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Basic Background
Basic Background
Model
System
Theory
Real Perform Experiments
Test
Experimental
System Results
Theoretical
Prediction
Length and Time Scales
Heavy Coarse
graining
F=ma
Phase-space Trajectory
Energy
p
r Simulation Time
7
Atomistic MD (Classical)
• Uses Born-Oppenheimer Approximation
• Atoms are assumed in their ground electronic states
Born-Oppenheimer Approximation
𝑚𝑒
Total wavefunction, Ψ(𝐑 𝑖 , 𝐫𝛼 ) = Φ(R i )𝜙(𝐫𝛼 , 𝐑 𝑖 ) as 𝑀
→0
• Macrostate
(NVT), (NPT), (NVE), (µVT)
• Equation of state
Statistical Thermodynamics
• Microstate
{r1(t), r2(t)…ri(t)…rN(t);
v1(t), v2(t)…vi(t)…vN(t)}
Quantum Mechanics
Ψ(𝐑 𝑖 , 𝐫𝛼 ) = Φ(𝐑 𝑖 )𝜙(𝐫𝛼 , 𝐑 𝑖 )
MOLECULAR DYNAMICS (MD) SIMULATIONS
• Ab-initio (AI) Molecular Dynamics: N~500, t~100ps
Both electronic as well as nuclear degrees of freedom
are considered, also involves QM theory
• All-Atom (AA) Molecular Dynamics : N~106, t~1µs
Only nuclear motion is considered, electrons are assumed to be in ground
electronic/vibrational states, only classical/statistical mechanics theories
are applicable
• Coarse-Grained (CG) Molecular Dynamics: N~109, t~1ms
Motion of coarsed-grained beads is considered,
only classical/statistical mechanics theories are
applicable
Pre-Quantum Mechanics:
(i) Newton (1642-1727) introduced law of motion
Second law:-
𝑑𝑝Ԧ 𝑑𝑣Ԧ 𝑑 2 𝑟Ԧ
𝐹Ԧ = =𝑚 = 𝑚 2 = 𝑚𝑎Ԧ
𝑑𝑡 𝑑𝑡 𝑑𝑡
𝑚 2
𝐾= 𝑥ሶ + 𝑦ሶ 2 + 𝑧ሶ 2 ; 𝑉 = 𝑉(𝑥, 𝑦, 𝑧)
2
𝑳𝒂𝒈𝒓𝒂𝒏𝒈𝒊𝒂𝒏: 𝐿(𝑥,ሶ 𝑦,ሶ 𝑧,ሶ 𝑥, 𝑦, 𝑧) = 𝐾(𝑥,ሶ 𝑦,ሶ 𝑧)ሶ − 𝑉(𝑥, 𝑦, 𝑧)
𝑳𝒂𝒈𝒓𝒂𝒏𝒈𝒆 𝑬𝒒𝒖𝒂𝒕𝒊𝒐𝒏 𝒐𝒇 𝒎𝒐𝒕𝒊𝒐𝒏
𝑑 𝜕𝐿 𝜕𝐿
= 𝑎𝑛𝑑 𝑠𝑖𝑚𝑖𝑙𝑎𝑟𝑙𝑦 𝑓𝑜𝑟 𝑦 𝑎𝑛𝑑 𝑧
𝑑𝑡 𝜕𝑥ሶ 𝜕𝑥
(iii) Hamilton (1805-1865):
𝜕𝐻 𝜕𝐻
= 𝑞ሶ 𝑗 𝑎𝑛𝑑 = −𝑝ሶ𝑗
𝜕𝑝𝑗 𝜕𝑞𝑗
𝛙 = 𝐄𝛙
𝐇 Schrodinger Equation (Time independent)
First Law of Thermodynamics
The internal energy (U) of an isolated system is
constant (or conserved).
ADIABATIC/INSULATING WALL
SYSTEM
S
U=Const.
