Anharmonic Helmholtz free energy to O(lambdaâ ´) in the non- leading term approximation /|nby Leslie Wilk. -- 260 St. Catharines, Ont. : [s. n.],

Expressions for the anharmonic Helmholtz free energy contributions up to o( f ) ,valid for all temperatures, have been obtained using perturbation theory for a c r ystal in which every atom is on a site of inversion symmetry. Numerical calculations have been carried out in the high temperature limit and in the non-leading term approximation for a monatomic facecentred cubic crystal with nearest neighbour c entralforce interactions. The numbers obtained were seen to vary by a s much as 47% from thos e obtai.ned in the leading term approximati.on,indicating that the latter approximati on is not in general very good. The convergence to oct) of the perturbation series in the high temperature limit appears satisfactory.

On the Ewald method and the quartic Helmholtz free energy of an anharmonic metallic crystal

Thesis (M. Sc.) - Brock University, 1978.

An anharmonic contribution to the Helmholtz free energy O(lambda 6)

The anharmonic contributions of order A6 to the Helmholtz free energy for a crystal in which every atom is on a site of inversion symmetry, have been evaluated The cor~esponding diagrams in the various orders of the perturbation theory have been presented The validity of the expressions given is for high temperatures. Numerical calculations for the diagrams which contribute to the free energy have been worked out for a nearest-n~ighbour central-force model of a facecentered cubic lattice in the high-temperature limit and in the leading term and the Ludwig approximations. The accuracy of the Ludwig approximation in evaluating the Brillouin-zone sums has been investigated. Expansion for all diagrams in the high-temperature limit has been carried out The contribution to the specific heat involves a linear as well as cubic term~ We have applied Lennard-Jones, Morse and Exponential 6 types of potentials. A comparison between the contribution to the free energy of order A6 to that of order A4 has been made.

The Landau free energy of hard ellipses obtained from microscopic simulations

Systems of two-dimensional hard ellipses of varying aspect ratios and packing fractions are studied by Monte Carlo simulations in the generalised canonical ensemble. From this microscopic model, we extract a coarse-grained macroscopic Landau-de Gennes free energy as a function of packing fraction and orientational order parameter. We separate the free energy into the ideal orientational entropy of non-interacting two-dimensional spins and an excess free energy associated with excluded volume interactions. We further explore the isotropic-nematic phase transition using our empirical expression for the free energy and find that the nature of the phase transition is continuous for the aspect ratios we studied.

Solvatochromism in Binary Mixtures: First Report on a Solvation Free Energy Relationship between Solvent Exchange Equilibrium Constants and the Properties of the Medium

We have employed UV-vis spectroscopy in order to investigate details of the solvation of six solvatochromic indicators, hereafter designated as ""probes"", namely, 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (RB); 4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePM; 1-methylquinolinium-8-olate, QB; 2-bromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr, 2,6-dichloro-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (WB); and 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr,, respectively. These can be divided into three pairs, each includes two probes of similar pK(a) in water and different lipophilicity. Solvation has been studied in binary mixtures, BMs, of water, W, with 12 protic organic solvents, S, including mono- and bifunctional alcohols (2-alkoxyethanoles, unsaturated and chlorinated alcohols). Each medium was treated as a mixture of S, W, and a complex solvent, S-W, formed by hydrogen bonding. Values of lambda(max) (of the probe intramolecular charge transfer) were converted into empirical polarity scales, E(T)(probe) in kcal/mol, whose values were correlated with the effective mole fraction of water in the medium, chi w(effective). This correlation furnished three equilibrium constants for the exchange of solvents in the probe solvation shell; phi(W/S) (W substitutes S): phi(S-W/W) (S-W substitutes W), and phi(S-W/S) (S-W substitutes S), respectively. The values of these constants depend on the physicochemical properties of the probe and the medium. We tested, for the first time, the applicability of a new solvation free energy relationship: phi = constant + a alpha(BM) + b beta(BM) + s(pi*(BM) + d delta) + p log P(BM), where a, b, s, and p are regression coefficients alpha(BM), beta(BM), and pi*(BM) are solvatochromic parameters of the BM, delta is a correction term for pi*, and log P is an empirical scale of lipophilicity. Correlations were carried out with two-, three-, and four-medium descriptors. In all cases, three descriptors gave satisfactory correlations; use of four parameters gave only a marginal increase of the goodness of fit. For phi(W/S), the most important descriptor was found to be the lipophilicity of the medium; for phi(S-W/W) and phi(S-W/S), solvent basicity is either statistically relevant or is the most important descriptor. These responses are different from those of E(T)(probe) of many solvatochromic indicators in pure solvents, where the importance of solvent basicity is usually marginal, and can be neglected.

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.

Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of magnesium addition on the vacancy-Mg binding free enthalpy in Al-Cr alloys

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of collagen matrix saturation on the surface free energy of dentin using different agents

The surface free energy of conditioned-dentin is one of the factors that interfere with monomeric infiltration of the interfibrillar spaces. Saturation of the tooth matrix with different substances may modulate this energy and, consequently, the wettability of the dentin. To evaluate the influence of different substances used to saturate conditioned-dentin on surface free energy (SFE) of this substrate. Dentin blocks (4 × 7 × 1 mm, n = 6/ group), obtained from the roots of bovine incisors, were etched using phosphoric acid for 15 seconds, rinsed and gently dried. The surfaces were treated for 60 seconds with: ultra-purified water (H20-control); ethanol (EtOH), acetone (ACT), chlorhexidine (CHX), ethylenediaminetetraacetic acid (EDTA); or sodium hypochlorite (NaOCl). The tooth surfaces were once again dried with absorbent paper and prepared for SFE evaluation using three standards: water, formamide and bromonaphthalene. Analysis of variance (ANOVA) and Dunnet's tests (a = 0.05) were applied to the data. Ethylenediaminetetraacetic acid was the only substance that caused a change to the contact angle for the standards water and formamide, while only EtOH influenced the angles formed between formamide and the dentin surface. None of the substances exerted a significant effect for bromonaphtha-lene. In comparison to the control, only EDTA and NaOCl altered both polar components of the SFE. Total SFE was increased by saturation of the collagen matrix by EDTA and reduced when NaOCl was used. Saturation of the collagen matrix by EDTA and EtOH changed the surface free energy of the dentin. In addition, the use of NaOCl negatively interfered with the properties evaluated. The increase of surface free energy and wettability of the dentin surface would allow higher penetration of the the adhesive system, which would be of importance to the clinical success of resin-dentin union.

Nonanalyticity of the free energy in thermal field theory

We study, in a d-dimensional space-time, the nonanalyticity of the thermal free energy in the scalar phi(4) theory as well as in QED. We find that the infrared divergent contributions induce, when d is even, a nonanalyticity in the coupling alpha of the form (alpha)((d-1)/2) whereas when d is odd the nonanalyticity is only logarithmic.