Pattern formation in thin films of polymer solutions: Theory and simulations

Self-assembly has been recognized as an efficient tool for generating a wide range of functional, chemically, or physically textured surfaces for applications in small scale devices. In this work, we investigate the stability of thin films of polymer solutions. For low concentrations of polymer in the solution, long length scale dewetting patterns are obtained with wavelength approximately few microns. Whereas, for concentrations above a critical value, bimodal dispersion curves are obtained with the dominant wavelength being up to two orders smaller than the usual dewetting length scale. We further show that the short wavelength corresponds to the phase separation in the film resulting in uniformly distributed high and low concentration regions. Interestingly, due to the solvent entropy, at very high concentration values of polymer, a re-entrant behaviour is observed with the dominant length scale now again corresponding to the dewetting wavelength. Thus, we show that the binary films of polymer solutions provide additional control parameters that can be utilized for generating functional textured surfaces for various applications. (C) 2016 AIP Publishing LLC.

Population of nonnative states of lysozyme variants drives amyloid fibril formation.

The propensity of protein molecules to self-assemble into highly ordered, fibrillar aggregates lies at the heart of understanding many disorders ranging from Alzheimer's disease to systemic lysozyme amyloidosis. In this paper we use highly accurate kinetic measurements of amyloid fibril growth in combination with spectroscopic tools to quantify the effect of modifications in solution conditions and in the amino acid sequence of human lysozyme on its propensity to form amyloid fibrils under acidic conditions. We elucidate and quantify the correlation between the rate of amyloid growth and the population of nonnative states, and we show that changes in amyloidogenicity are almost entirely due to alterations in the stability of the native state, while other regions of the global free-energy surface remain largely unmodified. These results provide insight into the complex dynamics of a macromolecule on a multidimensional energy landscape and point the way for a better understanding of amyloid diseases.

Perturbation of the stability of amyloid fibrils through alteration of electrostatic interactions.

The self-assembly of proteins and peptides into polymeric amyloid fibrils is a process that has important implications ranging from the understanding of protein misfolding disorders to the discovery of novel nanobiomaterials. In this study, we probe the stability of fibrils prepared at pH 2.0 and composed of the protein insulin by manipulating electrostatic interactions within the fibril architecture. We demonstrate that strong electrostatic repulsion is sufficient to disrupt the hydrogen-bonded, cross-β network that links insulin molecules and ultimately results in fibril dissociation. The extent of this dissociation correlates well with predictions for colloidal models considering the net global charge of the polypeptide chain, although the kinetics of the process is regulated by the charge state of a single amino acid. We found the fibrils to be maximally stable under their formation conditions. Partial disruption of the cross-β network under conditions where the fibrils remain intact leads to a reduction in their stability. Together, these results support the contention that a major determinant of amyloid stability stems from the interactions in the structured core, and show how the control of electrostatic interactions can be used to characterize the factors that modulate fibril stability.

Role Of Convection Flow On The Pattern Formation In The Drying Process Of Colloidal Suspension

We study the macroscopic drying patterns of aqueous suspensions of colloidal silica spheres. It was found that convection strength can influence pattern formation. Uniformed films are obtained at weaker convection strength. In addition, we make clear that it is not reasonable to discuss individually the effect of temperature and humidity on the colloid self-assembly. The physical mechanism is that these factors have relationship with the evaporation rate, which can affect the convection strength.

Laser-induced wavy pattern formation in metal thin films

Laser-induced well-ordered and controllable wavy patterns are constructed in the deposited metal thin film. The micrometer-sized structure and orientation of the wavy patterns can be controlled via scanning a different size of rectangle laser spot on the films. Ordered patterns such as aligned, crossed, and whirled wave structures were designed over large areas. This patterning technique may find applications in both exploring the reliability and mechanical properties of thin films, and fabricating microfluidic devices. (C) 2004 American Institute of Physics.

A new dynamic model for study of dislocation pattern formation

Based on the principle given in nonlinear diffusion-reaction dynamics, a new dynamic model for dislocation patterning is proposed by introducing a relaxation time to the relation between dislocation density and dislocation flux. The so-called chemical potential like quantities, which appear in the model can be derived from variation principle for free energy functional of dislocated media, where the free energy density function is expressed in terms of not only the dislocation density itself but also their spatial gradients. The Linear stability analysis on the governing equations of a simple dislocation density shows that there exists an intrinsic wave number leading to bifurcation of space structure of dislocation density. At the same time, the numerical results also demonstrate the coexistence and transition between different dislocation patterns.

