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

• provide valuable insights into the mechanisms of lactose and protein deposition on aluminum surfaces, which can aid in the general understanding of protein corona formation. Keywords: all atomistic; aluminum; bionano interface; coarse grained model; lactose; milk protein; multiscale modelling; protein

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

• by this mechanism, as it is harder to penetrate. Coarse grained model for polyvinyl alcohol (PVA, C2H4O)x). Red atoms are oxygen, dark gray are carbon, and light gray are hydrogen. One green circle represents one coarse-grained particle, which replaces the group of atoms C2H4O. Snapshot of the

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

• Lukasz Baran Wojciech Rzysko Edyta Slyk Department for Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin, Poland. 10.3762/bjnano.11.73 Abstract We introduce a molecular dynamics (MD) coarse-grained model for the description of

• diffraction pattern and average association number. Keywords: 2D materials; coarse-grained model; molecular simulations; self-assembly; structural characterization; tripod building blocks; Introduction On-surface synthesis is a newly developing field in chemistry that aims at making use of solid surfaces as

• directions of interparticle interactions [37][39], as well as for linear, V-shape, and tetraphenylethylene derivatives [40]. In this work, we want to show that the possibilities of our MD coarse-grained model are not limited to these geometries but can also be used for tripod molecules. In addition to that

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

• fibrils with the PDB IDs 2LMO [39], 2M4J [40] and 2MVX [41] and two Aβ42 with the PDB IDs 5OQV [42], and 2NAO [43]. The only available structure for α-syn is the one with PDB ID: 2N0A [44]. The coarse-grained model In our CG model, each amino acid is represented by a bead located at the Cα-atom position

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

• conjunction with a coarse-grained elastic-network model based on SNNFGAILSS fibrils [29], which showed that the bending rigidity increases up to a critical length; however, it is not possible to assess the importance of defects within such a coarse-grained model. For direct comparison between the different