Heat-induced morphological changes in silver nanowires deposited on a patterned silicon substrate

• Elyad Damerchi,
• Sven Oras,
• Edgars Butanovs,
• Allar Liivlaid,
• Mikk Antsov,
• Boris Polyakov,
• Annamarija Trausa,
• Veronika Zadin,
• Andreas Kyritsakis,
• Loïc Vidal,
• Karine Mougin,
• Siim Pikker and
• Sergei Vlassov

Beilstein J. Nanotechnol. 2024, 15, 435–446, doi:10.3762/bjnano.15.39

• process, fragmentation in either adhered or suspended parts can dominate. Experiments were supported by finite element method and molecular dynamics simulations. Keywords: diffusion; finite element method; heat treatment; molecular dynamics simulations; morphological changes; scanning electron microscopy

• were then heated to different temperatures in air, and the behavior of suspended as opposed to the adhered part under heating was compared. Experiments are supplemented with molecular dynamics (MD) and finite element method (FEM) simulations. Materials and Methods Preparation of samples Silver NWs with

•  1. Molecular dynamics simulations were performed with the large-scale atomic/molecular massively parallel simulator (LAMMPS) [40]. Interactions between the atoms were governed by the embedded atom method (EAM) potential [41] for silver atoms. Visualization was performed with the Open Visualization

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

Multiscale modelling of biomolecular corona formation on metallic surfaces

• Parinaz Mosaddeghi Amini,
• Ian Rouse,
• Julia Subbotina and
• Vladimir Lobaskin

Beilstein J. Nanotechnol. 2024, 15, 215–229, doi:10.3762/bjnano.15.21

• modelling of the interaction between various surfaces, that is (100), (110), and (111), of fcc aluminum with the most abundant milk proteins and lactose. Our approach combines atomistic molecular dynamics, a coarse-grained model of protein adsorption, and kinetic Monte Carlo simulations to predict the

• surfaces derived from explicit all-atom molecular dynamics simulations utilizing a previously established scheme [2][24][28]. These PMFs provide the input required to determine the adsorption energies between milk proteins and aluminum surfaces by using multiscale UA CG model, spanning from the atomistic

Density functional theory study of Au-fcc/Ge and Au-hcp/Ge interfaces

• Olga Sikora,
• Małgorzata Sternik,
• Benedykt R. Jany,
• Franciszek Krok,
• Przemysław Piekarz and
• Andrzej M. Oleś

Beilstein J. Nanotechnol. 2023, 14, 1093–1105, doi:10.3762/bjnano.14.90

• differences between the polytypes are very small [14][25]. In contrast, molecular dynamics simulations of metallic nanowires show a phase transformation from fcc to hcp below a critical diameter [26]. These findings support the feasibility of obtaining new hexagonal structures under conditions where surface

Fragmentation of metal(II) bis(acetylacetonate) complexes induced by slow electrons

• Janina Kopyra and
• Hassan Abdoul-Carime

Beilstein J. Nanotechnol. 2023, 14, 980–987, doi:10.3762/bjnano.14.81

• visit to Siedlce University, Siedlce (Poland) from the European Union via the COST Action CM1301 (CELINA). The research was conducted in the frame of the COST action CA18212 Molecular Dynamics in the GAS phase (MD-GAS) and action CA20129 "MultIChem".

Ultralow-energy amorphization of contaminated silicon samples investigated by molecular dynamics

• Grégoire R. N. Defoort-Levkov,
• Alan Bahm and
• Patrick Philipp

Beilstein J. Nanotechnol. 2023, 14, 834–849, doi:10.3762/bjnano.14.68

• contaminant, water, sputtered by ultralow-energy ion beams, ranging from 50 to 500 eV and covering the full range of incidence angles, using molecular dynamics simulations with the ReaxFF potential. We show that the expected sputtering yield trends are maintained down to the lowest sputtering yields. A region

• . Keywords: angle dependency; argon; contamination; energy dependency; ion bombardment; low energy; molecular dynamics; silicon; simulations; water; Introduction Low-energy ion beams offer substantial improvements and possibilities to reduce the damage production on the surface of samples [1][2]. In recent

• . Our aim is to determine the optimal conditions to reduce damage formation near the surface while also retaining a high degree of contaminant removal. All bombardments have been simulated using a reactive force field (ReaxFF) [27][28][29] and the molecular dynamics (MD) code LAMMPS [30][31]. While low

Thermal transport in kinked nanowires through simulation

• Alexander N. Robillard,
• Graham W. Gibson and
• Ralf Meyer

Beilstein J. Nanotechnol. 2023, 14, 586–602, doi:10.3762/bjnano.14.49

• completely understood. The behaviour of the conductance is examined as kinks of varying angular intensity are included into nanowires. The effects on thermal transport are evaluated through molecular dynamics simulations, phonon Monte Carlo simulations and classical solutions of the Fourier equation. A

