A. Theory and Simulation

CHEME 7740: Principles of Molecular Simulation

Instructor: Escobedo, F.

Semester: Spring

Introduction to molecular simulation methods, Molecular Dynamics and Monte Carlo. Understanding options for interatomic and intermolecular modeling and appropriate representation of materials.
CHEM 7870: Computational Methods of Physical Chemistry

Instructor: Hines, M.

Semester: Fall

This course will introduce students to analytical and computational methods useful for graduate-level research in both experimental and theoretical physical chemistry. These methods will be developed in Mathematica and will be used to explore interesting topics in quantum mechanics and statistical mechanics. The goal of this course is to bridge the gap between the analytical techniques taught in introductory courses and the computational (and visualization) methods required for modern research problems. Topics explored will include Scientific Programming and Visualization, Numerical Solution of the Schrödinger Equation, Variational Methods, Linear and Nonlinear Optimization Techniques, Self-Consistent Field Solutions to the Hartree-Fock Equations, Stochastic/Monte Carlo Methods, 2D Ising Model, and Molecular Dynamics. No previous programming experience will be assumed
PHYS 6562: Statistical Physics I

Instructor: Sethna, J.

Semester: Spring

A broad, graduate-level view of statistical mechanics, with applications to not only physics and chemistry, but to computation, mathematics, dynamical and complex systems, and biology. Some traditional focus areas will not be covered in detail (thermodynamics, phase diagrams, perturbative methods, interacting gasses, and liquids).  
CHEME 7310: Advanced Fluid Mechanics and Heat Transfer

Instructor: Koch, D.

Semester: Fall

Topics include derivation of conservation equations; conductive heat transfer; low Reynolds number fluid dynamics; lubrication theory; inviscid fluid dynamics; boundary layer theory; forced convection; and introduction to non-Newtonian fluid mechanics (polymeric liquids and suspensions), microfluidics, stability analysis, and turbulent flow.
CHEME 7510: Mathematical Methods in Chemical Engineering

Instructor: Hormozi, S.

Semester: Fall

This course will focus on analytical and numerical solutions to differential equations, emphasizing their applications in transport phenomena and chemical and biomolecular engineering problems and it comes into three parts:

1. Analytical solutions to linear partial differential equations

2. Analytical solutions to systems of nonlinear differential equations

3. Numerical methods to solve differential equations

PHYS 7601: Foundations of Fluid Mechanics I

Instructor: Desjardins, O.

Semester: Fall

Foundations of fluid mechanics from an advanced viewpoint, including formulation of continuum fluid dynamics; kinematic descriptions of fluid flow, derivation of the Navier-Stokes equations and energy equation for compressible fluids; and sound waves, viscous flows, boundary layers, and potential flows.
CS 5780: Introduction to Machine Learning

Instructor: De Sa, C.

Semesters: Fall, Spring

The course provides an introduction to machine learning, focusing on supervised learning and its theoretical foundations. Topics include regularized linear models, boosting, kernels, deep networks, generative models, online learning, and ethical questions arising in ML applications.
CS 5787: Deep Learning

Instructor: Kanan, C.

Semester: Spring

Students will learn deep neural network fundamentals, including, but not limited to, feed-forward neural networks, convolutional neural networks, network architecture, optimization methods, practical issues, hardware concerns, recurrent neural networks, dataset acquisition, dataset bias, adversarial examples, current limitations of deep learning, and visualization techniques. We still study applications to problems in computer vision and to a lesser extent natural language processing and reinforcement learning. There will also be a session on understanding publications in deep learning, which is a critical skill in this fast-moving area.
CHEM 7960: Statistical Mechanics

Instructor: Loring, R.

Semester: Spring

Introduces the fundamentals of statistical mechanics: ensembles, distributions, averages, and fluctuations, building to the treatment of systems of interacting molecules. Topics from equilibrium statistical mechanics include structure and thermodynamics of molecular liquids, critical phenomena, and computational statistical mechanics. Topics from nonequilibrium statistical mechanics include spectroscopy, chemical kinetics, transport, and the microscopic origins of irreversibility.
MSE 5830: Thermodynamics of Condensed Systems

Instructor: Thompson, M.

