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If you have any question feel free to post them in the comment section below. Terms offered: Spring , Spring , Spring This course covers deformation and fracture behavior of engineering materials for both monotonic and cyclic loading conditions. Terms offered: Fall , Spring , Fall Surface interactions. Fundamentals of contact mechanics. Friction theories. Types of measurement of wear.
Response of materials to surface tractions. Delamination wear. Microstructural effects in wear processes. Mechanics of layered media.
Solid film and boundary liquid film lubrication. Friction and wear of polymers and fiber-reinforced polymeric composites. Brief introduction to metal cutting and tool wear mechanisms. Terms offered: Spring , Spring , Spring Response of composite materials fiber and particulate-reinforced materials to static, cyclic, creep and thermomechanical loading. Manufacturing process-induced variability, and residual stresses. Fatigue behavior,fracture mechanics and damage development. Role of the reinforcement-matrix interface in mechanical behavior.
Environmental effects. Dimensional stability and thermal fatigue. Application to polymer, metal, ceramic, and carbon matrix composites. Terms offered: Spring , Spring , Spring Fundamental principles of magnetics, electro-magnetics, and magnetic materials as applied to design and operation of electro-mechanical devices.
Type of device to be used in a particular application and dimensions of parts for the overall design will be discussed. Typical applications covered will be linear and rotary actuators, stepper motors, AC motors, and DC brush and brushless motors. A design project is required. Terms offered: Fall Advanced optimization, polyhedra manipulation, and multiparametric programming.
Robust Invariant set theory. Analysis and design of model predictive controllers MPC for linear and nonlinear systems. Stochastic MPC. Learning MPC. Computational oriented models of hybrid systems. Analysis and design of constrained predictive controllers for hybrid systems. Course Objectives: The course is designed for graduate students who want to expand their knowledge on model predictive control.
Terms offered: Prior to Theoretical development of the common methods in control system robustness analysis, including general dissipative systems and supply rates, structured singular value, and integral quadratic constraints.
Transforming theory into pragmatic algorithms. Use cases in industrial examples. Course Objectives: The course is designed for graduate students who want to quickly expand their knowledge on robustness analysis comprising one part of a complete validation process for complex feedback systems.
Students will learn about theory, algorithms, applications and existing software. Student Learning Outcomes: Students will gain a deep understanding of the modeling assumptions and precise results offered by current state-of-the-art robustness analysis techniques. The wide applicability as well as the limitations of the techniques will be emphasized.
The course concludes with a self-directed project, covering a theoretical, algorithmic or applications-oriented issue of interest to each individual student.
The student will master skills needed to apply linear control design and analysis tools to classical and modern control problems. In particular, the participant will be exposed to and develop expertise in two key control design technologies: frequency-domain control synthesis and time-domain optimization-based approach.
Terms offered: Spring , Spring , Fall , Spring Experience-based learning in the design, analysis, and verification of automatic control systems. The course emphasizes the use of computer-aided design techniques through case studies and design tasks. The student will master skills needed to apply advanced model-based control analysis, design, and estimation to a variety of industrial applications. The role of these specific design methodologies within the larger endeavor of control design is also addressed.
Terms offered: Fall , Fall , Fall Input-output and state space representation of linear continuous and discrete time dynamic systems. Controllability, observability, and stability. Modeling and identification. Design and analysis of single and multi-variable feedback control systems in transform and time domain.
State observer. Application to engineering systems. Emphasis is on the effect that model uncertainty has on the design process. Terms offered: Spring , Fall , Spring This course provides preparation for the conceptual design and prototyping of mechanical systems that use microprocessors to control machine activities, acquire and analyze data, and interact with operators. The architecture of microprocessors is related to problems in mechanical systems through study of systems, including electro-mechanical components, thermal components, and a variety of instruments.
Terms offered: Spring Physical understanding of automotive vehicle dynamics: simple lateral, longitudinal and ride quality models. An overview of active safety systems will be intros including basic concepts and terminology, the state-of-the-art development, and basic principles of systems such as ABS, traction control, dynamic stability control, and roll stability control.
Course Objectives: Develop skills in using professional computer-aided control system design and analysis tools, e. Develop the analytical skills necessary to quantitatively predict the behavior of open-loop and closed-loop systems. Experimental design will be complemented with a careful analysis of the performance by simulation.
Present and motivate the appropriate level of dynamic modeling that is required to analyze the performance of vehicle control systems. The development of such models is as much of an art as a science in that the models must be kept as simple as possible so that real-time controller implementation can be achieved while retaining the fundamental stability and dynamic response characteristics.