• Fourier model. Keywords: ballistic transport; kinked nanowire; molecular dynamics; phonon Monte Carlo; thermal transport; Introduction The thermal conductivity of semiconductor nanostructures is of great interest because of potential applications in a wide variety of fields, such as thermal control

• angling of the wire should result in reduced quantities of unrestricted ballistic transport. Gradually increasing the angle effectively reduces the quantity of unobstructed line of sight (LoS) paths from one end of a nanowire to the other. We use molecular dynamics (MD) [25] to study an atomistic approach

Transferability of interatomic potentials for silicene

• Marcin Maździarz

Beilstein J. Nanotechnol. 2023, 14, 574–585, doi:10.3762/bjnano.14.48

• needed, for example, molecular dynamics/statics. For these methods, the quality of the used interatomic potentials (IAPs) is crucial. Because of the importance of silicon, as well as its complexity, dozens of potentials have been proposed for it. In the very well-known NIST Interatomic Potentials

• potentials, a series of molecular dynamics (MD) simulations (200 atoms and 10000 timesteps, NVE ensemble) and LAMMPS’s built-in function timesteps/s were used. The results were then normalized relative to the longest run time. Interatomic potentials The parameterizations of the potentials listed below were

• , ReaxFF and MEAM2011, give the best quantitative performance measured by the total mean absolute percentage error (MAPE), see Table 6. Regarding the cost of calculations in terms of relative performance measured as normalized timesteps per second in molecular dynamics (MD) simulations, the EDIP and

New trends in nanobiotechnology

• Pau-Loke Show,
• Kit Wayne Chew,
• Wee-Jun Ong,
• Sunita Varjani and
• Joon Ching Juan

Beilstein J. Nanotechnol. 2023, 14, 377–379, doi:10.3762/bjnano.14.32

• SARS-CoV-2 receptor binding domain by molecular docking” [6]. This research work showcases peptides that are capable to bind and neutralize the SARS-CoV-2 virus through molecular docking. The latest developments of the molecular docking of peptides by molecular dynamics were investigated to understand

The influence of structure and local structural defects on the magnetic properties of cobalt nanofilms

• Alexander Vakhrushev,
• Aleksey Fedotov,
• Olesya Severyukhina and
• Anatolie Sidorenko

Beilstein J. Nanotechnol. 2023, 14, 23–33, doi:10.3762/bjnano.14.3

• materials; molecular dynamics; nanocomposites; nanofilms; spintronics; Introduction The analysis of phase transitions and related critical phenomena in condensed media is a complex, time-consuming, and often a high-cost process from a technological point of view [1][2][3]. On the one hand, this is due to

• , simultaneous equations of classical molecular dynamics are used, which are supplemented by considering the spin vectors si for each atom. The motion equation for atoms and spins is written in the following form: where ri is the vector characterizing the position of the particle i; si,and sj are the spin

• magnetic properties based on the combined model of molecular dynamics and magnetization dynamics. The technique used includes simulations of atomic magnetic spins associated with lattice vibrations. The dynamics of these magnetic spins can be used to simulate a wide range of phenomena related to

Atmospheric water harvesting using functionalized carbon nanocones

• Fernanda R. Leivas and
• Marcia C. Barbosa

Beilstein J. Nanotechnol. 2023, 14, 1–10, doi:10.3762/bjnano.14.1

• occurs due to the presence of hydrophilic sites at the nanocone entrance. The functionalization, together with the high mobility of water inside nanostructures, leads to a fast water flow through the nanostructure. We show using molecular dynamics simulations that this device is able to collect water if

• molecular dynamics simulations the process of capturing and collecting water in a functionalized carbon nanocone. The process is analyzed in a system in which the larger diameter of the cone is in contact with a vapor reservoir and the smaller diameter is in contact with an initially empty reservoir. The

• ). Molecular dynamics simulations were performed using the LAMMPS [48] package using an NVT ensemble with a timestep of 0.1 fs. The TIP4P/2005 [49] water model was used since it provides a satisfactory description of self-diffusion coefficient [50], phase diagram, vapor–liquid equilibria [51][52], vapor

Bending and punching characteristics of aluminum sheets using the quasi-continuum method

• Man-Ping Chang,
• Shang-Jui Lin and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2022, 13, 1303–1315, doi:10.3762/bjnano.13.108

• , since it is very challenging to experimentally control every parameter in the nanoscale, the atomistic computational simulation methods are often used. The most commonly used simulation method is molecular dynamics (MD), which has been conducted to investigate many nanoscale processes [22][23]. Although

