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Gas-grain modeling for interstellar chemistry

Project 09

Aix-Marseille University
Master space 2015-2016

Supervise by- Marco MINISSALE P. THEULE

April, 22, 2016

1 |Introduction

2 |Theoretical approach

3 |Experimental approach
3.1 Experimental setup . . . . . . . . . . . . . . . . . . . . . . . . 10
3.2 Temperature-programmed desorption (TPD) . . . . . . . . . 12
3.3 Deposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4 |Experiments
4.1 H2 O ( m
e = 18) experiment . . . . . . . . . . . . .
4.1.1 Experimental data and simulation fitting
4.1.2 Discussion on H2 O . . . . . . . . . . . . .
4.1.3 Conclusion: . . . . . . . . . . . . . . . . .
4.2 CO ( m
e = 28) Experiment . . . . . . . . . . . . .
4.2.1 Experimental data and simulation fitting
4.2.2 Discussion on CO . . . . . . . . . . . . .
4.2.3 Conclusion . . . . . . . . . . . . . . . . .
4.3 CO2 ( m
e = 44) Experiment . . . . . . . . . . . .
4.3.1 Experimental data and simulation fitting
4.3.2 Discussion on CO2 . . . . . . . . . . . . .
4.3.3 Conclusion . . . . . . . . . . . . . . . . .
4.4 Experiment: Mixture of CO2 with H2 O . . . . .
4.4.1 Deposition of mixture and discussion . . .
4.4.2 Result . . . . . . . . . . . . . . . . . . . .









5 |Conclusion


6 |References


7 |Acknowledgment


Objective of this project is:
Discussion on importance of gas grain modeling in astrophysics.
Simulate adsorption and desorption model in multi-layer regime.
Perform temperature programmed desorption (TPD) experiment
in lab.
Extract desorption rate of different species.
Compare the simulation and experimental result and make a
analysis on desorption energy and discuss the physical significance.


The life-cycle of stars, recycles the matter of universe in galaxies (shown

in fig 1). During intermediate life of star, heavy elements creates in the
interior of star, while during death of star these elements scattered in Interstellar medium (ISM). So we can say, ISM is actually matter that exists
in between stars and galaxies. This matter includes gas in ionic, atomic,
molecular phase and dust as well as cosmic rays. All these phases of gases
blends smoothly in the surrounding intergalactic space. This means we
have all phases of gases everywhere. But spectroscopic observations verifies,
this smoothness is not uniformly distributed as we thinks, It depends on
surrounding temperature where matter resides. Alternatively, in all phases,
ISM is tenuous by terrestrial standards. In hot, diffuse regions (near to
developed star) matter is in ionized form. In cool dense regions (where
star is in forming state) matter is in molecular form and forms a molecular

Figure 1: Life-cycle of star, credit: Minissale M. presention(lecture1)

Over the last decades it is clear and proven experimentally and observationally, purely gas phase study cannot explain the variety and richness
of chemistry finds in ISM. Specially in star forming regions, in such a environment gas-grains plays an important role. For example formation of most
abundant molecules hydrogen and water is not clear in gas-phase model
but formation of these species is clear in gas-grain model, In which grain
(dust: graphite, silicate) surface work like a catalyst to perform reaction
more stably.
Star forming region is best environment to form dust and then in such
a cool and dense environment molecules get stuck and froze on the surface
of dust-grains and form ice mantles. This ice is effected by cosmic rays,
ultraviolet photosynthesis and shock waves, these process transfers energy to
mantles consequently different molecules (species, atoms) form on icy grains.

During cloud collapse or due to enough cosmic ray hits and else, when grain
surface get enough temperature then molecules on grains transform their
phase (solid to gas) and these gas phase species we observed in observational
spectroscopy. To evaluating these environment it is necessary to understand
sublimation behavior of every particular species and ice mantles such that
understanding of sublimation behavior is aim of this project.
we studied in our course till today 180 chemical compound found in ISM
and all these evidences comes from observational spectroscopy. Spectroscopy
also points, in ISM dust is only 1 percent and gas 99 percent and experiments
says this 1 percent dust plays a very important role in molecule formation.
we studied H2 O, CO, CO2 and mixture of H2 O CO2 in order to explain
the importance of dust and sublimation behavior of molecules in ISM environment. But before I start about project, I would like to give some key
process and definitions, those are important to understand physics of gasgrain modeling. There are many more processes those takes place to form
molecules but for project purpose solid-gas interaction and surface physics
processes are important, These processes are following:
Before I discuss these processes in brief, I would like to mention temperature
and density places an important role to explain these processes. Temperature control the residence time of species on surface. If surface is hot they
bounce and if surface is cool they stick for long time. Density controls the
probability of interaction, thus more dense cloud means more probability of
sticking molecules.
1. Adsorption: In this process gas phase particle stuck on grain surface and transform their phase gas to solid. There are two kind of
adsorption, physical adsorption and chemical adsorption. For physics
purpose, we will totally focus on physisorption (physical adsorption).
In physisorption we talk about inter-molecular forces, these intermolecular forces comes due to potential difference that arises due to
structure of molecules. There are two kinds of potential one is due
to Van der waals interaction force other is due to Pauli repulsive potential. Combined forces is defined by Lennard-Jones potential.
Fig(2) explains the adsorption process and Fig(3) explains the limit of

