Modeling of nanoparticle coatings for medical applications

Abstract Gold nanoparticles (AuNPs) have been shown to possess properties beneficial for the treatment of cancerous tumors by acting as radiosensitizers for both photon and ion radiation. Blood circulation time is usually increased by coating the AuNPs with poly(ethylene glycol) (PEG) ligands. The effectiveness of the PEG coating, however, depends on both the ligand surface density and length of the PEG molecules, making it important to understand the structure of the coating. In this paper the thickness, ligand surface density, and density of the PEG coating is studied with classical molecular dynamics using the software package MBN Explorer. AuNPs consisting of 135 atoms (approximately 1.4 nm diameter) in a water medium have been studied with the number of PEG ligands varying between 32 and 60. We find that the thickness of the coating is only weakly dependent on the surface ligand density and that the degree of water penetration is increased when there is a smaller number of attached ligands

Special issue: Dynamics of systems on the nanoscale (2018). Editorial

The structure, formation and dynamics of both animate and inanimate matter on the nanoscale are a highly interdisciplinary field of rapidly emerging research engaging a broad community encompassing experimentalists, theorists, and technologists. It is relevant for a large variety of molecular and nanosystems of different origin and composition and concerns numerous phenomena originating from physics, chemistry, biology, or materials science. This Topical Issue presents a collection of original research papers devoted to different aspects of structure and dynamics on the nanoscale. Some of the contributions discuss specific applications of the research results in several modern technologies and in next generation medicine. Most of the works of this topical issue were reported at the Fifth International Conference on Dynamics of Systems on the Nanoscale (DySoN) – the premier forum for the presentation of cutting-edge research in this field that was held in Potsdam, Germany in October of 2018

Two center multipole expansion method: application to macromolecular systems

We propose a new theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well known fast multipole method. Its efficiency, accuracy and applicability to macromolecular systems is analyzed and discussed in detail.Comment: 23 pages, 7 figures, 1 tabl

Physics of ion beam cancer therapy: a multi-scale approach

We propose a multi-scale approach to understand the physics related to ion-beam cancer therapy. It allows the calculation of the probability of DNA damage as a result of irradiation of tissues with energetic ions, up to 430 MeV/u. This approach covers different scales, starting from the large scale, defined by the ion stopping, followed by a smaller scale, defined by secondary electrons and radicals, and ending with the shortest scale, defined by interactions of secondaries with the DNA. We present calculations of the probabilities of single and double strand breaks of DNA, suggest a way to further expand such calculations, and also make some estimates for glial cells exposed to radiation.Comment: 18 pag,5 fig, submitted to PR

Ab initio study of alanine polypeptide chains twisting

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles Phi and Psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.Comment: 24 pages, 10 figure

Role of exchange interaction in self-consistent calculations of endohedral fullerenes

Results of the self-consistent calculation of electronic structure of endohedral fullerene Ar@C$_{60}$ within the Hartree-Fock and the local density approximations are presented. Hartree-Fock approximation is used for the self-consistent description for the first time. It is shown that the accurate account of the exchange interaction between all electrons of the compound leads to the significant modification of the atomic valent shell which causes the noticeable charge redistribution inside the endohedral compound.Comment: 5 figures, Proceedings of the 5th Conference on Elementary Processes in Atomic Systems (CEPAS 2011), submitted to Nuclear Instruments and Methods in Physics Research Section

Atomistic modelling and structural characterisation of coated gold nanoparticles for biomedical applications

This study presents the results of atomistic structural characterisation of 3.7-nm-diameter gold nanoparticles (NP) coated with polymer polyethylene glycol-based ligands of different lengths (containing 2–14 monomers) and solvated in water. The system size and composition are selected in connection to several experimental studies of radiosensitisation mechanisms of gold NPs. The coating structure and water distribution near the NP surface are characterised on the atomistic level by means of molecular dynamics simulations. The results of simulations carried out in this study, combined with the results of our recent study (Verkhovtsev et al. in J Phys Chem A 126:2170–2184, 2022) and those from the field of polymer physics, are used to calculate key structural parameters of the coatings of radiosensitising gold NPs. On this basis, connections between the coating structure and distribution of water are established for different NP sizes as well as lengths and surface densities of coating molecules. The quantitative analysis of water distribution in the vicinity of coated metal NPs can be used to evaluate the radiosensitising effectiveness of a particular NP system based on the proximity of water to the NP metal core, which should impact the production of hydroxyl radicals and reactive oxygen species in the vicinity of metal NPs exposed to ionising radiation. Graphical abstract

Synthesis of a fullerene-based one-dimensional nanopolymer through topochemical transformation of the parent nanowire

Large-scale practical applications of fullerene (C60) in nanodevices could be significantly facilitated if the commercially-available micrometer-scale raw C60 powder were further processed into a one-dimensional (1D) nanowire-related polymer displaying covalent bonding as molecular interlinks and resembling traditional important conjugated polymers. However, there has been little study thus far in this area despite the abundant literature on fullerene. Here we report the synthesis and characterization of such a C60-based nanowire polymer, (-C60TMB-)n, where TMB=1,2,4-trimethylbenzene, which displays a well-defined crystalline structure, exceptionally large length-to-width ratio and excellent thermal stability. The material is prepared by first growing the corresponding nanowire through a solution phase of C60 followed by a topochemical polymerization reaction in the solid state. Gas chromatography, mass spectrometry and 13C nuclear magnetic resonance evidence is provided for the nature of the covalent bonding mode adopted by the polymeric chains. Theoretical analysis based on detailed calculations of the reaction energetics and structural analysis provides an in-depth understanding of the polymerization pathway. The nanopolymer promises important applications in biological fields and in the development of optical, electrical, and magnetic nanodevices.Comment: 30 pages, 12 figures, 2 table

Evolution of electronic and ionic structure of Mg-clusters with the growth cluster size

The optimized structure and electronic properties of neutral and singly charged magnesium clusters have been investigated using ab initio theoretical methods based on density-functional theory and systematic post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. We have systematically calculated the optimized geometries of neutral and singly charged magnesium clusters consisting of up to 21 atoms, electronic shell closures, binding energies per atom, ionization potentials and the gap between the highest occupied and the lowest unoccupied molecular orbitals. We have investigated the transition to the hcp structure and metallic evolution of the magnesium clusters, as well as the stability of linear chains and rings of magnesium atoms. The results obtained are compared with the available experimental data and the results of other theoretical works.Comment: 30 pages, 10 figures, 3 table

Molecular dynamics study of accelerated ion-induced shock waves in biological media

We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model