics in developmental biology, from early development to later organogenesis of the central nervous, cardiovascular, musculoskeletal, respiratory, and gastrointestinal systems. Subdivided into modules on patterning (conversion of diffusible cues into cell fates) and morphogenesis (shaping of tissues), the course will include lectures, problem sets, reading of primary literature, and a final project

BMENE4400WAVELET APPL-BIOMED IMAGE PROC. 3.00 points.

An introduction to methods of wavelet analysis and processing techniques for the quantification of biomedical images and signals. Topics include frames and overcomplete representations, multiresolution algorithms for denoising and image restoration, multiscale texture segmentation and classification methods for computer-aided diagnosis

BMENE4410PRIN OF ULTRASOUND IN MEDICINE. 3.00 points.

Lect: 3.

Prerequisites: (MATHUN1202) or MATH V1202 or equivalent,
Fourier analysis. Physics of diagnostic ultrasound and principles of ultrasound imaging instrumentation. Propagation of plane waves in lossless medium; ultrasound propagation through biological tissues; single-element and array transducer design; pulse-echo and Doppler ultrasound instrumentation, performance evaluation of ultrasound imaging systems using tissue-mimicking phantoms, ultrasound tissue characterization; ultrasound nonlinearity and bubble activity; harmonic imaging; acoustic output of ultrasound systems; biological effects of ultrasound

BMENE4420SIGNAL MODELING. 3.00 points.

Lect: 3.

Prerequisites: (ELENE3801) and (APMAE2101) or (APMAE3101) or ELENE3801 and either APMAE2101 or E3101 or instructor's permission
Fundamental concepts of signal processing in linear systems and stochastic processes. Estimation, detection and filtering methods applied to biomedical signals. Harmonic analysis, auto-regressive model, Wiener and Matched filters, linear discriminants, and independent components. Methods are developed to answer concrete questions on specific data sets in modalities such as ECG, EEG, MEG, Ultrasound. Lectures accompanied by data analysis assignments using MATLAB

BMENE4430PRIN OF MAG RESONANCE IMAGING. 3.00 points.

Lect: 3.

Prerequisites: (PHYSUN1403) and (APMAE2101) or PHYS C1403 and APAM E2101 or instructors' permission.
Fundamental principles of Magnetic Resonance Imaging (MRI), including the underlying spin physics and mathematics of image formation with an emphasis on the application of MRI to neuroimaging, both anatomical and functional. The examines both theory and experimental design techniques

BMENE4440PHYSIOLOGICAL CONTROL SYSTEM. 3.00 points.

Lect: 3.

Prerequisites: (MEBME4439) and (APMAE2101)
Fundamentals of time and frequency domains analyses and stability. Frequency domain controller design. Cardiovascular and respiratory systems simulation. Endogenous control systems: baroreflex, chemoreflex, thermoregulation, pupillary light reflex. Open and closed loop physiological systems. Exogenous control systems: ventilators, infusion pumps. Nonlinear actuators and delayed feedback systems. Acute disease simulation and clinical decision support in the intensive care unit. MATLAB and Simulink environments utilized

BMENE4450DENTAL ＆ CRAN TISSUE ENG. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (MSAEE3103) and (BMENE4210) and (BMENE4501) or equivalent.
Fundamentals of time and frequency domains analyses and stability. Frequency domain controller design. Cardiovascular and respiratory systems simulation. Endogenous control systems: baroreflex, chemoreflex, thermoregulation, pupillary light reflex. Open and closed loop physiological systems. Exogenous control systems: ventilators, infusion pumps. Nonlinear actuators and delayed feedback systems. Acute disease simulation and clinical decision support in the intensive care unit. MATLAB and Simulink environments utilized

BMENE4460Deep Learning in Biomedical Imaging. 3.00 points.

Pre-requisites: MATH UN 1202 and APMA E2101. Background in Python programming is highly recommended.Not offered during 2023-2024 academic year.

