Felice C. Simeone's research while affiliated with Institute of Science and Technology for Ceramics and other places

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Publications (33)


FIG. 1
FIG. 2
FIG. 3 The use of Supervised and Unsupervised Machine ML in predictive nanoinformatics: Supervised ML methods (Decision Trees, Random Forest, Neural Networks etc.) are often used to create or improve predictive models, while Unsupervised ML methods (Clustering, Self-Organizing Maps, etc.) are more often used to group and explore nanomaterials properties or in combination with Supervised ML methods.
FIG. 5 (a) All-atom MD of nanoparticle/membrane/water system, (b) all-atom MD binding free energy for three different sizes of Ag nanoparticles, (c) all-atom MD binding free energy for silica for three nanoparticle sizes (graphs reproduced from Ref. [120] with permission from the Royal Society of Chemistry). (d) Standard uniform CG model and the new core-shell CG model, reproduced with permission from Singhal et al., MDPI Nanomaterials, 2022[158]. (e) With increasing hydrophobicity, the mechanism of direct insertion into the model lung membrane switches to a wrapping mechanism..
FIG. 6 (a) Schematic atomistic model of an NPC. A "soft corona" layer (dashed line) of loosely bound proteins surrounds a "hard" corona layer (continuous black line), proximal to the ENM's surface. Even for spherical nanoparticles, the overall shape and biophysical properties of the NPC surface will depend on its composition. (b) Comparing values of the SASA H for various coronas around a 4 nm spherical silica nanoparticle (dashed) with the values calculated for similar protein aggregates without including a nanoparticle (continuous). (c) Atomistic corona models allow the identification of protein residues that may play significant roles at the nanoparticle-protein interfaces. (d-e-f) Building an atomistic model of an NPC by sequential docking of protein structures (mucin, preequilibrated using MD) on a spherical silica nanoparticle. Mesoscopic descriptors such as SASA H can be estimated as statistical averages over results from docking multiple representative structures.

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A computational view on nanomaterial intrinsic and extrinsic features for nanosafety and sustainability
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  • Full-text available

June 2023

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266 Reads

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5 Citations

Materials Today

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Alicja Mikolajczyk

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In recent years, an increasing number of diverse Engineered Nano-Materials (ENMs), such as nanoparticles and nanotubes, have been included in many technological applications and consumer products. The desirable and unique properties of ENMs are accompanied by potential hazards whose impacts are difficult to predict either qualitatively or in a quantitative and predictive manner. Alongside established methods for experimental and computational characterisation, physics-based modelling tools like molecular dynamics are increasingly considered in Safe and Sustainability-by-design (SSbD) strategies that put user health and environmental impact at the centre of the design and development of new products. Hence, the further development of such tools can support safe and sustainable innovation and its regulation. This paper stems from a community effort and presents the outcome of a four-year-long discussion on the benefits, capabilities and limitations of adopting physics-based modelling for computing suitable features of nanomaterials that can be used for toxicity assessment of nanomaterials in combination with data-based models and experimental assessment of toxicity endpoints. We review modern multiscale physics-based models that generate advanced system-dependent (intrinsic) or time- and environment-dependent (extrinsic) descriptors/features of ENMs (primarily, but not limited to nanoparticles, NPs), with the former being related to the bare NPs and the latter to their dynamic fingerprinting upon entering biological media. The focus is on (i) effectively representing all nanoparticle attributes for multicomponent nanomaterials, (ii) generation and inclusion of intrinsic nanoform properties, (iii) inclusion of selected extrinsic properties, (iv) the necessity of considering distributions of structural advanced features rather than only averages. This review enables us to identify and highlight a number of key challenges associated with ENMs’ data generation, curation, representation and use within machine learning or other advanced data-driven models to ultimately enhance toxicity assessment. Finally, the set up of dedicated databases as well as the development of grouping and read-across strategies based on the mode of action of ENMs using omics methods are identified as emerging methodologies for safety assessment and reduction of animal testing.

