Classification and application of metal-based nanoantioxidants in medicine and healthcare

• Nguyen Nhat Nam,
• Nguyen Khoi Song Tran,
• Tan Tai Nguyen,
• Nguyen Ngoc Trai,
• Nguyen Phuong Thuy,
• Hoang Dang Khoa Do,
• Nhu Hoa Thi Tran and
• Kieu The Loan Trinh

Beilstein J. Nanotechnol. 2024, 15, 396–415, doi:10.3762/bjnano.15.36

• ]. Pharmacokinetic analysis of curcumin-loaded polymeric nanoparticles after oral delivery in mice demonstrated a 20-fold decrease in dose requirement compared to natural curcumin [140]. Both experimental and molecular dynamics simulation studies suggested an optimal ferulic acid (an antioxidant in plants

Comparative molecular dynamics simulations of thermal conductivities of aqueous and hydrocarbon nanofluids

• Adil Loya,
• Antash Najib,
• Fahad Aziz,
• Asif Khan,
• Guogang Ren and
• Kun Luo

Beilstein J. Nanotechnol. 2022, 13, 620–628, doi:10.3762/bjnano.13.54

• thermophysical properties of nanofluids using a simulation environment. Moreover, this comparison introduces data on aqueous and nonaqueous suspensions in one study. Keywords: alkanes; aqueous solutions; CuO; hydrocarbon solutions; molecular dynamics simulation; nanoparticles; thermal conductivity

• constructed with 36 CuO molecules bonded by the COMPASS force field. This constructed nanoparticle size was 0.4 nm, as shown in Figure 1b. A molecular dynamics simulation of paraffin (i.e., eicosane C20H42) was also conducted for comparison with the aqueous solution. In the alkane/CuO nanofluid simulation

A review on slip boundary conditions at the nanoscale: recent development and applications

• Ruifei Wang,
• Jin Chai,
• Bobo Luo,
• Xiong Liu,
• Jianting Zhang,
• Min Wu,
• Mingdan Wei and
• Zhuanyue Ma

Beilstein J. Nanotechnol. 2021, 12, 1237–1251, doi:10.3762/bjnano.12.91

• Beskok compared a slip-modified theoretical model with the molecular dynamics simulation results. They found that the slip enhancement in the electro-osmotic flow is independent of the channel height, which can provide a theoretical basis for membrane fabrication of electrically assisted nanofiltration

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF₃)₄

• Alexey Prosvetov,
• Alexey V. Verkhovtsev,
• Gennady Sushko and
• Andrey V. Solov’yov

Beilstein J. Nanotechnol. 2021, 12, 1151–1172, doi:10.3762/bjnano.12.86

Reducing molecular simulation time for AFM images based on super-resolution methods

• Zhipeng Dou,
• Jianqiang Qian,
• Yingzi Li,
• Rui Lin,
• Jianhai Wang,
• Peng Cheng and
• Zeyu Xu

Beilstein J. Nanotechnol. 2021, 12, 775–785, doi:10.3762/bjnano.12.61

• can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning. Keywords: atomic force microscopy; Bayesian compressed sensing; convolutional neural network; molecular dynamics simulation; super resolution; Introduction Atomic force microscopy methods

• . The energy maps of the interaction between several tips and samples under different conditions are simulated in dynamic and quasi-static modes. The molecular dynamics simulation details and main steps of reconstruction algorithms are presented. Then, several reconstruction results are conducted to

• simulated image [35]. Filters of spatial sizes of 9 × 9, 5 × 5, and 5 × 5 were used. The flow chart of the proposed SRCNN reconstruction method is shown in Figure 4. First, we use molecular dynamics simulation to obtain energy maps of the tip–sample interaction with low-resolution. Different from the full

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

• 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

• modeling of nanoparticle dynamics has been performed by means of either classical theory of continuum mechanics or molecular dynamics simulation, the nonclassical theory of continuum mechanics is employed to study the dynamical behavior of cylindrical nanoparticles. In addition, a developed version of the

• dynamics simulation and a multiscale approach, Korayem et al. investigated geometrical effects on the manipulation of carbon allotropes [24]. Ghattan Kashani et al. presented a new method to overcome the adhesion force between the tip and nanoparticle while releasing the nanoparticle. They created 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