Student Learning Outcomes: Assess the stability of dynamic systems using differential equation theory, apply frequency-response methods to assess system response to external disturbances, sensor noise and parameter variations. Terms offered: Fall , Spring , Spring , Spring Distributed systems and PDE models of physical phenomena propagation of waves, network traffic, water distribution, fluid mechanics, electromagnetism, blood vessels, beams, road pavement, structures, etc.
Fundamental solution methods for PDEs: separation of variables, self-similar solutions, characteristics, numerical methods, spectral methods. Stability analysis. Adjoint-based optimization. Lyapunov stabilization. Differential flatness. Viability control. Hamilton-Jacobi-based control. Prerequisites: Engineering 77, Mathematics 54 or equivalent , or consent of instructor. Terms offered: Fall , Fall , Fall This course is a room share with ME, and teaches students the dynamic analysis and control of unmanned aerial vehicles UAVs.
The course covers modeling and dynamics of aerial vehicles, common control strategies, sensing and estimation. A laboratory sequence allows students to apply knowledge on a real quadcopter system, by programming a microcontroller to control a UAV. Prerequisites: Introductory control Mechanical Engineering or similar , Dynamics Mechanical Engineering or similar.
Credit Restrictions: Student will not receive credit for this course if they have taken Mechanical Engineering Terms offered: Spring , Spring , Fall Fundamental properties of nonlinear systems. Controllability and observability of nonlinear systems. Controller design of nonlinear systems including feedback linearization and sliding mode control.
Design of nonlinear discrete and adaptive controllers. Nonlinear observers and compensators. To develop controller synthesis methods for nonlinear and uncertain dynamic systems. Student Learning Outcomes: The ability to design, evaluate and implement closed loop controllers for highly nonlinear and uncertain systems. Terms offered: Spring , Spring , Spring Basic graduate course in nonlinear systems. Nonlinear phenomena, planar systems, bifurcations, center manifolds, existence and uniqueness theorems.
Input-to-state and input-output stability, and dissipativity theory. Computation techniques for nonlinear system analysis and design. Feedback linearization and sliding mode control methods. Prerequisites: MATH 54 undergraduate level ordinary differential equations and linear algebra.
Terms offered: Fall , Fall , Fall This course will provide students with a solid understanding of robotic locomotion and the use of dynamics, control and embedded microcomputers in designing artificial legs such as prosthetics, orthotics and exoskeletons.
Terms offered: Fall , Spring , Spring This course introduces a probabilistic description of ocean waves and wave loads acting on marine structures. These topics are followed with discussion of structural strength and reliability analysis.
Terms offered: Spring , Fall , Spring This course is concerned with the structural response of marine structures to environmental loads. Overall response of the structure as well as the behavior of its members under lateral and compressive loads are discussed. Boundary-layer theory, laminar, and turbulent. Frictional resistance. Boundary layer over water surface. Separated flow modeling. Steady and unsteady flow. Momentum theorems. Three-dimensional water-wave theory.
Formulation of wave resistance of ships. Michell's solution. Wave patterns. Student Learning Outcomes: Students with ocean- and marine-related interest will develop the necessary theoretical and experimental background to keep up with existing literature and begin research on contemporary topics.
Terms offered: Spring , Spring , Fall Momentum analysis for bodies moving in a fluid. Added-mass theory. Matched asymptotic slender-body theory. Small bodies in a current. Theory of motion of floating bodies with and without forward speed.
Radiation and diffraction potentials. Wave forces. Hydro-elasticity formulation. Ocean-wave energy. Memory effects in time domain. Second-order formulation. Impact hydrodynamics, Hydrofoil theory and lifting surface.
Terms offered: Spring Viscous-fluid flow, boundary-layer theory surface waves, ship waves, and applications. Ocean environment. Course Objectives: To provide training of mechanical engineers to understand the unique characteristics of the ocean environment, local and global scale, and to provide background on engineering and design tools that are commonly used by engineers working with system and component designs of ocean, marine energy, and ship systems.
Student Learning Outcomes: At the end of the course, the students should understand general scientific properties that characterize the main body of the oceans; understand components of drags that contribute to the resistance of a marine vehicle and the associated engineering skills in model-testing that quantify the drag characteristics of a ship hull; comprehend simple harmonic surface-wave theory, with strong realization of the underlying concepts of wave kinematics, wave energy, and group velocity.
Terms offered: Spring , Fall , Spring Analytical and numerical methods in free-surface problems. Elements of inviscid external lifting and nonlifting flows. Analytical solutions in special coordinates systems.
Integral-equation methods: formulations and implementations. Multiple-bodies interaction problems. Free-surface Green functions in two and three dimensions. Hybrid integral-equation methods. Finite-element formulations. Variational forms in time-harmonic flows. Finite-difference forms, stability, and accuracy. Boundary-fitted coordinates methods. Unsteady linearized wave-body interaction in time domain.
