This readme file was generated on [2024-09-06] by [KE SUN]




GENERAL INFORMATION



Title of Dataset: Data_Nanoparticle_Adhesion_at_Liquid_Interfaces




Author/Principal Investigator Information

Name: Ke Sun

ORCID: 0000-0003-4144-7485

Institution: Durham University

Address: Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom

Email: ke.sun@durham.ac.uk



Author/Associate or Co-investigator Information

Name: Kislon Voïtchovsky

ORCID: 0000-0001-7760-4732

Institution: Durham University

Address: Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom

Email: kislon.voitchovsky@durham.ac.uk



Author/Alternate Contact Information

Name: Halim Kusumaatmaja

ORCID: 0000-0002-3392-9479

Institution: The University of Edinburgh

Address: Institute for Multiscale Thermofluids, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3FB, United Kingdom

Email: halim.kusumaatmaja@ed.ac.uk



Date of data collection: 2022-09-01 to 2024-05-14


Geographic location of data collection: Durham, United Kingdom



Information about funding sources that supported the collection of the data: 
EPSRC Centre for Doctoral Training in Soft Matter for Formulation and Industrial Innovation (SOFI2), EP/S023631/1.
UKRI Engineering and Physical Sciences Research Council, EP/V034154/1.
Leverhulme Trust, RPG-2022-140.
UKRI Engineering and Physical Sciences Research Council. EP/S028234/1.



SHARING/ACCESS INFORMATION



Licenses/restrictions placed on the data: 



Links to publications that cite or use the data: 



Links to other publicly accessible locations of the data: 



Links/relationships to ancillary data sets: 



Was data derived from another source? None

If yes, list source(s): 



Recommended citation for this dataset: 





DATA & FILE OVERVIEW



File List:
B2T6_AFM_exp, sample AFM force curve measurement showing amplitude, deflection, and force result.
AFM_simulation_line_tension, quantitative comparison between experiment and simulation, with line tension consideration.
Cone_angle_AFM_simulation, experiment and simulation data for varied cone angle.
Contact_angle_AFM_simulation, experiment and simulation data for varied contact angle.
Sqone and tilt, simulation data for varied shape factor and tilt angle.
Imperfect_particle, experiment data for two sample imperfect tips.
Velocity_test_SI, experiment data for varied tip velocity.
Repeatability_test_SI, experiment data for repeat measurement.
AFM_data_processing_SI, sample afm data processing.
Tip_truncation_SI, tip with sharp or sphere end, simulation.
Contact_angle_interface_energy_SI, explanation of the energy contribution from different interfaces when the contact angle is varied, simulation.
Sqone_normalisation_SI, choice of normalisation for sqone, simulation.
EM_images_of_tips, electron microscopy images of the tips.
Contact_angle_image, contact angle measurement images.
AFM_imaging_Pt_film, AFM image of the Pt film, for roughness calculation.


Relationship between files, if important: Each directory corresponds to a figure. Some data are used in more than one figure, so it may appear in multiple directories.


Additional related data collected that was not included in the current data package: None


Are there multiple versions of the dataset? No

If yes, name of file(s) that was updated: 

Why was the file updated? 

When was the file updated?





METHODOLOGICAL INFORMATION



Description of methods used for collection/generation of data:
AFM experiments were conducted in dynamic amplitude modulation mode to control tip indentation. Tip parameters were calibrated on a clean glass surface using the thermal method(Ref: Butt, H.-J., Jaschke, M., 1995. Calculation of thermal noise in atomic force microscopy. Nanotechnology 6, 1. https://doi.org/10.1088/0957-4484/6/1/001).
Simulation is built on the Surface Evolver (Ref: Brakke, K.A., 1992. The surface evolver. Exp. Math. 1, 141–165).


