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Dive into the world of molecular simulation to quantify physical properties crucial for science and engineering applications. Explore how molecular models and simulation methods play a vital role in material behavior analysis. Enhance your knowledge of molecular dynamics and Monte Carlo simulation techniques. Discover the application of molecular simulation in designing materials and processes effectively. Uncover the role of boundary conditions and energy separation in simulated systems. Engage with Etomica, a graphical development environment for simulations, and learn about Application Programming Interface (API) for simulation assembly.
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CE 400 Honors SeminarMolecular Simulation Class 1 Prof. Kofke Department of Chemical Engineering University at Buffalo, State University of New York
Course Information • Instructor • Prof. Kofke • Office: 510 Furnas Hall • Contact: kofke@eng.buffalo.edu • Aims • To learn about molecular simulation • To better understand Nature • Assessment • Occasional assignments: 50% • Semester project: 50%
Discussion • Who are you? • Name, home town, major • What do you know? • Experience with computers and programming • Strength in physics (mechanics) and calculus • Knowledge of physical chemistry / thermodynamics • What do you expect? • Why did you select this course? • What do you think you’ll learn? • What is molecular simulation? • Molecular simulation: what’s it good for? • Accessible length and time scales?
Physical Properties • Quantify material behavior • Examples • What physical properties are needed for science and engineering, and why?
Physical Properties • Quantify material behavior • Examples • Density (sizing equipment) • Vapor pressure (separations equipment design) • Thermal conductivity (heat exchanger design) • Viscosity (pipe and pump sizing; analysis of flow systems, including complex media such as paint or blood) • Diffusivity (analysis of mixing; reacting systems) • Freezing/melting points (equipment/process design; handling of petroleum mixtures; cryogenic applications) • Solubility (design of mixtures; separations equipment design) • Heat capacity (heating/cooling, energy requirements) • Electronic/photonic properties (laser, LED device design) • Surface tension (wetting, colloidal systems, mixing, droplets, foams, aerosols)
Engineering Method • Desired to design and construct a material or process that achieves some goal • Example: Separation of methanol from water • Large catalog of general methods exists for many such goals • Adsorption, absorption, crystallization, distillation • Engineer selects an approach based on experience • Distillation • Design of equipment or material requires quantitative knowledge of material behavior • Vapor pressure of each component as a function of composition • Given physical property data, design of process can proceed routinely • Usually!
Physical Property Information • Experiment • The definitive source • Expensive and inconvenient for design purposes • Semi-empirical formulas • Intelligently interpolates or extrapolates experimental measurements • Two inputs to a semiempirical formula • Functional form • Parameters specific to the substance of interest • Example: Antoine formula for vapor pressure
Role of Molecular Simulation model and treatment Theory Experiment test treatment test model Simulation • Molecular simulation is the only means to “measure” the macroscopic behavior of a molecularly modeled system • Example • Model: molecules behaves as billiard balls (hard spheres) • Treatment: Carnahan-Starling equation for hard-sphere fluid
Test of Hard-Sphere Treatments Carnahan-Starling equation
What is Molecular Simulation? • Molecular simulation is a computational “experiment” conducted on a molecular model. • Many configurations are generated, and averages taken to yield the “measurements.” One of two methods is used: • Molecular dynamics Monte Carlo • Integration of equations of motion Ensemble average • Deterministic Stochastic • Retains time element No element of time • Molecular simulation has the character of both theory and experiment • Applicable to molecules ranging in complexity from rare gases to polymers to electrolytes to metals 10 to 100,000 or more atoms are simulated (typically 500 - 1000)
What is a Molecular Model? • A molecular model postulates the interactions between molecules • More realistic models require other interatomic contributions • Intramolecular • stretch, bend, out-of-plane bend, torsion, +intermolecular terms • Intermolecular • van der Waals attraction and repulsion (Lennard-Jones form) • electrostatic • multibody A typical two-body, spherical potential (Lennard-Jones model) Energy e Separation s
Boundary Conditions • Impractical to contain system with a real boundary • Enhances finite-size effects • Artificial influence of boundary on system properties • Instead surround with replicas of simulated system • “Periodic Boundary Conditions” (PBC) • Click here to view an applet demonstrating PBC
Etomica • GUI-based development environment • Simulation is constructed by piecing together elements • No programming required • Result can be exported to run stand-alone as applet or application • Application Programming Interface (API) • Library of components used to assemble a simulation • Can be used independent of development environment • Invoked in code programmed using Emacs (for example) • Written in Java • Widely used and platform independent • Features of a modern programming language • Object-oriented
Class Project • Design, construct, test and deploy a molecular simulation • Must demonstrate a non-trivial collective behavior • Incorporation of game-like features is encouraged • Work in teams of three students • Details to follow… • For now, think about possibilities