Figure 2: Adsorption and desorption on grain surface, Credit:Philip Hofmann

Figure 3: physisorption, credit: Minissale M. presentation(lecture 1)

2. Desorption: When the temperature of grain surface exceeds the sublimation temperature of stuck species then they transform solid to gas.
Alternatively, I could say, due to thermal changes, when molecules gets
sufficient energy to cross the activation barrier (create due to potential
difference) of desorption they leads to gases phase. Fig(2) shows a hint
of desorption.
3. Sticking: It is the most important factor that helps in forming molecules

on grain surface. It is calculated by sticking coefficient.

[sticking coef f icient] =

[molecules adsorb]
[molecules spread on surf ace]

sticking depend on mass of specie, kinetic energy of specie, structure

of specie, surface temperature and surface coverage. Molecules that I
used in my experiment has sticking coefficient nearly equal to 1. [Ref:
Bishop et al. 2006]
4. Diffusion: In this process atoms and molecules comes to the surface
and diffuse (sit or stick) on surface vacancies more than the usual
residence time, then wait until perfect pair of specie comes. once the
perfect pair comes they both get react and form a new molecule. I
will not discuss this process further but just mentioning because most
abundant hydrogen molecule form by this way.
There are two kinds of reaction that can take place after species adsorb
on the surface to form another molecule:
Exothermic reaction: When system release (transfer) energy to surrounding in form of heat after reaction.
Endothermic reaction: When system absorbs energy from surrounding
after reaction to make molecule stable.Endothermic reactions cannot
possible in ISM because of low temperature.
When any reaction take place that has to follow specific pattern shown
in fig(4).

Figure 4: A potential energy profile of exothermic reaction. The height of

the barrier between reactant and product is the activation energy of reaction.
image credit: P.Theule (lecture notes)

Above figure shows, whichever is the reaction, to form a product it has

to cross the activation barrier. To cross this activation barrier either we
increase the temperature of surface or we introduce the catalyst. Increasing
temperature is not possible all the time but in presence of catalyst by giving
the small amount of energy, reactant can cross the the activation barrier
and product forms. This exact process that I talked in second paragraph
of introduction i.e. grain behave like catalyst by little heat from cosmic ray
or else, they form new molecules. All this discussion shows the importance
of gas-grain modeling in ISM physics. All above points are very basic and
important point to understand the gas-grain modeling.

|Theoretical approach

In second section of the project our goal was to develop the standard simulation for absorption and desorption rate for specific desorption energies
(taken from literature). For this purpose we used Polanyi-Wigner Equation:
Rdes =

= N n exp(


= Heating ramp rate (Kelvin/min)
T = Temperature of surface (Kelvin)
Edes = Desorption energy (Kelvin)
n = Order of desorption (for multilayer its zero). There are three order
of desorption: mono-layer (n = 1), sub-mono-layer (n = 2) and multilayer(n = 0)
N = Number of molecules per square cm
A = Frequency factor or normalization constant. Its unit depend on order
of desorption. But we can write base unit as molecules1n cm2+2n sec1 .
2 1 ), In experiment it is desorpdt = Rate of desorption (molecules cm K
tion signal.

Figure 5: simulation sample of adsorption and desorption for different ramp


Figure clearly explains the behavior of adsorption and desorption, initially when molecules adsorb on surface and surface temperature is not high
enough to desorb them, we see full coverage in graph, as temperature increases desorption takes place and coverage start falling at the same point
desorption peaks start rising. Figure 5 is simple model created by using
python code from equation (1), code is described below


import numpy a s np
import m a t p l o t l i b . p y p l o t a s p l t
import s c i p y a s sp
from s c i p y . i n t e g r a t e import o d e i n t

we a r e making s i m u l a t i o n f o r :
r a t e = (A/B) (N^n ) exp (E/kT)
dt f o r H2O
TPD s p e c t r a from a s e r i e s o f ( a ) z e r o t h o r d e r (A= 10^30
cm2 s 1 )
A i s i n s e c ^1
B = b e t a = ramp r a t e = K/min
N = no . o f m o l e c u l e s / s q u r e cm
n = order of desorption
Eads = a d s o r p t i o n enegy i n K
K = boltzmann c o n t a n t

A = 10.013
B = 10
C = [ 2 , 5 , 1 0 , 2 0 , 5 0 , 1 0 0 ] # no . o f mo no lay er s i n m u l t i l a y e r s
n = 0.0 # for zeroth order ( multilayer )
E = 5900.
#d e s o r p t i o n e n e r g y
k = 8 . 6 1 6 10( 5)
T1 = 2 0 . 0