Semester: Fall

Introduces the three laws of thermodynamics as the fundamental basis for thermal and chemical equilibrium, coupled with statistical mechanical interpretations for entropy.  Applies these principles to understand the equilibrium behavior of matter, with a focus on condensed liquid and solid phases.  Develops concepts of phase equilibria, phase diagrams, chemical reactions, solution behavior, and electrochemistry.  Includes an introduction to statistical mechanics and applications in ideal gas behavior, gas and crystal heat capacity, and electron Fermi-Dirac statistics.  Applications and examples will be drawn from a range of sub-disciplines spanning metallurgy to polymers. Extended assignments and independent study of advanced concepts are required.
MSE 5340: Particulate Science and Engineering: Fundamentals and Applications

Instructor: Murtagh, M.

Semester: Spring

This course is designed for senior undergraduates and graduate students in the fields of MSE, CBE, MAE. The course will focus on recent advances in particulate science and engineering (PSE) and its applications. These advances offer insight into the underlying principles of the ensemble of interacting particles undergoing transport ranging from nanometers to millimeters, which are relevant to particulate systems in various product applications. Lectures will draw from state-of-the-art research and industrial practice. Phenomenological modeling and numerical simulation methods will be introduced focusing on population balance modeling (PBM), discrete element method (DEM), and computational fluid dynamics (CFD). Students will attend lectures and participate in group reviews on current static and dynamic particle characterization methods, as well as team-based additive manufacturing (3D printing) projects.

CHEME 6880: Industrial Big Data Analytics and Machine Learning

Instructor: You, F.

Semester: Spring

This course covers the basic concepts, models and algorithms of Bayesian learning, classification, regression, dimension reduction, clustering, density estimation, artificial neural networks, deep learning, and reinforcement learning. Application and methodology topics include process monitoring, fault diagnosis, preventive maintenance, root cause analysis, soft sensing, quality control, machine learning for process optimization, data-driven decision making under uncertainty, missing data imputation, data de-noising, and anomaly/outlier detection.

CHEME 6888: Deep Learning

Instructor: You, F.

Semester: Summer

Covers the basic concepts, models, methods, and applications of deep learning. Topics include the basics of artificial neural networks, training of neural networks, convolutional neural networks, recurrent neural networks, generative models, deep reinforcement learning, and deep learning hardware and software packages. Application and methodology topics include deep learning for pharmaceutical discovery, deep learning for process control, deep learning for molecular design, deep learning for material screening, deep learning for product yield and quality estimation, and deep learning for optimization.

B. Soft Matter in the Life Sciences

CHEME 7770: Advanced Principles of Biomolecular Engineering

Instructors: Paszek, M.; Varner, J.

Semester: Spring

This course will cover the physical principles required for understanding the molecular basis of life and its use in biotechnologies. Emphasis will be placed on deconstructing biological phenomena from a quantitative perspective of core engineering principles. Specific topics will include:  thermodynamics and kinetics of gene expression and genetic circuitry, biophysical principles of molecular interaction, molecular mechanisms in the definition of cell state and differentiation, molecular modes of cellular communication, and biophysical considerations for multicellular life.
MAE 6670: Soft Tissue Biomechanics II: Viscoelasticity and Phasic Theory

Instructor: Andarawis-Puri, N.

Semester: Spring

Application of mechanics and materials principles to orthopaedic soft tissues. Mechanical properties of cartilage, tendon, and ligaments; applied viscoelasticity theory for cartilage, tendon, and ligament; cartilage, tendon, and ligament biology; tendon and ligament wound healing; osteoarthritis
MAE 5650: Biofluid Mechanics

Instructor: Lewis, K.

Semester: Fall

The transport of energy, mass, and momentum is essential to the function of living systems. Changes in these processes often underlie pathological conditions. This course covers the understanding and analysis of micro-macroscopic fluid flow phenomena within the human body and the relation between fluid flow and physiological processes. The topics covered in this course span from the cellular level to organs under healthy and diseased conditions.
AEP 5700: Biophysical Methods

Instructor: Lambert, G.

