Nanomechanics of few-layer materials: do individual layers slide upon folding?

• Ronaldo J. C. Batista,
• Rafael F. Dias,
• Ana P. M. Barboza,
• Alan B. de Oliveira,
• Taise M. Manhabosco,
• Thiago R. Gomes-Silva,
• Matheus J. S. Matos,
• Andreij C. Gadelha,
• Cassiano Rabelo,
• Luiz G. L. Cançado,
• Ado Jorio,
• Hélio Chacham and
• Bernardo R. A. Neves

Beilstein J. Nanotechnol. 2020, 11, 1801–1808, doi:10.3762/bjnano.11.162

• folded 2D material. In principle, the model describes any 2D material, and its predictions are corroborated by comparison with classical molecular dynamics simulations and to results of previous investigations on graphene and talc. Because folds naturally occur in flakes of varying thickness

Three-dimensional solvation structure of ethanol on carbonate minerals

• Hagen Söngen,
• Ygor Morais Jaques,
• Peter Spijker,
• Christoph Marutschke,
• Stefanie Klassen,
• Ilka Hermes,
• Ralf Bechstein,
• Lidija Zivanovic,
• John Tracey,
• Adam S. Foster and
• Angelika Kühnle

Beilstein J. Nanotechnol. 2020, 11, 891–898, doi:10.3762/bjnano.11.74

• Information File 1, where we also discuss the robustness and reproducibility of the AFM results. Molecular dynamics simulations We employed molecular dynamics simulations to model both calcite and magnesite with their (10.4) surface exposed as a nine layer crystal with three surface unit cells in the

Quantitative determination of the interaction potential between two surfaces using frequency-modulated atomic force microscopy

• Nicholas Chan,
• Carrie Lin,
• Tevis Jacobs,
• Robert W. Carpick and
• Philip Egberts

Beilstein J. Nanotechnol. 2020, 11, 729–739, doi:10.3762/bjnano.11.60

• mechanics models [22][23][24][25] to allow better visualization of surface interactions. While useful insights can be obtained using fully atomistic simulations, such as molecular dynamics simulations or density functional theory, these techniques are impractical for describing larger contacts with a large

A novel dry-blending method to reduce the coefficient of thermal expansion of polymer templates for OTFT electrodes

• Xiangdong Ye,
• Bo Tian,
• Yuxuan Guo,
• Fan Fan and
• Anjiang Cai

Beilstein J. Nanotechnol. 2020, 11, 671–677, doi:10.3762/bjnano.11.53

• the influence of fullerene (C60) on the CTE of Araldite LY 5052/Aradur HY 5052 cross-linked epoxy resin by molecular dynamics simulations. The CTE was minimized by adding a maximum of 15.9 wt % fullerene to the LY/HY/C60 epoxy system. Liu et al. [14] selected MCM-41 mesoporous silica nanoparticles

Understanding nanoparticle flow with a new in vitro experimental and computational approach using hydrogel channels

• Armel Boutchuen,
• Dell Zimmerman,
• Abdollah Arabshahi,
• John Melnyczuk and
• Soubantika Palchoudhury

Beilstein J. Nanotechnol. 2020, 11, 296–309, doi:10.3762/bjnano.11.22

• applicable for modeling smaller NP systems or optimizing less detailed simulations due to their increased complexity and computational cost [17]. The coarse grained molecular dynamics simulations can characterize larger systems over time scales greater than 1 ms [21]. These slightly coarser models simulate a

Nonclassical dynamic modeling of nano/microparticles during nanomanipulation processes

• Moharam Habibnejad Korayem,
• Ali Asghar Farid and
• Rouzbeh Nouhi Hefzabad

Beilstein J. Nanotechnol. 2020, 11, 147–166, doi:10.3762/bjnano.11.13

• of nanoparticles. To model this process, previous studies employed classical continuum mechanics and molecular dynamics simulations which had certain limitations; the former does not consider size effects at the nanoscale while the latter is time consuming and faces computational restrictions. To

Internalization mechanisms of cell-penetrating peptides

• Ivana Ruseska and
• Andreas Zimmer

Beilstein J. Nanotechnol. 2020, 11, 101–123, doi:10.3762/bjnano.11.10

• peptides to directly cross the cellular membranes involves the formation of pores. A theoretical model using molecular dynamics simulations was proposed for the translocation of the TAT peptide, which explains the relevance of peptide–phosphate interaction during the pore formation [47]. This theoretical