T2 = 3 0 0 . 0



f u n c t i o n s t o c a l u c u l a t e P ol an yi Wigner Equation f o r d i f f e r e n t


d e f e q u a t i o n ( t h i t a , T) : # f u n c t i o n f o r b e t a 10
n0 = t h i t a [ 0 ]
r = ((A 6 0 . ) / 1 0 . ) ( n0 ) np . exp(E/ (T) )
return r
T = np . l i n s p a c e ( T1 , T2 , 1 0 0 0 )
ec = 1.0
s 1 = o d e i n t ( e q u a t i o n , ec , T) #c a l c u l a t i n g c o v e r a g e
T3 = ( T2 T1 ) / 1 0 0 0 .
s 2 = np . z e r o s ( l e n ( s 1 ) )
f o r i i n r a n g e ( l e n ( s 1 ) 1) :
s 2 [ i ] = ( s 1 [ i +1] s 1 [ i ] ) / T3 # c a l c u l a t i o n f o r d e s o r p t i o n


d e f e2 ( t h i t a , T) : # f u n c t i o n f o r b e t a 6
n0 = t h i t a [ 0 ]
r 2 = ((A 6 0 . ) / 6 . ) n0 np . exp(E/ (T) )
return r2
T = np . l i n s p a c e ( T1 , T2 , 1 0 0 0 )
ec = 1.0
s 1 2 = o d e i n t ( e2 , ec , T)
T3 = ( T2 T1 ) / 1 0 0 0 .
s 2 2 = np . z e r o s ( l e n ( s 1 2 ) )
f o r i i n r a n g e ( l e n ( s 1 2 ) 1) :
s 2 2 [ i ] = ( s 1 2 [ i +1] s 1 2 [ i ] ) / T3


d e f e3 ( t h i t a , T) : # f u n c t i o n f o r b e t a 4
n0 = t h i t a [ 0 ]
r 3 = ((A 6 0 . ) / 4 . ) n0 np . exp(E/ (T) )
return r3
T = np . l i n s p a c e ( T1 , T2 , 1 0 0 0 )
ec = 1.0
s 1 3 = o d e i n t ( e3 , ec , T)
T3 = ( T2 T1 ) / 1 0 0 0 .
s 2 3 = np . z e r o s ( l e n ( s 1 3 ) )
f o r i i n r a n g e ( l e n ( s 1 3 ) 1) :
s 2 3 [ i ] = ( s 1 3 [ i +1] s 1 3 [ i ] ) / T3



. p l o t (T, s1 , . )
. xlim ( T1 , T2 )
. p l o t (T, s2 , c o l o r= b l a c k )
. p l o t (T, s22 , c o l o r = r e d )
. p l o t (T, s23 , c o l o r = g r e e n )



p l t . x l a b e l ( Temperature (K) > )

p l t . y l a b e l ( H2O d e s o r p t i o n r a t e ( m o l e c u l e s cm^2 K^1) > )
p l t . l e g e n d ( ( Coverage , b e t a 10 K/m , b e t a 6 K/m , b e t a 4 K/
m ) , l o c =0)
p l t . t i t l e ( s i m u l a t i o n sample )
p l t . g r i d ( True )
p l t . s a v e f i g ( s i m u l a t i o n _ s a m p l e . png , format= png )
p l t . show ( )


|Experimental approach
Experimental setup

Instrument consist of stainless steal ultra-high-vacuum (UHV) chamber that

operates on 9.3 109 mbar pressure and cooled by helium till 4K, this provides very similar conditions those found in ISM [Ref: Helen J. Fraser et al.
2001]. The chamber equipped with two instrument, effusive gas disposition
system, a quadrupole mass spectrometer (QMS) and a mid infrared spectrometer (MIR) (cooled by liquid nitrogen), Fig(6) shows the experimental
setup used in experiment.


Figure 6: Experimental septup

QMS is used for temperature-programmed desorption (TPD) experiment

(I will discuss about this in next subsection). Mid infra-red (MIR) spectrometer for monitoring the film of icy species on sample. We used copper sample
coated by gold film, capable to reach 10K (approx) and free to rotate on 360
degrees. TPD over this sample (when covered by species ice) is controlled
by positive feedback loop from the Lakeshore instrument (see in fig(7)),
this instrument control the temperature of sample during TPD and capable
to work under 10K to 340K.


Figure 7: Lakeshore instrument, Image credit: Lake Shore Cryotronics, Inc.


Temperature-programmed desorption (TPD)

Adsorbed molecules bound to surface in potential well of depth Edes , Probability that molecule will desorb at any one temperature, to produce an
equilibrium vapor pressure, is governed by Boltzmann statistics. Once the
desorption starts, QMS handles the TPD. QMS principle: It consists
of four parallel metal rods. Each opposing rod pair is connected together
electrically, and a radio frequency (RF) voltage with a DC offset voltage
is applied between one pair of rods and the other. Ions travel down the
quadrupole between the rods. Only ions of a certain mass-to-charge ratio
will reach the detector for a given ratio of voltages: other ions have unstable trajectories and will collide with the rods. This permits selection of
an ion with a particular m/e that allows the operator to scan for a range
of m/e-values by continuously varying the applied voltage (see in fig 8b).
During TPD formation, a linear temperature ramp is applied on sample by
lakeshore. when sample get heated, species start transforming there phase
from solid to gas and Mass spectrometer (QMS) measured the amount of
adsorbate that desorbs as a function of temperature.