Semester: Fall

Overview of the diversity of modern biophysical experimental techniques used in the study of biophysical systems at the molecular, cellular, and population level. Emphasis is placed on groundbreaking methods behind recent Nobel Prizes and other techniques likely to be encountered in cutting-edge research and industry. Topics include: 1) super-resolution, multi-photon, and single-molecule microscopy, 2) crystallography and structural biology methods used to characterize DNA, RNA, proteins, cells, tissues, 3) microfluidics, “lab-on-a-chip”, and single-cell culture techniques, 4) molecular dynamics simulations, stochastic modeling, and physical models of a cell, and 5) next-generation sequencing, protein engineering, synthetic biology, genome editing, and other experimental techniques at the intersection of applied physics and biological engineering.
BME 5830: Cell-Biomaterials Interactions

Instructor: Saikia, M.

Semester: Spring

Biological principles underlying biomaterial design and cellular adhesive behavior, incorporating biomechanical analysis across the molecular, cellular, and tissue length scales. We will take an in-depth look at design considerations and biomaterials analysis, incorporating reading from the primary literature as well as the text.
BME 6410: Cell and Molecular Mechanobiology

Instructor: Lammerding, J.

Semester: Spring

Mechanobiology describes how cells and tissues sense and respond to their physical environment. Examples range from muscle cells growing in response to exercise, bones adapting to mechanical load, and mechanical forces modulating immune cell function to the distribution of fluid shear stress determining the sites of atherosclerosis or tissue stiffness promoting the risk of cancer. This course will introduce examples of mechanobiology in physiology and disease, explain the cell and molecular components involved in mechanosensing and the cell/tissue response to mechanical stimuli, highlight experimental tools and approaches to study mechanobiology at the cell, molecular, and tissue level, analyze representative data of mechanobiology experiments, and discuss current limitations and engineering challenges to advance to the field.
MSE/ BME 5620: Biomineralization

Instructor: Estroff, L.

Semester: Spring

This course will examine the wide variety of mineralized materials made by biological organisms including mollusk shells, sea urchins, mammalian bone and teeth, siliaceous sponges and diatoms, and magnetotactic bacteria. The focus will be on the molecular and biological mechanisms that lead to the formation of these materials as well as their unique mechanical, optical and optical properties.

C. Soft Matter, Polymers and Interfaces

CHEME 6400: Polymeric Materials

Instructor: Alabi, C.

Semester: Spring

Covers chemistry and physics of the formation and characterization of polymers; principles of fabrication.
MAE 5670: Polymer Mechanics

Instructor: Silberstein, M.

Semester: Spring

This course will provide foundations of polymer mechanics building from the basics of mechanics of materials. The focus will be split between experimental methods/data interpretation and modeling approaches. Topics will include hyper-elasticity, viscoelasticity, glass transition temperature, and plasticity with applications to both synthetic and biological materials. There will also be a scientific literature reading component through which students will be able to pick their own focus areas in the latter part of the semester.
CHEM 6700: Fundamental Principles of Polymer Chemistry

Instructor: Stache, E.

Semester: Fall

Emphasizes general concepts and fundamental principles of polymer chemistry.
MSE 5230: Physics of Soft Materials

Instructor: Wiesner, U.

Semester: Fall

An introduction to general aspects of (i) structure, (ii) order, and (iii) dynamics of soft materials /biomaterials. Typical representative materials discussed include polymers, thermo- and lyotropic liquid crystals, and gels. Following the development of structural aspects of these materials, a general formalism for the description of partially ordered systems in terms of orientation distribution functions will be introduced, including various techniques to measure these parameters. Finally, dynamics of soft materials will be discussed including transport and flow behavior, and aspects of the local dynamics. Structure, order, and dynamic characterization techniques available at Cornell, such as NMR and x-ray scattering, will be emphasized.
MSE 5440: Soap Bubbles, Snowflakes, and Steps: Interfacial and Surface Phenomena in Materials Science

Instructor: Umbach, C.

Semester: Spring

Surface and interface phenomena play a critical role in the processing and performance of advanced materials. Students and the instructor will identify topics of joint interest that build on the fundamentals of surfaces and interfaces contained in the core materials science curriculum (diffusion and growth, surface structure and energy, adhesion, etc.) and that address phenomena such as interfacial electronic states, gas adsorption at surfaces and surface forces in air and liquid. Course content will be organized collaboratively with necessary background provided in lectures and readings, and with students contributing oral presentations and student-led active learning exercises.
MSE 5840: Kinetics, Diffusion, and Phase Transformation

Instructor: Dshemuchadse, J.