Introduction to methods in deep learning, with focus on applications to quantitative problems in biomedical imaging and Artificial Intelligence (AI) in medicine. Network models: Deep feedforward networks, convolutional neural networks and recurrent neural networks. Deep autoencoders for denoising. Segmentation and classification of biological tissues and biomarkers of disease. Theory and methods lectures will be accompanied with examples from biomedical image including analysis of neurological images of the brain (MRI), CT images of the lung for cancer and COPD, cardiac ultrasound. Programming assignments will use tensorflow / Pytorch and Jupyter Notebook. Examinations and a final project will also be required

BMENE4470Deep Learning for Biomedical Signal Processing. 3.00 points.

Introduction to methods in deep learning, focus on applications to biomedical signals and sequences. Review of traditional methods for analysis of signals and sequences. Temporal convolutional neural networks and recurrent neural networks. Long-short term memory (LSTM) models and deep state-space models. Theory and methods lectures accompanied with examples from biomedical signal and sequence analysis, including analysis of electroencephalogram (EEG), electrocardiogram (ECG/EKG), and genomics. Programming assignments use tensorflow/keras. Exams and final project required

BMENE4480Statistical machine learning for genomics. 3.00 points.

Prerequisites: Intro to Applied Mathematics (APMA E2101), Calculus IV (MATH UN1202), Linear Algebra (MATH UN2010). Proficiency in Python/R programming. Background in probability/statistics. Intro to Machine Learning (COMS W4771) is recommended.

Prerequisites: see notes re: points
Introduction to statistical machine learning methods using applications in genomic data and in particular high-dimensional single-cell data. Concepts of molecular biology relevant to genomic technologies, challenges of highdimensional genomic data analysis, bioinformatics preprocessing pipelines, dimensionality reduction, unsupervised learning, clustering, probabilistic modeling, hidden Markov models, Gibbs sampling, deep neural networks, gene regulation. Programming assignments and final project will be required

BMENE4490Magnetic Resonance Spectroscopy: A Window to the Living Brain. 3.00 points.

Introduction to use of magnetic resonance spectroscopy (MRS) with focus on brain. Covers all aspects of in vivo MRS from theory to experiment, from data acquisition to the derivation of metabolic signatures, from study design to clinical interpretation. Includes theoretical concepts, hands-on training in MRS data literacy and direct experimental experience using a 3T MR scanner

BMENE4500Functional Genomics: Methods and Applications. 3.00 points.

Introduces approaches for the functional genomic analysis of biological systems and their use to define genotype-phenotype relationships. Genetic variation, gene expression and regulation at the epigenome, chromatin organization level, and link between gene and protein expression covered. Case studies covered: study of cancer and cancer-associated processes, neuro-biology, and organismal development. The presented methods study these events at the genome, epigenome, transcriptome, and proteome levels.Approaches that increase the resolution of functional genomic assays to the level of individual cells, spatial profiling, integration with genetic and chemical screening methods, and their application to chemical genomic approaches also studied. Programming assignments and a final project required

BMENE4501Biomaterials and Scaffold Design. 3.00 points.

Lect: 3.

Prerequisites: (BIOLUN2005) and (BIOLUN2006) and (BMENE4001) and (BMENE4002)
An introduction to the strategies and fundamental bioengineering design criteria in the development of biomaterials and tissue ngineered grafts. Materials structuralfunctional relationships, biocompatibility in terms of material and host responses. Through discussions, readings, and a group design project, students acquire an understanding of cell-material interactions and identify the arameters critical in the design and selection of biomaterials for biomedical applications

BMENE4502TISSUE ENGINEERING II. 3.00 points.

BMENE4510TISSUE ENGINEERING. 3.00 points.

Lect: 3

Prerequisites: (BIOLUN2005) and (BIOLUN2006) and (BMENE4001) and (BMENE4002)
An introduction to the strategies and fundamental bioengineering design criteria behind the development of cell-based tissue substitutes. Topics include biocompatibility, biological grafts, gene therapy-transfer, and bioreactors

BMENE4520SYNTHETIC BIOLOGY:PRIN GENETIC CIRCUITS. 3.00 points.

