I.

Abstract: The overall goal of this research project was to develop a reliable method that simulates polymer adsorption onto rough surface using LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator). The surfaces were generated using a three-dimensional cosine wave developed in MATLAB while the polymers were generated in C. The purpose of the simulation was to test if polymer adsorption levels would be dependent on the degree of polymerization, the wavelength of the surface, or the interactive energy between the surface and the polymer. While maintaining the polymer density, the atom-to-surface area ratio, and the average bond length of the surface, we measured how well the polymers adsorbed onto the rough surfaces. This was determined by calculating the distance from the surface at which polymers were most dense and the average center of mass of each polymer. We found that all three variables did indeed affect the average distance between the polymers and the surfaces.

II.

Background: Polymer adsorption is a process in which a polymer adheres or sticks onto a surface due to intermolecular attraction forces. This phenomenon is seen in countless processes in many different applications such as paints, adhesives, plastics, etc. These polymers adsorb onto a surface and although some surfaces appear to be smooth on the macro-scale, all surfaces are actually rough on the nano-scale. Much research has been done on polymer adsorption onto smooth surfaces; however, almost no research has been done on rough surfaces due to the complexity and multitude of parameters that must be held constant throughout the experiment. Therefore, this projects focus has been to discover how polymer adsorption is affected by both surface roughness and the degree of polymerization by maintaining the polymer density, the monomerto-surface area ratio, and the average bond length of the surface throughout the experiment. Surface roughness is an important parameter in polymer adsorption; how the polymer adsorbs onto the surface is dependent on interaction energy between the monomers of the polymer and the monomers that make up the surface. These interaction energies can be represented using the Lennard-Jones Equation:

V = Energy R = distance between two particles Epsilon = Interactive energy parameter Sigma = average diameter of the two particles interacting and also the distance at which the intermolecular potential between the two particles is zero [1] This equation relates the potential energy between two particles with the distance between them. The graphical representation of this equation can be seen in Figure 1:

Lennard-Jones Potential
30 25 Potential Energy (J) 20 15 10 5 0 -5 -10 0 1 2 3 4 5 6 7 8

Disance between particles ()

Figure 1: The graphical representation of the Lennard-Jones Equation.

As a result, the particles have a certain distance that results in a point of lowest potential energy. At this location both particles require energy to be moved. This concept can be applied with polymer adsorption with interactive energies between monomers rather than particles. The point of lowest potential energy between the surface and the polymer is the distance at which the polymer adsorbs. Since the energy is dependent on the distance between the monomers of the polymer and the atoms of the surface, the shape and roughness of the surface will affect the adsorption levels of the polymer. During the experiment, two different sinusoidal surfaces were generated using the equation: z = Amplitude*cos((2*pi/Wavelength)*x)*cos((2*pi/Wavelength)*y)

As a result, both amplitude and wavelength would affect the roughness of the surface. For this experiment, amplitude was kept constant and the wavelengths of the surfaces were manipulated to study how polymer adsorption levels are affected by the roughness of the surface. Another parameter that affects polymer adsorption levels is the degree of polymerization or the average length of the polymer chains adsorbing onto the surface. As was said before, polymer adsorption occurs due to interactions between the polymer and the surface. Thus, the amount of monomers in both the polymer and the amount of atoms in the surface affect the adsorption levels of the polymer. As a result, two different degrees of polymerization were used during this experiment to find how the degree of polymerization affected these polymers ability to adsorb. This was controlled by creating two different groups of polymers. The short polymers had a range of 37-48 monomers per chain. The long polymers had a range of 116-138 monomers per chain. Since there are so many different parameters in this experiment, many parameters had to be held constant during the simulations. The first parameter held constant was the average bond length of the surface. Since the bond length of a molecule is one of its key characteristics, bond length had to be held constant in order to guarantee that the polymers were adsorbing onto surfaces with the same material properties. Another parameter that had to be held constant was the ratio between the atoms within the surface and the surface area. This was to ensure the polymers would experience the same amount of energy per unit area for each surface during adsorption. Lastly, the polymer density had to remain constant throughout the simulations, as well. Polymer density is the amount of monomers per unit area where the area is the area of the projection of the surface onto the XY plane. This is important to maintain, because if the polymer density changes throughout the experiment, then the monomers of the polymers adsorbing would experience different levels of interactive energies from the monomers of different polymers throughout the simulations.