Effects of surface charge and boundary slip on time-periodic pressure-driven flow and electrokinetic energy conversion in a nanotube

• Mandula Buren,
• Yongjun Jian,
• Yingchun Zhao,
• Long Chang and
• Quansheng Liu

Beilstein J. Nanotechnol. 2019, 10, 1628–1635, doi:10.3762/bjnano.10.158

• independent of the surface charge. However, recent theoretical and experimental results have shown that the surface charge affects the slip length. Joly et al. [18] used molecular dynamics simulations to find the relationship between slip length and surface charge density. The reason is that there exists an

Choosing a substrate for the ion irradiation of two-dimensional materials

• Egor A. Kolesov

Beilstein J. Nanotechnol. 2019, 10, 531–539, doi:10.3762/bjnano.10.54

• taking place considering the yield, one should refer to the solid curves for sputtering in Figure 1 within the range specified in Table 1. The results presented in Table 1 are in agreement with molecular dynamics simulations on the subject [1]. It should be noted that the sputtered substrate atoms can

Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

• Adolfo B. Poma,
• Horacio V. Guzman,
• Mai Suan Li and
• Panagiotis E. Theodorakis

Beilstein J. Nanotechnol. 2019, 10, 500–513, doi:10.3762/bjnano.10.51

• , Figure 7c presents the RMSF results for all fibrils. We observe that the disordered domains (N- and C-terminus) in α-syn are very flexible in comparison with Aβ fibrils. Conclusion We have carried out molecular dynamics simulations to study the elastic properties of two families of biological fibrils

Sub-wavelength waveguide properties of 1D and surface-functionalized SnO₂ nanostructures of various morphologies

• Venkataramana Bonu,
• Binaya Kumar Sahu,
• Arindam Das,
• Sankarakumar Amirthapandian,
• Sandip Dhara and
• Harish C. Barshilia

Beilstein J. Nanotechnol. 2019, 10, 379–388, doi:10.3762/bjnano.10.37

• section. OTS molecules are more reactive with –OH groups on the metal oxide surfaces [31][32][33]. Molecular dynamics simulations revealed that the OB site of SnO2 was the most preferable site for the formation of –OH groups [34][35]. Thus, OTS binds dominantly at OB sites over the OP sites of SnO2 NPs

Mechanism of silica–lysozyme composite formation unravelled by in situ fast SAXS

• Tomasz M. Stawski,
• Daniela B. van den Heuvel,
• Rogier Besselink,
• Dominique J. Tobler and
• Liane G. Benning

Beilstein J. Nanotechnol. 2019, 10, 182–197, doi:10.3762/bjnano.10.17

• close to that of the protein molecule [22][53]. Su et al. [54] found that at small surface coverage the lysozyme attaches to silica NPs in a side on orientation, and recently the molecular dynamics simulations by Hildebrand et al. [55] also further confirmed that the side-on orientation of lysozyme with

Sputtering of silicon nanopowders by an argon cluster ion beam

• Xiaomei Zeng,
• Vasiliy Pelenovich,
• Zhenguo Wang,
• Wenbin Zuo,
• Sergey Belykh,
• Alexander Tolstogouzov,
• Dejun Fu and
• Xiangheng Xiao

Beilstein J. Nanotechnol. 2019, 10, 135–143, doi:10.3762/bjnano.10.13

• nanowires. There are many molecular dynamics simulations using the collision cascade theory and, at the same time, only a few experimental studies on the interaction of monomer and cluster projectiles with nanodimensional systems. Using a MD simulation, Kissel et al. [16] have studied the effect of the

Accurate control of the covalent functionalization of single-walled carbon nanotubes for the electro-enzymatically controlled oxidation of biomolecules

• Naoual Allali,
• Veronika Urbanova,
• Mathieu Etienne,
• Xavier Devaux,
• Martine Mallet,
• Brigitte Vigolo,
• Jean-Joseph Adjizian,
• Chris P. Ewels,
• Sven Oberg,
• Alexander V. Soldatov,
• Edward McRae,
• Yves Fort,
• Manuel Dossot and
• Victor Mamane

