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Nanomaterials, i.e., materials that are manufactured at a very small spatial scale, can possess unique physical and chemical properties and exhibit novel characteristics as compared to the same material without nanoscale features. The reduction of size down to the nanometer scale leads to the abundance of potential applications in different fields of technology. For instance, tailoring the physicochemical properties of nanomaterials for modification of their interaction with a biological environment has been reflected in a number of biomedical applications.
Strategies to choose the size and the composition of nanoscale systems are often hindered by a limited understanding of interactions that are difficult to study experimentally. However, this goal can be achieved by means of advanced computer simulations. This thesis explores, from a theoretical and a computational viewpoints, stability, electronic and thermo-mechanical properties of nanoscale systems and materials which are related to biomedical applications.
We examine the ability of existing classical interatomic potentials to reproduce stability and thermo-mechanical properties of metal systems, assuming that these potentials have been fitted to describe ground-state properties of the perfect bulk materials.
It is found that existing classical interatomic potentials poorly describe highly-excited vibrational states when the system is far from the potential energy minimum. On the other hand, construction of a reliable computational model is essential for further development of nanomaterials for applications. A new interatomic potential that is able to correctly reproduce both the melting temperature and the ground-state properties of different metals, such as gold, platinum, titanium, and magnesium, by means of classical molecular dynamics simulations is proposed in this work. The suggested modification of a many-body potential has a general nature and can be utilized for similar numerical exploration of thermo-mechanical properties of a broad range of molecular and solid state systems experiencing phase transitions.
The applicability of the classical interatomic potentials to the description of nanoscale systems, consisting of several tens-hundreds of atoms, is also explored in this study. This issue is important, for instance, in the case of nanostructured materials, where grains or nanocrystals have a typical size of about a few nanometers. We validate classical potentials through the comparison with density-functional theory calculations of small
atomic clusters made of titanium and nickel. By this analysis, we demonstrate that the classical potentials fitted to describe ground-state properties of a bulk material can describe the energetics of nanoscale systems with a reasonable accuracy.
In this work, we also analyze electronic properties of nanometer-size nanoparticles made of gold, platinum, silver, and gadolinium; nanoparticles composed of these materials are of current interest for radiation therapy applications. We focus on the production of low-energy electrons, having the kinetic energy from a few electronvolts to several tens of electronvolts. It is currently established that the low-energy secondary electrons of such energies play an important role in the nanoscale mechanisms of biological damage resulting from ionizing radiation. We provide a methodology for analyzing the dynamic response of nanoparticles of the experimentally relevant sizes, namely of about several nanometers, exposed to ionizing radiation. Because of a large number of constituent atoms (about 1000 −10000 atoms) and consequently high computational costs, the electronic properties of such systems can hardly be described by means of ab initio methods based on a quantum-mechanical treatment of electrons, and this analysis should rely on model approaches. By comparing the response of smaller systems (of about 1 nm size) calculated within the ab initio- and the model framework, we validate this methodology and make predictions for the electron production in larger systems.
We have revealed that a significant increase in the number of the low-energy electrons emitted from nanometer-size noble metal nanoparticles arises from collective electron excitations formed in the systems. It is demonstrated that the dominating mechanisms of electron yield enhancement are related to the formation of plasmons excited in a whole system and of atomic giant resonances formed due to excitation of valence d electrons in individual atoms of a nanoparticle. Being embedded in a biological medium, the noble metal nanoparticles thus represent an important source of low-energy electrons, able to produce a significant irrepairable damage in biological systems.
A general methodology for studying electronic properties of nanosystems is used to make quantitative predictions for electron production by non-metal nanoparticles. The analysis illustrates that due to a prominent collective response to an external electric field, carbon nanoparticles embedded in a biological medium also enhance the production of low-energy electrons. The number of low-energy electrons emitted from carbon nanoparticles is demonstrated to be several times higher as compared to the case of liquid water.

