Mechanistic insights into endosomal escape by sodium oleate-modified liposomes

• Ebrahim Sadaqa,
• Satrialdi,
• Fransiska Kurniawan and
• Diky Mudhakir

Beilstein J. Nanotechnol. 2024, 15, 1667–1685, doi:10.3762/bjnano.15.131

• . These findings confirm that SO is effective at promoting membrane fusion under acidic conditions to achieve targeted fusogenicity, making it a promising candidate for enhancing endosomal escape in drug delivery applications. MD simulation of OLA and AUR interaction with lipid bilayers The MD simulations

• enhanced escape into the cytosol. This empirical evidence correlates with our MD simulation findings, providing a molecular basis for the observed decrease in colocalization. Protonated OLA was shown in simulations to integrate deeply into the lipid bilayer of the endosomal membrane, resulting in increased

Interaction of graphene oxide with tannic acid: computational modeling and toxicity mitigation in C. elegans

• Romana Petry,
• James M. de Almeida,
• Francine Côa,
• Felipe Crasto de Lima,
• Diego Stéfani T. Martinez and
• Adalberto Fazzio

Beilstein J. Nanotechnol. 2024, 15, 1297–1311, doi:10.3762/bjnano.15.105

• configuration in water without TA. Figure 4a and Figure 4b show the charge density plot of the functions f+ and f− of GO before and after NPT MD simulation in an aqueous environment at 300 K. We observed an augmentation of sheet folding and the occurrence of broken bonds, which increased the reactivity of the

Atomistic insights into the morphological dynamics of gold and platinum nanoparticles: MD simulations in vacuum and aqueous media

• Evangelos Voyiatzis,
• Eugenia Valsami-Jones and
• Antreas Afantitis

Beilstein J. Nanotechnol. 2024, 15, 995–1009, doi:10.3762/bjnano.15.81

• placed in vacuum, and the systems are cooled down to 100 K following the single-step procedure of Martin et al. [49]. In each step, the temperature is decreased instantaneously by 100 K, and the systems are relaxed by performing a MD simulation of 20 ns in the NVT ensemble. In total, this procedure is

Effects of cutting tool geometry on material removal of a gradient nanograined CoCrNi medium entropy alloy

• Yu-Sheng Lu,
• Yu-Xuan Hung,
• Thi-Xuyen Bui and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2024, 15, 925–940, doi:10.3762/bjnano.15.76

• carried out with time steps of 0.001 ps and a 10 ps equilibrium process. Table 1 shows the MD simulation parameters of the GNG CoCrNi MEA cutting process for this study. The embedded atom method (EAM) potential from Farkas et al. [11] was utilized for modeling the atomic interaction of the atoms in the

• of 300 K. (a–e) Crystal structure evolution in CoCrNi MEAs for various tool rake angles and (f) the total dislocation density during cutting with a cutting depth of 1 nm, a tool cutting-edge radius of 1 nm, a cutting speed of 10 m/s, and at a temperature of 300 K. MD simulation parameters in this

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

• fragmentation of NWs during the heat treatment. Molecular dynamics model of the NW: (a) initial conditions, (b) results of the compression cycle, (c) results of the tensile deformation; (d) amorphization of the central part of the NW as a result of heat-treatment cycles: TEM image (left) and MD simulation frame

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

• simulations. This is equivalent to a system of finite depth but with perfectly specular surfaces perpendicular to that direction. This polygon takes into account any variations in width at the joins that occur from the joints used in the MD simulation. The supplementary sketches in Figure 2 illustrate this

Transferability of interatomic potentials for silicene

• Marcin Maździarz

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

• height h (Å), 2D elastic constants Cij (N/m), 2D Kelvin moduli Ki (N/m), mean absolute percentage error (MAPE) (%), and relative performance measured as normalized timesteps/second in molecular dynamics (MD) simulation. Supporting Information Crystallographic Information Files (CIF) for polymorphs of

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

• the MD simulation can be effectively applied to simulations at the nanoscale, it still has limitations [14]. Therefore, in recent years, the multiscale simulation approach, which combines atomistic and continuum simulations, has received more and more attention [24][25][26][27][28][29][30][31][32