(a) schematic diagram of TPD mechanism

image credit:Trustees of Wellesley College

(b) schematic diagram of QMS mechanism

Figure 8: QMS working principle and TPD extraction internal view

TPD can give us certain information:
Heat of adsorption (if adsorption and desorption are reversible nondissociative processes). Alternatively, temperature range of adsorption
in which molecules could remain on surface.
coverage information.
Energy information.
Kinetic information about desorption process.



In this section I will try to explain the whole procedure that we followed
in order to obtain TPD of species : Before taking any step towards experiment, we need to note down pressure in sample chamber, if it is above 10 7
mbar, we can not proceed for experiment. For doing experiment we follow
following steps:
STEP-1: In specimen chamber, first we take fixed amount of particular
molecules. The amount taken in experiment is measured by pressure difference in specimen chamber. In all experiments we have taken only 10mbar
STEP-2:Spray these molecules on copper sample.
STEP-3:Turn our sample toward MIR spectrometer for taking spectrum in
order to verify species on sample.
STEP-4:Turn sample towards QMS to start TPD.
STEP-5:Start QMS software by giving mass no. of species (taken for experiment).
STEP-6:Set temperature in lakeshore (according to particular sample), then
we wait to obtain TPD by QMS.
In experiments we fixed the amount of molecules in each case but we obtain
TPD for two different cases:
For different exposure at fixed ramp rate(). for example we spray
molecules on sample for 20 sec at 10 K/min ramp, then in next experiment we sprayed molecules for 25 sec at same ramp and so on.
For different ramp rate but at fix exposure of molecules. For example
we sprayed molecules for 20 sec for 10 K/min ramp. Then in next
experiment we sprayed molecules again for 20 sec for 6 K/min ramp
and so on.
These are the two conditions that we followed for pure molecules H2 O, CO2
and CO, to analyze the changes in TPD and how these changes effect the
kinetics of desorption and adsorption.
For Mixture of H2 O CO2 we repeat the experiment for different ratio
of mixture (1:10 and 1:1) on fix ramp rate but In this case spraying time
depend on pressure in specimen chamber (In order to not to break QMS).
Mixture preparation: We followed few steps: We have two tube in
specimen chamber both are connected and separated by valves. First we
will pump-out all tubes (evacuation of all gasses, those are already available
in tubes). Second: we open valve of tube one and fill gas1 for certain pressure
then close the valve. Next step is to open valve of another tube and fill gas2
according to the ratio which we want for our experiment. After filling gases

in both tube, we will close all other valves and open the valve of both tubes
(to connect tubes) in order to mix gases. We left gases to mix for some
seconds or for a minute then mixture is ready to use in experiment.



H2 O ( me = 18) experiment

We repeated H2 O experiment four time, three time for different exposure

time by fixing ramp rate. Two time for different ramp-rate for fix exposure
time. We have taken 10mbar amount of molecules in each case. Deposition
start at 80K and desorption was started at 140K and finished before 200K.
For analysis, I used Simple matplotlib library, numpy and scipy modules in python programming
For energy calculation direct conversion of equation(1)
For area calculation, I use simple trapezoidal rule.
For uncertainty in measurement, I used statistical error analysis function for large dataset (normal distribution):
The average of all data values

i=0 Ri

Ravg =

where R is desorption signal and N is the total no. of observed points.

Uncertainty in a single measurement of R is given by equation (2):


Error = x = =

Ravg )2

i=0 (Ri


For calculating average time in which process occur and residence time
of surface ( ), I followed following equation:




equation 2 gives Average time in which process occur.
K = A exp(

= o exp(



where o is A1 . Equation 3 gives the residence time of surface. Every

coefficient has there usual meaning.
[Ref:http : // aces/scc/scat26 .htm]
Number of mono-layers I have calculated by langmuir (L). I use following equation [Ref:wikkipedia]:
layers =

P ressure time

Where pressure is in torr. (1bar = 750.062 torr)

1L = 106 torr sec



Results are shown below:

Figure 9: Result of H2O experiment: Energy is in Kelvin, pre-exponential

factor (A) is in sec1 ,Area is in cm2 , unit of x-peak and y-peak is same as
temperature and desorption signal respectively.

Experimental data and simulation fitting

Figure:10,11,12,13 shows the best fitted experimental data by simulation

for energies 535561.53K, 540055.7K, 545549.34K and 542059.00K respectively with pre-exponential factor (frequency-factor) shown in table-1

Figure 10: Fitting plot of H2 O for 20sec exposure and beta 10K/min; unit
of Y-axis is molecules cm2 K 1


Figure 11: Fitting plot of H2 O for 25sec exposure and beta 10K/min; unit
of Y-axis is molecules cm2 K 1

Figure 12: Fitting plot of H2 O for 30sec exposure and beta 10K/min; unit
of Y-axis is molecules cm2 K 1


Figure 13: Fitting plot of H2 O for 30sec exposure and beta 6K/min ; unit
of Y-axis is molecules cm2 K 1

Conclusion: On the basis of this I concluded H2 O has desorption energy (E) 5407.5 56.7 kelvin with pre-exponential factor (A) 10121 sec1 .
Desorption peaks are in between 177K to 182K, these result are nearly same
as available in literature [Ref: J.A. Noble et al.].