Methods for processing the data:
Most AFM data were obtained using the Cypher ES AFM. Position data were first calculated from position intervals. Tip bending was then corrected, followed by alignment and averaging at the bridge rupture point. Deflection data were converted to force, and results were computed from extension-retraction measurements.
A few AFM data sets were obtained using the JPK AFM. For these, a low-pass filter was applied to some data; see the online supplementary information for details.
Simulation data consisted of energy measurements. The data were divided into two segments: the curve segment where the tip is in contact with the liquid and the flat segment where the tip is fully withdrawn. The curve segment was fitted with a cubic spline, and the resulting force was obtained as the first derivative of this fit. It is then connected to a plateau representing the fully withdrawn state.



Instrument- or software-specific information needed to interpret the data:
Cypher ES (Oxford Instruments, USA)
JPK NanoWizard 3 (Bruker, USA)
The Surface Evolved (2.70)
Python 3.8 (with matplotlib, BaselineRemoval, scipy, pandas, numpy, os, re)


Standards and calibration information, if appropriate: 
B2T6_AFM_exp, Sensitivity = 80 nm/V (already input), Spring_constant = 1.97 nN/nm.
AFM_simulation_line_tension/AFM, Sensitivity = 80 nm/V (already input), Spring_constant = 1.97 nN/nm (same tip B2T6).
Cone_angle_AFM_simulation/AFM, B2T6 Sensitivity = 80 nm/V (already input), Spring_constant = 1.97 nN/nm, B1T8 Sensitivity = 80.48 nm/V(already input), Spring_constant = 1.81 nN/nm.
Contact_angle_AFM_simulation/AFM, Sensitivity already input, Spring_constant_in_water = 2.65 nN/nm, Spring_constant_air = 2.57 nN/nm.
Imperfect_particle, B4T1 tip Sensitivity = 73.95 nm/V, Spring_constant = 1.53 nN/nm.
Velocity_test_SI, Sensitivity = 76.26 nm/V, Spring_constant = 1.58 nN/nm.
Repeatability_test_SI, Sensitivity = 76.26 nm/V, Spring_constant = 1.58 nN/nm (same tip as Velocity_test_SI).


Environmental/experimental conditions: 
B2T6_AFM_exp, 30°C.
AFM_simulation_line_tension/AFM, 30°C.
Cone_angle_AFM_simulation/AFM, 30°C.
Contact_angle_AFM_simulation/AFM, 30°C.
Imperfect_particle, B4T1_0.5_u_avg_Defl.txt, 30°C.
Velocity_test_SI, 30°C.
Repeatability_test_SI, 30°C.


Describe any quality-assurance procedures performed on the data: 
During AFM measurements, we continuously monitored the frequency of the cantilever and ensured that it matched the intrinsic frequency specified by the manufacturer. This step was crucial for verifying that the cantilever was operating under optimal conditions and that the measurements were reliable. In data processing, we conducted noise control and reproducibility validation as shown in the online supplementary information. In simulation, our script allows sufficient iteration cycles with energy difference condition set to make sure the system is near quasi-static.



People involved with sample collection, processing, analysis and/or submission: 
Ke Sun




DATA-SPECIFIC INFORMATION FOR: [B2T6_AFM_exp]




Number of variables: 3



Number of cases/rows: 9937(extension data), 10004(retraction data)



Variable List: 
For amplitude files, the y-axis Ampltitude, reflecting the amplitude, the unit is m, labelled as amplitude.
For deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
For both amplitude deflection files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.



Missing data codes: None



Specialized formats or other abbreviations used: None




DATA-SPECIFIC INFORMATION FOR: [AFM_simulation_line_tension]




Number of variables: 6



Number of cases/rows: see each data file



Variable List: 

AFM deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
AFM deflection std files, the y-axis Deflection std, reflecting the vertical deflection std of the AFM tip, the unit is m, labelled as deflection std.
AFM deflection files and std files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.
Simulation and line_tension files, the first column is the tip position, the unit is simulation position unit, labelled as position.
Simulation and line_tension files, the second column is the system energy, the unit is simulation energy unit, labelled as energy.
Simulation and line_tension files, the third column is the energy difference ratio to the last calculated energy, the unit is none (since it is a ratio), not in use in the figure, thus no label.