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Figure 1. Viability of RAW 264.7 cells versus amount of ZnO. Dots: Experimental values. Thin curve: least-squares fitting curve, 95% confidential (dashes) and prediction interval (small dashes). Thick curve: Bayesian fitting curve (i.e. mean values of EC 50 and s.) Triangles: predicted responses at doses not measured experimentally surrounded by a visual representation (violins) of the probability of the values drawn from the posterior probability: the width of a violin is proportional to the frequency of the values of the response.
Figure 3. Fitting curves for the sub-datasets containing individual responses at doses 4, 16, 64 mg/L of ZnO nanoparticles (sampling Scheme 2). Dots: experimental response; least-squares fitting curve obtained with the values of EC 50 and s reported in each plot. The symbol '.#R' indicates the inability for the algorithm to calculate confidence intervals; Bayesian curves were obtained by using (mean) values of EC50 and s reported. Full output in Table S7.
Figure 4. Fitting curves for the datasets generated by sampling Scheme 4 (doses 32, 64, and 128 mg/L of ZnO nanoparticles). Dots: experimental response; least-squares fitting curves obtained with the values of EC 50 and s reported in each plot. The symbol '.#R' indicates the inability for the algorithm to calculate confidence intervals; Bayesian curves were obtained by using the (mean) values of EC 50 and s reported. Results detailed in Table S8.
Figure 5. Fitting curves for the sub-datasets containing individual responses for the central doses 16 and 32 mg/L of ZnO nanoparticles. Dots: experimental response; least-squares fitting curves obtained with the values of EC50 and s reported in each plot. The symbol '.#R' indicates the inability for the algorithm to calculate confidence intervals; Bayesian mean curve obtained by using the mean values of EC 50 and s reported. Results detailed in Table S10.
Quantifying uncertainty in dose–response screenings of nanoparticles: a Bayesian data analysis

March 2022

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39 Reads

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1 Citation

Fitting theoretical models to experimental data for dose-response screenings of nanoparticles yields values of several hazard metrics that can support risk management. In this paper, we describe a Bayesian approach to the analysis of dose-response data for nanoparticles that takes into account multiple sources of uncertainty. Specifically, we develop a Bayesian model for the analysis of data for the cytotoxicity of ZnO nanoparticles that follow the log-logistic equation. This model reproduces the unequal variance across doses observed in the experimental data, incorporates information about the sensitivity of the cytotoxicity assay used (i.e. resazurin), and complements experimental data with historical information about the system. The model determines probability distributions for multiple values of toxicity potency (EC50), and exponential decay (the slope s); these distributions provide a direct measure of uncertainty in terms of probabilistic credibility intervals. By substituting these distributions in the log-logistic equation, we determine upper and lower limits of the benchmark dose (BMD), corresponding to upper and lower limits of credibility intervals with 95% probability given the experimental data, multiple sources of uncertainty, and historical information. In view of a reduction of costs and time of dose-response screenings, we use the Bayesian model for the cytotoxicity of ZnO nanoparticles to identify the experimental design that uses the minimum number of data while reducing uncertainty in the estimation of both fitting parameters and BMD.



Assessment of Cytotoxicity of Metal Oxide Nanoparticles on the Basis of Fundamental Physical-Chemical Parameters: a Robust Approach to Grouping

August 2019

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54 Reads

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21 Citations

Environmental science. Nano.

Due to their sizes, nanoparticles can penetrate into biological systems easily; anticipating their harmful interactions at the cellular level makes it possible to safeguard workers, consumers, and the environment effectively. Decades of research have identified key properties of nanomaterials that induce adverse responses, and this evidence suggests that the toxicity of a nanoparticle can be inferred from its abiotic behavior. Experimental physical-chemical characterization of nanoparticles, however, is complex and time consuming, and the absence of any standardized method has generated controversial results. This paper shows how known adverse modes of action of nanoparticles arise from fundamental physical-chemical parameters that don’t need any experimental quantification. We show that cytotoxicity of metal oxides in different types of in-vitro systems, which include E. coli, rat alveolar macrophages, human bronchial epithelial cells, Daphnia magna, and Aliivibrio fisheri, can be foreseen on the basis of the values of oxidation number (Z) and ionic potential (IP) of the cation, and surface reducibility (SR), and redox reactivity (RR) of the oxide. Importantly, the values of these fundamental physical-chemical parameters can be easily deduced from the chemical formula of the nanoparticle with the help of a periodic table. Combining these parameters in a naïve Bayes classifier, a robust probabilistic model that can be run on a pocket calculator, makes it possible to determine the most probable level of toxicity of a nanoparticle given its composition. Results indicate that the probability that nano-oxides exhibit very high cytotoxicity (EC50 < 10-3 mol∙L-1) decreases with increasing oxidation number Z of the cation; high values of Z, however, may become unstable and activate adverse redox processes; in contrast, stable, redox-inert reducible oxides tend to be, probabilistically, less toxic than oxidizable ones.