Discussion on H2 O

We deposited H2 O molecules on sample at 80K for each TPD extraction.

Fig:14 shows the change in the intensity of desorption signal as the sample
get heated. Plot clearly shows the rising edge of TPD coincide and peak
temperature increases with the exposure time. This signifies intensity (area
under curve) increases as more and more material condensed on sample but
in every case desorption take place on same temperature. The shift in peak
temperatures occur due to desorption rate(eq:1) increases exponentially with
temperature, rate increases until all the layers get sublimate then it drop
down rapidly. A simple comment I would like to make on multi-layer and
mono-layer regime is: monolayer is much more tightly bound from the surface than the multilayer, consequently we may find desorption peak of monolayer TPD at higher temperature than the multilayer regime ***********.
I would also point, I tried to de-convolve monolayer from multilayer TPD
(by integrating area under peak and comparing area covered at each small
temperature deference) but I couldnt successful. so I will say multilayer
desorption process is independent of number of molecules that covered the
sample. However, If we look on above subsection figures, multilayer simulation provides a good estimated fit to data (this simulation doesnt contain
contain the no. of molecules) so its verified we worked in multilayer regime

and its independent of coverage.

Peak desorption signal for any curve is in between 177K to 182K, which
co-relate our experiment with published result and verifies or experiment.
Below fig shows the amount of area covered in each exp. and there peak

Figure 14: Experiment of H2 O for 20, 25, 30sec exposure and beta 10K/min;
unit of Y-axis is molecules cm2 K 1

Figure(15) shows, the there is slight shoulder observed at leading edges

of each TPD around 154K. This is due to phase transition of H2 O from
amorphous to crystalline. With this we can conclude, TPD peak of amorphous ice will occur at low temperature, this is due to vapor pressure in
amorphous ice is 3-time grater than the crystalline ice. Although, crystalline ice peaks dominates the TPD because amorphous phase transition
is for very little time always in such conditions. With this we can conclude
amorphous water is hard to find in such conditions, its so quickly transform
in crystalline phase.


Figure 15: Amorphous water desorption peak at 154K; unit of Y-axis is

molecules cm2 K 1

Fig16 shows the condition of different ramp rate () for fix exposure time.
In this we seen desorption leading edges totally overlap therefore desorption
take place at same time for different ramp, but Area covered by beta 6 is
much lesser than the area covered by beta 10, peak intensity also shifted by
the difference of 4. Difference in area under curve is due to some mistake
in experiment (for beta 10 we have taken farady integration and for beta 6
we have taken sel configuration) otherwise as we seen in simulation sample
whatever is the beta area covered by curves will be same always. Intensity
peak shifted towards the left is natural when we slow the ramp rate. This
signifies that when we have high ramp (means high temperature) therefore
time spent on each kelvin will be more thus high signal and vice-versa .


Figure 16: H2 O experiment for 30sec exposure and beta 10K/min and

In case of H2 O (mass 18), we can see one more interesting feature during
TPD formation, Some time we find isotope of H2 O (mass 17). This is due
to diffuse discharge electrons from electronics some time ionize the H2 O
(mass 18) molecule and form H2 O+ (mass 17) but probability of happening
this phenomenon is very less. Below figure(17) shows the condition of this
stage. In figure we could clearly see mass-17 has very less signal (due to
less probability) but desorption take place at same temperature, desorption
peaks also coincide. simulation fits the mass-17 for energy 5520100K with
frequency factor 10121 sec1 .


Figure 17: mass17 and mass18 H2 O comparison; unit of Y-axis is

molecules cm2 K 1



we studied desorption energy and behavior of crystalline and amorphous

H2 O under the conditions same as observed in denser region of interstellar
clouds. The result implies: In dense ISM, H2 O desorption occur at high temperature (182K) with desorption energy 5407.557.7 K and frequency factor
10121 sec1 . These types of results observed in hot-cores, which are very
dense clumps of gas and remnants of a collapsing cloud that form the massive star. We know from observation in such conditions trapped radiation
and pressure heats the core at 100K to 300K, such that water ice evaporate
and we trace that in observed spectra with other tracers (molecules) [Ref:
Millar 1993]. Our experimental data shows the same conditions as observation. But point to be noted here is, TPD temperature peak may not similar
to the observation because of the chemistry (mixture of molecules) find in
ISM (we worked for pure H2O ice) but initial and final range of desorption
temperature will be same or in between.
we followed same procedure, same equations for calculations in
each set of experiment as in H2 O.


CO ( me = 28) Experiment

We performed CO experiment four times, three time for different exposure

time (10s, 15, 20s) at same ramp rate (10K/min) then twice for different
different ramp (10 and 6K/min) by keeping exposure time fix at 20sec. We
started deposition at 20K and desorption started at 25K and finished at

45K. (we set set-point between 20 to 80K for CO).