Not offered during 2023-2024 academic year.

Prerequisites: (BIOLUN2005) and (MATHUN2030) or (APMAE2101)
Basic principles of synthetic biology and survey of the field. Fundamentals of biological circuits, including circuit design, modern techniques for DNA assembly, quantitative characterization of genetic circuits, and ODE modeling of biological circuits with MATLAB. Knowledge of biology, ordinary differential equations, and MATLAB will be assumed. Intended for advanced undergraduate and graduate students

BMENE4525Advanced Cell and Tissue Engineering: From Concepts to Translation. 3.00 points.

Covers advancements in the fields of cellular and developmental biology, molecular biology and materials science towards the development of “tissue engineered” therapies. Emphasis on tissue engineering therapies applied to musculoskeletal tissues, such as bone, cartilage, and skeletal muscle, and nervous tissues (central and peripheral nervous system). Design considerations and concepts in market analysis examined

BMENE4530DRUG AND GENE DELIVERY. 3.00 points.

Prerequisites: BME I (BMENE3010)
Application of polymers and other materials in drug and gene delivery, with focus on recent advances in field. Basic polymer science, pharmaco*kinetics, and biomaterials, cell-substrate interactions, drug delivery system fabrication from nanoparticles to microparticles and electrospun fibrous membranes. Applications include cancer therapy, immunotherapy, gene therapy, tissue engineering, and regenerative medicine. Course readings include textbook chapters and journal papers. Homework assignments take format of assay responding to open-ended question. Term paper and 30-minute PowerPoint presentation required at end of semester

BMENE4535Immunoengineering with Biomaterials and Nanotechnology. 3.00 points.

Introduction to fundamental aspects of immunology and engineering strategies to modulate the immune system to improve human health. We will cover the innate and adaptive immune system and current methods to characterize the immune response. Applications focus on cancer, vaccines, and autoimmune disorders

BMENE4540BIOELECTROCHEMISTRY. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (CHEMUN3079) and (CHEMUN2443) or equivalent.
Application of electrochemical kinetics to interfacial processes occurring in biomedical systems. Basics of electrochemistry, electrochemical instrumentation, and relevant cell and electrophysiology reviewed. Applications to interpretation of excitable and nonexcitable membrane phenomena, with emphasis on heterogeneous mechanistic steps. Examples of therapeutic devices created as a result of bioelectrochemical studies

BMENE4550MICRO/NANO STRUCT CELL ENG. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (BIOLUN2005) and (BIOLUN2006) or BIOL C2005 and BIOL C2006 or equivalent
Design, fabrication, and application of micro-/nanostructured systems for cell engineering. Recognition and response of cells to spatial aspects of their extracellular environment. Focus on neural, cardiac, coculture, and stem cell systems. Molecular complexes at the nanoscale

BMENE4560DYNAMICS OF BIOLOGCL MEMBRANES. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (BIOLUN2005) and (BMENE4001) or equivalent.
The structure and dynamics of biological (cellular) membranes are discussed, with an emphasis on biophysical properties. Topics include membrane composition, fluidity, lipid asymmetry, lipid-protein interactions, membrane turnover, membrane fusion, transport, lipid phase behavior. In the second half of the semester, students will lead discussions of recent journal articles

BMENE4580FOUND OF NANOBIOSCI/NANOBIOTECH. 3.00 points.

Lect: 3.

Prerequisites: (BIOLUN2005) and (BIOLUN2006) and (BMENE4001) or (BMENE4002) instructor permission
Fundamentals of nanobioscience and nanobiotechnology, scientific foundations, engineering principles, current and envisioned applications. Includes discussion of intermolecular forces and bonding, of kinetics and thermodynamics of self-assembly, of nanoscale transport processes arising from actions of biomolecular motors, computation and control in biomolecular systems, and of mitochondrium as an example of a nanoscale factory

BMENE4590BIOMEMS:CELL/MOLECULAR APPLIC. 3.00 points.

