Non-quantized minimum free energy in untranslated region exons

In an attempt to improve automated gene prediction in the untranslated region of a gene, we completed an in-depth analysis of the minimum free energy for 8,689 sub-genetic DNA sequences. We expanded Zhang's classification model and classified each sub-genetic sequence into one of 27 possible motifs. We calculated the minimum free energy for each motif to explore statistical features that correlate to biologically relevant sub-genetic sequences. If biologically relevant sub-genetic sequences fall into distinct free energy quanta it may be possible to characterize a motif based on its minimum free energy. Proper characterization of motifs can lead to greater understanding in automated genefinding, gene variability and the role DNA structure plays in gene network regulation.

Our analysis determined: (1) the average free energy value for exons, introns and other biologically relevant sub-genetic sequences, (2) that these subsequences do not exist in distinct energy quanta, (3) that introns exist however in a tightly coupled average minimum free energy quantum compared to all other biologically relevant sub-genetic sequence types, (4) that single exon genes demonstrate a higher stability than exons which span the entire coding sequence as part of a multi-exon gene and (5) that all motif types contain a free energy global minimum at approximately nucleotide position 1,000 before reaching a plateau. These results should be relevant to the biochemist and bioinformatician seeking to understand the relationship between sub-genetic sequences and the information behind them.

Machine to die for: the quest for free energy

This is about the search for 'perpetual motion' and 'free energy'. Conventional science claims that it is impossible, yet generations of inventors have been mesmerised by the promise of an engine that powers itself. The world's reliance on diminishing fossil fuel resources and the associated problems of pollution serve to spur them on. It showcases a number of dedicated, sometimes eccentric, and always obsessive individuals who have devoted their lives to this quest.

Monte Carlo calculations of the free energy of binary SII hydrogen clathrate hydrates for identifying efficient promoter molecules

The thermodynamics of binary sII hydrogen clathrates with secondary guest molecules is studied with Monte Carlo simulations. The small cages of the sII unit cell are occupied by one H2 guest molecule. Different promoter molecules entrapped in the large cages are considered. Simulations are conducted at a pressure of 1000 atm in a temperature range of 233?293 K. To determine the stabilizing effect of different promoter molecules on the clathrate, the Gibbs free energy of fully and partially occupied sII hydrogen clathrates are calculated. Our aim is to predict what would be an efficient promoter molecule using properties such as size, dipole moment, and hydrogen bonding capability. The gas clathrate configurational and free energies are compared. The entropy makes a considerable contribution to the free energy and should be taken into account in determining stability conditions of binary sII hydrogen clathrates.

Different thermal analysis technique application in determination of fold surface-free energy

In this work, the crystallization rates and spherulitic growth rate of miscible blends of poly(vinylidene fluoride) (PVDF) and acrylic rubber (ACM) were determined using differential scanning calorimetry (DSC), real-time FTIR, and optical microscopy. FTIR results suggest that blending does not induce the creation of polymorphic crystalline forms of PVDF. SAXS data demonstrate the formation of interlamellar structure after blending. The fold surface-free energy (σ e) was analyzed and compared using different thermal analysis techniques. The isothermal crystallization curves obtained using real-time FTIR and DSC explored in two different methods: t 1/2 or Avrami equation. While the Avrami equation is more widespread and precise, both analytical methods gave similar free energy of folding values. However, it was found that the direct optical method of measuring spherulitic growth rate yields σ e values 30-50 % lower than those obtained from the overall crystallization rate data. Conversely, the σ e values were found to increase with increasing amorphous ACM phase content regardless of the analytical methods.

Miscibility, crystallization κinetics and real-time small-Angle x-ray scattering investigation of the semicrystalline morphology in thermosetting polymer blends of epoxy resin and poly(ethylene oxide)

Thermosetting polymer blends of poly(ethylene oxide) (PEO) and bisphenol-A-type epoxy resin (ER) were prepared using 4,4′-methylenebis(3-chloro-2,6-diethylaniline) (MCDEA) as curing agent. The miscibility and crystallization behavior of MCDEA-cured ER/PEO blends were investigated by differential scanning calorimetry (DSC). The existence of a single composition-dependent glass transition temperature (Tg) indicates that PEO is completely miscible with MCDEA-cured ER in the melt and in the amorphous state over the entire composition range. Fourier-transform infrared (FTIR) investigations indicated hydrogen-bonding interaction between the hydroxyl groups of MCDEA-cured ER and the ether oxygens of PEO in the blends, which is an important driving force for the miscibility of the blends. The average strength of the hydrogen bond in the cured ER/PEO blends is higher than in the pure MCDEA-cured ER. Crystallization kinetics of PEO from the melt is strongly influenced by the blend composition and the crystallization temperature. At high conversion, the time dependence of the relative degree of crystallinity deviated from the Avrami equation. The addition of a non-crystallizable ER component into PEO causes a depression of both the overall crystallization rate and the melting temperature. The surface free energy of folding σe displays a minimum with variation of composition. The spherulitic morphology of PEO in the ER/PEO blends exhibits typical characteristics of miscible crystalline/amorphous blends, and the PEO spherulites in the blends are always completely volume-filling. Real-time small-angle X-ray scattering (SAXS) experiments reveal that the long period L increases drastically with increasing ER content at the same temperatures. The amorphous cured ER component segregates interlamellarly during the crystallization process of PEO because of the low chain mobility of the cured ER. A model describing the semicrystalline morphology of MCDEA-cured ER/PEO blends is proposed based on the SAXS results. The semicrystalline morphology is a stack of crystalline lamellae; the amorphous fraction of PEO, the branched ER chains and imperfect ER network are located between PEO lamellae.