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

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

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

• 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

• stabilized within a few millikelvins. Snapshot of the molecular dynamics simulation showing the different atom types. ‘Normal’ gold atoms are drawn in blue, ‘tip boundary’ atoms in green and ‘surface boundary’ atoms in red. Determination of surface atom positions via geometric argumentation: The two panels

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

• 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

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 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

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

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

A nanocomplex of C₆₀ fullerene with cisplatin: design, characterization and toxicity

• Svitlana Prylutska,
• Svitlana Politenkova,
• Kateryna Afanasieva,
• Volodymyr Korolovych,
• Kateryna Bogutska,
• Andriy Sivolob,
• Larysa Skivka,
• Maxim Evstigneev,
• Viktor Kostjukov,
• Yuriy Prylutskyy and
• Uwe Ritter

Beilstein J. Nanotechnol. 2017, 8, 1494–1501, doi:10.3762/bjnano.8.149

• complexation were investigated by calculating the energy-minimized spatial structure of their complex, shown in Figure 3. The initial location coordinates of Cis above the C60 fullerene surface were taken from the ab initio structure [39]. Then we performed the molecular dynamics simulation of this nanocomplex

First examples of organosilica-based ionogels: synthesis and electrochemical behavior

• Andreas Taubert,
• Ruben Löbbicke,
• Barbara Kirchner and
• Fabrice Leroux

Beilstein J. Nanotechnol. 2017, 8, 736–751, doi:10.3762/bjnano.8.77

• molecular dynamics (AIMD) simulations in which the forces are calculated from the electronic structure on the fly were carried out as described previously [41] using the cp2k program packages [42]. AIMD simulation was started from a classical molecular dynamics simulation snapshot of 32 ion pairs of

Fracture behaviors of pre-cracked monolayer molybdenum disulfide: A molecular dynamics study

• Qi-lin Xiong,
• Zhen-huan Li and
• Xiao-geng Tian

Beilstein J. Nanotechnol. 2016, 7, 1411–1420, doi:10.3762/bjnano.7.132

• and Vibration, Xi’an Jiaotong University, Xi’an 710049, China 10.3762/bjnano.7.132 Abstract The fracture strength and crack propagation of monolayer molybdenum disulfide (MoS2) sheets with various pre-existing cracks are investigated using molecular dynamics simulation (MDS). The uniaxial tensions of

• model without finite size effect. Finally, the MDS results of monolayer MoS2 sheets with different angled crack are also analyzed based on the continuum fracture mechanics model. Keywords: crack propagation; fracture strength; molecular dynamics simulation; monolayer molybdenum disulfide; pre-existing

Free vibration of functionally graded carbon-nanotube-reinforced composite plates with cutout

• Mostafa Mirzaei and
• Yaser Kiani

Beilstein J. Nanotechnol. 2016, 7, 511–523, doi:10.3762/bjnano.7.45

• parameters. These parameters compensate for the errors generated due to the conventional rule of mixtures approach for a CNTRC. The values of these constants are obtained by matching the data obtained according to the above formula with those obtained based on the molecular dynamics simulation. It is worth

• present modified rule of mixtures approach and the molecular dynamics simulations of other researchers. A molecular dynamics simulation was performed by Han and Elliott [41]; however, since the condition of maximum thickness for CNTs was not satisfied in this research, their simulations were re-examined

Plasticity-mediated collapse and recrystallization in hollow copper nanowires: a molecular dynamics simulation

• Amlan Dutta,
• Arup Kumar Raychaudhuri and
• Tanusri Saha-Dasgupta

Beilstein J. Nanotechnol. 2016, 7, 228–235, doi:10.3762/bjnano.7.21

• copper nanowires using molecular dynamics simulation. We find that the plasticity-mediated structural evolution leads to transformation of the initial hollow structure to a solid wire. The process involves three distinct stages, namely, collapse, recrystallization and slow recovery. We calculate the time

• molecular dynamics simulation. The results reveal that the hollow nanowire undergoes a rapid collapse, thereby transforming into a structure of reduced diameter consisting of disordered atoms and some residual crystalline parts with stacking faults. The crystalline parts act as nucleation centers for the