Beilstein J. Nanotechnol. 2018, 9, 2750–2762, doi:10.3762/bjnano.9.257

• impurities in the case of mediated electron transfer play no role in the oxidation of NADH, contrary to what has been presented in the literature for other systems. We also underline the interest of using molecular dynamics simulations to evaluate the important role of the linker, which certainly depends on

Surface energy of nanoparticles – influence of particle size and structure

• Dieter Vollath,
• Franz Dieter Fischer and
• David Holec

Beilstein J. Nanotechnol. 2018, 9, 2265–2276, doi:10.3762/bjnano.9.211

• particle size. Different approaches, such as classical thermodynamics calculations, molecular dynamics simulations, and ab initio calculations, exist to predict this quantity. Generally, considerations based on classical thermodynamics lead to the prediction of decreasing values of the surface energy with

• be expected by the formation of a disordered or quasi-liquid layer at the surface. The atomistic approach, based either on molecular dynamics simulations or ab initio calculations, generally leads to values with an opposite tendency. However, it is shown that this result is based on an insufficient

• and becomes liquid-like. Therefore, as γliquid < γsolid is always valid, an increase of the surface energy with decreasing particle size cannot be expected. Approach to the surface energy from atomistic calculations Molecular dynamics simulations Molecular dynamics simulations describe the spatial

The inhibition effect of water on the purification of natural gas with nanoporous graphene membranes

• Krzysztof Nieszporek,
• Tomasz Pańczyk and
• Jolanta Nieszporek

Beilstein J. Nanotechnol. 2018, 9, 1906–1916, doi:10.3762/bjnano.9.182

• Department of Analytical Chemistry and Instrumental Analysis, Maria Curie-Sklodowska University, M. C. Sklodowska sq. 3, 20-031 Lublin, Poland 10.3762/bjnano.9.182 Abstract Molecular dynamics simulations are used to investigate the inhibiting effect of water on the natural gas separation with nanoporous

Free-radical gases on two-dimensional transition-metal disulfides (XS₂, X = Mo/W): robust half-metallicity for efficient nitrogen oxide sensors

• Chunmei Zhang,
• Yalong Jiao,
• Fengxian Ma,
• Sri Kasi Matta,
• Steven Bottle and
• Aijun Du

Beilstein J. Nanotechnol. 2018, 9, 1641–1646, doi:10.3762/bjnano.9.156

• meV and 3 Å, suggesting that water is physically adsorbed on the surface of the WS2 nanosheet. Monolayer MoS2 [38] and multilayer MoS2 field effect transistors [17] for sensing NO at room temperature have been fabricated experimentally. In this work, the ab initio molecular dynamics simulations at

Atomic-level characterization and cilostazol affinity of poly(lactic acid) nanoparticles conjugated with differentially charged hydrophilic molecules

• María Francisca Matus,
• Martín Ludueña,
• Cristian Vilos,
• Iván Palomo and
• Marcelo M. Mariscal

Beilstein J. Nanotechnol. 2018, 9, 1328–1338, doi:10.3762/bjnano.9.126

• determine the spatial distribution of cilostazol in polymeric NPs and to explore its potential use in this kind of drug delivery system. Experimental Characterization of copolymer structures by all-atom molecular dynamics simulations The poly(lactic acid) core PLA polymer chains were built in three

Dynamics and fragmentation mechanism of (C₅H₄CH₃)Pt(CH₃)₃ on SiO₂ surfaces

• Kaliappan Muthukumar,
• Harald O. Jeschke and
• Roser Valentí

Beilstein J. Nanotechnol. 2018, 9, 711–720, doi:10.3762/bjnano.9.66

• molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our

• originally bonded to Pt, fragments and bonds to the adjacent vacant site, as observed in the 3 × 3 × 4 cell (see Figure 2d and Figure 3e). These DFT relaxed structures (as shown in Figure 3b–e) are considered as starting point for molecular dynamics simulations. The trajectory of the MD simulations for the

• methylcyclopentadienyl ring. Removal of the methylcyclopentadienyl ring from (C5H4CH3)Pt(CH3)3 has an activation energy of +0.771 eV, which leaves the Pt(CH3)3 part of the precursor bound to the substrate. The formation of Pt(CH3)3 in vacuum is observed in our molecular dynamics simulations. However, neither its

Review: Electrostatically actuated nanobeam-based nanoelectromechanical switches – materials solutions and operational conditions