III.

Method: In order to test whether the degree of polymerization, the roughness of the surface, or the interactive energy between the surface and polymer affect adsorption levels, polymers were generated using a program in C and surfaces were generated using MATLAB. To test whether the degree of polymerization has an effect on the adsorption levels of the polymers, a program in C was developed that creates a set of 48 polymer chains with different amounts of total monomers in the set, thus varying the degree of
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polymerization. This code generated two sets of polymers, the first with 2,043 monomers designated as the short polymer group (Degree of Polymerization: 42.5625) and the second with 6,129 monomers designated as the long polymer group (Degree of Polymerization: 127.6875). These polymers maintained a certain bond length and angle so that the physical properties of the polymers would remain constant. After, surfaces were created using the equation: z = Amplitude*cos((2*pi/Wavelength)*x)*cos((2*pi/Wavelength)*y) There are two sets of surfaces that use this equation. The first set of surfaces will use the short polymers, while the second set of surfaces will use the long polymers. To vary the roughness of these surfaces, two different wavelengths of 25 and 37.5 were used while maintaining an amplitude of 5 for both surfaces. The number of points on the surface represents atoms within the surface. To create the first rough surface to be used with the short polymers, a MATLAB code was developed that created a surface with inputs of amplitude of 5, wavelength of 25 , and a desire bond length of 3 . The MATLAB code then changed the domain and range of the surface (domain and range are equal) while maintaining the same amount of points until the bond length was the desired length. The domain and range of the surface became [-40.49 , 40.49 ]. After, the same MATLAB code found the surface area of the surface using the fact that the cross product between two vectors of the same vertex gives the area of the parallelogram that the vectors create. As a result, the surface area was found and the atom-to-surface area ratio was calculated to be 0.1189 atoms/ 2. The first surface created (hereafter referred to as surface A) can be seen in Figure 2 below.

Figure 2: Surface A. Amplitude of 5 , Wavelength of 25 , domain and range values of [-40.49 , 40.49 ] and atom-to-surface area ratio of 0.1189.

However, if a surface was created with a different wavelength but with the same domain and range values, the characteristics of the surfaces such as bond length and atom-to-surface area ratio would be different, as seen in both Figures 3 and 4.

Average Bond Length vs. Wavelength

0.435 0.43

Bond Length ()

0.425 0.42 0.415 0.41 0 2 4 6 8 10 12 14 Wavelength ()

Figure 3: The relationship between Average Bond Length of the surface and the wavelength of that surface when amplitude is held constant at 1 .

Surface Area vs. Wavelength

2750 Surface Area (^2) 2700 2650 2600 2550 2500 2450 0 2 4 6 8 10 12 14 Wavelength ()

Figure 4: The relationship between surface area and wavelength when the amplitude is held constant at 1 .

As a result, another MATLAB code was developed that created three surfaces that maintained the average bond length, the atom-to-surface area ratio, and the polymer density. This MATLAB code had inputs such as the domain and range of the original surface, the atom-to-surface area ratio of the original surface, the desired bond length, the desired wavelength, and the amplitude. This code then found a second surface within the first set of surfaces that maintained bond length and the atom to surface area ratio by changing the domain and range of the new surface while maintaining the same amount of points. Although these parameters were held constant, changing the domain and range values did change the polymer density. As, a result, wavelengths of 25 and 37.5 were chosen to vary roughness, because as wavelength increases the difference between the domain and range values of the surfaces decreases. However, the wavelengths could not be increased too much, because this would decrease the amount of periods within the domain and range. Thus, 25 and 37.5 were chosen, because they minimize the difference between the domain and range values, while maintaining the bond length and atom-to-surface area ratio. This created the second surface (hereafter referred to as surface B) with an amplitude of 5 , wavelength of 37.5 , bond length of 2.9758 , domain and range values of [-42.79 , 42.79 ], with a calculated ratio of 0.1210.