Lect: 3.

Prerequisites: (MATHUN1201) and (BIOLUN2005) and (BIOLUN2006) and (CHEMUN3443) or (CHEMUN2545) or or equivalent. Chemistry.
Topics include biomicroelectromechanical, microfluidic, and lab-on-a-chip systems in biomedical engineering, with a focus on cellular and molecular applications. Microfabrication techniques, biocompatibility, miniaturization of analytical and diagnostic devices, high-throughput cellular studies, microfabrication for tissue engineering, and in vivo devices

BMENE4601CELLULAR ELECTRICITY. 3.00 points.

Lect: 2. Lab: 1.Not offered during 2023-2024 academic year.

Bioelectricity of the cell membrane. Basis of cell resting voltage, voltage changes that lead to the action potential and electrical oscillations used in sensing systems. Laboratory includes building electronic circuits to measure capacitance of artificial membranes and ion pumping in frog skin. Lab required

BMENE4738TRANSDUCTN/ACQ OF BIOMED DATA. 3.00 points.

Lect: 2. Lab: 1.Not offered during 2023-2024 academic year.

Data transduction and acquisition systems used in biomedicine. Assembly of biotransducers and the analog/digital circuitry for acquiring electrocardiogram, electromyogram, and blood pressure signals. Each small group will develop and construct a working data acquisition board, which will be interfaced with a signal generator to elucidate the dynamics of timing constraints during retrieval of biodata. Lab required

BMENE4750SOUND AND HEARING. 3.00 points.

Lect: 3.

Prerequisites: (PHYSUN1401) and (MATH UN1105) and (MATH UN1106) PHYSC1401 and MATH V1105 - MATH V1106.
Introductory acoustics, basics of waves and discrete mechanical systems. The mechanics of hearing - how sound is transmitted through the external and middle ear to the inner ear, and the mechanical processing of sound within the inner ear

BMENE4810ARTIFICIAL ORGANS. 3.00 points.

Analysis and design of replacements for the heart, kidneys, and lungs. Specification and realization of structures for artificial organ systems

BMENE4840FUNCTIONAL IMAGING BRAIN. 3.00 points.

Lect: 3. Lab: 1.

Prerequisites: (APMAE2101) and (APMAE4200) and (ELENE3801) or instructor's permission.
Fundamentals of modern medical functional imaging. In depth exploration of functional magnetic resonance imaging (fMRI), arterial spin labeling (ASL), and positron emission tomography (PET). Human brain anatomy, physiology, and neurophysiological bases underlying each functional imaging. Statistical and digital signal processing methods specific for functional image analysis. Final cumulative project requiring coding in MATLAB, Python, R, or C

BMENE4894BIOMEDICAL IMAGING. 3.00 points.

Lect: 3.

Covers image formation, methods of analysis, and representation of digital images. Measures of qualitative performance in the context of clinical imaging. Algorithms fundamental to the construction of medical images via methods of computed tomography, magnetic resonance, and ultrasound. Algorithms and methods for the enhancement and quantification of specific features of clinical importance in each of these modalities

BMENE4895Analysis and Quantification of Medical Images. 3 points.

Lect: 3.

Prerequisites: (BMENE4894)
Corequisites: BMENE4894

Novel methods of mathematical analysis applied to problems in medical imaging. Design requirements for screening protocols, treatment therapies, and surgical planning. Sensitivity and specificity in screening mammography and chest radiographs, computer aided diagnosis systems, surgical planning in orthopaedics, quantitative analysis of cardiac performance, functional magnetic resonance imaging, positron emission tomography, and echocardiography data.

BMENE4898BIOPHOTONICS. 3.00 points.

Lect: 3.

Prerequisites: (BMENE4894) and (PHYSUN1403) or instructor's permission.
Provides a broad-based introduction into the field of Biophotonics. Fundamental concepts of optical, thermal, and chemical aspects of the light-tissue interactions will be presented. The application of these concepts for medical therapy and diagnostics will be discussed. The course includes theoretical modeling of light-tissue interactions as well as optical medical instrument design and methods of clinical data interpretation

BMENE4899Research Training. 0.00 points.