We obtained following results:

Figure 18: Result of CO experiment: Energy is in Kelvin, pre-exponential

factor (A) is in sec1 ,Area is in cm2 . Unit of x-peak and y-peak is same
as temperature and desorption signal respectively. * shows there was some
connection problem in pressure measurement equipment, so we could not
get appropriate readings, that is why I estimated there is error in layer


Experimental data and simulation fitting

Fig: 19,20,21,22 shows best fitted experimental data by simulation for the
energies 93039K, 106052.61K, 94539.11K and 106030K respectively
with pre-exponential factor (A) shown in fig 18. I tried but, in some cases,
I was unable to fit onset position.

Figure 19: Fitting plot of CO for 10sec exposure and beta 10K/min; y-axis:
CO desorption signal molecules cm2 K 1 , x-axis: temperature


Figure 20: Fitting plot of CO for 15sec exposure and beta 10K/min; y-axis:
CO desorption signal, x-axis: temperature

Figure 21: Fitting plot of CO for 20sec exposure and beta 10K/min; y-axis:
CO desorption signal molecules cm2 K 1 , x-axis: temperature


Figure 22: Fitting plot of CO for 15sec exposure and beta 6K/min;y-axis:
CO desorption signal molecules cm2 K 1 , x-axis: temperature

NOTE: I missed my y-axis title due to zoom in matplot.


Discussion on CO

Figure:23 shows the TPD formation of CO for different exposure on fix ramp.
we could clearly see as we increase exposure time, all leading edges concide
and peak temperature of TPD increases, this increment in peak signifies as
we deposit (condensed) more material on sample, intensity increases just
because more material more desorption signal.
The shift in peak temperatures occur due to desorption rate(eq:1) increases
exponentially with temperature, rate increases until all the layers get sublimate then it does not drop down rapidly, since in CO since energy is not as
high enough as in H2 O desorption, that is why we have smooth curves both
Area covered by TPD increases as be condensed more molecules (increased
There is second peak (right side) in each TPD but more clearly visible in
20sec TPD. This peak has no significance, Its just the disambiguation of
QMS, as I mentioned (sec-3.2) QMS work on mass no. so when it found
molecules of similar mass like CO, which has mass no. equal to nitrogen N2 ,
it disambiguate and showed us two peaks since CO simulation fits the first
peak we could say first peak is due to CO. But there can be another reason,
this N2 signal comes from any outside layer or leakage in chamber.
We found peak desorption signal in each TPD signal is in between 32K
to 37K, which co-relate the results with literature and verify our experiment.[Ref: J.A. Noble et al.]

Figure 23: CO experiment for 10, 15, 20sec exposure and beta 10K/min;
y-axis: CO desorption signal molecules cm2 K 1 , x-axis: temperature

Below fig shows the condition of different ramp rate (10 and 6K/min)
with fix exposure (15sec). We could see desorption of leading edges overlaps
therefore desorption take place at same time, Area covered by both peaks
is nearly equal of difference 0.04 106 . This result verifies the simulation
(Fig:5). Again I would mention this little difference is due to non precise
measurement in exposure time while spraying molecules otherwise TPD has
to cover same area. We can verify our mistake by looking on no. of layers
in these two experiments (see in figure 18). Shift in the peak occur due
to slowdown in ramp, signifies the same reason as I mentioned in H2O (its


Figure 24: CO experiment for 15sec exposure and beta 10K/min and



On the basis of this I conclude CO has desorption energy (E) 98736K with
frequency factor 10121 sec1 . Desorption arises in between 32K to 37K,
this environment typically observed around young stars.


CO2 ( me = 44) Experiment

As usual we performed CO2 experiment four time, thrice for different exposure (15s, 20s, 25s) by keeping fix ramp rate at 10K/min and then two times
for different ramp rate (10 and 6K/min) on fixed exposure time. We started
deposition of molecules at 50K and desorption start at 85K and finished
at 102K. The peak of TPD is in between 95 to 100K which is very similar
that we finds in available literature. In this experiment we fixed set points
in between 50 to 130K. We obtained certain results:

Figure 25: Result of CO2 experiment: Energy is in Kelvin, pre-exponential

factor (A) is in sec1 ,Area is in cm2 . Unit of x-peak and y-peak is same as
temperature and desorption signal respectively.



Experimental data and simulation fitting

Figure: 26,27,28,29 shows the best fitted data by modeled simulation for
desorption energy 2550250K, 2450250K, 248030K and 2500165K respectively. Pre-exponent factor is shown in figure 25.