Fig. 1. Schematic representation of the pilot plant for continuous sonochemical functionalization of textiles with bactericidal nanoparticles.
Criteria for assigning exposure scores based on fre- quency of processing of nanoparticles.
Criteria for assigning exposure scores based on duration of operation.
Criteria for assigning exposure scores for processing of nanoparticles.
Hazard scores for bactericidal nanoparticles based on their expected toxicities.
Assessing occupational risk in designs of production processes of nano-materials

March 2019

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63 Reads

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18 Citations

NanoImpact

Building safe production places can protect workers more effectively than managing risks in a plant that has been conceived without taking into account safety upfront. In this paper, we describe an approach to assessing potential risks already at the stage of design of production processes of nano-enabled products. In a chemical plant, risk results from the combination of hazard of the chemicals and exposure of workers to them. Toxicological profiles of novel nanomaterials, however, are generally unknown; in addition, the impossibility of measuring exposure in a plant that does not exist yet exacerbates the challenge of designing safe production processes. This paper describes a simple method to formulate realistic hypotheses about the toxicity of untested nanoparticles and derives a simplified model of exposure that enables non-specialists (e.g., managers, engineers) to analyze potential risks in projects of future production plants. As an example of analysis of risk in the absence of experimental data, the paper describes the procedure to generate maps of risks of two envisaged production chains of antibacterial textiles: 1) sonochemical synthesis and deposition of bactericidal nanoparticles, and 2) spray deposition of suspension of bactericidal nanoparticles.



Hazard Screening Methods for Nanomaterials: A Comparative Study

February 2018

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361 Reads

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23 Citations

International Journal of Molecular Sciences

Hazard identification is the key step in risk assessment and management of manufactured nanomaterials (NM). However, the rapid commercialisation of nano-enabled products continues to out-pace the development of a prudent risk management mechanism that is widely accepted by the scientific community and enforced by regulators. However, a growing body of academic literature is developing promising quantitative methods. Two approaches have gained significant currency. Bayesian networks (BN) are a probabilistic, machine learning approach while the weight of evidence (WoE) statistical framework is based on expert elicitation. This comparative study investigates the efficacy of quantitative WoE and Bayesian methodologies in ranking the potential hazard of metal and metal-oxide NMs—TiO2, Ag, and ZnO. This research finds that hazard ranking is consistent for both risk assessment approaches. The BN and WoE models both utilize physico-chemical, toxicological, and study type data to infer the hazard potential. The BN exhibits more stability when the models are perturbed with new data. The BN has the significant advantage of self-learning with new data; however, this assumes all input data is equally valid. This research finds that a combination of WoE that would rank input data along with the BN is the optimal hazard assessment framework.



Fabrication of Paper-Templated Structures of Noble Metals

February 2017

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78 Reads

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20 Citations

Advanced Materials Technologies

Advanced Materials Technologies

This manuscript describes a simple and rapid method for fabricating free-standing structures composed primarily (>94% w/w, and 55–80 at%) of noble metals (e.g., gold, silver, platinum, etc.) and having physical morphologies that resemble paper, thread, or fabric. In this method, templates (i.e., pieces of paper, or cotton fabric) are loaded with aqueous solutions of salts of noble metals, and then the cellulosic component is burned off in a furnace held at high temperatures (i.e., from 550 °C to 800 °C, depending on the procedure, in air). Even though the environment in a furnace is ostensibly oxidizing (e.g., hot air), the metal ions are reduced to elemental metal and form paper-templated or fabric-templated structures that have morphologies similar to that of the material from which they were derived (i.e., paper or fabric). Paper-templated structures are fibrous, permeable to gases and liquides, electrically conductive, and in some cases (e.g., paper-templated gold and paper-templated platinum structures), their surfaces are electroactive. The surface areas of paper-templated structures are more than 20 times higher than their projected areas. Paper-templated structures thus have properties that make them potentially useful in catalysis, sensing, and electroanalysis.