Figure 5: Surface B. Amplitude of 5 , Wavelength of 37.5 , domain and range values of [-42.79 , 42.79 ] and the atom to surface area ratio is 0.1210.

After, the same code developed the second set of surfaces that maintained the polymer densities of the first two surfaces by increasing the domain and range of the first set of surfaces. This was done, because the amount of monomers for the first set of surfaces was 2043 monomers while the amount of monomers for the second set of surfaces was 6129 monomers. The third surface was based on the first surface where the wavelength was 25 and it was created by maintaining the first surfaces lattice length (grid length between points), or the distance in x between two points within the surface, and increasing the domain a range of the surface until the polymer density of the third surface equals that of the first. Doing this process does not affect the average bond length and the atom to surface area ratio of the surface. Thus the third surface has 3025 atoms with an amplitude of 5 , a wavelength of 25 , domain and range values of [-70.13 70.13 ], a bond length of 3.0152 , and a ratio of 0.1166. Since the third surface (Hereafter referred to as surface B) maintains the same atom to surface ratio, bond length, and polymer density, it is virtually the same surface and as a result This surface can be seen in Figure 6.

Figure 6: This surface has 3025 atoms with an amplitude of 5 , a wavelength of 25 , domain and range values of [-70.13 70.13 ], a bond length of 3.0152 , and a ratio of 0.1166.

The same process is then used to create the fourth surface which has 3025 atoms with an amplitude of 5 , a wavelength of 37.5 , domain and range values of [-74.11 74.11 ], a bond length of 2.9667 , and a ratio of 0.1190. This surface can be seen in Figure 7.

Figure 7: This surface has 3025 atoms with an amplitude of 5 , a wavelength of 37.5 , domain and range values of [-74.11 74.11 ], a bond length of 2.9667 , and a ratio of 0.1190.

After these polymers and surfaces were created, information for both the polymers and surfaces such as the molecule number, atom type, coordinates of the polymers and surfaces were exported into data files that would later be submitted into the Large Scale Atomic Molecular Massively Parallel Simulator (LAMMPS) for simulations. LAMMPS is a program that simulates either atomic or molecular interaction and can be run on different operating systems such as Windows or Linux, however, for this project LAMMPS was run on Linux. In order to run a LAMMPS simulation, each simulation required a data file and an input file. The data file, as previously stated, was created on MATLAB and contained all of the information needed for both the polymer and surface so that the LAMMPS simulation could take place. The data file lists the information about each atom in the surface where each atom is given a unique atom number. Then the atom is given a molecule number to differentiate between the 48 different polymer chains as well as from the surface. A molecule number of 1 indicated the atom belonged to the surface, while a molecule number of 2 to 49 indicated the atom belonged to one of the polymers. After this, the atom is then given an atom type where the surface atoms were given an atom type of 1 and the monomers of the polymers were given an atom type of 2. Finally, the atoms of both the polymers and the surface are given initial x, y, and z coordinates. The input file was created on LAMMPS and it contains parameters that were utilized during the simulation. First, it describes the types of atoms that are being simulated. For these simulations, the atoms were described as molecular with harmonic bonds, harmonic angles, and Lennard-Jones pairwise interactions. This means that the bonds and angles varied slightly from the desired values according to a Gaussian curve during the simulation. It also means that the Lennard-Jones equation should be applied to all of the atoms in the system to determine how they interact with one another. Next, the input file lists which data file to read from and which coefficients to use for this data file. There are three coefficients which need to be defined: pair coefficients, bond coefficients, and angle coefficients. The pair coefficients are the input values for the Lennard-Jones equation. They are the interactive energy parameter and the sigma values for both the surface to surface and the surface to polymer atoms. The interactive energy parameter, or Epsilon represents the measure of how strong two particles are attracted to each other. This is how the interactive energy parameter was changed during the experiment. For each simulation, the appropriate interactive energy was inputted to test whether the interactive energy parameter would have an effect on the adsorption distance of the polymers. Sigma represents the diameter of the atoms interacting and the distance at which the intermolecular potential between the two particles is zero. The bond coefficients describe the average bond length and the harmonic constant or the amount of variance that the bond length is allowed. The angle coefficients are the
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same as the bond coefficients and they represent the average angle value and the amount of variance the angles can have. After, the masses of the atoms are given as well as the name of the dump and restart files. The dump and restart files are the outputs of the simulations where the dump files are used for analysis and they detail where each atom is located at each time step. The restart files contain all of the same information as the data file and can be used to rerun the simulation. When both the data files and the input files are finished, they are run on LAMMPS. LAMMPS uses molecular dynamics to move the atoms of the polymer around the surface, according to Lennard-Jones interactions. These simulations used a time step of 1 for 10,000,000 runs. This means that the atoms of the polymer were moved and analyzed 10,000,000 different times and every 1000 time steps the data was outputted into the dump files. 8 different simulations were run with this amount of time steps in order to test the effect the degree of polymerization, the roughness of the surface, and the interactive energy parameter have on the adsorption levels of the polymers. The different simulations run with the certain polymer type, surface type, and interactive energy parameter can be seen in Table 1 below.
Table 1: Experimental Process