Research training course. Recommended in preparation for laboratory related research

BMENE4999FIELDWORK. 1.00-2.00 points.

Prerequisites: Obtained internship and approval from faculty advisor. BMEN graduate students only.
Only for BMEN graduate students who need relevant work experience as part of their program of study. Final reports required. May not be taken for pass/fail credit or audited

BMENE6000Graduate Special Topic. 3 points.

Lect: 3.

Current topics in biomedical engineering. Subject matter will vary by year. Instructors may impose prerequisites depending on the topic.

BMENE6001TOPICS IN BIOMED NANOTECHNOLOGY. 3.00 points.

Review and critical discussion of recent literature in nanobiotechnology and synthetic biology. Experimental and theoretical techniques, critical advances. Quality judgments of scientific impact and technical accuracy. Styles of written and graphical communication, the peer review process

BMENE6003COMP MODELING-PHYSIOL SYSTEMS. 3.00 points.

Lect: 3.

Prerequisites: (BMENE4001) and (BMENE4002) and (APMAE4200) or equivalent.
Advanced computational modeling and quantitative analysis of selected physiological systems from molecules to organs. Selected systems are analyzed in depth with an emphasis on modeling methods and quantitative analysis. Topics may include cell signaling, molecular transport, excitable membranes, respiratory physiology, nerve transmission, circulatory control, auditory signal processing, muscle physiology, data collection and analysis

BMENE6005Biomedical Innovation I. 3 points.

Lect: 3.

Prerequisites: Master's students only.

Project-based design experience for graduate students. Elements of design process, including need identification, concept generation, concept selection, and implementation. Development of design prototype and introduction to entrepreneurship and implementation strategies. Real-world training in biomedical design and innovation.

BMENE6006BIOMEDICAL DESIGN II. 3.00 points.

Lect. 3.

Second semester of project-based design experience for graduate students. Elements of design process, with focus on skills development, prototype development and testing, and business planning. Real-world training in biomedical design, innovation, and entrepreneurship

BMENE6007LAB-TO-MARKET. 3.00 points.

Introduction to and application of commercialization of biomedical innovations. Topics include needs clarification, stakeholder analysis, market analysis, value proposition, business models, intellectual property, regulatory, and reimbursem*nt. Development of path-to-market strategy and pitch techniques

BMENE6301MODELING OF BIOL TISS WITH FEM. 3.00 points.

Lect: 3.

Prerequisites: (MECEE6422) or (ENME E6315) or equivalent.
Structure-function relations and linear/nonlinear constitutive models of biological tissues: anisotropic elasticity, viscoelasticity, porous media theories, mechano-electrochemical models, infinitesimal and large deformations. Emphasis on the application and implementation of constitutive models for biological tissues into existing finite element software packages. Model generation from biomedical images by extraction of tissue geometry, inhom*ogeneity and anisotropy. Element-by-element finite element solver for large-scale image based models of trabecular bone. Implementation of tissue remodeling simulations in finite element models

BMENE6400Analysis and quantification of medical images. 3 points.

Lect: 3.

Novel methods of mathematical analysis applied to problems in medical imaging. Design requirements for screening protocols, treatment therapies, and surgical planning. Sensitivity and specificity in screening mammography and chest radiographs, computer aided diagnosis systems, surgical planning in orthopaedics, quantitative analysis of cardiac performance, functional magnetic resonance imaging, positron emission tomography, and echocardiography data.

BMENE6410Principles and Practices of In Vivo Magnetic Resonance Spectroscopy. 3.00 points.

