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

• modeling, including reactive classical molecular dynamics and ab initio calculations, we reveal that TA preferentially binds to the most reactive sites on GO surfaces via the oxygen-containing groups or the carbon matrix; van der Waals interaction forces dominate the binding energy. TA exhibits a dose

• are useful to predict and interpret experimental results. We performed, therefore, a multilevel study with different theory levels; reactive classical molecular dynamics enabled the exploration of the chemical and conformational changes of TA and GO, whereas ab initio calculations provided information

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

• , 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

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

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

Nanomechanics of few-layer materials: do individual layers slide upon folding?

• Ronaldo J. C. Batista,
• Rafael F. Dias,
• Ana P. M. Barboza,
• Alan B. de Oliveira,
• Taise M. Manhabosco,
• Thiago R. Gomes-Silva,
• Matheus J. S. Matos,
• Andreij C. Gadelha,
• Cassiano Rabelo,
• Luiz G. L. Cançado,
• Ado Jorio,
• Hélio Chacham and
• Bernardo R. A. Neves

Beilstein J. Nanotechnol. 2020, 11, 1801–1808, doi:10.3762/bjnano.11.162

• folded 2D material. In principle, the model describes any 2D material, and its predictions are corroborated by comparison with classical molecular dynamics simulations and to results of previous investigations on graphene and talc. Because folds naturally occur in flakes of varying thickness

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

• : 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 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

• 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

• permeation rate due to hydrogen-bonding with the nanopore rim. In this paper, by means of classical molecular dynamics, we discuss such an inhibiting effect of water on the gas permeability. Employing different nanopores functionalized by hydrogen and nitrogen atoms, we conduct theoretical studies on the

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

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

• molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free

• organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical

The difference in the thermal conductivity of nanofluids measured by different methods and its rationalization

• Aparna Zagabathuni,
• Sudipto Ghosh and
• Shyamal Kumar Pabi

Beilstein J. Nanotechnol. 2016, 7, 2037–2044, doi:10.3762/bjnano.7.194

• phononic heat exchange during the collision. In order to do so Karthik et al. [23] used a continuum approach rather than classical molecular dynamics (CMD) approach to estimate the energy exchange between the nanoparticles and wall, because in the CMD approach the movement of electrons cannot be considered

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

• more advanced surface features, including steps, are unclear at this point. The present work addresses the mechanical behavior around a gallium nitride (GaN) step employing a combination of classical molecular dynamics (MD) simulations with a finite element (FEM) approach and CR-AFM experiments. GaN is

Dissipation signals due to lateral tip oscillations in FM-AFM

• Michael Klocke and
• Dietrich E. Wolf

Beilstein J. Nanotechnol. 2014, 5, 2048–2057, doi:10.3762/bjnano.5.213

• of a more realistic model, where tip and substrate consist of many atoms. The interaction is given by the summation over pair potentials as they are used in molecular dynamics. In classical molecular dynamics, atomic bonding is described by empirical potentials. We used the potential of Fumi and Tosi

Classical molecular dynamics investigations of biphenyl-based carbon nanomembranes

• Andreas Mrugalla and
• Jürgen Schnack

Beilstein J. Nanotechnol. 2014, 5, 865–871, doi:10.3762/bjnano.5.98

• : biphenyls; carbon nanomembranes; classical molecular dynamics; Introduction Freestanding carbon nanomembranes are produced from molecular precursors such as biphenylthiols (BPT). The precursors self-assemble in monolayers on gold surfaces and are then polymerized by irradiation with electrons [1][2][3

• ., a lattice structure as in solids cannot be assumed, a quantum mechanical simulation is virtually impossible. In this article we therefore resort to classical molecular dynamics simulations, which allow to simulate up to several millions of carbon atoms. In order to account for the very flexible spn

• configuration that is laterally linked through carbon bonds of broken phenyls. We show that such structures indeed form in our simulations. The article is organized as follows. In the next two sections we shortly repeat the essentials of our classical molecular dynamics simulations. The main section discusses

Direct monitoring of opto-mechanical switching of self-assembled monolayer films containing the azobenzene group

• Einat Tirosh,
• Enrico Benassi,
• Silvio Pipolo,
• Marcel Mayor,
• Michal Valášek,
• Veronica Frydman,
• Stefano Corni and
• Sidney R. Cohen

Beilstein J. Nanotechnol. 2011, 2, 834–844, doi:10.3762/bjnano.2.93

• the data previously obtained. This is due to the upright orientation of the molecules in the SAM, which makes the bending unable to absorb the external compression. Molecular dynamics approach The problem of calculating the relative stiffness can also be treated through a classical molecular dynamics

• The investigation of the relative stiffness of the azobenzene SAM at the molecular level was also approached by computational modeling. The problem was modeled within two different schemes, one based on a quantum mechanical (QM) description of the single molecule, and the other on classical molecular

• dynamics (MD) simulations of the SAM. In the QM approach, the stiffness of the SAM is first related to a molecular quantity, the weighted molecular force constant , through a simple model. Then, is obtained by rigorous ab initio calculations (details in Experimental section). The molecular