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

• under-cosine shape, in other words, the atoms are sputtered mostly in the lateral direction [5]. This effect results in another prominent phenomenon called surface smoothing. Using molecular dynamics (MD) and Monte Carlo simulations it has been shown that the effect of the cluster impact depends on the

• 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

Hydrogen-induced plasticity in nanoporous palladium

• Markus Gößler,
• Eva-Maria Steyskal,
• Markus Stütz,
• Norbert Enzinger and
• Roland Würschum

Beilstein J. Nanotechnol. 2018, 9, 3013–3024, doi:10.3762/bjnano.9.280

• lower surface areas measured after compression tests [47]. Therefore, in our case of nanoporous palladium under compression a coarsening of the structure can be expected, giving rise to the length contraction. It has been shown using molecular dynamics (MD) simulations that plastic deformation at

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

• , the role of the PEG linker in the good electrochemical response was studied by molecular dynamics, which show that favorable interaction between the ETG units and water molecules prevents π-stacking of the ferrocene unit on the surface of the CNTs, therefore allowing for a good electron transfer

• simulation (structure and diameter close to that of (11,5)). The FcETG2 molecule grafted at the surface of the SWCNT model was oriented to simulate a ferrocene group in a π-stacking interaction (see below the molecular dynamics simulation) since the analysis is done in ultra-high vacuum. The distance between

• alkyl linker is completely inefficient for the mediated electron transfer process, while the polyethylene glycol spacers are efficient regardless of their length (in the range examined in this work) was puzzling, so we decided to investigate the role of the linker by molecular dynamics computation. The

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

• particle size is found. The main conclusion of this work is that surface energy values for the equivalent bulk materials should be used if detailed data for nanoparticles are not available. Keywords: ab initio calculations; classical thermodynamics; molecular dynamics simulation; surface energy; surface

Metal-free catalysis based on nitrogen-doped carbon nanomaterials: a photoelectron spectroscopy point of view

• Mattia Scardamaglia and
• Carla Bittencourt

Beilstein J. Nanotechnol. 2018, 9, 2015–2031, doi:10.3762/bjnano.9.191

• molecular dynamics combined with analytical potential and density functional theory methods, Lehtinen et al. reported on the influence of the ion kinetic energy and mass on the probability of defect formation during irradiation of suspended graphene sheets and single-walled CNTs [86]. Being proportional to

• . There are many other nonradiative relaxation channels in nanosystems that affect the excitation lifetimes. Reproduced with permission from [83], copyright 2010 American Institute of Physics. (d–i) Production of defects in graphene under ion irradiation as revealed by the analytical potential molecular

• dynamics: (d) simulation setup. (e, h) Probability for the formation of single and double vacancies as a function of the ion energy. The insets show the atomic structures of the reconstructed vacancies. (f) Average area of defects as a function of the ion energy. The areas corresponding to single vacancies

Recent highlights in nanoscale and mesoscale friction

• Andrea Vanossi,
• Dirk Dietzel,
• Andre Schirmeisen,
• Ernst Meyer,
• Rémy Pawlak,
• Thilo Glatzel,
• Marcin Kisiel,
• Shigeki Kawai and
• Nicola Manini

Beilstein J. Nanotechnol. 2018, 9, 1995–2014, doi:10.3762/bjnano.9.190

• mechanisms of structural lubricity. This crucial importance of the edge was also demonstrated by molecular dynamics (MD) simulations for Kr islands adsorbed on Pb(111). Here, depending on size and shape of the islands, the edge generates a barrier for the unpinning and successive advancement of the edge

Defect formation in multiwalled carbon nanotubes under low-energy He and Ne ion irradiation

• Santhana Eswara,
• Jean-Nicolas Audinot,
• Brahime El Adib,
• Maël Guennou,
• Tom Wirtz and
• Patrick Philipp

Beilstein J. Nanotechnol. 2018, 9, 1951–1963, doi:10.3762/bjnano.9.186

• improved mechanical properties which is similar to the one of collagen found in nature [7]. Vacancy formation and interconnections forming between CNTs have also been observed in molecular dynamics (MD) simulations during the irradiation of SWCNTs supported by silica [8]. MD simulations have been used to

