From the double-stranded helix to the chiral nematic phase of B-DNA: a molecular model

B-DNA solutions of suitable concentration form left-handed chiral nematic phases (cholesterics). Such phases have also been observed in solutions of other stiff or semiflexible chiral polymers; magnitude and handedness of the cholesteric pitch are uniquely related to the molecular features. In this work we present a theoretical method and a numerical procedure which, starting from the structure of polyelectrolytes, lead to the prediction of the cholesteric pitch. Molecular expressions for the free energy of the system are obtained on the basis of steric and electrostatic interactions between polymers; the former are described in terms of excluded volume, while a mean field approximation is used for the latter. Calculations have been performed for 130 bp fragments of B-DNA. The theoretical predictions provide an explanation for the experimental behavior, by showing the counteracting role played by shape and charge chirality of the molecule.Comment: 42 pages, 6 figure

Range separation: The divide between local structures and field theories

This work presents parallel histories of the development of two modern theories of condensed matter: the theory of electron structure in quantum mechanics, and the theory of liquid structure in statistical mechanics. Comparison shows that key revelations in both are not only remarkably similar, but even follow along a common thread of controversy that marks progress from antiquity through to the present. This theme appears as a creative tension between two competing philosophies, that of short range structure (atomistic models) on the one hand, and long range structure (continuum or density functional models) on the other. The timeline and technical content are designed to build up a set of key relations as guideposts for using density functional theories together with atomistic simulation.Comment: Expanded version of a 30 minute talk delivered at the 2018 TSRC workshop on Ions in Solution, to appear in the March, 2019 issue of Substantia (https://riviste.fupress.net/index.php/subs/index

Heuristic molecular lipophilicity potential for computer-aided rational drug design

In my thesis research, I suggest a heuristic molecular lipophilicity potential (HMLP), a structure-based technique requiring no empirical indices of atomic lipophilicity, for computer-aided drug design. The input data used in this approach are molecular geometries and molecular surfaces. The HMLP is a modified electrostatic potential, combined with the averaged influences from the molecular environment. Quantum mechanics is used in calculating the electron density function ñ(r) and the electrostatic potential V(r), and from this information a lipophilicity potential L(r) is generated. The HMLP is a unified lipophilicity and hydrophilicity potential. The interactions of dipole and multipole moments, hydrogen bonds, and charged atoms in molecules are included in the hydrophilic interactions in this model. The HMLP is used to study hydrogen bonds and water-octanol partition coefficients in several examples. The calculated results show that HMLP gives qualitatively and quantitatively correct, as well as chemically reasonable results in cases where comparisons are available. These comparisons indicate that the HMLP has advantages over the empirical lipophilicity potential in many aspects. Three possible screening functions and parameters used in them are tested and optimized in this research. The power screening function, bi||Ri - r||ã, and the exponential screening function, biexp(-||Ri - r|| / d0), give satisfactory results. A new strategy for drug design and combinatory chemistry is presented based on HMLP, and is used in the study of a small molecular system, pyrazole and its derivatives. The mechanism of inhibition of LADH caused by pyrazole and its derivatives is explained based on the calculation results of HMLP indices. Good results are achieved in this example. Further improvements of screening function and visualization of HMLP by computer graphics are discussed. I suggest two possible visualization approaches of HMLP: a two-color system and a three-color system. Their possible applications are discussed. HMLP is suggested as a potential tool in computer-aided three-dimensional drug design, studies of 3D-QSAR, active structure of proteins, and other types of molecular interactions

The Lippmann Equation and the Ideally Polarizable Electrode

The Lippmann equation for the ideally polarizable interface is normally derived by thermodynamics, using the Gibbs dividing surface. Therefore, the quantities appearing in the Lippmann equation can have no reference to the actual charge distribution in the interfacial region. For example, the quantity referred to as surface charge is actually a sum of surface excesses, rather than the integral of a true charge density. In this article we derive, by statistical mechanical methods, the Lippmann equation for a model at the molecular level, thus giving a precise physical definition to all quantities which appear. First, we derive the conditions for mechanical equilibrium for a system (the interface between metal and solution) in which an electric field is present, and whose properties are inhomogeneous and anisotropic. From the balance of forces, we obtain equations for the surface tension. in terms of the pressure, electric field, electric charge density, and electric polarization at each point within the system. Considering a spherically symmetric system (mercury drop), we then proceed to a direct calculation of the change in the surface tension produced by a change in the potential drop across the interface, maintaining thermal equilibrium, constant temperature, and the pressure and chemical composition in homogeneous regions (on the boundaries of the interfacial region). Since an ideally polarizable interface does not permit charge transport across it, we introduce a surface within the interface on which the charge density is always zero. This surface serves to divide the interfacial region into two parts, thus allowing the surface charge to be defined as the integral of the charge density over the metal side of the interface. Only the solution side is treated by statistical mechanics. Boltzmann distributions for charged and polarizable species (solute and solvent) are used to guarantee thermal equilibrium. The Lippmann equation is obtained (a) considering only ions and supposing a dielectric constant equal to that of vacuum and (b) considering ions and molecules in thermal equilibrium, and a dielectric constant varying from point to point and changing with field. Finally, the response of our system to an imposed alternating potential is considered. A direct calculation of the impedance shows that it behaves, in the low-frequency limit, as a pure capacitance, and that the value of this capacitance is the derivative of the previously defined surface charge density with respect to the potential drop across the interface