Multifunctional layered magnetic composites

• Maria Siglreitmeier,
• Baohu Wu,
• Tina Kollmann,
• Martin Neubauer,
• Gergely Nagy,
• Dietmar Schwahn,
• Vitaliy Pipich,
• Damien Faivre,
• Dirk Zahn,
• Andreas Fery and
• Helmut Cölfen

Beilstein J. Nanotechnol. 2015, 6, 134–148, doi:10.3762/bjnano.6.13

• illustrates the association of the two ion cluster types to collagen and typical configurations as obtained from relaxation in aqueous solution based on 100 ps molecular dynamics simulation runs. While the FeIII(OH)3 ion clusters bind as stable moieties to the biomolecule, the association of FeII(OH)2 to

Nanometer-resolved mechanical properties around GaN crystal surface steps

• Jörg Buchwald,
• Marina Sarmanova,
• Bernd Rauschenbach and
• Stefan G. Mayr

Beilstein J. Nanotechnol. 2014, 5, 2164–2170, doi:10.3762/bjnano.5.225

• these results to the molecular dynamics simulation with the same radius (Figure 4), a similar behavior for the indentation modulus could be found. However, there was an even more pronounced increase for y < 0 that was also dependent on the step height, in contrast to our MD simulations results

Resonance of graphene nanoribbons doped with nitrogen and boron: a molecular dynamics study

• Ye Wei,
• Haifei Zhan,
• Kang Xia,
• Wendong Zhang,
• Shengbo Sang and
• Yuantong Gu

Beilstein J. Nanotechnol. 2014, 5, 717–725, doi:10.3762/bjnano.5.84

• discussed. A systematic study of the vibrational properties of graphene doped with nitrogen and boron is performed by means of a molecular dynamics simulation. The influence from different density or species of dopants has been assessed. It is found that the impacts on the quality factor, Q, resulting from

• the resonance of graphene with different dopants, which may benefit their application as resonators. Keywords: dopant; graphene; molecular dynamics simulation; natural frequency; quality factor; resonance; Introduction Graphene has drawn intensive interest since its discovery in 2005 [1]. It has

Tensile properties of a boron/nitrogen-doped carbon nanotube–graphene hybrid structure

• Kang Xia,
• Haifei Zhan,
• Ye Wei and
• Yuantong Gu

Beilstein J. Nanotechnol. 2014, 5, 329–336, doi:10.3762/bjnano.5.37

• materials. Keywords: doping; graphene; molecular dynamics simulation; nanotubes; tension; Young’s modulus; Introduction In recent years, low-dimensional structures such as carbon nanotubes (CNT) and graphene have attracted huge attention of the scientific community, because of their excellent performance

Nanoglasses: a new kind of noncrystalline materials

• Herbert Gleiter

Beilstein J. Nanotechnol. 2013, 4, 517–533, doi:10.3762/bjnano.4.61

• in the nanoglass is caused by negative spin polarized sp-like itinerant electrons [21][22][23][24]. Molecular dynamics simulation of the consolidation of a nanoglass at 300 K [27]. The nanoglass is obtained by sintering nanometer-sized (5 nm diameter) glassy spheres (of Ge) at a pressure of 5 GPa. (e

Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

• Hlengisizwe Ndlovu,
• Alison E. Ashcroft,
• Sheena E. Radford and
• Sarah A. Harris

Beilstein J. Nanotechnol. 2013, 4, 429–440, doi:10.3762/bjnano.4.50

• carbon-α atoms was used to monitor convergence of the MD simulations. This was achieved within 20 and 40 ns for the 8 × 2 and 16 × 2 models, respectively. Steered molecular dynamics simulation The details of the SMD protocol used are identical to those we have described elsewhere [23]; only a summary is

• binding free energy of the intersheet interface and also the enthalpy of the fibril complex devoid of solvent molecules. The three polymorphs of SNNFGAILSS sequence fibrils in the Class1-P (red), Class2-P (green) and Class6-AP (blue) symmetry-packing classes. (a) Models before the molecular dynamics

• simulation; (b) the structural changes in each model at the conclusion of 20 ns of MD in explicit solvent (water molecules omitted for clarity). Schematic representation of the four pulling geometries used to mechanically probe the fibril models. The centre of mass of the carbon-α atoms in the peptide marked