• found in experiments. Molecular dynamics (MD) simulations would be able to provide an atomistic description of the sputter processes, which has already been done for several systems [48], however experimental fluences are beyond their possibilities. BCA-based simulations have already been used for the

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

• ; hydrogen bonds; molecular dynamics; separation; Introduction Modern separation techniques require energy-efficient and environmentally friendly solutions. Very promising, but not yet widely considered to be practical, is the utilization of nanochemistry achievements. An example would be the utilization of

• hydrated ions and liquid water with porous graphene [12]. Sun et al. [7] studied the purification of natural gas using nanoporous graphene with the help of classical molecular dynamics. Similarly to most papers that deal with the application of nanoporous graphene, they demonstrated that the efficiency of

Quantitative comparison of wideband low-latency phase-locked loop circuit designs for high-speed frequency modulation atomic force microscopy

• Kazuki Miyata and
• Takeshi Fukuma

Beilstein J. Nanotechnol. 2018, 9, 1844–1855, doi:10.3762/bjnano.9.176

• ], we discussed the origin of this region in detail. By comparing the AFM images with the molecular dynamics simulation results, we proposed that the transition region is most likely to be a Ca(OH)2 layer. In this study, this transition region was newly observed by direct imaging using high-speed FM-AFM

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

• suggest that the combination of molecular dynamics ReaxFF simulations and blind docking techniques can be used as an explorative tool prior to experiments, which is useful for rational design of new drug delivery systems. Keywords: drug delivery; PEGylated nanoparticle; PLA; polymeric nanoparticle

• , cilostazol [32][33]. PEG chains typically create an interface between the NP core (PLA) and the hydrophilic environment, where the drug encapsulation is largely dependent on the intrinsic affinity between the drug and the PLA core [31]. All-atom molecular dynamics (MD) simulations were performed using the

• 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

Induced smectic phase in binary mixtures of twist-bend nematogens

• Anamarija Knežević,
• Irena Dokli,
• Marin Sapunar,
• Suzana Šegota,
• Ute Baumeister and
• Andreja Lesac

Beilstein J. Nanotechnol. 2018, 9, 1297–1307, doi:10.3762/bjnano.9.122

• investigate how conformational disorder of terminal chains might affect induction of the smectic phase we performed a molecular dynamics simulation of BB at 80 K with a time step of 1 fs for a total duration of 10 ps using the Turbomole program package [48] at the PBE/def2-TZVP level of theory using the RI

• molecular dynamics. Snapshots were taken every 0.2 ps from a 10 ps molecular dynamics simulation at 80 K. To illustrate the motion of the alkyl chain separately from the motion of the remainder of the molecule, the snapshots are shown with the benzene ring of each geometry aligned, and only the alkyl chain

Atomistic modeling of tribological properties of Pd and Al nanoparticles on a graphene surface

• Alexei Khomenko,
• Miroslav Zakharov,
• Denis Boyko and
• Bo N. J. Persson

Beilstein J. Nanotechnol. 2018, 9, 1239–1246, doi:10.3762/bjnano.9.115

• insight into the fundamental origin of sliding friction. Results: Using molecular dynamics we investigate frictional properties of aluminum and palladium nanoparticles deposited on a graphene layer. We study the time evolution of the total momentum of the system, the total and potential energies, the

• the friction dynamics of metallic nanoparticles [14] makes it virtually impossible to construct a general and reliable analytical theory of the phenomena under consideration. Therefore, computer modeling, in particular molecular dynamics (MD), is a useful tool for the theoretical study of friction and

• coordinates of metal atoms with maximum and minimum values along the x,y,z-axes. The substrate in our model is a graphene sheet that is parallel to the xy-plane with armchair and zigzag fixed edges along the x- and y-directions (Figure 1). Snapshots in this paper were taken by using the Visual Molecular

Fatigue crack growth characteristics of Fe and Ni under cyclic loading using a quasi-continuum method

• Ren-Zheng Qiu,
• Yi-Chen Lin and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2018, 9, 1000–1014, doi:10.3762/bjnano.9.93

