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CE 400 Honors Seminar Molecular 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

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ce 400 honors seminar molecular simulation

CE 400 Honors SeminarMolecular Simulation

Class 1

Prof. Kofke

Department of Chemical Engineering

University at Buffalo, State University of New York

course information
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%
  • 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
Physical Properties
  • Quantify material behavior
  • Examples
    • What physical properties are needed for science and engineering, and why?
physical properties5
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
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
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
Role of Molecular Simulation

model and treatment



test treatment

test model


  • 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
Test of Hard-Sphere Treatments

Carnahan-Starling equation

what is molecular simulation
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
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)





boundary conditions
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
  • 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
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