Expected Fair Allocation in Farsighted Network Formation

I consider cooperation situations where players have network relations. Networks evolve according to a stationary transition probability matrix and at each moment in time players receive payoffs from a stationary allocation rule. Players discount the future by a common factor. The pair formed by an allocation rule and a transition probability matrix is called expected fair if for every link in the network both participants gain, marginally, and in discounted, expected terms, the same from it; and it is called a pairwise network formation procedure if the probability that a link is created (or eliminated) is positive if the discounted, expected gains to its two participants are positive too. The main result is the existence, for the discount factor small enough, of an expected fair and pairwise network formation procedure where the allocation rule is component balanced, meaning it distributes the total value of any maximal connected subnetwork among its participants. This existence result holds for all discount factors when the pairwise network formation procedure is restricted. I finally provide some comparison with previous models of farsighted network formation.

Forward-looking Pairwise Stability in Networks with Externalities

We consider cooperation situations where players have network relations. Networks evolve according to a stationary transition probability matrix and at each moment in time players receive payoffs from a stationary allocation rule. Players discount the future by a common factor. The pair formed by an allocation rule and a transition probability matrix is called a forward-looking network formation scheme if, first, the probability that a link is created is positive if the discounted, expected gains to its two participants are positive, and if, second, the probability that a link is eliminated is positive if the discounted, expected gains to at least one of its two participants are positive. The main result is the existence, for all discount factors and all value functions, of a forward-looking network formation scheme. Furthermore, we can always nd a forward-looking network formation scheme such that (i) the allocation rule is component balanced and (ii) the transition probabilities increase in the di erence in payo s for the corresponding players responsible for the transition. We use this dynamic solution concept to explore the tension between e ciency and stability.

Recognition of double helical DNA by purine oligonucleotides via triple helix formation

Oligonucleotide-directed triple helix formation is one of the most versatile methods for the sequence specific recognition of double helical DNA. Chapter 2 describes affinity cleaving experiments carried out to assess the recognition potential for purine-rich oligonucleotides via the formation of triple helices. Purine-rich oligodeoxyribonucleotides were shown to bind specifically to purine tracts of double helical DNA in the major groove antiparallel to the purine strand of the duplex. Specificity was derived from the formation of reverse Hoogsteen G•GC, A•AT and T•AT triplets and binding was limited to mostly purine tracts. This triple helical structure was stabilized by multivalent cations, destabilized by high concentrations of monovalent cations and was insensitive to pH. A single mismatched base triplet was shown to destabilize a 15 mer triple helix by 1.0 kcal/mole at 25°C. In addition, stability appeared to be correlated to the number of G•GC triplets formed in the triple helix. This structure provides an additional framework as a basis for the design of new sequence specific DNA binding molecules.

In work described in Chapter 3, the triplet specificities and required strand orientations of two classes of DNA triple helices were combined to target double helical sequences containing all four base pairs by alternate strand triple helix formation. This allowed for the use of oligonucleotides containing only natural 3'-5' phosphodiester linkages to simultaneously bind both strands of double helical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depended on whether the binding site sequence was 5'-(purine)_m (pyrimidine)_n-3' or 5'- (pyrimidine)_m (purine)_n-3'.

In Chapter 4, the ability of oligonucleotide-cerium(III) chelates to direct the transesterfication of RNA was investigated. Procedures were developed for the modification of DNA and RNA oligonucleotides with a hexadentate Schiff-base macrocyclic cerium(III) complex. In addition, oligoribonucleotides modified by covalent attachment of the metal complex through two different linker structures were prepared. The ability of these structures to direct transesterification to specific RNA phosphodiesters was assessed by gel electrophoresis. No reproducible cleavage of the RNA strand consistent with transesterification could be detected in any of these experiments.