Studies of probe tip materials by atomic force microscopy: a review

• Ke Xu and
• Yuzhe Liu

Beilstein J. Nanotechnol. 2022, 13, 1256–1267, doi:10.3762/bjnano.13.104

• without compromising the carbon nanotubes' aspect ratio, strength and size. The mechanical response of these composite beams under bending is studied in molecular dynamics simulations and nanomanipulation experiments. The behavior of this system has been studied at both theoretical and experimental levels

Influence of water contamination on the sputtering of silicon with low-energy argon ions investigated by molecular dynamics simulations

• Grégoire R. N. Defoort-Levkov,
• Alan Bahm and
• Patrick Philipp

Beilstein J. Nanotechnol. 2022, 13, 986–1003, doi:10.3762/bjnano.13.86

• by molecular dynamics (MD) simulations how one of the most commonly found residual contaminations in vacuum chambers (i.e., water adsorbed on a silicon surface) influences sputtering by 100 eV argon ions. The incidence angle was changed from normal incidence to close to grazing incidence. For the

• ; molecular dynamics; silicon; simulations; water; Introduction Focused ion beams (FIB) play an increasingly important role in materials research areas such as nanoanalysis (e.g., secondary ion mass spectrometry (SIMS) [1][2][3] and sample preparation for transmission electron microscopy (TEM) [4], atom

• extreme cases. Nowadays, very little is known about the influence of contaminations on the amorphization process under ion irradiation. Thanks to molecular dynamics (MD) simulations, a wide range of materials properties and process parameters can be reproduced [27][28][29]. In this paper, we are using MD

Modeling a multiple-chain emeraldine gas sensor for NH₃ and NO₂ detection

• Hana Sustkova and
• Jan Voves

Beilstein J. Nanotechnol. 2022, 13, 721–729, doi:10.3762/bjnano.13.64

• gradient approximated (GGA) Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional was used. Guo et al. [5] investigated the graphene/polyaniline adsorption energy of NH3, CO, NO, and H2 using DFT and molecular dynamics computations. From this, graphene/PANI is highly sensitive to NH3 in comparison

• chosen fixed positions of ammonia and nitrogen dioxide molecules. We have computed the local energy minima through molecular dynamics, which results in the optimized position and orientation of the gas molecule. The spatial orientation of the gas molecules was estimated by these optimizations. Next, one

• as well. The I–V characteristics were computed for several molecule positions near the doped and near the undoped nitrogen atoms, see above. The molecule orientation was estimated through molecular dynamics optimization. The resistance from the linear part of the I–V characteristics was used to

Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking

• Kendra Ramirez-Acosta,
• Ivan A. Rosales-Fuerte,
• J. Eduardo Perez-Sanchez,
• Alfredo Nuñez-Rivera,
• Josue Juarez and
• Ruben D. Cadena-Nava

Beilstein J. Nanotechnol. 2022, 13, 699–711, doi:10.3762/bjnano.13.62

• variants of SARS-CoV-2. This research work will be focused on the molecular docking of peptides by molecular dynamics, in addition to an analysis of the possible interaction of these peptides with physiological proteins. This methodology could be extended to design peptides that are active against other

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

• ., alkane) the thermal conductivity was increased three times (from 0.1 to 0.4 W·m−1·K−1). This approach to determine the thermal conductivity of metal oxide nanoparticles in aqueous and nonaqueous fluids using visual molecular dynamics and interactive autocorrelations demonstrate a great tool to quantify

• 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

• molecules [1]. The molecular dynamics (MD) simulation method is a tool that has been used to effectively predict nanofluid thermal properties with relative accuracy [38][39][40][41][42]. The method relies on computationally solving basic equations of Newton’s laws of motion for interacting particles at the

Investigation of electron-induced cross-linking of self-assembled monolayers by scanning tunneling microscopy

• Patrick Stohmann,
• Sascha Koch,
• Yang Yang,
• Christopher David Kaiser,
• Julian Ehrens,
• Jürgen Schnack,
• Niklas Biere,
• Dario Anselmetti,
• Armin Gölzhäuser and
• Xianghui Zhang

Beilstein J. Nanotechnol. 2022, 13, 462–471, doi:10.3762/bjnano.13.39

• with a scanning tunneling microscope. As the irradiation dose was increased, the cross-linked regions continued to grow and a large number of subnanometer voids appeared. Their equivalent diameter is 0.5 ± 0.2 nm and the areal density is ≈1.7 × 1017 m−2. Supported by classical molecular dynamics

• cross-linked regions appear darker than the structurally ordered domains. At high doses, subnanometer-sized voids are formed preferably in regions of lower structural order and lower density in the monolayer. The formation of carbon nanomembranes was also modeled using classical molecular dynamics

