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

• Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam 10.3762/bjnano.10.51 Abstract We perform molecular dynamics simulation on several relevant biological

• experimental observations. Keywords: β-amyloid; atomic force microscopy, mechanical deformation; molecular simulation; proteins; α-synuclein; Introduction All-atom molecular dynamics (MD) simulations have been employed to study the physical and chemical behaviour of the fundamental biomolecules of life (e.g

• native state, P0, as a function of the temperature T. We define the temperature of thermodynamic stability, Tf (folding temperature in our model), for the case P0 = 1/2. To study the thermodynamic properties of the biological fibrils, we carried out overdamped Langevin dynamics simulations. The

Biocompatible organic–inorganic hybrid materials based on nucleobases and titanium developed by molecular layer deposition

• Leva Momtazi,
• Henrik H. Sønsteby and
• Ola Nilsen

Beilstein J. Nanotechnol. 2019, 10, 399–411, doi:10.3762/bjnano.10.39

• , compared to uncoated glass coverslips using alamarBlue® proliferation assay [23]. The current contribution describes the growth of the films based on nucleobases in more detail. Results The growth dynamics of all three systems were investigated using in situ QCM, as shown in Figure 2 and Figure 3 and

• mode dominates the overall film growth. Such a CVD contribution is limited when a practical growth mode is considered sufficient. When highlighting the overall growth dynamics, rather long pulse and purge times for all precursors are used. In this case, a pulse scheme of 7 s TTIP, 10 s purge, 15 s

• and Ti-L-aspartic acid films where a contact angle of approximately 30° was measured on the surface of these materials in our previous study [22]. The growth dynamics of the individual systems were further investigated by adding an extra water pulse after the organic precursor to shed light on the

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

Transport signatures of an Andreev molecule in a quantum dot–superconductor–quantum dot setup

• Zoltán Scherübl,
• András Pályi and
• Szabolcs Csonka

Beilstein J. Nanotechnol. 2019, 10, 363–378, doi:10.3762/bjnano.10.36

• spectrum and the dynamics. Several previous works on similar systems completely neglect the possibility of EC processes [7][52][53][54][71][72]. In other works EC coupling is taken into account [44][61][64][65][67][68][73], but in most of the cases it is defined as a constant coupling term that is

Intuitive human interface to a scanning tunnelling microscope: observation of parity oscillations for a single atomic chain

• Sumit Tewari,
• Jacob Bakermans,
• Christian Wagner,
• Federica Galli and
• Jan M. van Ruitenbeek

Beilstein J. Nanotechnol. 2019, 10, 337–348, doi:10.3762/bjnano.10.33

• –machine augmented system in which the operator and the machine are connected by a real-time simulation. Here, a 3D motion control system is integrated with an ultra-high vacuum (UHV) low-temperature scanning tunnelling microscope (STM). Moreover, we coupled a real-time molecular dynamics (MD) simulation

• and combined it with a molecular dynamics (MD) simulator that simulates in real-time the manipulation process going on in the STM. The MD simulation not only provides information about the atomic scale structure of the junction, but also serves as a visual feedback to the operator in real-time who can

• the operator does not use any feedback from the current while the manipulation is executed and thus cannot influence the trajectory in order to respond to the complex dynamics of the tip/adatom/surface system during the manipulation. In contrast, in our setup the operator receives a continuous visual

Heating ability of magnetic nanoparticles with cubic and combined anisotropy

• Nikolai A. Usov,
• Mikhail S. Nesmeyanov,
• Elizaveta M. Gubanova and
• Natalia B. Epshtein

Beilstein J. Nanotechnol. 2019, 10, 305–314, doi:10.3762/bjnano.10.29

• ][31] governs the dynamics of the unit magnetization vector of the ith single-domain nanoparticle of the cluster where γ is the gyromagnetic ratio, κ is phenomenological damping parameter, γ1 = γ/(1+κ2), is the effective magnetic field and is the thermal field. The effective magnetic field acting on

• on the behavior of fractal clusters of nanoparticles arising often within the biological cells or in the intracellular space [13][24][25]. This can be done using the stochastic LL equation [22][28][29][30][31] that describes the dynamics of the particle magnetic moments taking into account both the

