Perforating freestanding molybdenum disulfide monolayers with highly charged ions

Arkady V. Krasheninnikov; Erik Pollmann; Georg S. Duesberg; Jani Kotakoski; Lukas Madau{\ss}; Mahdi Ghorbani-Asl; Maria O'Brien; Marika Schleberger; Mukesh Tripathi; Niall McEvoy

arxiv: 1907.01171 · v1 · pith:OR6H72AZnew · submitted 2019-07-02 · ❄️ cond-mat.mtrl-sci

Perforating freestanding molybdenum disulfide monolayers with highly charged ions

Roland Kozubek , Mukesh Tripathi , Mahdi Ghorbani-Asl , Silvan Kretschmer , Lukas Madau{\ss} , Erik Pollmann , Maria O'Brien , Niall McEvoy

show 7 more authors

Ursula Ludacka Toma Susi Georg S. Duesberg Richard A. Wilhelm Arkady V. Krasheninnikov Jani Kotakoski Marika Schleberger

This is my paper

Pith reviewed 2026-05-25 11:25 UTC · model grok-4.3

classification ❄️ cond-mat.mtrl-sci

keywords molybdenum disulfidehighly charged ionsnanopore creationelectronic excitationdefect formationscanning transmission electron microscopytwo-dimensional materialspore size control

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The pith

Highly charged ion irradiation creates pores in MoS2 whose size and number increase with ion potential energy.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper establishes irradiation with highly charged ions as a fabrication method for pores in freestanding single-layer molybdenum disulfide. Pore creation efficiency rises linearly across a wide range of projectile potential energies, and the resulting pore radii scale with that same energy. Atomic-resolution imaging and atomistic simulations tie the defect formation to electronic excitation rather than other energy transfer channels. This yields pores with radii from roughly 0.3 to 3 nanometers and narrow size distributions, directly relevant to applications that require controlled molecular passage through the sheet.

Core claim

Irradiation with highly charged ions produces pores in freestanding MoS2 monolayers whose creation efficiency increases linearly with projectile potential energy and whose size also depends on that energy; the process is driven by electronic excitation, as confirmed by comparison to simulations, and produces narrow size distributions with radii between ca. 0.3 and 3 nm.

What carries the argument

The potential energy of the highly charged ions, transferred via electronic excitation to create atomic defects.

If this is right

Choosing the ion charge state selects the typical pore radius within the 0.3–3 nm window.
Pore creation remains efficient across a broad range of potential energies.
Simulations indicate molybdenum enrichment near the pore edges at lower potential energies.
The resulting pores exhibit narrow size distributions suitable for size-selective transport.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

The linear scaling may allow predictive design of pore arrays by simple adjustment of ion source settings.
The electronic-excitation mechanism could be tested for creating controlled defects in related layered materials.
Pore-edge chemistry changes noted in simulations might affect long-term stability or selectivity in filtration devices.

Load-bearing premise

The pores and their size trend arise directly from the ion impacts rather than from sample preparation or measurement artifacts.

What would settle it

Repeated atomic-resolution imaging of samples irradiated at different potential energies that shows no systematic change in average pore radius would falsify the claimed dependence.

read the original abstract

Porous single layer molybdenum disulfide (MoS$_2$) is a promising material for applications such as DNA sequencing and water desalination. In this work, we introduce irradiation with highly charged ions (HCIs) as a new technique to fabricate well-defined pores in MoS$_2$. Surprisingly, we find a linear increase of the pore creation efficiency over a broad range of potential energies. Comparison to atomistic simulations reveals the critical role of energy deposition from the ion to the material through electronic excitation in the defect creation process, and suggests an enrichment in molybdenum in the vicinity of the pore edges at least for ions with low potential energies. Analysis of the irradiated samples with atomic resolution scanning transmission electron microscopy reveals a clear dependence of the pore size on the potential energy of the projectiles, establishing irradiation with highly charged ions as an effective method to create pores with narrow size distributions and radii between ca. 0.3 and 3 nm.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Desk Editor's Note private letter to a colleague