Polymer Type

Surface Type A

Short B Long A B

Interactive energy 0.0935 0.187 0.2805 0.0935 0.187 0.2805 0.0935

The dump files were then analyzed using C programs developed by Dr. Vikram Kuppa. The C programs analyzed the density of monomers within certain ranges of z values in the space above the surface in order to represent the distance at which most polymers tend to be accumulating. To further understand the distance of the polymers to the surface, the center of mass of each of the polymers were calculated and averaged for the 10,000 dump files created and thus an average z value for each polymer was found. This data was then used to prove whether the degree of polymerization, surface roughness, or interactive energy have an effect on the adsorption levels of the polymers. IV. Results: It was found that the degree of polymerization, surface roughness and interaction energy parameter did affect polymer adsorption onto rough surfaces.
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A. Degree of Polymerization To begin, the degree of polymerization affected the adsorption levels of the polymers. This was studied by comparing polymers of different sizes when they are adsorbing onto the same surfaces. First, the long and short polymers were simulated to interact with Surface A. Figure 8a displays the density profile of this adsorption and shows that the distance at which the shorter polymers are most dense is closer to the surface than the longer polymers distance. This is confirmed by the center of mass calculations, which can be seen in Table 2. The short polymer with an interactive energy 0.0935 while adsorbing onto surface A had a smaller average z value for center of mass than the long polymer in the same conditions. Since the average center of mass is greater for the long polymer, it adheres less closely than the short polymers on rougher surfaces. An explanation for these results could be that shorter polymers are better able to fit inside the depressions of the rougher surface. The radius of gyration for the long polymer, or the collective size of the polymer may be greater than the radius of the valleys in the surface, which would lead to the polymer not being able to closely adhere to the surface. However, there is a completely opposite correlation for the simulated interactions between the long and short polymers and surface B. Figure 9b displays the density profile of the polymers as a function of distance from the surface. This showed there was tendency towards greater adsorption of longer polymers than shorter polymers onto surface B. The average center of masses in the z direction again confirmed this which can be seen Table 2. The center of mass calculations confirm that short polymers with an interaction energy of 0.0935 adhere less closely than their longer counterparts. In fact, short polymers had an average center of mass of 27.7381 angstroms from the surface and long polymers had an average center of mass of 26.3915 angstroms away from the surface. A possible explanation for this is that the longer polymers are able to fit within the depressions of the surface due to the increase in wavelength. Thus, if the longer polymers can fit, then they have more monomers to interact with the atoms in the surface than the short polymers. Thus, the longer polymers have a larger total interaction energy and would subsequently adsorb closer on the surface.