In the present work, the problem of protein folding is addressed from the point of view of equilibrium thermodynamics. The conformation of a globular protein in solution at common temperatures is quite complicated without any geometrical symmetry, but it is an ordered state in the sense of its biological activity. This complicated conformation of a single protein molecule is destroyed upon increasing the temperature or by the addition of appropriate chemical agents, as is revealed by the loss of its activity and change of the physical properties, and so on. Once the complicated native structures having biological activity are lost, it would be natural to suppose that the native structure could hardly be restored. Nevertheless, pioneers, such as Anson and Mirsky, recognized as early as in 1925 that this was not always the case. If one defines the folded and unfolded states of a protein as two distinct phases of a system, then under the variation of temperature the system is transformed from one phase state into another and vice versa. The process of protein folding is accompanied by the release or absorption of a certain amount of energy, corresponding to the first-oder-type phase transitions in the bulk. Knowing the partition function of the system one can evaluate its energy and heat capacity under different temperatures. This task was performed in this work. The results of the developed statistical mechanics model were compared with the results of molecular dynamic simulations of alanine poylpeptides. In particular, the dependencies on temperature of the total energy of the system and heat capacity were compared for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. The good correspondence of the results of the theoretical model with the results of molecular dynamics simulations allowed to validate the assumptions made about the system and to establish the accuracy range of the theory. In order to perform the comparison of the results of theoretical model and the molecular dynamics simulations it is necessary to perform the efficient analysis of the results of molecular dynamics simulations. This task was also addressed in the present work. In particular, different ways to obtain dependence of the heat capacity on temperature from molecular dynamics simulations are discussed and the most efficient one is proposed. The present thesis reports the result of molecular dynamic simulations for not only alanine polypeptides by also for valine and leucine polypeptides. In valine and leucine polypeptides, it is also possible to observe the helix↔random coil transitions with the increase of temperature. The current thesis presents a work that starts with the investigation of the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. Then this knowledge is applied for the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized for the case of proteins in water environment and the comparison of the results of the statistical mechanics model with the experimental measurements of the heat capacity on temperature dependencies for two globular proteins is performed. The presented formalism is based on fundamental physical properties of the system and provides the possibility to describe the folding↔unfolding transitions quantitatively. The combination of these two facts is the major novelty of the presented approach in comparison to the existing ones. The “transparent” physical nature of the formalism provides a possibility to further apply it to a large variety of systems and processes. For instance, it can be used for investigation of the influence of the mutations in the proteins on their stability. This task is of primary importance for design of novel proteins and drug delivering molecules in medicine. It can provide further insights into the problem of protein aggregation and formation of amyloids. The problem of protein aggregation is closely associated with various illnesses such as Alzheimer and mad cow disease. With certain modifications, the presented theoretical method can be applied to the description of the protein crystallization process, which is important for the determination of the structure of proteins with X-Rays. There many other possible applications of the ideas described in the thesis. For instance, the similar formalism can be developed for the description of melting and unzipping of DNA, growth of nanotubes, formation of fullerenes, etc.