Core-shell particles and their application for superhydrophobic surfaces

During the last years great effort has been devoted to the fabrication of superhydrophobic surfaces because of their self-cleaning properties. A water drop on a superhydrophobic surface rolls off even at inclinations of only a few degrees while taking up contaminants encountered on its way. rnSuperhydrophobic, self-cleaning coatings are desirable for convenient and cost-effective maintenance of a variety of surfaces. Ideally, such coatings should be easy to make and apply, mechanically resistant, and long-term stable. None of the existing methods have yet mastered the challenge of meeting all of these criteria.rnSuperhydrophobicity is associated with surface roughness. The lotus leave, with its dual scale roughness, is one of the most efficient examples of superhydrophobic surface. This thesis work proposes a novel technique to prepare superhydrophobic surfaces that introduces the two length scale roughness by growing silica particles (~100 nm in diameter) onto micrometer-sized polystyrene particles using the well-established Stöber synthesis. Mechanical resistance is conferred to the resulting “raspberries” by the synthesis of a thin silica shell on their surface. Besides of being easy to make and handle, these particles offer the possibility for improving suitability or technical applications: since they disperse in water, multi-layers can be prepared on substrates by simple drop casting even on surfaces with grooves and slots. The solution of the main problem – stabilizing the multilayer – also lies in the design of the particles: the shells – although mechanically stable – are porous enough to allow for leakage of polystyrene from the core. Under tetrahydrofuran vapor polystyrene bridges form between the particles that render the multilayer-film stable. rnMulti-layers are good candidate to design surfaces whose roughness is preserved after scratch. If the top-most layer is removed, the roughness can still be ensured by the underlying layer.rnAfter hydrophobization by chemical vapor deposition (CVD) of a semi-fluorinated silane, the surfaces are superhydrophobic with a tilting angle of a few degrees. rnrnrnAufgrund der selbstreinigenden Eigenschaft von superhydrophoben Oberflächen wurde in den letzten Jahren viel Arbeit in deren Herstellung gesteckt. Ein Tropfen Wasser perlt von einer um nur wenige Grad geneigten superhydrophoben Oberfläche ab, während er Verunreinigungen auf seinem Weg mitnimmt.rnSuperhydrophobe, selbstreinigende Beschichtungen sind eine mögliche Lösung für den kostengünstigen Erhalt vieler Oberflächen. Idealerweise sind diese Beschichtungen einfach in der Herstellung, mechanisch resistent und Langzeitstabil. Bisher konnte keine Methode gefunden werden alle diese Kriterien zur gleichen Zeit zu erfüllen.rnSuperhydrophobizität steht in direkter Beziehung zur Oberflächenrauigkeit. Das Lotusblatt mit einer zweifach skalierten Oberflächenrauigkeit ist ein Beispiel für eine der effizientesten superhydrophobe Oberflächen.rnIn der vorliegenden Arbeit wurde eine neue Technik zur Herstellung hydrophober Oberflächen vorgestellt. Zwei Längenskalen der Rauheit wurden durch das Aufbringen von Silikapartikel (~ 100 nm im Durchmesser) auf Mikrometer große Polystyrolpartikel durch die bekannte Stöber Synthese dargestellt. Mechanische Stabilität der Partikel wurde durch die dünne Silika Schale auf der Oberfläche der resultierenden „Himbeeren“ erzeugt. Neben der einfachen Darstellung und Handhabbarkeit bieten diese Partikel die Möglichkeit einer verbesserten technischen Anwendung: zum einen sind sie in Wasser dispergierbar und zum anderen können Doppelschichten durch Auftropfmethoden auf selbst sehr rauen Oberflächen erzeugt werden. Die Lösung des Hauptproblems – der Stabilität der Multilagen – liegt im Design der Partikel: Die Schalen, obwohl mechanisch stabil, sind porös genug um Polystyrol aus dem Kern durchzulassen. Im THF Dampf können sich Polystyrolbrücken zwischen den Partikeln ausbilden, die durch das Verkleben der Partikel untereinander für eine Stabilität der Multilagenschicht sorgen. Multilagenschichten sind vielversprechend im Einsatz für kratzbeständige Oberfläche. Wenn die oberste Schicht beschädigt wird, kann die definierte Rauigkeit immer noch durch die darunterliegende Schicht gewährleistet werden. rnChemical Vapour Deposition (CVD) mit semi-fluorierten Silanen bewirkt eine Superhydrophobisierung der Oberflächen mit einem Neigungswinkel von wenigen Grad.rnr