Prerequisites: Quantitative Physiology I or II
Magnetic resonance spectroscopy (MRS) allows the detection and quantification of chemical compounds from localized regions in living tissue, e.g., the brain, in a noninvasive fashion. It thereby provides a powerful tool to assess key aspects of brain metabolism and function. The repertoire of measurable compounds along with the quantitative character of the derived information makes MRS a versatile tool for the identification of clinical conditions, for longitudinal patient monitoring and for treatment control and monitoring of virtually all disorders with a metabolic signature. This educational course comprises all aspects of in vivo MRS from theory to experiment, from data acquisition to the derivation of metabolic signatures, and from study design to clinical interpretation, with special focus on applications in the human brain. Anyone interested in gaining an understanding of MRS techniques, their potential and the limitations of their application in vivo will find this course useful. The course bridges the gap between theoretical concepts, hands-on training in MRS data literacy and direct experimental experience on a human 3T MR scanner. This combined academic course and practical “boot-camp” will provide novices in MRS the requisite know-how for future engagement in MRS research and diagnostics

BMENE6420ADV MICROSCOPY APPLICATIONS. 3.00 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (PHYSUN1401) and (PHYSUN1402) and (PHYSUN1403) or (PHYSUN1601) and (PHYSUN1602) and (PHYSUN2601) or (PHYSUN2801) and (PHYSUN2802) or equivalent (general Physics sequence).

Fundamentals of techniques including confocal, two-photon, atomic force and electron microscopy. Application of methods to modern biomedical imaging targets. Analysis and interpretation of microscopy data. Enrollment beyond the cap must be completed using an add/drop form in consultation with class instructor.

BMENE6500TISSUE/MOLECULAR ENGI LAB. 4.00 points.

Lect: 1. Lab: 4.

Prerequisites: (BIOLUN2005) and (BIOLUN2006) or permission of instructor.
Hands-on experiments in molecular and cellular techniques, including fabrication of living engineered tissues. Covers sterile technique, culture of mammalian cells, microscopy, basic subcloning and gel electrophoresis, creation of cell-seeded scaffolds, and the effects of mechanical loading on the metabolism of living cells or tissues. Theory, background, and practical demonstration for each technique will be presented. Lab required

BMENE6505Advanced Biomaterials for Tissue Engineering. 3.00 points.

Prerequisites: (BMENE4501) or BMENE4501 or equivalent.
Corequisites: BMENE4001 or BMENE4002
Advanced biomaterial selection and biomimetic scaffold design for tissue engineering and regenerative medicine. Formulation of bio-inspired design criteria, scaffold characterization and testing, and applications on forming complex tissues or organogenesis. Laboratory component includes basic scaffold fabrication, characterization and in vitro evaluation of biocompatibility. Group projects target the design of scaffolds for select tissue engineering applications

BMENE6510STEM CELL, GENOME ENG ＆ REGEN MED. 3.00 points.

Lect: 3.

Prerequisites: (BMENE4001) or (BMENE4002) and Biology, Cell Biology
General lectures on stem cell biology followed by student presentations and discussion of the primary literature. Themes presented include: basic stem cell concepts; basic cell and molecular biological characterization of endogenous stem cell populations; concepts related to reprogramming; directed differentiation of stem cell populations; use of stem cells in disease modeling or tissue replacement/repair; clinical translation of stem cell research

BMENE6520Instructive Biomaterials. 3.00 points.

Covers biomaterials that are instructive or have been designed or engineered to be instructive; structure-function-property relationships in natural and synthetic biomaterials. Advances in understanding of material properties emphasized; including electroactivity, chemical, mechanical, geometry/architecture, and the modification of material surfaces and context of their effect on biological function. Evolving field of smart biomaterials discussed. Exercises/demonstrations using materials characterization equipment conducted

BMENE8001TOPICS IN NANOBIOTCEHNOLOGY. 3.00 points.

Lect: 3.

Targeted toward graduate students; undergraduate student may participate with permission of the instructor. Review and critical discussion of recent literature in nanobiotechnology and synthetic biology. Experimental and theoretical techniques, critical advances. Quality judgments of scientific impact and technical accuracy. Styles of written and graphical communication, the peer review process.