Electromagnetic analysis of the lasing thresholds of hybrid plasmon modes of a silver tube nanolaser with active core and active shell

• Denys M. Natarov,
• Trevor M. Benson and
• Alexander I. Nosich

Beilstein J. Nanotechnol. 2019, 10, 294–304, doi:10.3762/bjnano.10.28

• -field with the active regions. To obtain a fuller vision of the dynamics of LEP eigenvalues on the plane (λ, γ) for the plasmonic silver nanotube laser, we have computed their trajectories for a device with an active core radius a = 30 nm and an active shell thickness d = 10 nm as the tube wall

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

Scanning probe microscopy for energy-related materials

• Rüdiger Berger,
• Benjamin Grévin,
• Philippe Leclère and
• Yi Zhang

Beilstein J. Nanotechnol. 2019, 10, 132–134, doi:10.3762/bjnano.10.12

• dynamics in order to study charge carrier lifetimes. This contribution focuses on a mathematical model to calculate time constants [3]. Such a model is critical for understanding the photophysics at the nanometer scale. Amelie Axt and co-workers discuss the applicability and reliability of different ways

A comparison of tarsal morphology and traction force in the two burying beetles Nicrophorus nepalensis and Nicrophorus vespilloides (Coleoptera, Silphidae)

• Liesa Schnee,
• Benjamin Sampalla,
• Josef K. Müller and
• Oliver Betz

Beilstein J. Nanotechnol. 2019, 10, 47–61, doi:10.3762/bjnano.10.5

• secretion in N. nepalensis compared with that of N. vespilloides [3]. Since under the dynamics of friction regimes, the generated shear stress is largely determined by the viscosity of the fluid [46], such higher viscosities might be responsible for the observed higher friction forces of N. nepalensis on

Bidirectional biomimetic flow sensing with antiparallel and curved artificial hair sensors

• Claudio Abels,
• Antonio Qualtieri,
• Toni Lober,
• Alessandro Mariotti,
• Lily D. Chambers,
• Massimo De Vittorio,
• William M. Megill and
• Francesco Rizzi

Beilstein J. Nanotechnol. 2019, 10, 32–46, doi:10.3762/bjnano.10.4

• real-time using our flow sensor platform could possibly further reduce mechanically unfavourable flow dynamics in the wake. When compared to flow sensors which are based on the same electrical measurement procedure (piezoresistive, strain gauge) and mechanical structure (bent cantilever), the achieved

• Applied Sciences Kaiserslautern for her help with experimental measurements. We owe gratitude to Friedrich Muhs from Rhine-Waal University of Applied Sciences for his data acquisition improvements and Prof. Giovanni Lombardi from University of Pisa for his invaluable suggestions on fluid dynamics. Claudio

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

Characterization of the microscopic tribological properties of sandfish (Scincus scincus) scales by atomic force microscopy

• Weibin Wu,
• Christian Lutz,
• Simon Mersch,
• Richard Thelen,
• Christian Greiner,
• Guillaume Gomard and
• Hendrik Hölscher

Beilstein J. Nanotechnol. 2018, 9, 2618–2627, doi:10.3762/bjnano.9.243

• sand swimming. Reviewing literature and our recent results it now seems likely that the dynamics of the sandfish locomotion as well as the elastic properties of the epidermis are important factors and not exceptional low friction and wear of the scales alone. Consequently, it will be important to

• consider not only scales but also the tissue underneath the epidermis as well as the dynamics of the swimming sandfish. Such experiments might hold the key for understanding the fabulous swimming abilities combined with low wear rates. It is possible that sandfish scales are not primarily designed to lower

• friction (a friction coefficient of 0.2 is comparably low for a dry sliding contact already) but to reduce wear in combination with the specific dynamics of sandfish. The latter is a significant technological challenge with high industrial impact that might lead to new robots which could swim through

Pattern generation for direct-write three-dimensional nanoscale structures via focused electron beam induced deposition

• Lukas Keller and
• Michael Huth

Beilstein J. Nanotechnol. 2018, 9, 2581–2598, doi:10.3762/bjnano.9.240

• pattern files for 3D FEBID depositions. Here, we present our approach to generating such a pattern-definition file using some general rules of precursor dynamics. The algorithms, reflecting successful writing strategies as discussed below, are implemented in C++ for speed, flexibility and independence