• , strong materials. Considerable attention has been focused on the investigation of the fatigue crack growth behavior in single crystals under cyclic loading using molecular dynamics (MD), which is an effective tool for analyzing the mechanical deformation and mechanical properties of materials at the

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

• beam pretreated surfaces. Hence, in order to extend the knowledge on the adsorption and to address the open questions in the deposition process, in this study we use DFT and finite temperature DFT-based molecular dynamics (MD) simulations and investigate the adsorption behavior of (C5H4CH3)Pt(CH3)3 on

• 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

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

• switches is mostly focused on developing experimental approaches for device prototype fabrication and testing in laboratory environment and theoretical modelling based on continuum mechanics and molecular dynamics, allowing simulations to be performed on the processes occurring in NEM switching devices and

• 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

• into lift-off lithography removal mechanisms and outcomes of the lift-off process at the atomic scale, we simulated lift-off using molecular dynamics and density functional theory. We determined the energetics of this complex system during lift-off. The simulations were used to predict the

• 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

Interface conditions of roughness-induced superoleophilic and superoleophobic surfaces immersed in hexadecane and ethylene glycol

• Yifan Li,
• Yunlu Pan and
• Xuezeng Zhao

Beilstein J. Nanotechnol. 2017, 8, 2504–2514, doi:10.3762/bjnano.8.250

• of roughness by using AFM. Results show that the slip length enhanced with larger RMS roughness, as the increasing roughness could magnify the intrinsic wetting properties of surface. In addition, the published studies based on LB simulation and molecular dynamics (MD) also show that roughness could

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

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

• scratch conditions were studied by molecular dynamics (MD) simulations. The type of grain boundary is the main factor in the control of the substrate atoms with respect to the size of dislocations since the existence of the grain boundary itself restricts the movement associated with dislocations. In this

• nanoindentation results (i.e., indentation on the upper area) of the vertical grain boundary showed that the force was translated along the grain boundary, thereby producing intergranular fractures. Keywords: indentation; molecular dynamics; nanograin boundary; nanoscratch; Introduction The recent developments

• ][18][19][20][21]. Molecular dynamics (MD) simulation is an effective tool for studying material behavior and system design at the nanometer scale while avoiding experimental noise and turbulence issues. Landman et al. [7] studied the interactional properties (i.e., the characteristics of deformation

Au₅₅, a stable glassy cluster: results of ab initio calculations

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

Beilstein J. Nanotechnol. 2017, 8, 2221–2229, doi:10.3762/bjnano.8.222

• means of molecular dynamics or ab initio modeling. These studies resulted in puzzling and often contradictory conclusions regarding the nanoparticle structure: crystalline vs non-crystalline, icosahedral vs cuboctahedral or even unspecific shapes. Doye and Wales [16] described their resulting Au55

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

Velocity dependence of sliding friction on a crystalline surface

• Christian Apostoli,
• Giovanni Giusti,
• Jacopo Ciccoianni,
• Gabriele Riva,
• Rosario Capozza,
• Rosalie Laure Woulaché,
• Andrea Vanossi,
• Emanuele Panizon and
• Nicola Manini

Beilstein J. Nanotechnol. 2017, 8, 2186–2199, doi:10.3762/bjnano.8.218

• of the atomic force microscope (AFM) and its friction force microscope (FFM) variant [6][7][8], as well as the extensive usage of atomistic molecular dynamics (MD) simulations and modeling made possible by the vastly increased computing power availability [9][10][11][12][13][14][15][16]. Despite this

Modelling focused electron beam induced deposition beyond Langmuir adsorption

• Dédalo Sanz-Hernández and
• Amalio Fernández-Pacheco

Beilstein J. Nanotechnol. 2017, 8, 2151–2161, doi:10.3762/bjnano.8.214

• model to simulate gas flow surface distribution when delivered from an injector [24], code that analytically and numerically solves FEBID continuum models [25], a hybrid Monte Carlo-continuum model to predict and guide the growth of 3D nanostructures [26], and a molecular dynamics model to give an