Nanotechnology Engineering

Activity type

Attività formative affini o integrative

SSD

FIS/01

Year

N/D

Semester

N/D

CFU

3

Hours distribution

30 classroom hours

Lecturers

GIUSEPPE ZOLLO

Activity type

Attività formative affini o integrative

SSD

ING-IND/06

Year

N/D

Semester

N/D

CFU

3

Hours distribution

30 classroom hours

Lecturers

ALBERTO GIACOMELLO

The main purpose of the course is to transfer to the students the basic knowledge concerning the multidisciplinary topics that found the atomistic simulations. The course is focussed on the main aspects of the classical models and the principal quantum models. Numerical laboratories and exercises will help the students to develop the needed technical skills.

Expected learning outcomes:

Knowledge and understanding (Dublin descriptor I)
At the end of the course the student will have the basic knowledge on the main atomistic simulations methods and techniques used to study, from an atomistic point of view, the nano-structures and systems of interest. They will then be able to understand the environment that surrounds it from the point of view of its microscopic and macroscopic structure. He will also be aware of the way the atomistic structure affects the materials properties and its relationship with other scientific disciplines and the need for continuous updating on the state of the art, due to the continuous progress of scientific knowledge and technology.

Applying knowledge and understanding (descriptor II)
At the end of the course of study the student will have developed the ability to understand the inner atomistic nature of some physical and chemical properties and their relations with the macroscopic properties of materials.

Making judgements (descriptor III)
At the end of the course the student will have to possess the tools to critically evaluate the limits of the different techniques and their potentiality.

Communication skills (descriptor IV)
At the end of the course the student must have acquired a good language property, especially with regards to a specific scientific terminology, so as to be able to clearly communicate their knowledge and conclusions to an audience composed from people with (or without) expertise in the field.

Learning skills (descriptor V)
At the end of the course the student must have developed a learning ability that will allow him to study and deepen the chemical aspects related to the field of nanotechnology in an autonomous way.

Knowledge and understanding (Dublin descriptor I)
At the end of the course the student will have the basic knowledge on the main atomistic simulations methods and techniques used to study , from an atomistic point of view, the nano-structures and systems of interest. They will then be able to understand the environment that surrounds it from the point of view of its microscopic and macroscopic structure. He will also be aware of the way the atomistic structure affects the materials properties and its relationship with other scientific disciplines and the need for continuous updating on the state of the art, due to the continuous progress of scientific knowledge and technology.

Applying knowledge and understanding (descriptor II)
At the end of the course of study the student will have developed the ability to understand the inner atomistic nature of some physical and chemical properties and their relation with the macrospoic properties of materials.

Making judgements (descriptor III)
At the end of the course the student will have to possess the tools to critically evaluate the limits of the different techniques and their potentiality.

Communication skills (descriptor IV)
At the end of the course the student must have acquired a good language property, especially with regards to a specific scientific terminology, so as to be able to clearly communicate their knowledge and conclusions to an audience composed from people with (or without) expertise in the field.

Learning skills (descriptor V)
At the end of the course the student must have developed a learning ability that will allow him to study and deepen the chemical aspects related to the field of nanotechnology in an autonomous way.

It is mandatory that the student has attended course "Atomistic Simulations and Molecular Dynamics" 6 CFU and given the exam successfully.
It is mandatory that the student has attended the course "Atomistic Simulations and Molecular Dynamics" (6 CFU) or Principi di meccanica quantistica con elementi di struttura della Materia simulazioni atomistiche (12 CFU) and given the exam successfully.

Module: Atomistic Simulations Laboratory
Fundamentals of scientific computation
Working environments: Linux, MacOsX, Unix
Finite difference operators: usage in Molecular Dynamic and MonteCarlo
Metropolis Montecarlo: practical implementation of a simple simulation code
Molecular Dynamics: practical implementation of a simple simulation code
Molecular dynamics packages: usage for materials in nanoscience
Molecular dynamics packages: usage for studying bio-systems
Semi-empirical quantum approaches
First Principles calculations based on the Density Functional Theory: some case studies and the usage of key parameters and features such as the energy cut-off, k-point sampling in the first Brillouin zone, pseudopotentials, etc..



Module: Micro-Nano Fluidics Simulations Laboratory
Module II: Micro-Fluidics Simulation Laboratory
1 - A UNIX primer: typical work session on a linux-box
1.a - Basic commands for the navigation of the filesystem, management of files and directories, including editing of files
1.b - Fundamental UNIX utilities for manipulating the simulation output: grep and awk
1.c - Execution and control of computational "jobs"

2 - Fluid mechanics at the nanoscale: particle-based simulation of fluids
2.a - Introduction to a Molecular Dynamics Engine for equilibrium and non-equilibrium simulations: LAMMPS
2.b - Preparation of a single and multiphase sample (liquid/solid, liquid/vapor, ...) at different thermodynamic conditions
2.c - Simulations of Couette and Poiseuille flows
2.d - Fluids in contact with rough surfaces: contact angle of a sessile droplet (superhydrophobicity), wetting of a cavity (wetting/recovery)

