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For most studies, you don’t want to study a nano-sized droplet of water!
Instead, you would like to study a “piece” of a large region of liquid water.
Why? Because the properties of water (and other molecules) at an
interface are very different from in the bulk
For example, water's surface is acidic. The hydronium ion prefers to sit at
the water surface rather than deep inside the liquid. Whereas H2O
molecules typically form four hydrogen bonds to their neighbours, H3O+ can
only form three. The three hydrogens can bind to other water molecules,
but the oxygen atom, where most of the positive charge resides, can no
longer act as a good 'acceptor' for hydrogen bonds.
For most studies, you don’t want to study a nano-sized droplet of water!
Instead, you would like to study a “piece” of a large region of liquid water.
Why? Because the properties of water (and other molecules) at an
interface are very different from in the bulk
Boundary Conditions
Snapshots (side view) of the
solution–air interface of 1.2 M
aqueous sodium halides and
density profiles (number densities)
of water oxygen atoms and ions
plotted vs. distance from the center
of the slabs in the direction normal
to the interface, normalized by the
bulk water density. From top to
bottom the systems are NaF, NaBr,
and NaI. The colors of the density
profiles correspond to the coloring
of the atoms in the snapshots (blue
for water and green for Na+ in all of
the plots, black for F, orange for Br,
and magenta for I). The
water density is scaled differently
from those of the ions so that it can
be easily displayed on the same
plots. Phys. Chem. Chem. Phys., 2008, 10, 4778 - 4784
Boundary Conditions
But there is a problem: with a finite number of variables all state functions
are analytic (no discontinuities).
You have to do simulations with
increasingly larger systems and
look for where the quantity of
interest begins to diverge.
J. Phys. A: Math. Gen. 35 (2002) 33–42
U
CV
T V
Molecular Dynamics Simulations
2 1
T 1
2 m v
i i
2
3k B N i1
One way to do this is to use the Anderson thermostat. In this method, the
system is coupled to a heat bath that imposes the desired temperature.
The coupling to a heat bath is represented by stochastic impulsive forces
randomly selected particles. These stochastic
that act occasionally on
collisions with the heat bath can be considered as Monte Carlo moves that
transport the system from one constant-energy shell to another.
Between stochastic collisions, the system evolves at constant energy
according to Newtonian mechanics. The stochastic collisions ensure that
all accessible constant-energy shells are visited according to their
Boltzmann weight.
Molecular Dynamics Simulations
We mean that the deviations from equilibrium are linearly related to the
perturbations that remove the system from equilibrium.
For example, consider an aqueous electrolyte solution. At equilibrium,
there is no net flow of charge; the average current <j> is zero.
C(0) A
2
behavior: at short times,
Look at the limiting
while at
long times A(t) is uncorrelated to A(0) , thus
C(t) A(0) A(t) 0 as t
This decay of correlations with increasing time is the “regression of
spontaneous fluctuations” referred to inOnsager’s hypothesis
Onsager’s regression hypothesis
and time correlation functions
By invoking the ergodic hypothesis, we can view the equilibrium average as
a time average, and write T
d A( ) A( t)
1
“sliding window” A(0) A(t) lim
T T
0
Fick’s 1st Law: the diffusive flux goes from regions of high concentration to
regions of low concentration, with a magnitude that is proportional to the
concentration gradient
J D
J is the flux: the amount of substance that will flow
through a small area in a small time interval
D is the diffusion constant
ϕ is the concentration
Fick’s 2nd Law: use the 1st law and mass conservation to get
D 2
t
Solutions to this partial differential equation describe
how concentration gradients relax in terms of a
parameter, the diffusion constant.
Application: (self-) diffusion
P(r,t)
As a result, we have
D P(r,t)
2
t
2
Now, consider R (t) r1 (t) r1 (0)
2
which is the mean squared
displacement of a tagged solute molecule in a time t.
Clearly, R2 (t) dr r 2
P(r,t)
Hence,
P(r,t)
dr r t P(r,t) 6 dr DP(r,t)
d
R2 (t) 2
dr r 2
D 2
dt
Application: (self-) diffusion
d
P(r,t) is normalized for any value of time, giving R 2 (t) 6D
dt
or, R 2 (t) 6Dt
This formula was first derived by Einstein
d d v( ) v( )
2
Hence R 2 (t) r (t) r1 (0)
1
0 0
t
R 2 (t) 2 d v(0) v( )
giving
d
dt 0
Since the left-hand side goes to 6D in the limit of large times, we have
D 1
3 d v(0) v( )
0