Friction reduction through biologically inspired scale-like laser surface textures

• Johannes Schneider,
• Vergil Djamiykov and
• Christian Greiner

Beilstein J. Nanotechnol. 2018, 9, 2561–2572, doi:10.3762/bjnano.9.238

• . In the case of lubricated contacts, we will also involve fluid dynamics modelling to understand and optimize the tribological behaviour of these surfaces. For dimpled surface morphologies, such simulations have recently been able to explain the beneficial effect of laser surface texturing [27][50

• elaborate fluid dynamics simulations. As far as the unlubricated experiments are concerned, the concept developed by Bowden and Tabor [51] points out that most frictional energy dissipation is due to plastic deformation of the subsurface layer. If one of the sliding partners is harder than the other, 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

Lead-free hybrid perovskites for photovoltaics

• Oleksandr Stroyuk

Beilstein J. Nanotechnol. 2018, 9, 2209–2235, doi:10.3762/bjnano.9.207

• luminescent Cs3Bi2X9 NCs [159]. A study of single-crystal and polycrystalline MABI showed that both materials have a long exciton lifetime and a high carrier mobility [161][163]. A transient absorption study of MABI crystals showed only a minor change of the exciton dynamics when the crystal size was reduced

• similar Voc (0.895 V) was reported for a MABI-based cell produced without HTLs with a single carbon back contact [86]. In this case, a top light conversion efficiency was only 0.054% (Table 1), indicating the crucial role of the hole transfer dynamics for the total cell performance. The efficiency of MABI

Influence of the thickness of an antiferromagnetic IrMn layer on the static and dynamic magnetization of weakly coupled CoFeB/IrMn/CoFeB trilayers

• Deepika Jhajhria,
• Dinesh K. Pandya and
• Sujeet Chaudhary

Beilstein J. Nanotechnol. 2018, 9, 2198–2208, doi:10.3762/bjnano.9.206

• , AF-based spintronics is gaining momentum because of the unique properties such as zero net magnetization, no stray fields, low magnetic susceptibility, large spin–orbit coupling, ultrafast dynamics and large magneto-transport effects [2][3][4][5][6]. Several of the effects such as tunnel anisotropic

• sample magnetometer (VSM) option. The magnetization dynamics of the films was studied using a broadband (5–13 GHz) ferromagnetic resonance setup employing a vector network analyzer (VNA) and co-planar waveguide (CPW) transmission line. Since the output microwave power of the VNA was set to 0 dBm, the

• amplitude of magnetization precession is small, which results in a nearly linear FMR response and thus the complicated non-linear magnetization dynamics is less likely in the films. The samples were mounted with the deposited film side directly facing down on to the CPW. The FMR spectra were recorded by

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

• 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

• sliding nanostructures. A first indication stems from nanomanipulation experiments performed for Sb nanoparticles on HOPG, where distinct contact-ageing effects were demonstrated. By characterizing the ageing dynamics as a function of the temperature, of the sliding velocity, and of the hold time in

• statically pinned state to an intermittent stick–slip dynamics to a sliding regime (possibly characterized by superlubric motion) has not been explicitly carried out. Recently, thanks to state-of-the-art experimental setups [82][148][149][150], artificial tribology emulators have taken friction experiments

Electromigrated electrical optical antennas for transducing electrons and photons at the nanoscale

• Arindam Dasgupta,
• Mickaël Buret,
• Nicolas Cazier,
• Marie-Maxime Mennemanteuil,
• Reinaldo Chacon,
• Kamal Hammani,
• Jean-Claude Weeber,
• Juan Arocas,
• Laurent Markey,
• Gérard Colas des Francs,
• Alexander Uskov,
• Igor Smetanin and
• Alexandre Bouhelier

Beilstein J. Nanotechnol. 2018, 9, 1964–1976, doi:10.3762/bjnano.9.187

• thermal radiation of an out-of-equilibrium heated electron distribution, which is promoted by the electron–electron interaction dynamics. Both light-emission mechanisms may be observed in the electromigrated junctions discussed in the previous section as illustrated in Figure 5. Prevalence of inelastic

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