Tunneling Across SAMs Containing Oligophenyl Groups

April 2016

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103 Reads

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45 Citations

The Journal of Physical Chemistry C

This paper reports rates of charge tunneling across self-assembled monolayers (SAMs) of compounds containing oligophenyl groups, supported on gold and silver, using Ga2O3/EGaIn as the top electrode. It compares the attenuation constant, β, and the pre-exponential parameter, J0, of the simplified Simmons equation, across oligophenyl groups (R = Phn; n = 1, 2, 3), with three different anchoring groups (thiol, HSR; methanethiol, HSCH2R; and acetylene, HC≡CR) that attach R to the template-stripped gold or silver substrates. The results demonstrate that the structure of the molecular linker between the anchoring group (-S- or -C≡C-) and the oligophenyl moiety significantly influences rates of charge transport. SAMs of SPhn and C≡CPhn on gold show similar values of β and log|J0| (β = 0.28 ± 0.03 Å-1 and log|J0| = 2.7 ± 0.1 for Au/SPhn; β = 0.30 ± 0.02 Å-1 and log|J0| = 3.0 ± 0.1 for Au/C≡CPhn). The introduction of a single intervening methylene (CH2) group between the anchoring sulfur atom and the aromatic units generates SAMs of SCH2Phn, and increases β to ~0.66 ± 0.06 Å-1 on both gold and silver substrates. (For n-alkanethiolates on gold the corresponding values are β = 0.76 ± 0.03 Å-1 and log|J0| = 4.2 ± 0.2). Density Functional Theory (DFT) calculations indicate that the highest occupied molecular orbitals (HOMOs) of both SPhn and C≡CPhn extend beyond the anchoring group and onto the phenyl rings; SAMs composed of these two groups of molecules result in indistinguishable rates of charge transport. The introduction of the CH2 group, to generate SCH2Phn, disrupts the delocalization of orbitals, localizes the HOMO on the anchoring sulfur atom, and results in the experimentally observed increase in β to a value closer to that of a SAM of n-alkylthiolate molecules.


Citations (27)


... eNanomapper, Nanosafety Data Interface) to FAIRify and harmonize nanotoxicity data (Furxhi et al., 2020a;Furxhi, 2022;Jeliazkova et al., 2021;Papadiamantis et al., 2020). Through the FAIRification of nanotoxicity (meta)data, it can be (re)used, retrieved and stored more efficiently within databases for modelling purposes (Mancardi et al., 2023;Scott-Fordsmand & Amorim, 2023;Yan et al., 2023). ...

Reference:

Building species trait-specific nano-QSARs: Model stacking, navigating model uncertainties and limitations, and the effect of dataset size
A computational view on nanomaterial intrinsic and extrinsic features for nanosafety and sustainability

Materials Today

... Also, being positively charged and bearing a quaternary ammonium group, HEC is reported to be highly active in preventing Gram (− ) bacteria infection and resistance (Alfei and Schito, 2020;Jain et al., 2014;Kenawy et al., 2007). AgHEC has shown to be a good alternative to chloroquine, considering their risk/benefit profile, for use as antimicrobial (against Escherichia coli) and antiviral (against SARS-COV-2) agent in solution, as fabric coating and embedded in hydrogel scaffolds (Costa et al., 2022). Further, AgHEC showed enhanced antimicrobial activity against pathogenic strains compared to commercial Ag NMs (Marassi et al., 2018), i.e. improved product performance. ...

Eco design for Ag-based solutions against SARS-CoV-2 and E. coli

Environmental science. Nano.

... Mn 2+ ions are considered to be safe than other oxidation states due to their involvement in the enzymatic reactions in the body. The higher oxidation might have increased reactivity which will influence the biocompatibility and also can induce antioxidant behavior [120]. Mn 2+ ions are good in providing T 1 relaxation enhancement which is favorable for enhancing the signal intensity in MRI. ...

Assessment of Cytotoxicity of Metal Oxide Nanoparticles on the Basis of Fundamental Physical-Chemical Parameters: a Robust Approach to Grouping
  • Citing Article
  • August 2019

Environmental science. Nano.

... This means that this method had not been evaluated and investigated before and therefore the bias of the results of this method can be justified. On the other hand, the number of activities investigated in this study was very high compared to other studies (Simeone et al. 2019). About Boccuni et al.'s study (2020) it can be said that this study, in addition to using one of the important CB-based methods (ISO/TS 12901), used a new method designed by the authors, and the high risk of bias can be attributed to it (Boccuni et al. 2020). ...