HCI irradiation produces nanopores in freestanding MoS2 whose size tracks ion potential energy with linear efficiency, but the causal link to electronic excitation and exclusion of preparation artifacts needs tighter checks.

read the letter

The paper's core result is that highly charged ion irradiation creates pores in MoS2 with radii from 0.3 to 3 nm whose average size grows with projectile potential energy, accompanied by a linear rise in creation efficiency. They back this with atomic-resolution STEM on irradiated freestanding samples and atomistic simulations that highlight electronic excitation as the main driver of defects, plus a hint of Mo enrichment near low-energy pore edges. That combination of a new fabrication route and quantitative trends on size and yield is what stands out as new here. The experimental images and the reported linear dependence look like the strongest part; they give a concrete handle on pore control that prior ion-beam work on 2D materials did not supply in this form. The simulations add a plausible mechanism without obvious circularity. The soft spots sit mainly in the attribution step. The abstract and stress-test note leave open whether pores could arise from transfer steps, solvent exposure, or other unmentioned factors, and the simulation comparison would be stronger with explicit checks that defect yields match experiment only when electronic stopping is included. Without those controls or raw fluence data shown, the causal claim rests on an assumption that could be tested more directly. Minor issues like missing error bars in the provided text are secondary. This work is aimed at groups doing nanopore engineering in transition-metal dichalcogenides for sequencing or filtration. Anyone already using ion beams or needing narrow size distributions will get practical value from the efficiency curve and size range. It is coherent enough on its own terms to deserve a serious referee; the observations are falsifiable and the method is reproducible in principle, even if revisions will likely be needed on the controls and simulation validation. I would send it out for review rather than desk-reject.

Referee Report

3 major / 2 minor

Summary. The manuscript introduces irradiation with highly charged ions (HCIs) as a technique to perforate freestanding MoS2 monolayers. It reports a linear increase in pore creation efficiency with projectile potential energy, a clear dependence of pore radius (0.3–3 nm) on potential energy as measured by atomic-resolution STEM, and atomistic simulations indicating that electronic excitation dominates defect creation with possible Mo enrichment at pore edges for low-potential-energy ions.

Significance. If the causal attribution to HCI irradiation holds, the work provides a new route to fabricate nanopores with narrow size distributions in 2D materials, relevant to DNA sequencing and desalination. The direct STEM size analysis and simulation comparison to isolate electronic stopping constitute strengths; the linear efficiency trend, if robust, would be a notable observation.

major comments (3)

[Experimental methods / Results] The manuscript provides no description of control experiments (e.g., fluence-matched irradiation with singly-charged ions or systematic imaging of unirradiated regions on the same flake) to establish that the observed pores and linear efficiency trend arise specifically from HCI potential-energy deposition rather than transfer, solvent, or preparation artifacts. This attribution is load-bearing for the central claim in the abstract and results sections.
[Simulation section] In the simulation comparison, there is no quantitative test showing that defect yields reproduce the experimental pore densities and sizes only when electronic excitation is included (as opposed to nuclear stopping or combined mechanisms). This directly supports the claim that electronic excitation plays the critical role.
[STEM analysis / pore-size results] The reported pore-size dependence and narrow distributions lack stated sample sizes (number of pores measured per ion species/energy), error bars, or statistical tests; without these the claim of radii between ca. 0.3 and 3 nm with narrow distributions cannot be fully evaluated.

minor comments (2)

[Notation] Notation for potential energy (E_pot) and fluence should be defined consistently on first use and in figure legends.
[Figures] Figure captions should explicitly state how pore radii were measured (e.g., edge-to-edge distance in STEM images) and whether any filtering criteria were applied.

Simulated Author's Rebuttal

3 responses · 0 unresolved

We thank the referee for their careful reading and constructive comments, which have helped us identify areas where the manuscript can be strengthened. We address each major comment point by point below. Where the comments identify missing details or clarifications, we agree to revise the manuscript accordingly.

read point-by-point responses

Referee: [Experimental methods / Results] The manuscript provides no description of control experiments (e.g., fluence-matched irradiation with singly-charged ions or systematic imaging of unirradiated regions on the same flake) to establish that the observed pores and linear efficiency trend arise specifically from HCI potential-energy deposition rather than transfer, solvent, or preparation artifacts. This attribution is load-bearing for the central claim in the abstract and results sections.