Figure 26: Fitting plot of CO2 for 15sec exposure and beta 10K/min; unit
of Y-axis is molecules cm2 K 1

Figure 27: Fitting plot of CO2 for 20sec exposure and beta 10K/min; unit
of Y-axis is molecules cm2 K 1


Figure 28: Fitting plot of CO2 for 25sec exposure and beta 10K/min; unit
of Y-axis is molecules cm2 K 1

Figure 29: Fitting plot of CO2 for 20sec exposure and beta 6K/min; unit of
Y-axis is molecules cm2 K 1


Discussion on CO2

Fig: 30 shows the TPD formation of CO2 observed in same conditions as

in ISM. Experiment has done for three different exposure (15s,20s,25s)on
fix ramp of 10K/min. I will first point-out there is some mistake in 25sec
TPD experiment, we may have done huge mistake in calculating the time
during spraying molecules. We were running out of time so we couldnt

repeat this experiment. But still I can try to concluded, as happened in

other cases here also leading edges coincide and peak intensity increases as
we condensed more material on sample, significance of same natural reason
as discussed in above two experiment.
we can see in figure area covered by TPD increases as we increase the exposure.
Peak desorption signal occurs in between 96K to 99K which co-relate or
result with standard published result [Ref: J.A. Noble et al.].

Figure 30: CO2 experiment for 15, 20, 25sec exposure and beta 10K/min;
unit of Y-axis is molecules cm2 K 1 ; x-axis is in Kelvin

Below fig:31 express the condition of different ramp rate 10K/min and
6K/min at fix exposure time of 20sec. I dont have idea why every time
area differ with different ramp, according to model it should not differ only
peaks has to shift. figure clearly points, desorption takes place at same time
at same temperature for different ramp.


Figure 31: CO2 experiment for 20sec exposure and beta 10K/min and



Since CO2 is the second most abundant molecule mixed in interstellar ices
according to spitzer observations(Oberg et al. 2011). Therefore it is important to understand the sublimation behavior of pure CO2 . I concluded,
the desorption energy that governed the CO experiment is 249550K with
pre exponential factor of order 10121 sec1 . For experiment taken by us
desorption peaks arises in between 95K to 99K which verifies the accuracy
of experiment from available literature.


Experiment: Mixture of CO2 with H2 O

As I discussed earlier in introduction section, In pre-stellar cores, cold outer

proto-stellar envelop and proto-planetary disks, most molecules frozen out
on dust grains, forming ice mantles. The main component of young stellar
objects is H2 O with the mixture of CO and CO2 according to spitzer observations(Oberg et al. 2011). Near Infra-red (NIR) observation shows the
evidence of it [Ref: Oberg et al. (2001), Knez et al. (2005)]. Therefore it is
important to understand mixture desorption.


Deposition of mixture and discussion

Figure:32 shows the experiment of mixture in two different conditions.


1. When we mixed CO2 with H2 O for 1:1 respectively. The amount of

molecules taken in experiment is 10mb. Exposure time is 25sec with
ramp rate 10K/min.
2. When we mixed CO2 with H2 O for 1:10 respectively. The amount
that we have taken is approx 25mb. Exposure time is 10sec with ramp
10K/min. we reduced exposure, In order to not to destroy QMS,
because after mixing for ratio 1:10 pressure in specimen chamber was
Preparation of mixture is discussed in section 3.3 . In both of the cases we
deposited mixture on sample at 80K. we run our TPD for 80K to 200K.
Experiment shows mixture of CO2 with H2 O dose not behave as pure
CO2 and H2 O. This is due to interaction behavior of CO2 with H2 O, this behavior differ the binding energies of mixture molecules consequently we see
different results then pure molecule TPD. CO2 known as volatile molecule,
due to its volatile nature its traps in H2 O and desorbs twice in single experiment. Trapping fraction depend on the ratio of mixture. If volatile molecule
fraction increases with H2 O tapped fraction decreases. Theoretical model
that defines such behavior is three phase model. In this model, gas-grain
interactions are addressed by considering three phases: the gas phase, the
surface of the ice and the bulk/mantle of the ice. (this model is bit hard
to explain systematically but this will my future work), still I would like to
point diffusion plays a key role in this condition. This diffusion focused on
two important conditions: the energy barrier that volatile molecule has to
overcome to swap the neighboring molecule and fraction of mantle molecules
close enough to participate in swapping surface molecules. [Ref: Edith C.
Fayolle at al.(2011)]


(a) CO2 - H2 O mixture of (1:1)

(b) CO2 - H2 O mixture of (1:10)

Figure 32: Mixture desorption experiment; x-axis is in kelvin; Y-axis is in

molecules cm2 K 1
In the cases of mixture we observed CO2 desorbs twice or more than
twice. As we could see in the ratio of 1:1 mixture, CO2 has more than two
peaks, the first peak that arise nearly 90K is due to pure CO2 nature and
other rest peaks are due to trapping behavior. In mixture 1:10 (CO2 and
H2 O resp.) we seen CO2 desorption twice, both peaks shows the behavior
of CO2 and H2 O chemistry.
We usually discuss on two peaks because 1:1 ratio is not that much
recommended in ISM (nearly we can not find such condition). First desorption peak of CO2 is called molecular volcano: Molecules those are not
trapped deeply in surface easily diffused in ice mental and desorbs so we de34

tect them. There is another strong reason, when H2 O transform amorphous

to crystalline phase there is sudden leakage CO2 from upper layers and we
observed this peak. That is why, it is named as molecular volcano. Second
peak of CO2 is due to co-desorption: This is due to trapping of CO2 in the
deep layers of H2 O. This signifies mixing can change sublimation temperature of molecules or this is due to, diffusion quickly slowdown as the surface
layers saturate with H2 O molecules or alternatively all accessible pores have
been emptied with which CO2 were diffusing and sublimating.


