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

• flexible behavior. Also, for manipulating multiple nanowires, they presented a method based on graph theory that saved significant time owing to being independent from intermediate scanning [22]. Mahdjour Firouzi et al. tried to simulate the manipulation of biological nanoparticles using molecular dynamics

• required repulsive force for releasing nanoparticles via high electrostatic voltage. The method was proposed for a conductive tip and nanoparticles, and the efficiency of the proposed method was studied using a combination of molecular dynamics simulation and FEM [25]. To examine the size dependence in the

Molecular architectonics of DNA for functional nanoarchitectures

• Debasis Ghosh,
• Lakshmi P. Datta and
• Thimmaiah Govindaraju

Beilstein J. Nanotechnol. 2020, 11, 124–140, doi:10.3762/bjnano.11.11

• designed a porphyrin-tethered single-DNA duplex as a transmembrane ion channel [94]. Their minimalistic design approach involved the attachment of six porphyrin units along the oligonucleotide sequence that facilitated the movement of ions through the channel. The schematic of molecular dynamics simulation

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

Formation of metal/semiconductor Cu–Si composite nanostructures

• Natalya V. Yumozhapova,
• Andrey V. Nomoev,
• Vyacheslav V. Syzrantsev and
• Erzhena C. Khartaeva

Beilstein J. Nanotechnol. 2019, 10, 2497–2504, doi:10.3762/bjnano.10.240

• 10.3762/bjnano.10.240 Abstract Molecular dynamics modelling of the formation of copper and silicon composite nanostructures was carried out by using the many-particle potential method. The dependences of the internal structure on the cooling rate and the ratio of elements were investigated. The

• content of 50 atom %. Additionally, an estimation of the effective experimental cooling rate was made. Keywords: composite nanoparticle; gas-phase synthesis; molecular dynamics modelling; Introduction In recent years, due to the development of various methods of synthesis, it has become possible to

• approach to modelling the formation of metal/semiconductor core–shell nanoparticles was described in [18]. There, a core–shell particle was obtained by spraying the outer shell on an already formed core. The molecular dynamics calculation of such a procedure showed the possibility of the formation of Cu–Si

Abrupt elastic-to-plastic transition in pentagonal nanowires under bending

• Sergei Vlassov,
• Magnus Mets,
• Boris Polyakov,
• Jianjun Bian,
• Leonid Dorogin and
• Vahur Zadin

Beilstein J. Nanotechnol. 2019, 10, 2468–2476, doi:10.3762/bjnano.10.237

• flexible polymer composite materials. Keywords: finite element method; mechanical properties; molecular dynamics; nanowires; Introduction Nanostructures comprised of noble metals with face centered cubic (FCC) crystal structure (Au, Ag and Cu according to the most common physical definition) prepared via

• : Classical molecular dynamics (MD) simulations were conducted to investigate the atomic deformation behavior of the penta-twinned Ag NW under bending. The large-scale open-source molecular dynamics simulator, LAMMPS, developed by Sandia National Laboratories, was adopted [35]. The interatomic interactions

• the present work are comparable, but do not exceed the theoretical yield strength value of bulk Au, which is about 8 GPa in accordance with the empirical relation E/10 based on atomic bonding considerations [41]. Molecular dynamics results Figure 8 depicts the loading curve of the penta-twinned NW

Mobility of charge carriers in self-assembled monolayers

• Zhihua Fu,
• Tatjana Ladnorg,
• Hartmut Gliemann,
• Alexander Welle,
• Asif Bashir,
• Michael Rohwerder,
• Qiang Zhang,
• Björn Schüpbach,
• Andreas Terfort and
• Christof Wöll

Beilstein J. Nanotechnol. 2019, 10, 2449–2458, doi:10.3762/bjnano.10.235

• conductivity within self-assembled monolayers was further corroborated by Bashir et al. through the application of molecular dynamics simulation where the charge transport was taken explicitly into account [29]. The theoretical study on the optimized model of HBC by using the Ehrenfest (mean field) approach

Design of a nanostructured mucoadhesive system containing curcumin for buccal application: from physicochemical to biological aspects

• Sabrina Barbosa de Souza Ferreira,
• Gustavo Braga,
• Évelin Lemos Oliveira,
• Jéssica Bassi da Silva,
• Hélen Cássia Rosseto,
• Lidiane Vizioli de Castro Hoshino,
• Mauro Luciano Baesso,
• Wilker Caetano,
• Craig Murdoch,
• Helen Elizabeth Colley and
• Marcos Luciano Bruschi

Beilstein J. Nanotechnol. 2019, 10, 2304–2328, doi:10.3762/bjnano.10.222

• spectral emission (Table 1). Anisotropy is considered a powerful technique to investigate the molecular dynamics of fluorescent solutes, such as CUR. During the fluorescence analysis, the molecules are excited by linearly polarized light, and they absorb and emit the fluorescence in a polarized way. If the

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

Graphynes: an alternative lightweight solution for shock protection

• Kang Xia,
• Haifei Zhan,
• Aimin Ji,
• Jianli Shao,
• Yuantong Gu and
• Zhiyong Li

Beilstein J. Nanotechnol. 2019, 10, 1588–1595, doi:10.3762/bjnano.10.154

• ][13][14]. Based on in silico molecular dynamics (MD) tensile tests, the recorded failure strength values for different types of GYs range between 32.48 and 63.17 GPa [2][15][16]. According to a first-principle study, the failure strain of GY reaches 20% [17]. A high Young’s modulus of 532.5 GPa is

Green fabrication of lanthanide-doped hydroxide-based phosphors: Y(OH)₃:Eu³⁺ nanoparticles for white light generation

• Tugrul Guner,
• Anilcan Kus,
• Mehmet Ozcan,
• Aziz Genc,
• Hasan Sahin and
• Mustafa M. Demir

Beilstein J. Nanotechnol. 2019, 10, 1200–1210, doi:10.3762/bjnano.10.119

• atoms slightly enlarges (0.5%) the bonds between neighboring atoms belonging to the Y(OH)3 crystal. Regarding the stability or robustness of Eu dopants in the host material, molecular dynamics calculations show that Eu atoms, covalently attached to the host lattice with a binding energy of 2.34 eV

Mo-doped boron nitride monolayer as a promising single-atom electrocatalyst for CO₂ conversion

• Qianyi Cui,
• Gangqiang Qin,
• Weihua Wang,
• Lixiang Sun,
• Aijun Du and
• Qiao Sun

Beilstein J. Nanotechnol. 2019, 10, 540–548, doi:10.3762/bjnano.10.55

• electrocatalyst for nitrogen fixation with a very small overpotential of only 0.19 V. In addition, through molecular dynamics modeling, they demonstrated that Mo-doped BN synthesized in acidic conditions is stable at high temperature (500 K) [45]. In our previous reports, we have studied BN nanomaterials used as

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

• 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

• , 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

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

• potential energy, forces can be calculated using The force on an atom a is therefore given by (the derivation of this is given in Supporting Information File 1). Implementation The molecular dynamics simulation is written in C++ to guarantee high computational performance. A schematic flowchart of the

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