Adsorption on Surface

Description

This function analyzes the dynamics of the adsorption of a group of molecules onto a surface. The physical process analyzed is a simple physisorption where an atom is considered adsorbed at a given time when its distance from the surface is below a certain threshold (Contact distance input). Importantly, the function allows to define various zones on the surface and therefore perform the analysis for every zone separately. However, the group of molecules selected to be analyzed is considered as a single group. The results are based on residue statistics, meaning the smallest unit considered is the residue. For example, residue percentage is used to quantify the portion of the surface covered by molecules or the percentage of molecules adsorbed on the surface.

The analysis generates several types of data, divided into three categories:

  1. Time-dependent quantities: These are analyzed over the course of the simulation.

  2. Spatial quantities: These are averaged across frames.

  3. Nature of contacts: This category evaluates the nature of contacts between molecules and the surface. It includes additional analysis relevant specifically for polymers.

Time-dependant quantities

The following are analyzed as a function of simulation time:

  • The percentage of molecule residues adsorbed onto the surface.

  • For each surface zone, the percentage of surface residues covered by molecules, relative to the number of residues in that zone.

  • For each surface zone, the percentage of surface residues covered by molecules, relative to the total number of residues across all zones.

Spatial Quantities

The following are spatial properties averaged accross frames:

  • For each surface zone, a surface map shows the average percentage of coverage for every residue in the map (the center of mass of the residues in the surface plane is used to position the coverage).

  • The average density of molecules for every point in space.

Nature of Contacts

Two key quantities define the nature of the contacts between molecules and the surface:

  • A count of the atoms involved in the shortest contact between a molecule residue and the surface.

  • For polymers, an analysis of the nature of each residue in the polymer, categorized as one of the following: "Full Adsorbed", "Full Adsorbed Border", "Full Free", "Train", "Train Border", "Tail", "Loop", "Loop Border", and "Loop Bridge".

Since the last two quantities are of more complex nature, they deserve a more detailed explanation.

The shortest interaction count creates a matrix that records how many times (atom_name_res_name_molecule, atom_name_res_name_surface) iforms the shortest interaction between a residue in the molecule and the surface. For instance, the analysis might show that C1_RESA in the molecule connects N times to C2_RESB on the surface when considering the shortest distances between molecule and surface for each residue.

The residue classification for polymers is based on the role of each residue in the corresponding polymer chain:

  • Full Adsorbed: Residues in a polymer chain fully connected to the surface, always interacting with the same surface zone.

  • Full Adsorbed Border: Residues in a polymer chain fully connected to the surface, but interacting with more than one surface zone.

  • Full Free: Residues in a polymer chain that never connect to the surface.

  • Train: Residues that connect to the surface but are part of a chain only partially connected to the surface.

  • Train Border: Residues in a chain partially connected to the surface, where the connected part crosses more than one zone of the surface.

  • Tail: Residues not connected to the surface but part of a chain that is partially connected to the surface and not classified as *Loop`".

  • Loop: Residues not connected to the surface but located between two points of connection to the surface within the polymer chain.

  • Loop Border: Residues classified as "Loop", but the part they belong to connects to two different zones on the two sides.

  • Loop Bridge: “Loop” or “Loop Border” residues that bridge over another surface zone. For example, a “Loop Border” connects to “zone1” on one side and “zone2” on the other, while also passing above “zone3”, making those residues a “Loop Bridge”.

The analysis reports the number of each residue type per frame, averaged across frames.

Latest version

Allowed number of parents: 1

Parameter Description Value type Value restrictions Default value Units

Names of molecules

Indicate the name of the molecules whose adsorption will be analyzed

selector component

component types, “all”

N/A

N/A

Surface zone 1: name

Name to assign to the first selected zone

str

N/A

N/A

N/A

Surface zone 1: component names

The component names of the reference group for the first surface zone

selector_component

component types, “all”

N/A

N/A

Surface zone 1: residue names

The residue names of the reference group for the first surface zone

selector_residue

residue types, “all”

all

N/A

Surface zone 1: atom type

The atom types of the reference group for the first surface zone

selector_atom_type

atom_types, “all”

all

N/A

Surface zone 1: atom name

The atom names of the reference group for the first surface zone

selector_atom

atom_names, “all”

N/A

N/A

Surface zone 2: name

Name to assign to the second selected zone

str

N/A

N/A

N/A

Surface zone 2: component names

The component names of the reference group for the second surface zone

selector_component

component types, “all”

N/A

N/A

Surface zone 2: residue names

The residue names of the reference group for the second surface zone

selector_residue

residue types, “all”

all

N/A

Surface zone 2: atom type

The atom types of the reference group for the second surface zone

selector_atom_type

atom_types, “all”

all

N/A

Surface zone 2: atom name

The atom names of the reference group for the second surface zone

selector_atom

atom_names, “all”

N/A

N/A

Direction perpendicular to surface

The direction perpendicular to the surface

selector

“x”, “y”, “z”

“z”

N/A

Use PBC in direction perpendicular to surface

Whether to use periodic boundary conditions in a perpendicular direction to the surface

bool

True, False

True

N/A

Contact distance

Distance below which molecule and surface are considered in contact

float

>0

5

angstrom

Consider H

Indicate whether to consider hydrogen atoms in the analysis

bool

True, False

False

N/A

Perform conformation analysis

Whether to perform the conformation analysis on the molecule. It only makes sense if the molecule is a polymer.

bool

True, False

False

N/A