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0.25 Density of Polymers (g/cc) 0.2 0.15 0.1 0.05 0

Density of the Short and Long Polymer on Surface A

Short, A Long, A

0.0 3.5 7.0 10.4 13.9 17.4 20.9 24.4 27.8 31.3 34.8 38.3 41.7 45.2 48.7 52.2 55.7 59.1 62.6 66.1 69.6 73.1 76.5 80.0 83.5 87.0 90.4 93.9 97.4 100.9 Distance from Surface ()

Figure 8a: Density of Short and Long Polymers on Surface A

Table 2: Average Center of Mass (Derived from Figure 9a 9b 9c and 10)

Polymer Type

Surface Type A

Short B Long A B

Interactive Energy 0.0935 0.187 0.2805 0.0935 0.187 0.2805 0.0935

Z-Coordinate of Average Center of Mass () 24.4643 10.9657 9.3199 27.7381 17.0435 15.0720 29.0739 26.3915

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Average Center of Mass for an Interactive Energy of 0.0935

35 Average Center of Mass () 30 25 20 15 10 5 0 37 38 39 40 41 42 43 44 45 46 Chain Length (Number of Monomers) 47 48 A, Short, Epsilon = 0.0935 B, Short, Epsilon = 0.0935

Figure 9a: Average Center of Mass as a Function of Chain Length for Short Polymers with an Interactive energy of 0.0935

Average Center of Mass for an Interactive Energy of 0.187

20 18 16 14 12 10 8 6 4 2 0

Average Center of Mass ()

A, Short, Epsilon = 0.187 B, Short, Epsilon = 0.187

37

38

39

40 41 42 43 44 45 46 47 Chain Length (Number of Monomers)

48

Figure 9b: Average Center of Mass as a Function of Chain Length for Short Polymers with an Interactive energy of 0.187

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Average Center of Mass for an Interactive Energy of 0.2805

18 16

Average Center of Mass ()

14 12 10 8 6 4 2 0 1 2 3 4 5 6 7 8 9 10 11 12 A, Short, Epsilon = 0.2805 B, Short, Epsilon = .2805

Chain Length (Number of Monomers)

Figure 9c: Center of Mass as a Function of Chain Length for Short Polymers with an Interactive Energy of 0.2805

Average Center of Mass for an Interactive Energy of 0.0935

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Average Center of Mass ()

30 25 20 15 10 5 0 116 117 118 119 121 122 123 124 125 127 128 129 130 132 133 134 135 136 137 138 A, Long, Epsilon = 0.0935 B, Long, Epsilon = 0.0935

Chain Length (Number of Monomers)

Figure 10: Center of Mass as a Function of Chain Length for Long Polymers with an Interactive Energy of 0.0935

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B. Surface Roughness It was found that roughness does affect the adsorption levels for both the short and long polymers and this was found by holding the degree of polymerization constant while the surface roughness was changed. In Figure 8a it appears that as the roughness increases due to a decrease in wavelength from 37.5 A to 25 A the distance from the surface at which the monomers are most dense decreases. This might be because the short polymer can fit within the depression of the surface and interact with more atoms within the surface since the atoms are more available due to the curvature or roughness of the surface. Thus, more atoms of the surface and more monomers of the polymer are interacting creating a stronger total interaction force between them. Thus, as roughness of the surface increases, short polymers will adsorb more closely. Although roughness decreased the distance at which the short polymers were most dense, Figure 8b shows that roughness increased the distance from the surface at which the longer polymers were most dense. This phenomenon might be due to the longer chains inability to fit within the depressions of surface A, the rougher surface. Thus, the longer chains will be forced to sit on the top of the surface instead of penetrating into the depressions. As a result, it appears that as the roughness increases, the distance between the longer polymer chains and the surface will increase.