3 - Fluid mechanics at the microscale: continuum theory and simulations
3.a - Theory of planar, stationary flows
3.b - Equations of continuum fluid mechanics and fundamentals of their numerical solution
3.c - Introduction to a computational fluid dynamics engine: OpenFOAM
3.d - Setup of a numerical simulation
3.e - Lid-driven cavity: simulation and flow visualization
3.f - Poiseuille flow and Navier boundary conditions

Module: Atomistic Simulations Laboratory
material provided by the teacher


Module: Micro-Nano Fluidics Simulations Laboratory
MODULE II MICRO-NANO-FLUIDICS SIMULATIONS LABORATORY: instructor's notes

Module: Atomistic Simulations Laboratory
N/D
Module: Micro-Nano Fluidics Simulations Laboratory
Mark Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford Graduate Texts, 1st Edition

The course consists of five laboratories, primarily conducted in class. Initially, 3–30 hours are dedicated to teaching the principles of numerical computation, postponing, however, the in-depth study of the techniques involved in numerical labs.
The thematic laboratories, which cover the majority of the course (27–30 hours), will focus on topics covered theoretically in the introductory courses. For each of these broad topics, students will be given a laboratory assignment that involves scientific programming, algorithm validation, data production, and critical evaluation of the data produced, with discussion of the physical phenomena represented.

Beside not being formally mandatory, attending the class is strongly recommended due to the intrinsic difficulty of the themes treated.

The examination consists in an oral interview and shall ensure that the following objectives are met: he students are required to giva a talk on the various laboratories proposed and must demonstrate to have acquired the basic knowledge of the atomistic simulation theory and techniques, the ability of writing pieces of scientific codes, to produce scientific data concerning the laboratories and finally to analize in a critical way the data produced.
The evaluation is based on:
verifying of the acquired knowledge (40%) ("Knowledge and understanding" and "Applying knowledge and understanding")
verifying of language property and clarity of presentation (20%) ("Communication skills")
verifying of the ability to apply the acquired knowledge in the field of nanotechnology (40%) ("Learning skills")

1) discuss and specify the actions performed, the instructions introduced and the scientific programming choices employed to complete the codes for the various laboratories and scientific themes afforded in order to obtain the expected results.
2) discuss the scientific data obtained to draw the isotherms of a real gas using the Metropolis Montecarlo scheme, also in the light of the behaviour of an ideal gas in the same thermodynamic conditions.
3) discuss in details all the resuls obtained from the LCAO model of various Si phases in terms of the elastic properties. Illustrate and discuss also the electronic properties obtained.

Module: Atomistic Simulations Laboratory

• 1 h: Introduction to linux operative systems: commands from the terminal2 h: Introduction to scientific calculus: finite differences operators, data, commands with special emphasis on the modern versions of the Fortran language. 1h: Introductory laboratory and simple Fortran programs (input-output, data structures, control etc..)1h: Introduction to Lab 1: real gas isotherms by Metropolis Monte Carlo4h Lab 1 : real gas isotherms by Metropolis Monte Carlo   
  • Books: material provided by the teacher


• 1h:  Introduction to Lab 2.4h: Lab 2 molecular dynamics of a gaseous system: NVE and NVT examples with  the Verlet and the Velocity Verlet algorithms. Radial distribution functions and energy fluctcuations for the specific heath measurements. 
  • Books: material provided by the teacher


• 2h: Introduction to Lab 34h: Realistic potentials: Tersoff potential and calculation of the stability curves for three different solid phases of Si. 
  • Books: material provided by the teacher


• 1h: Introduction to Lab 4:3h: atomistic setup for a membrane and a membrane protein, hydration, equilibration and RMSD analysis. 
  • Books: material provided by the teacher


• 2h: Introduction to Lab 54h: The semi-empirical tight binding model for the electronic structure of materials and nano-structures. The Si case: Hamiltonian matrix, density of states and stability curves.
  • Books: material provided by the teacher

• Module II: Micro-Fluidics Simulation Laboratory1 - A UNIX primer: typical work session on a linux-box1.a - Basic commands for the navigation of the filesystem, management of files and directories, including editing of files1.b - Fundamental UNIX utilities for manipulating the simulation output: grep and awk1.c - Execution and control of computational "jobs"


• 2 - Fluid mechanics at the nanoscale: particle-based simulation of fluids2.a - Introduction to a Molecular Dynamics Engine for equilibrium and non-equilibrium simulations: LAMMPS2.b - Preparation of a single and multiphase sample (liquid/solid, liquid/vapor, ...) at different thermodynamic conditions


• 2.c - Simulations of Couette and Poiseuille flows


• 2.d - Fluids in contact with rough surfaces: contact angle of a sessile droplet (superhydrophobicity), wetting of a cavity (wetting/recovery)


• 3 - Fluid mechanics at the microscale: continuum theory and simulations3.a - Theory of planar, stationary flows3.b - Equations of continuum fluid mechanics and fundamentals of their numerical solution 3.c - Introduction to a computational fluid dynamics engine: OpenFOAM3.d - Setup of a numerical simulation3.e - Lid-driven cavity: simulation and flow visualization


• 3.f - Poiseuille flow and Navier boundary conditions