SURROUNDINGS
• The internal energy (U) of a system can be changed either
by doing work on the system or by heating the system
Ӎ + d𝑤
d𝑈𝑆𝑦𝑠 = d𝑞 Ӎ
Supply Do some
Heat Work
Ӎ + d𝑤
d𝑈𝑆𝑦𝑠 = d𝑞 Ӎ
Supply Do some
Heat
SURROUNDINGS
Work
SYSTEM
Ӎ
U+dU
S
d𝑤
dU >0
ADIABATIC WALL
SURROUNDINGS
SYSTEM
S
U
SURROUNDINGS
Ӎ
d𝑞
Diathermal Wall
ADIABATIC WALL SYSTEM
U+dU
S
dU >0
ADIABATIC WALL
When energy is transferred to the When a system does work,
surroundings as heat, the transfer it stimulates orderly motion
stimulates random motion of the
in the surroundings.
atoms in the surroundings.
Transfer of energy from the
surroundings to the system makes
use of random motion (thermal
motion) in the surroundings.
Entropy and Second Law of Thermodynamics
S
Equilibrium (Reversible)
Smax
dS=0
dS>0
time
Spontaneous
(Irreversible)
Δ𝑈 = 𝑞𝑉 Δ𝑈 = 𝑞𝑉
Δ𝐻 = 𝑞𝑃 Δ𝐻 = 𝑞𝑃
Δ𝐹 =? Δ𝐹 = 𝑤max
Δ𝐺 =? Δ𝐺 = 𝑤𝑎𝑑𝑑,max
The Helmholtz and Gibbs energies
Consider a system in thermal equilibrium with its surroundings at a temperature T. When a
change in the system occurs and there is a transfer of energy as heat between the system and
the surroundings, the Clausius inequality
Criteria for spontaneity 𝑑𝑞Ӎ
𝑑𝑆 ≥ 𝑑𝑆 ≥ 0 for an isolated system
(Clausius inequality) 𝑇
𝑑𝑈 𝑑𝐻
𝑑𝑆 − ≥0 𝑑𝑆 − ≥0
𝑇 𝑇
𝑇𝑑𝑆 − 𝑑𝑈 ≥ 0 𝑇𝑑𝑆 − 𝑑𝐻 ≥ 0
𝑇𝑑𝑆 ≥ 𝑑𝑈 𝑇𝑑𝑆 ≥ 𝑑𝐻
Constant internal energy (dU=0) or constant At either constant enthalpy or constant entropy
entropy (dS=0) this inequality becomes
Constant internal energy (dU=0) or constant At either constant enthalpy or constant entropy
entropy (dS=0) this inequality becomes
𝑑𝑆𝑈,𝑉 ≥ 0 𝑑𝑆𝐻,𝑃 ≥ 0
In a system at constant volume and constant The entropy of the system at constant pressure
internal energy (such as an isolated system), must increase if its enthalpy remains constant
the entropy increases in a spontaneous (for there can then be no change in entropy of
change. the surroundings).
𝑑𝑈𝑆,𝑉 ≤ 0 𝑑𝐻𝑆,𝑃 ≤ 0
If the entropy and volume of the system are The enthalpy must decrease if the entropy of
constant, then the internal energy must the system is constant, for then it is essential to
decrease in a spontaneous change. have an increase in entropy of the
i.e. if the entropy of the system is surroundings.
unchanged, then there must be an increase in
entropy of the surroundings, which can be
achieved only if the energy of the system
decreases as energy flows out as heat.
CRITERIA FOR SPONTANEITY
Constant Volume Condition Constant Pressure Condition
𝑑𝑈 − 𝑇𝑑𝑆 ≤ 0 𝑑𝐻 − 𝑇𝑑𝑆 ≤ 0
When the state of the system changes at constant temperature, the two
properties change as follows:
𝑑𝐹 = 𝑑𝑈 − 𝑇𝑑𝑆 𝑑𝐺 = 𝑑𝐻 − 𝑇𝑑𝑆
𝑑𝐹𝑇,𝑉 ≤ 0 𝑑𝐺𝑇,𝑃 ≤ 0
Some remarks on the Helmholtz energy Some remarks on the Gibbs energy
𝑑𝐹𝑇,𝑉 = 0 𝑑𝐺𝑇,𝑃 = 0
𝑑𝐹 = 𝑑𝑤max