Statistical Mechanics of thermal denaturation of DNA oligomers

Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.Comment: Appeared in Proceeding of Conference on "Liquid Crystals and other Soft materials", held at RRI, Bangalore Indi

Vibronic Lineshapes of PTCDA Oligomers in Helium Nanodroplets

Oligomers of the organic semiconductor PTCDA are studied by means of helium nanodroplet isolation (HENDI) spectroscopy. In contrast to the monomer absorption spectrum, which exhibits clearly separated, very sharp absorption lines, it is found that the oligomer spectrum consists of three main peaks having an apparent width orders of magnitude larger than the width of the monomer lines. Using a simple theoretical model for the oligomer, in which a Frenkel exciton couples to internal vibrational modes of the monomers, these experimental findings are nicely reproduced. The three peaks present in the oligomer spectrum can already be obtained taking only one effective vibrational mode of the PTCDA molecule into account. The inclusion of more vibrational modes leads to quasi continuous spectra, resembling the broad oligomer spectra

Mechanism for the stabilization of protein clusters above the solubility curve

Pan, Vekilov and Lubchenko[\textit{J. Phys. Chem. B}, 2010, \textbf{114}, 7620] have proposed that dense stable protein clusters appearing in weak protein solutions above the solubility curve are composed of protein oligomers. The hypothesis is that a weak solution of oligomer species is unstable with respect to condensation causing the formation of dense, oligomer-rich droplets which are stabilized against growth by the monomer-oligomer reaction. Here, we show that such a combination of processes can be understood using a simple capillary model yielding analytic expressions for the cluster properties which can be used to interpret experimental data. We also construct a microscopic Dynamic Density Functional Theory model and show that it is consistent with the predictions of the capillary model. The viability of the mechanism is thus confirmed and it is shown how the radius of the stable clusters is related to physically interesting quantities such as the monomer-oligomer rate constants

Ferroelectric characterization and growth optimization of thermally evaporated vinylidene fluoride thin films

Organic thin films have numerous advantages over inorganics in device processing and price. The large polarization of the organic ferroelectric oligomer vinylidene fluoride (VDF) could prove useful for both device applications and the investigation of fundamental physical phenomena. A VDF oligomer thin film vacuum deposition process, such as thermal evaporation, preserves film and interface cleanliness, but is challenging, with successful deposition occurring only within a narrow parameter space. We report on the optimal deposition parameters for VDF oligomer thin films, refining the parameter space for successful deposition, resulting in a high yield of robust ferroelectric films. In particular, we investigate the influence of deposition parameters on surface roughness, and the role that roughness plays in sample yield. The reliable production of ferroelectric films allowed us to perform detailed measurements of previously unreported properties, including the Curie temperature, the temperature and thickness dependence of the coercive field, the melting temperature, and the index of refraction. The ability to successfully grow robust, switchable, well-characterized films makes VDF oligomer a viable candidate in the field of organic ferroelectrics

Thermal and Flame Properties of Polyethylene and Polypropylene Nanocomposites Based on an Oligomerically–Modified Clay

An oligomerically-modified clay was made using a surfactant which is the ammonium salt of an oligomer. The newly modified clay contains 37.5% inorganic clay and 62.5% oligomer. Polyethylene and polypropylene nanocomposites were made by melt blending the polymer with the oligomerically-modified clay in a Brabender mixer at various clay loadings. The structure of the nanocomposites was characterized by X-ray diffraction and transmission electron microscopy. Mechanical testing showed that the polyethylene nanocomposites had an enhanced Young\u27s modulus and slightly decreased elongation, while the changes for polypropylene nanocomposites are small compared with the virgin polymers. The thermal stability and flame properties were evaluated using thermogravimetric analysis and cone calorimetry, respectively. The plasticising effect of the oligomer was suppressed because of the increased inorganic content. The maximum reduction in peak heat release rate is about 40%

Role of electrostatic interactions in amyloid beta-protein (Abeta) oligomer formation: A discrete molecular dynamics study

Pathological folding and oligomer formation of the amyloid beta-protein (Abeta) are widely perceived as central to Alzheimer's disease (AD). Experimental approaches to study Abeta self-assembly are problematic, because most relevant aggregates are quasi-stable and inhomogeneous. We apply a discrete molecular dynamics (DMD) approach combined with a four-bead protein model to study oligomer formation of the amyloid beta-protein (Abeta). We address the differences between the two most common Abeta alloforms, Abeta40 and Abeta42, which oligomerize differently in vitro. We study how the presence of electrostatic interactions (EIs) between pairs of charged amino acids affects Abeta40 and Abeta42 oligomer formation. Our results indicate that EIs promote formation of larger oligomers in both Abeta40 and Abeta42. The Abeta40 size distribution remains unimodal, whereas the Abeta42 distribution is trimodal, as observed experimentally. Abeta42 folded structure is characterized by a turn in the C-terminus that is not present in Abeta40. We show that the same C-terminal region is also responsible for the strongest intermolecular contacts in Abeta42 pentamers and larger oligomers. Our results suggest that this C-terminal region plays a key role in the formation of Abeta42 oligomers and the relative importance of this region increases in the presence of EIs. These results suggest that inhibitors targeting the C-terminal region of Abeta42 oligomers may be able to prevent oligomer formation or structurally modify the assemblies to reduce their toxicity.Comment: Accepted for publication at Biophysical Journa

The synthesis, characterization and thermal chemistry of modified norbornenyl PMR endcaps

As part of a program to further the understanding of the polymerization of Nadic-Endcapped PMR systems, a series of model Norbornenyl-Imides has been synthesized and their thermal behavior explored. Their syntheses and characterizations as well as their rearrangement and polymerization chemistry are described. Monomer isomerization at temperatures as low as 125 C and oligomer formation at somewhat higher temperatures are observed. Approximate relative rates for competing isomerization pathways are established and some information is obtained about the details of oligomer formation. The relationship of this data to current PMR systems is briefly discussed

Synthesis of imide/arylene ether copolymers for adhesives and composite matrices

A series of imide/arylene ether copolymers were prepared from the reaction of an amorphous arylene ether oligomer and a semi-crystalline imide oligomer. These copolymers were thermally characterized and mechanical properties were measured. One block copolymer was endcapped and the molecular weight was controlled to provide a material that displayed good compression moldability and attractive adhesion and composite properties

Pressure-driven flow of oligomeric fluid in nano-channel with complex structure. A dissipative particle dynamics study

We develop a simulational methodology allowing for simulation of the pressure-driven flow in the pore with flat and polymer-modified walls. Our approach is based on dissipative particle dynamics and we combine earlier ideas of fluid-like walls and reverse flow. As a test case we consider the oligomer flow through the pore with flat walls and demonstrate good thermostatting qualities of the proposed method. We found the inhomogeneities in both oligomer shape and alignment across the pore leading to a non-parabolic velocity profiles. The method is subsequently applied to a nano-channel decorated with a polymer brush stripes arranged perpendicularly to the flow direction. At certain threshold value of a flow force we find a pillar-to-lamellar morphological transition, which leads to the brush enveloping the pore wall by a relatively smooth layer. At higher flow rates, the flow of oligomer has similar properties as in the case of flat walls, but for the narrower effective pore size. We observe stretching and aligning of the polymer molecules along the flow near the pore walls.Comment: 14 pages, 12 figure