Assessing occupational risk in designs of production processes of nano-materials

NanoImpact

... ML techniques can complete in vitro and in vivo toxicity assessment, reducing cost and time, minimizing the need for animal studies in toxicity tests, and improving toxicity prediction accuracy (Furxhi et al., 2019a). ML tools are gaining popularity for predicting toxicity because they integrate several information sources, such as physicochemical properties and exposure conditions to predict the safety of NPs (Schöning et al., 2018;Sheehan et al., 2018). ...

Hazard Screening Methods for Nanomaterials: A Comparative Study

International Journal of Molecular Sciences

... This Pt-modified carbon electrode showed excellent performance toward hydrogen evolution reaction (HER). By also using noble metals, Christodouleas fabricated highly conductive metallic free-standing sheets combining paper substrates, noble metal salts and pyrolysis (Christodouleas et al., 2017). Noble metal salts are added to filter paper and then treated at temperatures of around 550-800°C. ...

Fabrication of Paper-Templated Structures of Noble Metals
  • Citing Article
  • February 2017

Advanced Materials Technologies

Advanced Materials Technologies

... To thoroughly compare the impact of replacing anchoring groups, we analyzed the log |J| as a function of n C and fitted the data to eq 1 (Fig. 2H). The values of β = 0.91 ± 0.02 n C −1 and log |J 0 | = 2.10 ± 0.14 obtained for Se-SAMs are close to those of S-SAMs (β = 0.87 ± 0.03 n C −1 and log |J 0 | = 1.78 ± 0.18) and other SAMs composed of the alkyl chain formed by the nonthiolates system, NHCs (64), carboxyl (65), and alkyne (66). Thus, these junctions behave within error essentially the same and therefore we conclude that Se-SAMs form very similar tunneling barriers as Se-SAMs in agreement with the characterization results described above, from which we concluded that both types of SAMs have similar packing densities and heights. ...

Tunneling Across SAMs Containing Oligophenyl Groups
  • Citing Article
  • April 2016

The Journal of Physical Chemistry C

... The rectifying property was restored upon overnight white light irradiation. Charge transport through these Au-mSAM-MoS2-Pt-Ir probe junctions, considering the comparably long HS-C 10 H 21 molecule, was attributed to a combination of tunneling through a metal-semiconductor (MS) barrier and the mSAM layer [171]. The photoswitchable transport features were deduced from significant differences in the contact potentials of MoS2-trans-mSAM and MoS2-cis-mSAM ( Figure 14c). ...

Odd–Even Effects in Charge Transport across n -Alkanethiolate-Based SAMs
  • Citing Article
  • November 2014

Journal of the American Chemical Society

... We determined the thickness, d (in nm), of the nine monolayers using ADXPS.The values of d ( Figure S1) show that the nine monolayers have similar thickness (values of thickness are between 0.7 and 0.8 nm, AE 0.1 nm), which are comparable to the previously reported thickness (d = 0.9 nm) of octanoic acid on Ag TS . [19] This observation suggests the SAMs (of molecules 1-9)w ere formed with as imilar quality,d espite differences in saturation, and perhaps in conformation along the carbon backbone.Physisorbed molecules,such as solvent molecules,w ere not observed in the monolayers by XPS (Figures S2 and S3). ...

Replacing AgTSSCH2‐R with AgTSO2C‐R in EGaIn‐Based Tunneling Junctions Does Not Significantly Change Rates of Charge Transport
  • Citing Article
  • April 2014

Angewandte Chemie

... Because the surface Ga atoms of EGaIn readily form Ga-O bonds [27,30], the polar solvents containing oxygen atoms may cover the droplet's surface and cause it to behave similarly to a micelle. In contrast, in the non-polar solvents such as hexane and benzene, the surface of the EGaIn droplets is not likely to react with the solvent molecules to form Ga-C bonds [31]; however, it is still possible that the solvent molecules physically adsorb to the surface of the droplet. Thus, the interfacial energy of the EGaIn droplets in solvents is influenced by the types and polarity of solvents. ...

Introducing ionic and/or hydrogen bonds into the SAM//Ga2O3 top-interface of Ag(TS)/S(CH2)nT//Ga2O3/EGaIn junctions
  • Citing Article
  • May 2014

Nano Letters