• were analyzed by using an empirical fit. The lateral distribution of subnanometer voids was analyzed by partitioning the surface area into small segments and counting the number of voids in each segment. Classical molecular dynamics simulations The formation of a CNM was modelled using classical

Electrostatic pull-in application in flexible devices: A review

• Teng Cai,
• Yuming Fang,
• Yingli Fang,
• Ruozhou Li,
• Ying Yu and
• Mingyang Huang

Beilstein J. Nanotechnol. 2022, 13, 390–403, doi:10.3762/bjnano.13.32

• et al. [33] used molecular dynamics to compare the adsorption energies of GR-Au and GR-GR structures. The GR-GR structure has a higher adsorption energy of 307 mJ/m2. Mizuta et al. [7][35] assumed that the use of a GR-GR electrode structure could avoid the uncontrollable microscale interactions

Nanoscale friction and wear of a polymer coated with graphene

• Robin Vacher and
• Astrid S. de Wijn

Beilstein J. Nanotechnol. 2022, 13, 63–73, doi:10.3762/bjnano.13.4

• challenging problem due to the complex viscoelastic properties and structure. Using molecular dynamics simulations, we investigate how a graphene sheet on top of the semicrystalline polymer polyvinyl alcohol affects the friction and wear. Our setup is meant to resemble an AFM experiment with a silicon tip. We

• the polymer chains and reduces the indentation depth. Keywords: friction; graphene; molecular dynamics; polymer; Introduction Graphene is a two dimensional material that has remarkable properties, both electronic [1][2] and mechanical [3][4]. Even before anything was known about graphene, the

• . [27][28] show that graphene has a strong effect on the structure and dynamics of the polymer chains near the interface. In this work, we aim to develop our understanding of the frictional behavior of a polymer coated with graphene by using molecular dynamics simulations of a single sliding asperity at

Effect of lubricants on the rotational transmission between solid-state gears

• Huang-Hsiang Lin,
• Jonathan Heinze,
• Alexander Croy,
• Rafael Gutiérrez and
• Gianaurelio Cuniberti

Beilstein J. Nanotechnol. 2022, 13, 54–62, doi:10.3762/bjnano.13.3

• and velocity distribution are not well defined and one has to resort to an atomistic description, for example, via molecular dynamics (MD) simulations. Also, the contact mechanics at the nanoscale is very different from the macroscopic case since specific pair interactions have to be taken into

• only for better visibility since the actual thickness of the lubricant layer is 5.0–5.5 nm to ensure that the gears are immersed. Finally, the whole system is optimized by using the conjugate gradient method implemented within LAMMPS [58]. Molecular dynamics In this study, we use LAMMPS to perform the

Sputtering onto liquids: a critical review

• Anastasiya Sergievskaya,
• Adrien Chauvin and
• Stephanos Konstantinidis

Beilstein J. Nanotechnol. 2022, 13, 10–53, doi:10.3762/bjnano.13.2

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

• force [39][40][41][42]. However, compared with experimental methods, numerical simulations, such as the lattice Boltzmann method and molecular dynamics (MD) simulation, are more attractive in many aspects. First, numerical simulations can readily reach the system sizes and timescales of practical

• 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

• presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer

• deposition; irradiation-driven molecular dynamics; irradiation-induced chemistry; platinum nanostructures; reactive force fields; Introduction The controllable fabrication of nanostructures with nanoscale resolution remains a considerable scientific and technological challenge [1]. To address this challenge

• up to a few hundred atoms. This makes ab initio approaches of limited use to describe the irradiation-induced chemical transformations occurring during the FEBID process. A breakthrough into the atomistic description of FEBID has been achieved recently by means of irradiation-driven molecular

Effects of temperature and repeat layer spacing on mechanical properties of graphene/polycrystalline copper nanolaminated composites under shear loading

• Chia-Wei Huang,
• Man-Ping Chang and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2021, 12, 863–877, doi:10.3762/bjnano.12.65

• ) composites under shear loading are investigated by molecular dynamics simulations. The effects of different temperatures, graphene chirality, repeat layer spacing, and grain size on the mechanical properties, such as failure mechanism, dislocation, and shear modulus, are observed. The results indicate that

• . Keywords: dislocation; graphene/Cu; molecular dynamics; shear; self-healing; Introduction Graphene is a monolayered hexagonal thin film composed of sp2-bonded carbon atoms and has extraordinary properties for applications in nanoelectronics [1][2][3][4][5][6]. However, because of the two-dimensional

• this work, we focus on temperature and microstructure effects on graphene/polycrystalline copper nanolaminated (GPCuNL) composites. As mentioned above, the microstructure plays a crucial role for the mechanical behavior of GPCuNL composites. Thus, in the present study, molecular dynamics (MD