This thesis is devoted to the developement of a classical model for the study of the energetics and stability of carbon nanotubes. The motivation behind such a model stems from the fact that production of nanotubes in a well-controlled manner requires a detailed understanding of their energetics. In order to study this different theoretical approaches are possible, ranging from the computationally expensive quantum mechanical first principle methods to the relatively simple classical models. A wisely developed classical model has the advantage that it could be used for systems of any possible size while still producing reasonable results. The model developed in this thesis is based on the well-known liquid drop model without the volume term and hence we call it liquid surface model. Based on the assumption that the energy of a nanotube can be expressed in terms of its geometrical parameters like surface area, curvature and shape of the edge, liquid surface model is able to predict the binding energy of nanotubes of any chirality once the total energy and the chiral indices of it are known. The model is suggested for open end and capped nanotubes and it is shown that the energy of capped nanotubes is determined by five physical parameters, while for the open end nanotubes three parameters are sufficient. The parameters of the liquid surface model are determined from the calculations performed with the use of empirical Tersoff and Brenner potentials and the accuracy of the model is analysed. It is shown that the liquid surface model can predict the binding energy per atom for capped nanotubes with relative error below 0.3% from that calculated using Brenner potential, corresponding to the absolute energy difference being less than 0.01 eV. The influence of the catalytic nanoparticle on top of which a nanotube grows, on the nanotube energetics is also discussed. It is demonstrated that the presence of catalytic nanoparticle changes the binding energy per atom in such a way that if the interaction of a nanotube with the catalytic nanoparticle is weak then attachment of an additional atom to a nanotube is an energetically favourable process, while if the catalytic nanoparticle nanotube interaction is strong , it becomes energetically more favourable for the nanotube to collapse. The suggested model gives important insights in the energetics and stability of nanotubes of different chiralities and is an important step towards the understanding of nanotube growth process. Young modulus and curvature constant are calculated for single-wall carbon nanotubes from the paremeters of the liquid surface model and demonstrated that the obtained values are in agreement with the values reported earlier both theoretically and experimentally. The calculated Young modulus and the curvature constant were used to conclude about the accuracy of the Tersoff and Brenner potentials. Since the parameters of the liquid surface model are obtained from the Tersoff and Brenner potential calculations, the agreement of elastic properties derived from these parameters corresponds to the fact that both potentials are capable of describing the elastic properties of nanotubes. Finally, the thesis discuss the possible extension of the model to various systems of interest.

Nanocarbon structures, such as fullerenes and nanotubes, have generated considerable interest and research, due to their unique properties and potential applications. In this thesis, we present a study of the phase transition properties of nanocarbon clusters,in particular, we pay special consideration to fullerenes. The work presented in this thesis is largely theoretical and computational in nature, employing as a tool, molecular dynamics simulations to probe the dynamic stability of fullerenes and associated nanocarbon structures such as graphenes and nanotubes.

Atomistic molecular dynamics approach for channeling of charged particles in oriented crystals
(2015)

Der Gitterführungseffekt ist der Prozess der Ausbreitung von geladenen Teilchen entlang der Ebenen oder Achsen von kristallinen Materialien. Seit den 1960er Jahren ist dieser Effekt weitgehend theoretisch und experimentell untersucht worden. Dieser Effekt wurde für die Manipulation von Hochenergiestrahlen, die Hochpräzisionsstruktur- und -fehleranalyse von kristallinen Medien und die Herstellung von hochenergetischer Strahlung angewendet. Zur Abstimmung der Parameter der Gitterführung und Gitterführungsstrahlung wurde dieser Prozess für den Fall von künstlich nanostrukturierten Materialien, wie gebogenen Kristallen, Nanoröhren und Fullerit, angenommen. In den letzten Jahren wurde das Konzept des kristallinen Undulators formuliert und getestet, das besondere Eigenschaften der Strahlung aufgrund der Gitterführung von Projektilen in regelmäßig gebogenen Kristallen vorhersagt.
In dieser Arbeit werden die Prozesse der Gitterführung von Sub- und Multi-GeV-Elektronen und -Positronen durch den atomistischen Molekulardynamik-Ansatz untersucht. Die Ergebnisse dieser Studien wurden in einer Reihe von Artikeln während meiner Promotion in Frankfurt vorgestellt. Dieser Ansatz ermöglicht die Simulation komplexer Fälle von Gitterführung in geraden, gebogenen und periodisch gebogenen Kristallen aus reinen kristallinen Materialien und von gemischten Materialien wie Si-Ge-Kristallen, in mehrschichtigen und nanostrukturierten kristallinen Systemen. Die Arbeit beschreibt die Methode der Simulationen, stellt Ergebnisse von Simulationen für verschiedene Fälle vor und vergleicht die Ergebnisse von Simulationen mit aktuellen experimentellen Daten. Die Ergebnisse werden mit Schätzungen der dechanneling-Länge verglichen, dem Anteil der gittergeführten Projektile, der Winkelverteilung der ausgehenden Projektile und des Strahlungsspektrums.