The influence of geometry and wall character of pores on the permeation of ions and water through desalination membranes

The transport of water and ions across mimicked nanotube membranes with pseudo atoms is studied using molecular dynamics simulations under equilibrium conditions and hydrostatic pressure. Different pore surface properties are constructed by assigning partial charges on the sites of specified atoms to explore the influence of charges and polarity. The energetics of water and ion transports through the nanopores was calculated to evaluate their filterability to water. The simulation results show that the free energy barriers to water and ion conductions much depend on the charges at the pore entrance and the dipole within the pore. The membranes with hydrophobic pores and negatively charged entrances would be very efficient in the water transport and ion rejection. The charges and dipoles of the pore wall and the aligned dipoles of water molecules in the pore can create a significant force on ions.

Anisotropic wetting characteristics on submicrometer-scale periodic grooved surface

Submicrometer-scale periodic structures consisting of parallel grooves were prepared on azobenzene-containing multiarm star polymer films by laser interference. The wetting characteristics on the patterned surfaces were studied by contact angle measurements. Macroscopic distortion of water drops was found on such small-scale surface structures, and the contact angles measured from the direction parallel to the grooves were larger than those measured from the perpendicular direction. A thermodynamic model was developed to calculate the change in the surface free energy as a function of the instantaneous contact angle when the three-phase contact line (TPCL) moves along the two orthogonal directions. It was found that the fluctuations, i.e., energy barriers, on the energy versus contact angle curves are crucial to the analysis of wetting anisotropy and contact angle hysteresis. The calculated advancing and receding contact angles from the energy versus contact angle curves were in good agreement with those measured experimentally. Furthermore, with the groove depth increasing, both the degree of wetting anisotropy and the contact angle hysteresis perpendicular to the grooves increased as a result of the increase in the energy barrier. The theoretical critical value of the groove depth, above which the anisotropic wetting appears, was determined to be 16 nm for the grooved surface with a wavelength of 396 nm. On the other hand, the effect of the groove wavelength on the contact angle hysteresis perpendicular to the grooves was also interpreted on the basis of the thermodynamic model. That is, with the wavelength decreasing, the contact angle hysteresis increased due to the increase in the number of energy barriers. These results may provide theoretical evidence for the design and application of anisotropic wetting surface.

Nonisothermal Crystallization Behavior of Poly(m-xylene adipamide)/Montmorillonite Nanocomposites

This article reports the nonisothermal crystallization behavior of MXD6 and its clay nanocomposite system (MXD6/MMT) using differential scanning calorimetry (DSC). The DSC experimental data were analyzed by theoretical modeling of the crystallization kinetics using the Avrami, Ozawa, Jeziorny, and the combined Avrami―Ozawa semiempirical models. It has been determined that these models adequately described the crystallization behavior of the MXD6 nanocomposite at cooling rates below 20 °C/min, but there was a deviation from linear dependence at higher cooling rates. This was attributed to changes of both the free energy and the cooling crystallization function K(T) over the entire crystallization process, as well as possible relaxation effects leading to structural rearrangements. In addition, the activation energy determined using the differential isoconversional method of Friedman was also found to vary, indicating changes in both the free energy and crystallization mechanism. Despite the lack of a reliable theoretical model, the heterogeneous nucleating activity of the MMT nanoparticles was demonstrated and quantified using Dobreva's method (Φ = 0.71), and the crystallization rate for the nanocomposite system was found to be greater than pure MXD6 by up to 79% at 40 °C/min.

Adhesion of polymers

Most industrially applied polymer resins and composites have low surface free energy and lack polar functional groups on their surface, resulting in inherently poor adhesion properties. A strong research momentum to understand polymer adhesion in the last decade has been motivated by the growing needs of the automotive and aerospace industries for better adhesion of components and surface coatings. This paper reviews the recent research efforts on polymer adhesion with a special focus on adhesion mechanisms. It starts with an introduction to adhesion with explanatory notes on adhesion phenomena. Recent research on the adhesion mechanisms of mechanical coupling, chemical bonding and thermodynamic adhesion is then discussed. The area of adhesion promoters is reviewed with the focus on plasma and chemical treatments, along with direct methods for adhesion measurement. The topics of polymer blends and reactive polymerization are considered and the interactions with adhesion mechanisms are reported. The concluding section provides recommendations regarding future research on the contentious aspects of currently accepted adhesion mechanisms and on strategies for enhancing polymer adhesion strength.

Benzene adsorption at the aqueous (011) α-quartz interface : is surface flexibility important?

Atomistic simulations of molecular adsorption onto inorganic substrates under aqueous conditions can be used to guide the rational design of new materials, fabricated using biomimetic methods. The success of such work depends critically on the model used. Here, we investigate the impact of using a rigid structural model of the (0 1 1) ?-quartz surface, over a fully flexible model, on the calculated free energy change in the adsorption of a single molecule of benzene (a simple analogue of the amino acid phenylalanine) from liquid water. Subtle differences in the mobility of the adsorbate close to the surface result in the free energy of adsorption being overestimated by the rigid model, relative to the fully flexible case. Moreover, we find that the distribution of bound configurations of the adsorbate at their respective free energy minima is different between the two models.

Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model.

To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomolecules, detailed connections between adsorbed conformations and adsorption behaviour are needed. To elucidate these links, a key approach, in partnership with experimental techniques, is molecular simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chemistry of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biological FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calculations using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aqueous interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to determine the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomolecule-mediated, solution-based graphene processing and self-assembly strategies.