Missing data codes: None



Specialized formats or other abbreviations used: None



DATA-SPECIFIC INFORMATION FOR: [Cone_angle_AFM_simulation]




Number of variables: 6



Number of cases/rows: see each data file



Variable List: 

AFM deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
AFM deflection std files, the y-axis Deflection std, reflecting the vertical deflection std of the AFM tip, the unit is m, labelled as deflection std.
AFM deflection files and std files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.
Simulation files, the first column is the tip position, the unit is simulation position unit, labelled as position.
Simulation files, the second column is the system energy, the unit is simulation energy unit, labelled as energy.
Simulation files, the third column is the energy difference ratio to the last calculated energy, the unit is none (since it is a ratio), not in use in the figure, thus no label.



Missing data codes: None



Specialized formats or other abbreviations used: None


DATA-SPECIFIC INFORMATION FOR: [Contact_angle_AFM_simulation]




Number of variables: 6



Number of cases/rows: see each data file



Variable List: 

AFM deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
AFM deflection std files, the y-axis Deflection std, reflecting the vertical deflection std of the AFM tip, the unit is m, labelled as deflection std.
AFM deflection files and std files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.
Simulation files, the first column is the tip position, the unit is simulation position unit, labelled as position.
Simulation files, the second column is the system energy, the unit is simulation energy unit, labelled as energy.
Simulation files, the third column is the energy difference ratio to the last calculated energy, the unit is none (since it is a ratio), not in use in the figure, thus no label.



Missing data codes: None



Specialized formats or other abbreviations used: None



DATA-SPECIFIC INFORMATION FOR: [Sqone and tilt]




Number of variables: 3



Number of cases/rows: see each data file



Variable List: 

Simulation files, the first column is the tip position, the unit is simulation position unit, labelled as position.
Simulation files, the second column is the system energy, the unit is simulation energy unit, labelled as energy.
Simulation files, the third column is the energy difference ratio to the last calculated energy, the unit is none (since it is a ratio), not in use in the figure, thus no label.



Missing data codes: None



Specialized formats or other abbreviations used: None




DATA-SPECIFIC INFORMATION FOR: [Imperfect_particle]




Number of variables: 4



Number of cases/rows: 
'B4T1_0.5_u_avg_Defl.txt', 4023.
'speed_0.5_force-save-2022.07.06-16.06.37.660.txt', 8336.



Variable List: 

'B4T1_0.5_u_avg_Defl.txt' AFM deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
'B4T1_0.5_u_avg_Defl.txt' AFM deflection files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.
'speed_0.5_force-save-2022.07.06-16.06.37.660.txt' AFM deflection files, the y-axis Deflection (see column 13, note that number from 0), reflecting the vertical deflection of the AFM tip, the unit is N, labelled as vDeflection.
'speed_0.5_force-save-2022.07.06-16.06.37.660.txt' AFM deflection files, the x-axis position (see column 7, note that number from 0), reflecting the position of the AFM tip, the unit is m, labelled as measured height.
Note that there are many other variables in JPK AFM data file 'speed_0.5_force-save-2022.07.06-16.06.37.660.txt' that are not used for figures, thus not specified here.


Missing data codes: None



Specialized formats or other abbreviations used: None




DATA-SPECIFIC INFORMATION FOR: [Velocity_test_SI]




Number of variables: 2



Number of cases/rows: see each data file



Variable List: 

AFM deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
AFM deflection files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.



Missing data codes: None



Specialized formats or other abbreviations used: None


DATA-SPECIFIC INFORMATION FOR: [Repeatability_test_SI]




Number of variables: 3



Number of cases/rows: see each data file



Variable List: 

AFM deflection files, the y-axis Deflection, reflecting the vertical deflection of the AFM tip, the unit is m, labelled as deflection.
AFM deflection std files, the y-axis Deflection std, reflecting the vertical deflection std of the AFM tip, the unit is m, labelled as deflection std.
AFM deflection files and std files, the x-axis position interval (the last line), used to calculate the position of the AFM tip, the unit is m, the result is labelled as position in the figures.



