Ergodic Behavior and Statistical Ensembles

In this topic you will learn about the Ergodic behavior of atoms where the long time trajectories sample the entire phase-space necessary for thermodynamic ensemble behavior.

Force Field and Molecular Dynamics Methodology

In this topic you will learn about the force field models that describe the inter-atomic forces of attraction and repulsion and intra-atomic forces between collections of atoms forming molecules. These idealized potential functions, such as, Lenard Jones function provide simple pair-potentials used for solving Newton's second law of motion for the computational evolution of atomic trajectories.

Laws of Thermodynamics

In this topic, you will learn four laws of thermodynamics. The laws of thermodynamics define the relationship between the temperature, pressure and volume. The zeroth law defines the equilibrium of temperature, first law defines the relation between hear and work, second law describes the quality of heat and entropy and third law describes that the entropy behavior as we reach absolute zero temperature.


Overview of Molecular Dynamics and Computational Science

In this topic you will learn about the Ergodic behavior of atoms where the long time trajectories sample the entire phase-space necessary for thermodynamic ensemble behavior.

Physical System and Thermodynamics

The study in the computational science is done based on physical systems that describe the thermodynamic systems. The open and close systems, reversible and irreversible systems, and thermodynamic processes describe the properties of the physical systems. Once these physical systems are described in terms of thermodynamic intensive and extensive properties, then you can perform computational molecular dynamics on collection of atoms for discoveries in science.

Statistical Mechanics for Molecular Dynamics

In this topic you will learn about statistical mechanics, a branch of Physics that deals with the ensemble of micro-states. These ensembles of micro-states are connected with the thermodynamics variable, such as, micro canonical ensembles, canonical ensemble, and constant pressure ensemble and grand-canonical ensembles. Using the machinery of statistical mechanical under these ensembles molecular dynamics method can perform computational experiments.


Statistical Thermodynamics for Molecular Dynamics

The statistical thermodynamics connects collection of micro-states for statistical calculation of bulk properties. With collection of small number atoms in a given force field described by a potential function, molecular dynamics method can successfully calculate bulk properties of a matter. You will learn how to use statistical thermodynamics of partition functions for your MD experiments.

Thermodynamic Potentials

In this topic you will learn how thermodynamic variables that drive the thermodynamic processes. For example you will learn about temperature as thermodynamic driver for phase change from solid to liquid.

Thermodynamic Process and Degree of Freedom

In this topic you will learn about thermodynamics processes, such as, isothermal, isochoric, isobaric and adiabatic to define the work done in a thermodynamic cycle. The degree of freedom defines as number of possible dimensions for the motion of particles in a thermodynamic ensemble. The degrees of freedom also define the how we can apply equipartition theorem for the calculation of partition function and calculate bulk thermodynamic properties for the ensemble of atoms.


Thermodynamic Processes

There are four fundamental processes that describe the thermodynamic state of a system. In this topic you will learn change in internal energy U of the systems under isothermal (constant temperature T), isochoric (constant V), isobaric (constant pressure P), and adiabatic (constant heat Q) processes. The processes then define the thermodynamics ensemble to study thermodynamic processes using Molecular Dynamic simulations.