Density of Short Polymers on Surface A and Surface B

0.25 Density of Polymers (g/cc) 0.2 0.15 0.1 0.05 0 0.0 4.9 9.8 14.7 19.6 24.6 29.5 34.4 39.3 44.2 49.1 54.0 58.9 63.8 68.8 73.7 78.6 83.5 88.4 93.3 98.2 Short, A Short, B

Distance from Surface ()

Figure 11a: Density of Short Polymers on Surface A and Surface B

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Density of Long Polymers on Surface A and Surface B

Density of Polymers (g/cc) 0.2 0.15 0.1 Long, A 0.05 0 0.0 4.7 9.4 14.1 18.8 23.5 28.2 32.9 37.7 42.4 47.1 51.8 56.5 61.2 65.9 70.6 75.3 80.0 84.7 89.4 94.1 98.8 Long, B

Distance from Surface () Figure 11b: Density of Long Polymers on Surface A and Surface B

C. Interaction Energy Parameter It also appeared that the interaction energy parameter between the atoms of the surface and the monomers of the polymer effects the distance at which polymers adsorb for both surface A and B. In both Figures 12a and 12b it can be seen that as the interaction energy between the surface and polymer atoms and monomers increases, the distance at which the polymers are most dense decreases. This seems to be consistent with different surfaces and with previous understandings where the interaction energy represents how attracted the atoms are to each other. Thus, if the interaction energy between the atoms of the surface and the monomers of the polymer is increased, the distance at which the polymer will be most dense will decrease due to the stronger interaction energy.

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Surface A, Short Polymer with Varying Values of Epsilon

0.6

Density of Polymers (g/cc)

0.5 0.4 0.3 0.2 0.1 0 0.0 4.5 9.0 13.5 18.0 22.5 27.0 31.5 36.0 40.5 45.0 49.5 54.0 58.5 63.0 67.5 72.0 76.5 81.0 85.5 90.0 94.5 99.0 Epsilon = 0.0935 Epsilon = 0.187 Epsilon = 0.2805

Distance from Surface ()

Figure 12a: Surface A, Short Polymer with Varying Values of Epsilon

Surface B, Short Polymer with Varying Values of Epsilon

0.6 0.5 0.4 0.3 0.2 0.1 0 0.0 4.0 8.0 12.0 16.0 20.0 23.9 27.9 31.9 35.9 39.9 43.9 47.9 51.9 55.9 59.9 63.8 67.8 71.8 75.8 79.8 83.8 87.8 91.8 95.8 99.8 Epsilon = 0.0935 Epsilon = 0.187 Epsilon = 0.2805

Density of Polymers (g/cc)

Distance from Surface () Figure 12b: Surface B, Short Polymer with Varying Values of Epsilon

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V.

Conclusion: As a result, the degree of polymerization, the surface roughness, and the interactive energy parameter between the surface and the polymer all effected the average distance between the polymers and the surfaces. For a low degree of polymerization of 42.5625 average monomers per chain, as the surface roughness increased, the average distance between the polymers and the surface decreased. For a high degree of polymerization of 127.6875 average monomers per chain, as the surface roughness decreased, the average distance between the polymers and the surface decreased. For a rough surface of wavelength 25 , as the degree of polymerization decreased, the average distance between the polymers and the surface decreased. Likewise, for a smooth surface of wavelength 37.5 , as the degree of polymerization increased, the average distance between the polymers and the surface decreased. Lastly, for both rough and smooth surfaces, as the interactive energy increased between the surface and the polymer, the average distance between the polymers and the surface decreased. Although this research received great preliminary results, much more research has to be done to verify our work. Many more simulations will be run with different surfaces, different degrees of polymerization, and different interactive energy parameters. By completing these future simulations, a better understanding of polymer adsorption onto rough surfaces will ensue. As a result, with this information, materials can be tailored to either attract or repel polymer adsorption and polymers can be bettered developed to adsorb onto rougher surfaces. In all, great progress has been made in polymer adsorption that will lead to a better understanding of the world around us.

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Bibliography
[1] (2010). Lennard-Jones Potential,UCDavisChemWiki, <http://chemwiki.ucdavis.edu/Physical_Chemistry/Quantum_Mechanics/Atomic_Theory/Interm olecular_Forces/Lennard-Jones_Potential>(May 31, 2013).

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