Nanotribology and Nanomechanics of Thin Films Including Material Characterization, Mechanical Wear, Adhesion and Lubrication

The present work is dedicated to addressing nanotribological issues of ultra-thin (sub-10 nm) films at contacting interfaces. In devices such as micro-electro-mechanical systems (MEMS), thin films are deposited for specific functions. In some occasions, mechanical durability of the thin films is also important. Magnetic storage hard disk drives (HDD) are a good example where nanotribology at the head-disk interface (HDI) is extremely important. Especially in recent years, where the areal density increases exponentially and the write/read head has been brought as close to as less than 10 nm to the disk surface. As a result, direct contact is possible to occur at such small distance and such unfavorable contact will cause mechanical wear and demagnetization. Nanometer thick diamond like carbon (DLC) and lubricant films provide important protection and study of their failure mechanisms is necessary. The present thesis has conducted research to understand the nanotribology of thin films in the multilayered system used in HDDs. The majority of the work is measurement of the nanomechanical and nanotribological properties of the solid thin films with thickness of less than 20 nm. A method combining finite element analysis (FEA) and nanoindentation was proposed to extract nanomechanical properties from nanoindentation data for multilayered samples. A highly sensitive nanomechanical transducer was introduced to perform sub-5 nm shallow nanoindentation experiments on thin films deposited at different conditions. To study the tribological performance of DLC films at high temperatures up to 300 °C, the present work performs nanoscratch and nanowear tests on a 3-nm thick DLC film. The results show the wear rate of DLC films begin to increase abruptly at around 200°C and this degradation of wear resistance is irreversible. The present thesis also proposes a mathematical model to quantitatively predict the hydrodynamic lubrication effects of the molecularly thin lubricant between the head and the disk surfaces. After considering the nanorheological behavior of the lubricant, the model is able to make predictions of contacting forces and pressures and explain the tribological role of the lubricant in terms of continuum mechanics. Lastly, present thesis proposed a model considering Van der Waals forces between lubricants on the disk and on the head. The proposed model provides stricter criterion for onset of adhesion induced lubricant-transfer between the two wet surfaces and is in better agreement with Molecular Dynamics simulations than conventional models. In summary, the findings above center about nanomechanics and nanotribology at the interfaces of the magnetic storage hard disk. However, these findings can also extend their applications to other MEMS devices where tribology issues are of important concerns. The shallow nanoindentaton instrument and FEA-based characterization method can be applicable any other solid thin films. The high-temperature tribological properties of a ultra-thin DLC films utilize a unique test rig but the findings are generally instructive in understanding behaviors of DLC at high temperature. The nano-lubrication model for a lubricated single asperity can be an addition of current contact mechanics which usually neglects the presence of lubricants

Doctor of Philosophy

dissertationKaolinite is both a blessing and a curse. As an important industrial mineral commodity, kaolinite clays are extensively used in the paper, ceramic, paint, plastic and rubber industries. In all these applications the wettability, aggregation, dispersion, flotation and thickening of kaolinite particles are affected by its crystal structure and surface properties. It is therefore the objective of this research to investigate selected physical and surface chemical properties of kaolinite, specifically the surface charge of kaolinite particles. A pool of advanced analytical techniques such as XRD, XRF, SEM, AFM, FTIR and ISS were utilized to investigate the morphological and surface chemistry features of kaolinite. Surface force measurements revealed that the silica tetrahedral face of kaolinite is negatively charged at pH > 4, whereas the alumina octahedral face of kaolinite is positively charged at pH 8. Based on electrophoresis measurements, the apparent iso-electric point for kaolinite particles was determined to be less than pH 3. In contrast, the point of zero charge was determined to be pH 4.5 by titration techniques, which corresponds to the isoelectric point of between pH 4 and 5 as determined by surface force measurements. Results from kaolinite particle interactions indicate that the silica face-alumina face interaction is dominant for kaolinite particle aggregation at low and intermediate pH values, which explains the maximum shear yield stress at pH 5-5.5. Lattice resolution images reveal the hexagonal lattice structure of these two face surfaces of kaolinite. Analysis of the silica face of kaolinite showed that the center of the hexagonal ring of oxygen atoms is vacant, whereas the alumina face showed that the hexagonal surface lattice ring of hydroxyls surround another hydroxyl in the center of the ring. High resolution transmission electron microscopy investigation of kaolinite has indicated that kaolinite is indeed composed of silica/alumina bilayers with a c-spacing of 7.2 Å. The surface charge densities of the silica face, the alumina face and the edge surface of kaolinite all influence particle interactions, and thereby affect the mechanical properties of kaolinite suspensions. The improved knowledge of kaolinite surface chemistry from this dissertation research provides a foundation for the development of improved process strategies for both the use and disposal of clay particles such as kaolinite