• Liga Jasulaneca,
• Jelena Kosmaca,
• Raimonds Meija,
• Jana Andzane and
• Donats Erts

Beilstein J. Nanotechnol. 2018, 9, 271–300, doi:10.3762/bjnano.9.29

• experiment was carried out with an AFM in amplitude modulation mode complemented with molecular dynamics simulations. An exponential wear rate dependence on the peak force load was found, suggesting that lower contact forces are needed to reduce the wear rate. It should be noted that for soft materials

Patterning of supported gold monolayers via chemical lift-off lithography

• Liane S. Slaughter,
• Kevin M. Cheung,
• Sami Kaappa,
• Huan H. Cao,
• Qing Yang,
• Thomas D. Young,
• Andrew C. Serino,
• Sami Malola,
• Jana M. Olson,
• Stephan Link,
• Hannu Häkkinen,
• Anne M. Andrews and
• Paul S. Weiss

Beilstein J. Nanotechnol. 2017, 8, 2648–2661, doi:10.3762/bjnano.8.265

• found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure. Keywords: chemical patterning; hybrid material; monolayer; soft lithography; two-dimensional material; Introduction Chemical lift

• assumptions made above regarding the structure of Au–alkanethiolate monolayers on PDMS are in agreement with estimates of the stoichiometry of the Au–alkanethiolate monolayer calculated through molecular dynamics simulations. Atomic rearrangement during the CLL process was modeled using density functional

• agreement with indirect evidence that a monolayer of Au is removed during CLL, molecular dynamics simulations converged on a stoichiometry of ≤1.5 Au atoms per thiol. These simulations also demonstrate that the lifted-off Au atoms are in an environment distinct from that at the surface of the bulk Au and

Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips

• Sumit Tewari,
• Koen M. Bastiaans,
• Milan P. Allan and
• Jan M. van Ruitenbeek

Beilstein J. Nanotechnol. 2017, 8, 2389–2395, doi:10.3762/bjnano.8.238

• repeatable cycles, which is interpreted as evidence for a crystalline tip structure. This work on mechanical annealing was inspired by earlier break junction and STM experiments, supported by molecular dynamics simulations [25][27][28]. A first application of this approach for a Au STM tip over a graphene

• imaged, and we find that the shape of the STM tip evolves surprisingly smoothly and reproducibly towards an atomically sharp and symmetric structure of the second layer from the tip apex atom, starting from any random and poorly defined tip shapes. As has been illustrated by molecular dynamics

• simulations [25], the mechanical annealing cycles lead to a more regular atomic packing at both sides of the junction. The smooth evolution of this alignment observed here suggests that the process evolves through gradual shifts in packing and orientation of the layers farther away from the apex atom. Based

Molecular dynamics simulations of nanoindentation and scratch in Cu grain boundaries

• Shih-Wei Liang,
• Ren-Zheng Qiu and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2017, 8, 2283–2295, doi:10.3762/bjnano.8.228

Comprehensive investigation of the electronic excitation of W(CO)₆ by photoabsorption and theoretical analysis in the energy region from 3.9 to 10.8 eV

• Mónica Mendes,
• Khrystyna Regeta,
• Filipe Ferreira da Silva,
• Nykola C. Jones,
• Søren Vrønning Hoffmann,
• Gustavo García,
• Chantal Daniel and
• Paulo Limão-Vieira

Beilstein J. Nanotechnol. 2017, 8, 2208–2218, doi:10.3762/bjnano.8.220

• initio molecular dynamics simulations of focused electron beam induced deposition (FEBID) precursor molecules adsorbed on fully and partially hydroxylated SiO2 surfaces [24]. Electron-induced reactions in FEBID processes are initiated by low-energy secondary electrons rather than the high-energy primary

Atomic structure of Mg-based metallic glass investigated with neutron diffraction, reverse Monte Carlo modeling and electron microscopy

• Rafał Babilas,
• Dariusz Łukowiec and
• Laszlo Temleitner

Beilstein J. Nanotechnol. 2017, 8, 1174–1182, doi:10.3762/bjnano.8.119

• the ternary Mg–Cu–Y glasses. Gao et al. [11] performed ab initio molecular dynamics simulations of the structural evolution of a Mg65Cu25Y10 alloy from liquid to glass state. Moreover, Laws et al. [12] provided an analysis of the dynamic crystallization in Mg65Cu25Y10 bulk metallic glass using