Nanotechnology is a rapidly developing branch of science, which is focused on the study of phenomena at the nanometer scale, in particular related to the possibilities of matter manipulation. One of the main goals of nanotechnology is the development of controlled, reproducible, and industrially transposable nanostructured materials.
The conventional technique of thin-film growth by deposition of atoms, small atomic clusters and molecules on surfaces is the general method, which is often used in nanotechnology for production of new materials. Recent experiments show, that patterns with different morphology can be formed in the course of nanoparticles deposition process on a surface. In this context, predicting of the final architecture of the growing materials is a fundamental problem worth studying.
Another factor, which plays an important role in industrial applications of new materials, is the question of post-growth stability of deposited structures. The understanding of the post-growth relaxation processes would give a possibility to estimate the lifetime of the deposited material depending on the conditions at which the material was fabricated. Controllable post-growth manipulations with the architecture of deposited structures opens new path for engineering of nanostructured materials.
The task of this thesis is to advance understanding mechanisms of formation and post-growth evolution of nanostructured materials fabricated by atomic clusters deposition on a surface. In order to achieve this goal the following main problems were addressed:
1. The properties of isolated clusters can significantly differ from those of analogous clusters occurring on a solid surface. The difference is caused by the interaction between the cluster and the solid. Therefore, the understanding of structural and dynamical properties of an atomic cluster on a surface is a topic of intense interest from the scientific and technological point of view. In the thesis, stability, energy, and geometry of an atomic cluster on a solid surface were studied using a liquid drop approach which takes into account the cluster-solid interaction. Geometries of the deposited clusters are compared with those of isolated clusters and the differences are discussed.
2. The formation scenarios of patterns on a surface in the course of the process of cluster deposition depend strongly on the dynamics of deposited clusters. Therefore, an important step towards predicting pattern morphology is to study dynamics of a single cluster on a surface. The process of cluster diffusion on a surface was modeled with the use of classical molecular dynamics technique, and the diffusion coefficients for the silver nanoclusters were obtained from the analysis of trajectories of the clusters. The dependence of the diffusion coefficient on the system’s temperature and cluster-surface interaction was established. The results of the calculations are compared with the available experimental results for the diffusion coefficient of silver clusters on graphite surface.
3. The methods of classical molecular dynamics cannot be used for modeling the self-assembly processes of atomic clusters on a surface, because these processes occur on the minutes timescale, what would require an unachievable computer resource for the simulation. Based on the results of molecular dynamics simulations for a single cluster on a surface a Monte-Carlo based approach has been developed to describe the dynamics of the self-assembly of nanoparticles on a surface. This method accounts for the free particle diffusion on a surface, aggregation into islands and detachment from these islands. The developed method is allowed to study pattern formation of structures up to thousands nm, as well as the stability of these structures. Developed method was implemented in MBN Explorer computer package.
4. The process of the pattern formation on a surface was modeled for several different scenarios. Based on the analysis of results of simulations was suggested a criterion, which can be used to distinguish between different patterns formed on a surface, for example: between fractals or compact islands.This criteria can be used to predict the final morphology of a growing structure.
5. The post-growth evolution of patterns on a surface was also analyzed. In particular, attention in the thesis is payed to a systematical theoretical analysis of the post-growth processes occurring in nanofractals on a surface. The time evolution of fractal morphology in the course of the post-growth relaxation was analyzed, the results of these calculations were compared with experimental data available for the post-growth relaxation of silver cluster fractals on graphite substrate.
All the aforementioned problems are discussed in details in the thesis.