Nanotribology and Nanomechanics of Thin Films Including Material Characterization, Mechanical Wear, Adhesion and Lubrication

The present work is dedicated to addressing nanotribological issues of ultra-thin (sub-10 nm) films at contacting interfaces. In devices such as micro-electro-mechanical systems (MEMS), thin films are deposited for specific functions. In some occasions, mechanical durability of the thin films is also important. Magnetic storage hard disk drives (HDD) are a good example where nanotribology at the head-disk interface (HDI) is extremely important. Especially in recent years, where the areal density increases exponentially and the write/read head has been brought as close to as less than 10 nm to the disk surface. As a result, direct contact is possible to occur at such small distance and such unfavorable contact will cause mechanical wear and demagnetization. Nanometer thick diamond like carbon (DLC) and lubricant films provide important protection and study of their failure mechanisms is necessary. The present thesis has conducted research to understand the nanotribology of thin films in the multilayered system used in HDDs. The majority of the work is measurement of the nanomechanical and nanotribological properties of the solid thin films with thickness of less than 20 nm. A method combining finite element analysis (FEA) and nanoindentation was proposed to extract nanomechanical properties from nanoindentation data for multilayered samples. A highly sensitive nanomechanical transducer was introduced to perform sub-5 nm shallow nanoindentation experiments on thin films deposited at different conditions. To study the tribological performance of DLC films at high temperatures up to 300 °C, the present work performs nanoscratch and nanowear tests on a 3-nm thick DLC film. The results show the wear rate of DLC films begin to increase abruptly at around 200°C and this degradation of wear resistance is irreversible. The present thesis also proposes a mathematical model to quantitatively predict the hydrodynamic lubrication effects of the molecularly thin lubricant between the head and the disk surfaces. After considering the nanorheological behavior of the lubricant, the model is able to make predictions of contacting forces and pressures and explain the tribological role of the lubricant in terms of continuum mechanics. Lastly, present thesis proposed a model considering Van der Waals forces between lubricants on the disk and on the head. The proposed model provides stricter criterion for onset of adhesion induced lubricant-transfer between the two wet surfaces and is in better agreement with Molecular Dynamics simulations than conventional models. In summary, the findings above center about nanomechanics and nanotribology at the interfaces of the magnetic storage hard disk. However, these findings can also extend their applications to other MEMS devices where tribology issues are of important concerns. The shallow nanoindentaton instrument and FEA-based characterization method can be applicable any other solid thin films. The high-temperature tribological properties of a ultra-thin DLC films utilize a unique test rig but the findings are generally instructive in understanding behaviors of DLC at high temperature. The nano-lubrication model for a lubricated single asperity can be an addition of current contact mechanics which usually neglects the presence of lubricants

Characterization, modeling, and simulation of multiscale directed-assembly systems

Nanoscience is a rapidly developing field at the nexus of all physical sciences which holds the potential for mankind to gain a new level of control of matter over matter and energy altogether. Directed-assembly is an emerging field within nanoscience in which non-equilibrium system dynamics are controlled to produce scalable, arbitrarily complex and interconnected multi-layered structures with custom chemical, biologically or environmentally-responsive, electronic, or optical properties. We construct mathematical models and interpret data from direct-assembly experiments via application and augmentation of classical and contemporary physics, biology, and chemistry methods. Crystal growth, protein pathway mapping, LASER tweezers optical trapping, and colloid processing are areas of directed-assembly with established experimental techniques. We apply a custom set of characterization, modeling, and simulation techniques to experiments to each of these four areas. Many of these techniques can be applied across several experimental areas within directed-assembly and to systems featuring multiscale system dynamics in general. We pay special attention to mathematical methods for bridging models of system dynamics across scale regimes, as they are particularly applicable and relevant to directed-assembly. We employ massively parallel simulations, enabled by custom software, to establish underlying system dynamics and develop new device production methods