Nonlinear breaking waves calculations. Particle dynamics. Course Objectives: To present a relatively broad spectrum of analytical and numerical methods commonly used in tackling wave-body interaction problems. Topics covered include classical techniques in special coordinate systems, modern computational techniques based on boundary-integral, finite-element, and boundary-fitted coordinates methods.
Lectures focus on formulations and implementation techniques. Students are given opportunities to implement methods discussed in class on workstations or mainframe. Student Learning Outcomes: Students will be conversant and have abilities to handle fluid-structure interactions problems with free-surface present. Terms offered: Spring , Spring , Spring Covers dynamics of wave propagation in the ocean and the atmosphere. Terms offered: Fall , Spring , Fall Covers the fundamental principles of energy conversion processes, followed by development of theoretical and computational tools that can be used to analyze energy conversion processes.
Also introduces the use of modern computational methods to model energy conversion performance characteristics of devices and systems. Performance features, sources of inefficiencies, and optimal design strategies are explored for a variety of applications. Course Objectives: This class provides students with an understanding of the thermophysical principles that govern energy conversion processes of different types, and will introduce them to modern computational methods for modeling the performance of energy conversion processes, devices and systems.
This course is a capstone experience for ME students, synthesizing thermodynamics, fluid dynamics, heat transfer and computational analysis tools to facilitate engineering design analysis. Student Learning Outcomes: This course will provide a foundation for design analysis of energy conversion systems encountered in a variety of applications.
Prerequisites: Engineering 7, Mechanical Engineering 40, Mechanical Engineering , and Mechanical Engineering or their equivalents. Students will learn the fundamentals of particle image velocimetry, electrical impedance measurements, X-ray based multiphase flow measurements, and advanced measurement data processing and analysis techniques.
Different demos are conducted, students will work in teams in their labs, on both simple experiments, and on one major experiment design. The benchmark developed in this work will serve as an indispensable source to reach this goal. The structure detn.
Several methods based on docking to study protein complexes have also been well developed over the past few years.
Most of these approaches are not driven by exptl. An AIR is defined as an ambiguous distance between all residues shown to be involved in the interaction. The accuracy of our approach is demonstrated with three mol. For two of these complexes, for which both the complex and the free protein structures have been solved, NMR titrn. Mutagenesis data were used in the last example. The prediction of the quaternary structure of biomol. In the era of integrative structural biol.
We present here the updated version 2. With well over registered users and , jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biol. Scientific reports , 5 , ISSN:. Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate.
Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy.
It is indeed becoming increasingly evident that the time a drug spends in contact with its target aka residence time can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays.
We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold.
Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance. Engineering chem. In this context, the limitations of statically describing bimol. On the exptl. Thus, computer simulations, particularly mol. Unfortunately, MD-based approaches cannot yet describe complex events without incurring prohibitive time and computational costs.
Here, we present a new method for fully and dynamically simulating drug-target-complex formations, tested against a real world and pharmaceutically relevant benchmark set. The method, based on an adaptive, electrostatics-inspired bias, envisions a campaign of trivially parallel short MD simulations and a strategy to identify a near native binding pose from the sampled configurations. At an affordable computational cost, this method provided predictions of good accuracy also when the starting protein conformation was different from that of the crystal complex, a known hurdle for traditional mol.
Moreover, along the obsd. Overall, this methodol. Royal Society of Chemistry. Docking algorithms build multimol. This requires at least two steps, a rigid-body search that dets. The methods developed in the past twenty years yield native-like models in most cases, but always with many false positives that must be filtered out, and they fail when the conformation changes are large.
Assessment of PRedicted Interactions is a community-wide expt. It offers participants the opportunity to test their methods in blind predictions that are assessed against an unpublished exptl. The models submitted by predictor groups are judged depending on how well they reproduce the geometry and the residue-residue contacts seen in the target structure. In nine years of CAPRI, 42 target complexes have been subjected to prediction based on the components' unbound structures.
Good models have been submitted for 28 targets, and prediction has failed on 6. Both these successes and these failures have been fruitful, as they stimulated participant groups to develop new score functions to identify native-like solns.
The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation.
In order to elucidate the mol. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them.
The interplay of electron transfer and induced conformational changes seems to be crit. Nucleic Acids Res. Cuneo, Matthew J. Oxford University Press.
The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. Although structural data for the individual domains has been available, no structure of the complex has been detd. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation.
We report here the structures of both homodimer complexes as well as the heterodimer complex. This enhanced linker-mediated binding interface plays a significant role in the detn. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex. Scheuermann, Thomas H. National Academy of Sciences. In humans, HIF is critically important for the sustained growth and metastasis of solid tumors.