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

• 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

• of both nanofluids. Moreover, this research gives insights regarding the accuracy of thermal conductivities of aqueous and nonaqueous fluids predicted by molecular dynamic simulation. Finally, these MD simulation results were compared with experimental data [43] and previously reported simulation

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

• formation process between gears. Keywords: lubricants; MD simulation; rotational transmission; solid-state gears; Introduction In mechanical systems, lubrication is the most common way to reduce friction and wear [1][2][3][4]. The idea of lubricants is preventing direct contact between surfaces to avoid

• chosen in order to make the MD simulation feasible in terms of computation time. In fact, one might expect for that the result from MD simulations might be different for lower speeds. However, we expect that results in the low-speed regime would be qualitatively similar and would be somewhere between our

• instantaneous torque transfer and makes the simulation more realistic. Then we monitor how the second gear can follow the motion of the first one. The results from the MD simulation within 60 ps for different center-of-mass distances, dCM = 9.6, 9.9, 10.2 and 10.5 nm, are shown in Figure 2a,b,c and d

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

• length correspondingly decreases [23][46]. Joly et al. proposed an approximate model to describe the relationship between the slip length and surface charge density. They validated the model by using a MD simulation with an ionized solution system represented by models of ideal solvents and ions [46

• the liquid flows perpendicularly (θ = 0) and parallelly (θ = π/2) to the stripe orientation, respectively. As it can be seen from Figure 8, MD simulation results show good agreement with Equation 4 and the effective slip length monotonically increases with an increase in θ. 2.4.3 Gas bubbles

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

• removed, and remaining metal deposits are reorganized into more compact and dense structures. Both types of post-deposition processing, that is, annealing and further electron irradiation, can be simulated by means of MD as the last step of the computational protocol shown in Figure 1. MD simulation of

The role of gold atom concentration in the formation of Cu–Au nanoparticles from the gas phase

• Yuri Ya. Gafner,
• Svetlana L. Gafner,
• Darya A. Ryzkova and
• Andrey V. Nomoev

Beilstein J. Nanotechnol. 2021, 12, 72–81, doi:10.3762/bjnano.12.6

• composition; however, the size of the resulting particles varies significantly. To solve this issue, we studied the formation of Cu–Au nanoparticles with different chemical compositions from a gaseous medium using computer molecular dynamics (MD) simulation. The aim was to determine the effect of the

• MD simulation, it was concluded that an increase in the percentage of gold atoms in the initial vapor phase led to a decrease in the size of the synthesized nanoparticles. In addition, it was found that clusters with a size of more than 400–500 atoms, regardless of the chemical composition of the

• in a high-density buffer gas, collisions between atoms of the synthesized material occur in the nanosecond range, which is the maximum possible time interval for a MD simulation. Based on this, the analysis we present is only an attempt, at a qualitative level, to understand the main features of the

Three-dimensional solvation structure of ethanol on carbonate minerals

• Hagen Söngen,
• Ygor Morais Jaques,
• Peter Spijker,
• Christoph Marutschke,
• Stefanie Klassen,
• Ilka Hermes,
• Ralf Bechstein,
• Lidija Zivanovic,
• John Tracey,
• Adam S. Foster and
• Angelika Kühnle

Beilstein J. Nanotechnol. 2020, 11, 891–898, doi:10.3762/bjnano.11.74

• reveals a qualitatively similar ethanol arrangement on both carbonates, indicating the general nature of this finding. Keywords: 3D AFM; calcite; ethanol; magnesite; MD simulation; solvation structure; Introduction Sedimentary rocks including the minerals calcite and magnesite are abundant constituents

• reveals some minor differences that are within the variations typically seen for different tips. Thus, our experimental findings suggest these findings to be equally valid for the magnesite–ethanol interface. MD simulation results To allow for consistent comparisons between our experimental data and

• orientational preference (there is a slight preference for the OH to point away from the surface). Even broader peaks can be recognized in the profiles at larger distances from the surface, which is indicative of a faint third, fourth, etc. layer. From the MD simulation, we obtain a layer-to-layer distance of