BMENE9100MASTERS RESEARCH. 1.00-6.00 points.

Candidates for the M.S. degree may conduct an investigation of some problem in biomedical engineering. No more than 6 points in this course may be counted for graduate credit

BMENE9500DOCTORAL RESEARCH. 1.00-6.00 points.

Doctoral candidates are required to make an original investigation of a problem in biomedical engineering, the results of which are presented in the dissertation

BMENE9700BIOMEDICAL ENGINEERING SEMINAR. 0.00 points.

0 pts. Sem: 1.

All matriculated graduate students are required to attend the seminar as long as they are in residence. No degree credit is granted. The seminar is the principal medium of communication among those with biomedical engineering interests within the University. Guest speakers from other institutions, Columbia faculty, and students within the Department who are advanced in their studies frequently offer sessions

BMENE9800DOCTORAL RESEARCH INSTRUCTION. 3.00-12.00 points.

A candidate for the Eng.Sc.D. degree in biomedical engineering must register for 12 points of doctoral research instruction. Registration may not be used to satisfy the minimum residence requirement for the degree

BMENE9900DOCTORAL DISSERTATION. 0.00 points.

0 pts.

A candidate for the doctorate in biomedical engineering or applied biology may be required to register for this course in every term after the students course work has been completed and until the dissertation has been accepted

CBMFW4761COMPUTATIONAL GENOMICS. 3.00 points.

Lect: 3.

Prerequisites: Working knowledge of at least one programming language, and some background in probability and statistics.
Computational techniques for analyzing genomic data including DNA, RNA, protein and gene expression data. Basic concepts in molecular biology relevant to these analyses. Emphasis on techniques from artificial intelligence and machine learning. String-matching algorithms, dynamic programming, hidden Markov models, expectation-maximization, neural networks, clustering algorithms, support vector machines. Students with life sciences backgrounds who satisfy the prerequisites are encouraged to enroll

CBMFE6772Advanced machine learning. 0 points.

CHBME4321The genome and the cell. 3 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (BIOLUN2005) and (MATHUN2030)

The utility of genomic information lies in its capacity to predict the behavior of living cells in physiological, developmental, and pathological situations. The effect of variations in genome structure between individuals within a species, including those deemed healthy or diseased, and among species, can be inferred statistically by comparisons of sequences with behaviors, and mechanistically, by studying the action of molecules whose structure is encoded within the genome. This course examines known mechanisms that elucidate the combined effect of environmental stimulation and genetic makeup on the behavior of cells in homeostasis, disease states, and during development, and includes assessments of the probable effect of these behaviors on the whole organism. Quantitative models of gene translation and intracellular signal transduction will be used to illustrate switching of intracellular processes, transient and permanent gene activation, and cell commitment, development, and death.

EEBME6020METHODS OF COMPUT NEUROSCIENCE. 4.50 points.

Lect: 3.Not offered during 2023-2024 academic year.

Prerequisites: (BMEBW4020)
Formal methods in computational neuroscience including methods of signal processing, communications theory, information theory, systems and control, system identification and machine learning. Molecular models of transduction pathways. Robust adaptation and integral feedback. Stimulus representation and groups. Stochastic and dynamical systems models of spike generation. Neural diversity and ensemble encoding. Time encoding machines and neural codes. Stimulus recovery with time decoding machines. MIMO models of neural computation. Synaptic plasticity and learning algorithms. Major project(s) in MATLAB

EEBME6090TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Lect: 2.

Prerequisites: The instructor's permission.
Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090-6099

EEBME6091TPCS IN COMP NEUROSCI/ENGINEERING. 3.00 points.

Lect: 2.

Prerequisites: The instructor's permission.
Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090-6099. Topic: Devices and Analysis for Neural Circuits

EEBME6092TOPICS IN COMP NEUROSI ＆ ENG. 3.00 points.

Not offered during 2023-2024 academic year.

Prerequisites: The instructor's permission.
Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6093TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6094TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6095TOPICS IN COMP NEUROSI ＆ ENG. 3.00 points.

Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6096TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6097TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6098TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBME6099TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Lect: 2.

Prerequisites: The instructor's permission.
Selected advanced topics in computational neurscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090-6099

EEBMGR6250Field Methods in Wildlife Monitoring. 3 points.

This course provides a strong theoretical and practical background in the use of wildlife monitoring techniques to address ecological and conservation orientated questions. The course will conduct an overview of monitoring plan design and the conceptual background needed to understand and critique monitoring plans, and have the basic skills to develop and implement a monitoring program as part of an interdisciplinary team. During this course, we will examine a variety of research and monitoring techniques used by wildlife professionals. We will evaluate the theories, strengths, and weaknesses behind the use of these wildlife techniques and apply them in the field.

EEBME9070SEM IN COMP NEURO SCI＆NEUROENGINEERING. 3.00 points.

Lect: 3.

Prerequisites: (BMEBW4020) or permission of instructor.
Study of recent developments in computational neuroscience and neuroengineering

MEBME4439MODELING ＆ ID OF DYNAMIC SYST. 3.00 points.

Prerequisites: (APMAE2101) and (ELENE3801) or instructor's permission.
Corequisites: EEMEE3601
Generalized dynamic system modeling and simulation. Fluid, thermal, mechanical, diffusive, electrical, and hybrid systems are considered. Nonlinear and high order systems. System identification problem and Linear Least Squares method. State-space and noise representation. Kalman filter. Parameter estimation via prediction-error and subspace approaches. Iterative and bootstrap methods. Fit criteria. Wide applicability: medical, energy, others. MATLAB and Simulink environments

MEBME4440Physiological Controls. 3.00 points.

Prerequisites: (MEBME4439) and (APMAE2101) Fundamentals of time and frequency domains analyses and stability. Frequency domain controller design. Cardiovascular and respiratory systems simulation. Endogenous control systems: baroreflex, chemoreflex, thermoregulation, pupillary light reflex. Open and closed loop physiological systems. Exogenous control systems: ventilators, infusion pumps. Nonlinear actuators and delayed feedback systems. Acute disease simulation and clinical decision support in the intensive care unit. MATLAB and Simulink environments utilized

MEBME4703MOLECULAR MECHANICS IN BIOLOGY. 3.00 points.

Lect: 3.

Prerequisites: (ENMEE3105) and (APMAE2101) or instructor's permission.
Mechanical understanding of biological structures including proteins, DNA and RNA in cells and tissues. Force response of proteins and DNA, mechanics of membranes, biophysics of molecular motors, mechanics of protein-protein interactions. Introduction to modeling and simulation techniques, and modern biophysical techniques such as single molecule FRET, optical traps, AFM, and superresolution imaging, for understanding molecular mechanics and dynamics

MEBME4710MORPHOGENESIS:BIOL MAT SHP/STR. 3.00 points.

Prerequisites: Courses in mechanics, thermodynamics, and ordinary differential equations (for example, ENMEE3113, MECEE3301 and MATHUN3027) at the undergraduate level or instructor's permission.
Introduction to how shape and structure are generated in biological materials using engineering approach emphasizing application of fundamental physical concepts to a diverse set of problems. Mechanisms of pattern formation, self-assembly, and self-organization in biological materials, including intracellular structures, cells, tissues, and developing embryos. Structure, mechanical properties, and dynamic behavior of these materials. Discussion of experimental approaches and modeling. Course uses textbook materials as well as collection of research papers

MEBME6311MIXT THEORIES FOR BIOL TISSUES. 3.00 points.

Lect: 3.

Prerequisites: (MECEE6422) and (APMAE4200) or equivalent.
Development of governing equations for mixtures with solid matrix, interstitial fluid, and ion constituents. Formulation of constitutive models for biological tissues. Linear and nonlinear models of fibrillar and viscoelastic porous matrices. Solutions to special problems, such as confined and unconfined compression, permeation, indentation and contact, and swelling experiments