A Unifying model of strategic network formation

Documento de trabajo

Stability of Electrode-Electrolyte Interfaces during Charging in Lithium Batteries

In this thesis we study the growth of a Li electrode-electrolyte interface in the presence of an elastic prestress. In particular, we focus our interest on Li-air batteries with a solid electrolyte, LIPON, which is a new type of secondary or rechargeable battery. Theoretical studies and experimental evidence show that during the process of charging the battery the replated lithium adds unevenly to the electrode surface. This phenomenon eventually leads to dendrite formation as the battery is charged and discharged numerous times. In order to suppress or alleviate this deleterious effect of dendrite growth, we put forth a study based on a linear stability analysis. Taking into account all the mechanisms of mass transport and interfacial kinetics, we model the evolution of the interface. We find that, in the absence of stress, the stability of a planar interface depends on interfacial diffusion properties and interfacial energy. Specifically, if Herring-Mullins capillarity-driven interfacial diffusion is accounted for, interfaces are unstable against all perturbations of wavenumber larger than a critical value. We find that the effect of an elastic prestress is always to stabilize planar interfacial growth by increasing the critical wavenumber for instability. A parametric study results in quantifying the extent of the prestress stabilization in a manner that can potentially be used in the design of Li-air batteries. Moreover, employing the theory of finite differences we numerically solve the equation that describes the evolution of the surface profile and present visualization results of the surface evolution by time. Lastly, numerical simulations performed in a commercial finite element software validate the theoretical formulation of the interfacial elastic energy change with respect to the planar interface.

The impact of liberalizing cost-saharing on basic models of network formation

This paper studies the impact of "liberalizing " the cost-sharing of links on some basic models of network formation. This is done in a setting where both doubly supported and singly supported links are possible, and which includes the two seminal models of network formation by Jackson and Wolinsky and Bala and Goyal as extreme cases. In this setting, the notion of pairwise stability is extended and it is proved that liberalizing cost-sharing for doubly supported links widens the range of values of the parameters where the efficient networks formed by such type of links are pairwise stable, while the range of values of the parameters where the efficient networks formed by singly supported links are pairwise stable shrinks, but the region where the latter are e¢ cient and pairwise stable remains the same.

Effect of oxygen substitution by halide ions on structure, thermal stability and upconversion fluorescence in Er3(+)/Yb3(+)-codoped germanium-bismuth glasses

For the first time. effect of halide ions (F-, Cl-, Br-, and I-) introduction on structure, thermal stability, and upconversion fluorescence in Er3+/Yb3+-codoped oxide-halide germanium-bismuth glasses has been systematically investigated. The results show that halide ions modified germanium-bismuth glasses have lower maximum phonon energy and phonon density, worse thermal stability. longer measured lifetimes of I-4(l1/2) level, and stronger upconversion emission than germanium-bismuth glass. All these results indicate that halide ions play an important role in the formation of glass network, and have an important influence on the upconversion luminescence. The possible upconversion mechanisms of Er3+ ion are also evaluated. © 2005 Elsevier Ltd. All rights reserved.

Structure and thermal stability of novel fluorophosphate glasses

A systematic investigation on glass formation in the PbF2-InF3-BaHPO4 ternary system has been carried out. These glasses have characterized by IR spectra, Raman spectra and differential thermal analysis. The results show that the structure of these glasses is mainly affected by BaHPO4 and InF3 contents. With decreasing BaHPO4 content, the glass structure gradually transforms from metaphosphate to polyphosphate. When InF3 content is low, it mainly acts as network modifier, when its content is high; it enters glass matrix and forms In(O,F)(6) groups connecting the polymerized phosphorus oxygen species. PbF2 mainly acts as network modifier in this system. Systematic variations of the glass transition temperature and the thermal stability index agree well with these results. The most stable glass with Delta T = 230 degrees C and S = 21.79 K is obtained. (c) 2004 Elsevier B.V. All rights reserved.

Stability and molecular modeling of triplex DNA inhibiting DNA binding protein binding to the core promoter of hepatitis B virus.

Two three-dimensional structure models of the 21nt oligodeoxyribonucleotides, CPI (G3TG-2TGT2G5TG2TGT) and CP3 (TGTG2TGST2GTG2TG3), were constructed by InsightII (MSI) software in IRIS Indigo2 (SGI) workstation using the crystal structure of TAT tripler formation as the template. The initial structures subsequently were minimized by molecular mechanics. The final structures were believed as the dominant conformation. The results showed that the energy of CP1 is lower than that of CP3, and the former is more stable than the latter. Moreover, the results further proved that the 21nt oligodeoxyribo-nucleotide CP1 stably combines with the core promoter (Cp) fragment of hepatitis B virus (HBV) to form a tripler DNA, and CP1 specifically inhibits a specific cellular factor (DNA binding protein) binding to Cp fragment. These results indicated that specific repression of gene transcription of HBV DNA might be possible by tripler-formation DNA.