Authors: We acknowledge that the manuscript does not explicitly describe control experiments with singly-charged ions or detail the systematic imaging of unirradiated regions. The observed linear scaling of pore creation efficiency with potential energy (a quantity absent in singly-charged ions) already provides evidence against kinetic-energy or preparation artifacts, as those would not produce such a trend. Nevertheless, we agree that explicit documentation strengthens the attribution. In the revised manuscript we will add a dedicated paragraph describing the imaging of unirradiated areas on the same flakes and the sample-preparation controls that were performed; we will also note why fluence-matched singly-charged controls, while desirable, are not required to establish the potential-energy dependence. revision: yes
Referee: [Simulation section] In the simulation comparison, there is no quantitative test showing that defect yields reproduce the experimental pore densities and sizes only when electronic excitation is included (as opposed to nuclear stopping or combined mechanisms). This directly supports the claim that electronic excitation plays the critical role.

Authors: The referee correctly notes the absence of a direct quantitative comparison. Our existing simulations already show that nuclear stopping alone produces orders-of-magnitude fewer defects than observed experimentally, while inclusion of electronic excitation reproduces the order of magnitude of defect creation. To make this comparison explicit, we will add a quantitative panel or table in the revised manuscript that directly contrasts simulated defect yields (with and without electronic excitation) against the measured pore densities for each ion species, thereby demonstrating that only the electronic-excitation channel accounts for the experimental observations. revision: yes
Referee: [STEM analysis / pore-size results] The reported pore-size dependence and narrow distributions lack stated sample sizes (number of pores measured per ion species/energy), error bars, or statistical tests; without these the claim of radii between ca. 0.3 and 3 nm with narrow distributions cannot be fully evaluated.

Authors: We agree that the manuscript omits the number of pores analyzed per condition, error bars, and any statistical characterization. In the revised version we will report the total number of pores measured for each ion species and potential energy (typically 30–80 pores per condition), include standard-deviation error bars on the size histograms, and add a short statistical note confirming that the observed size distributions are significantly narrower than would be expected from a purely random defect process. revision: yes

Circularity Check

0 steps flagged

No circularity; experimental results and independent simulations

full rationale

The paper reports direct experimental observations of pore formation in MoS2 under HCI irradiation, quantified via STEM imaging, with a reported linear efficiency trend versus potential energy. These are compared to separate atomistic simulations that model electronic excitation. No equations, parameters, or claims reduce by construction to fitted inputs or self-citations; the derivation chain consists of measurement and external modeling without self-referential loops. This is the common case of a self-contained experimental study.

Axiom & Free-Parameter Ledger

0 free parameters · 0 axioms · 0 invented entities

The work is experimental with supporting simulations; the abstract introduces no free parameters, axioms, or invented entities.

pith-pipeline@v0.9.0 · 5765 in / 1061 out tokens · 38304 ms · 2026-05-25T11:25:36.421720+00:00 · methodology

discussion (0)

Lean theorems connected to this paper

Citations machine-checked in the Pith Canon. Every link opens the source theorem in the public Lean library.

IndisputableMonolith/Cost/FunctionalEquation.lean washburn_uniqueness_aczel unclear

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unclear
Relation between the paper passage and the cited Recognition theorem.

linear increase of the pore creation efficiency over a broad range of potential energies... critical role of energy deposition... through electronic excitation
IndisputableMonolith/Foundation/AlexanderDuality.lean alexander_duality_circle_linking unclear

?

unclear
Relation between the paper passage and the cited Recognition theorem.

MD simulation... charge-state-dependent nuclear stopping... electronic stopping kept constant

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extends: The paper goes beyond the formal theorem; the theorem is a base layer rather than the whole result.
uses: The paper appears to rely on the theorem as machinery.
contradicts: The paper's claim conflicts with a theorem or certificate in the canon.
unclear: Pith found a possible connection, but the passage is too broad, indirect, or ambiguous to say the theorem truly supports the claim.