Semester: Spring

Phenomenological and atomistic theories of diffusion in metals, alloys, ionic compounds, semiconductors and polymers. Introduction to general transport theory and non-equilibrium thermodynamics. Kinetic effects in solidification and solid-state transformations that determine structure and properties of materials including: interfaces and microstructure; nucleation, growth and coarsening; alloy solidification; and diffusional and diffusionless transformations in solids.
FDSC 6170: Food Chemistry I

Instructor: Brady, J.

Semester: Spring

Covers the chemistry of foods and food ingredients. Discusses the chemical and physical properties of water, proteins, lipids, carbohydrates, and other food components and additives in the context of their interactions and functional roles in foods.
FDSC 6040: Chemistry and Functional Properties of Food Ingredients

Instructor: Abbaspourrad, A.

Semester: Spring

This is a course with an emphasis on understanding the interactions of food ingredients and their role and functionality in the food product. This course is designed to enable students to utilize a step-by-step problem-solving approach to tackle challenges found in the food industry. Examples of these challenges will be presented as case studies obtained from literature and the food industry. Additionally, graduate students in this course will: perform a case study on a given product; investigate the role of each ingredient and determine their interactions; suggest solutions to solve the problem; and present their results on case studies in class.
MSE 5210: Properties of Solid Polymers

Instructor: Ober, C.

Semester: Fall

The course provides a general introduction to this diverse field including synthetic and natural polymers for engineering applications. Covers structure, order, and dynamics integrating aspects of chemistry, physics, and engineering as needed to understand macromolecular materials. Relationships between structure and properties are elucidated from a materials science perspective. Examples from the current literature are also discussed to expose students to the state-of-the-art in the field.

D. Scientific Communication

STS 2851: Communication, Environment, Science, and Health

Instructor: Schuldt, J.

Semester: Spring

Environmental problems, public health issues, scientific research-in each of these areas, communication plays a fundamental role. From the media to individual conversations, from technical journals to textbooks, from lab notes to the web, communication helps define scientifically based social issues and research findings. This course examines the institutional and intellectual contexts, processes, and practical constraints on communication in the sciences
COMM 2010: Oral Communication

Instructor: Cohen, J.

Semesters: Fall, Spring, Summer

The course focuses on face-to-face, public communication, but the principles and practices addressed transfer to all purposeful communication situations. While many assume a good speech rests in how well it is delivered, students will learn that a good speech is equally dependent on the development, structure, and integrity of one’s ideas. The objectives of the course are for students to speak effectively and ethically, and listen critically.
BIOMI 7970: Scientific Communication Skills

Instructor: Feaga, H.

Semesters: Fall, Spring

The ability to communicate effectively is essential for success as a scientist. The primary goal of this course is to provide students with an opportunity to develop self-confidence and refine their formal oral presentation skills. Students are asked to present topical seminars that are critically evaluated by the instructor. Feedback for improving the presentation and peer evaluations are emphasized.
ENGRC 3500: Engineering Communications

Instructor: Wang, H.

Semesters: Fall, Spring

Prepares students for important communication activities. They communicate using various types of documents (e.g., emails, memos, problem analyses, proposals, progress reports), give oral presentations, and incorporate graphics in their oral and written work. Students learn how to communicate specialized information to different audiences (e.g., technical and non-technical audiences, colleagues and clients, peers and supervisors, and in-house departments), work in teams, and address organizational and ethical issues. The course material is drawn from professional contexts, principally engineering, and it generates lively discussion. The class size ensures close attention to each student’s work.
ENTOM 7100: Mastering the Craft of Scientific Writing

Instructor: O’Grady, P.

Semester: Spring

This course will offer students an opportunity to develop skills necessary for writing scientific papers, progress reports, and grant proposals. Students will work on their own projects, as well as offer editorial comments on the work of other students in the course. MS and Ph.D. students at all stages are welcome in the course, from first-year students developing thesis proposals and grants to support their work, to senior students finishing their dissertations and applying for faculty and postdoctoral positions.