Missing data codes: None



Specialized formats or other abbreviations used: None




DATA-SPECIFIC INFORMATION FOR: [AFM_data_processing_SI]




Number of variables: 2



Number of cases/rows: 2833



Variable List: 
AFM deflection files, the y-axis Deflection (see column 9,note that number from 0), reflecting the vertical deflection of the AFM tip, the unit is N, labelled as vDeflection.
AFM deflection files, the x-axis position (see column 4,note that number from 0), reflecting the position of the AFM tip, the unit is m, labelled as measured height.
Note that there are many other variables in JPK AFM data file 'sa_rate_50kHz_force-save-2022.09.01-17.43.16.195.txt' that are not used for figures, thus not specified here.


Missing data codes: None



Specialized formats or other abbreviations used: None


DATA-SPECIFIC INFORMATION FOR: [Tip_truncation_SI]




Number of variables: 4



Number of cases/rows: 
2007_nongra_condition_0.0002_cone_angle_30_contact_angle_20.txt, 200.
tagent_sphere_condition_0.0002_cone_angle_30_contact_angle_20.txt, 70.



Variable List: 

Simulation file 2007_nongra_condition_0.0002_cone_angle_30_contact_angle_20.txt, the first column is the tip position, the unit is simulation position unit, labelled as position.
Simulation file 2007_nongra_condition_0.0002_cone_angle_30_contact_angle_20.txt, the second column is the system energy, the unit is simulation energy unit, labelled as energy.
Simulation file tagent_sphere_condition_0.0002_cone_angle_30_contact_angle_20.txt, the second column (column 1, as number from 0) is the sphere central position, labelled as position.
Simulation file tagent_sphere_condition_0.0002_cone_angle_30_contact_angle_20.txt, the third column (column 2, as number from 0) is the energy, labelled as energy.
Note that there are other variables in these simulation files that are not used for figures, thus not specified here.



Missing data codes: None



Specialized formats or other abbreviations used: None




DATA-SPECIFIC INFORMATION FOR: [Contact_angle_interface_energy_SI]




Number of variables: 5



Number of cases/rows: see each file.



Variable List: 
Simulation file, the first column (column 0, as number from 0) is the tip position, labelled as position.
Simulation file, the second column (column 1, as number from 0) is the total energy, labelled as E.
Simulation file, the last column (column -1) is the liquid-fluid interface energy, labelled as E_LF.
Simulation file, the second last column (column -2) is the liquid-solid interface energy, labelled as E_SL.
Simulation file, the third last column (column -3) is the fluid-solid interface energy, labelled as E_SF.
Note that there are other variables in these simulation files that are not used for figures, thus not specified here.



Missing data codes: None



Specialized formats or other abbreviations used: None



DATA-SPECIFIC INFORMATION FOR: [Sqone_normalisation_SI]




Number of variables: 3



Number of cases/rows: see each data file



Variable List: 

Simulation files, the first column is the tip position, the unit is simulation position unit, labelled as position.
Simulation files, the second column is the system energy, the unit is simulation energy unit, labelled as energy.
Simulation files, the third column is the energy difference ratio to the last calculated energy, the unit is none (since it is a ratio), not in use in the figure, thus no label.



Missing data codes: None



Specialized formats or other abbreviations used: None




DATA-SPECIFIC INFORMATION FOR: [EM_images_of_tips]




Number of variables: 1



Number of cases/rows: see each data file



Variable List: 

Different tips' electron microscopy images.



Missing data codes: None



Specialized formats or other abbreviations used: None



DATA-SPECIFIC INFORMATION FOR: [Contact_angle_image]




Number of variables: 1



Number of cases/rows: see each data file



Variable List: 

Contact angle measurements on different surfaces and fluids.



Missing data codes: None



Specialized formats or other abbreviations used: None



DATA-SPECIFIC INFORMATION FOR: [AFM_imaging_Pt_film]




Number of variables: 1



Number of cases/rows: see each data file



Variable List: 

AFM images of Pt film.



Missing data codes: None



Specialized formats or other abbreviations used: None