Simulations of the 2D self-assembly of tripod-shaped building blocks

• Łukasz Baran,
• Wojciech Rżysko and
• Edyta Słyk

Beilstein J. Nanotechnol. 2020, 11, 884–890, doi:10.3762/bjnano.11.73

• structures and computed the average association number, which can be found in Figure 5b. Conclusion We have shown MD simulation results of the self-assembly of different models of tripod building blocks. We have characterized the self-assembled structures regarding different structural parameters such as

Long-term entrapment and temperature-controlled-release of SF₆ gas in metal–organic frameworks (MOFs)

• Hana Bunzen,
• Andreas Kalytta-Mewes,
• Leo van Wüllen and
• Dirk Volkmer

Beilstein J. Nanotechnol. 2019, 10, 1851–1859, doi:10.3762/bjnano.10.180

• the fact that all calculated values formally correspond to a temperature of zero Kelvin. In the future, metadynamic MD simulation studies might be performed, which should take into account both the effects of different gas loading conditions as well as temperature-dependent lattice vibrations and

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

• protection in battle situations and shielding structure of spacecrafts that are exposed to space debris. Experimental In the MD simulation, a low initial temperature of 10 K was chosen to minimize the influence from environmental thermal fluctuations. The widely adopted adaptive intermolecular reactive

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

• fibril bending modulus (Yb) that depends on both YT and S. Our CG strategy can be used to extract and compare elastic properties in a systematic way. This significant advantage of CG simulations has motivated the current study, which employs MD simulation of a structure-based CG model [35][36][37][38] to

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

• adaptable trajectory is the only solution where the operator can continuously communicate with the experiment through the real-time MD simulation and define the trajectory at will using the motion control system. This human–machine augmented system thus provides a far better control of the manipulation

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

• 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

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

• between PLA chains, the optimal separation distance between them was evaluated. The separation distance between PLA chains was established in 7 Å (Figure 2). Thus, 10 PLA chains were packed in a 100 × 100 × 100 Å3 periodic box to assemble the PLA core by a MD simulation in vacuum. The initially packed

• monomer units after 2 ns of MD simulation and 20 PLA chains, 40 PLA chains, 80 PLA chains with 20 monomer units after 100 ps of simulation. Snapshots in time were taken from the MD simulation of PLA core formation with 10 PLA chains. Atoms are colored according to convention (carbon–gray; hydrogen–white

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

• ][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

• grain itself, thereby directing the destruction along the grain boundary rather than through the grain. This destruction phenomenon is denoted as intergranular fracture [20][21]. Cleri et al. [20] reported that the grain boundary in FCC Cu generates an asymmetric crack growth based on the MD simulation

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

• practical MD simulation cell, the dissipated energy accumulates in the phonons in the simulated sample, leading to a progressive overheating. Therefore this simulation procedure cannot address a steady sliding regime, but can at most identify the leading instabilities occurring and the most strongly coupled

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

• [BmimSO3H][PTS] under periodic boundary conditions. The snapshot can be obtained upon request. In the classical MD simulation the system was set up for a density of 1.6 g/cm3 and NPT simulations were performed resulting in a box size of 2349.41 pm3. The AIMD simulations we run at 440 K with massive

Calculating free energies of organic molecules on insulating substrates

• Julian Gaberle,
• David Z. Gao and
• Alexander L. Shluger

Beilstein J. Nanotechnol. 2017, 8, 667–674, doi:10.3762/bjnano.8.71

• distance between a step edge and the COM of a molecule. Averages were taken from 50 ns MD simulations at each separation R. The MD simulation time was then increased to 80 ns and 100 ns in order to check for convergence. Zero entropy was defined to be at a configuration where the force along the reaction

• state is more favourable than the other. However, the convergence of thermodynamic integration calculations must be checked thoroughly. When increasing the MD simulation time at each step along the reaction coordinate from 50 ns to 80 ns the calculated values for change in entropy differed only

• curves. Increasing the MD trajectory from 50 ns to 100 ns leads to a drop in the free energy of step adhesion from 0.5 eV to 0.35 eV. As MD simulation times are increased, the free energy continues to decrease as more and more of the higher-energy, low-probability configurational space is sampled. This