Given the essential role of PAS domains in forming active HIF heterodimers, these results suggest a presently uncharacterized ligand-mediated mechanism for regulating HIF2 activity in endogenous and clin. Argiriadi, Maria A. American Society for Biochemistry and Molecular Biology. The unique cytokine interleukin IL acts synergistically with IL to regulate T-helper 1 and 2 lymphocytes and, as such, seems to underlie the pathogenesis of various autoimmune and allergic diseases.
Several anti-IL agents are in clin. Here the authors report three crystal structures: the murine antibody H Fab fragment bound to human IL, at 1. IL thus exhibits plasticity that may be common to its interactions with other receptors. Related cytokines may exhibit similar plasticity. Second, ABT and H differ significantly in combining site character and architecture, thus explaining their ability to bind IL simultaneously at distinct epitopes.
These data allow the authors to define the likely ABT epitope and thereby explain the distinct neutralizing mechanisms of both antibodies. Third, given the high H potency, 10 well ordered water mols. Thus, counter-intuitively, tight and specific antibody binding may in some cases be water-mediated. Transient disulfide bond formation is increasingly recognized as an important mol. The results presented here suggest a paradigm in DNA repair in which the redox state of a scaffolding protein plays an active role in organizing the repair complex.
Clostridium perfringens iota-toxin Ia mono-ADP ribosylates Arg of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystd. Here we report high-resoln. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases.
The direct comparison of NMR and X-ray data shows that the epitope defined by the crystal structure encompasses predominantly those residues whose NMR resonances are severely perturbed upon complex formation. In this paper, we introduce the BiKi Life Sciences suite. This software makes it easy for computational medicinal chemists to run ad hoc mol. Wiley-Liss, Inc. Recent advances in hardware and software have enabled increasingly long mol.
Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions.
Here, the authors further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, the authors used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, the authors optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mech. Finally, the authors used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of exptl.
NMR measurements that directly probe side-chain conformations. Proteins A parallel message-passing implementation of a mol. Simulation with communication to and from left and right neighbors, but can run on any parallel system onto which a a ring of processors can be mapped and which supports PVM-like block send and receive calls.
The MD program can handle rectangular periodic boundary conditions with temp. The interactions that can be handled without modification are variable non-bonded pair interactions with Coulomb and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based on charge groups, and fixed bonded interactions of either harmonic or constraint type for bonds and bond angles and either periodic or cosine power series interactions for dihedral angles.
Special forces can be added to groups of particles for non-equil. Includes Appendix showing practical bearing configurations advantages and disadvantages. Physical interpretation of dynamic forces for circular centered whirl 14 p. Hydrodynamic fluid film bearings and their effect on the stability of rotating machinery Presentation in pdf form 42 p.
Equations of motion of a rigid rotor. The concept of force coefficients. Derivation of stiffness and damping coefficients for the short bearing.
Stability analysis and the effect of cross-coupled stiffness. Effect of rotor flexibility on stability and imbalance response.
Appropriate boundary conditions for a sound cavitation model. The basics of a universal cavitation model algorithm. A discussion on dynamic cavitation: air ingestion and entrapment. Universal cavitation model Single point relaxation. Mathcad file. Thermal analysis of finite length journal bearings including fluid inertia 59 p. Evaluation of dynamic force coefficients in finite length bearings using a perturbation of the flow equations.
Finite Element models: basic equations and their solution. Gives explanation about pad offset and preload. The nature of turbulence. Turbulence equations in thin film flows. Turbulence flow models. When fluid inertia effects are important. Bulk-flow model for inertial flows. Turbulence and inertia in short length journal bearings and open end dampers. MATHCAD program for prediction of threshold speed of instability and imbalance response of a rigid rotor supported on turbulent flow short length journal bearings no fluid inertia.
The complete set of bulk-flow equations for the analysis of turbulent flow fluid film bearings. Importance of thermal effects in process fluid applications. A CFD method for solution of the bulk-flow equations. High pressure floating ring seals 17p. Floating ring seals for compressors: leakage and force coefficients, seal lock up and effect on rotor stability, recommendations to reduce seal cross-coupled effects.
High pressure long oil seals 12p. Long oil seals as pressure barriers in industrial mixers: leakage and force coefficients, effect on rotor stability, recommendations for grooved seals with reduced leakage and lesser cross-stiffnesses. The mechanism of centering stiffness in seals. Force coefficients for short-length pressure seals. Design of annular seals: swirl brakes, impact on rotordynamics. Hydrostatic bearings in modern applications. The principle of hydrostatic lubrication.
Effects of recess volume-fluid compressibility on force coefficients for operation at low and high frequencies. Password recovery.
Recover your password. Get help. Fundamentals of Complex Analysis by Saff, E.
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