When we have ratio of mixture 1:1, we seen first desorption peak of

CO2 is at 93.11K. this is nearly the case of pure CO2 therefore its
shows the independence from coverage (thickness of layers) such that
we can conclude from the top layer of mixture CO2 desorbs at same
desorption temperature of pure CO2 .
H2 O peak is at 172 K which is in the range of pure H2 O desorption
range. CO2 second peak is at 149.83K. Therefore this second peak
shows the huge difference (by 50K) in the sublimation temperature of
CO2 in desorption process.
At the end I can point, for the mixture of equal ratio fist peak of CO2
and water peak behaves same as pure molecules. But CO2 second peak
shows the behavior of trapping and points on change in sublimation
temperature due to mixing.
When we have ratio of mixture 1:10 (CO2 and H2 O resp.). This experiment clearly shows the behavior of trapping and sublimation temperature of CO2 in mixture increased with huge factor, first peak observed
at 154.5K. This shows the clear dependency of desorption temperature on ratio of mixture. This implies, as the water start desorbing,
surface layers start saturating with H2 O molecules, consequently diffusion quickly slowdown or alternatively all accessible pores have been
emptied with which CO2 were diffusing and sublimating.
Its is also amazing to see second peak of CO2 coincide with H2 O,
both peak observed at 177.6K. This is due CO2 is less mobile in H2 O
Therefore, CO2 that has to sublimate before water spent more time
on each kelvin such that defines the science of trapping.
In the ratio of 1:1, area covered by CO2 : curve1 is 1.077109 curve2
is 6.1 1010 . Area covered in H2 O curve is 1.2 108 .
In the ratio of 1:10, area covered by CO2 : curve1 is 1.5471010 curve2
is 2.26 1010 . Area covered in H2 O curve is 1.2 108 . we seen with
this result area covered by both CO2 curves is same. This may signifies

that CO2 molecules that traps in deep layer of H2 O is same as in above

layers (less abundence but equal distribution of CO2 with H2 O).
For ration 1:1 mixture experiment sample was covered by 25 monolayers and in 1:10 mixture experiment sample was covered by 38


These experiment was aimed to extract the two important parameter desorption energy (Edes ) and pre-exponential factor A (frequency factor) from
each set of experiment. For pure molecule experiment, results are given

Figure 33: Energy is in Kelvin, pre-exponential factor (A) is in molecules

cm2 sec1 , Temperature is in Kelvin, residence time is in years.

While fitting simulation I found A and E both are co-related, so just for
curiosity I tried to find the co-relation between them, I found co-relation
coefficient 0.422.
These A and E parameters are so important for modeling interstellar environment specially in calculating the residence time of particular specie on
grains. I have calculated the residence time of H2 O, CO and CO2 at there
peak desorption temperature for the typical lifetime of inter-stellar cloud
107 years [Ref: Wikipedia inter-stellar clouds], results are shown in figure 33.
Results implies, at the peak desorption temperature of molecules, there residence time is huge. This means they take very long time to desorb but we
can see them because of there large number density. Due to huge residence
time, species have sufficient time to grown-up and perform reaction to form
new molecules in ice mantles on grain surface.
Future work: I would like to work more on Three-phase model and residence time co-relation in cloud collapse conditions.



[1] Thermal desorption of water ice in interstellar medium, (Helen J. Fraser

et al. 2001)
[2] Desorption of CO and O2 interstellar ice analogs (K. Acharya et al. 2014)
[3] J. A. Noble et al. 2011, Thermal desorption characteristic of CO, O2 and
CO2 on non porous water, crystalline water and silicate surface at submonolayer and multi coverage, Pg. no. 5 (reference for energies )
[4] Edith C. Fayolle et al. 2001, Laboratory H2 O:CO2 ice desorption: entrapment and its parameterization with an extended three-phase model "H2 O
CO2 ice desorption data, and three phase model"
[5] Astro-chemistry lecture notes by P. Theule.
[6] Marco Minissale master thesis
[7] https : //
[8] http : // aces/scc/scat26 .htm
[9] "error-analysis" lab manual of university of pennsylvania, Pg. no. 6
[10] Oberg et al. 2011



I am very thankful to my supervisor Marco Minissale and Co-supervisor P.

Theule for there consistent availability and fruitful discussion on my every
mode of difficulty. I am thankful to my colleague Ny kieu for helping in
doing experiment. Thanks for my mind, it was functioning properly (I hope
it functioned properly). If some thing is missing in report, I really apologies
to my supervisors please forgive me: "God tells me every day, see gauri If
you use your brain in more amount, It will finish fast, strictly speaking I
wont give you more again and again. so please control on yourself, you have
to survive till 100 years (with tongue smiley)" Thats the reason!!!