Browsing by Subject "Free energy"
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Item Open Access Chiral single-wall gold nanotubes(American Physical Society, 2004) Senger, R. T.; Dag, S.; Çıracı, SalimThe formation of freestanding and tip-suspended chiral-wall (n,m) nanotubes, which were composed of helical atomic strands, from gold atoms was investigated using first-principles calculations, where (n,m) notation defines the structure of the tube. The tubes with 3≤n≤5 were found to be stable and exhibited electronic and transport properties investigated. The (5,3) gold tube was energetically the most favourable. It was observed from the quantum ballistic conductance, band structure and charge density analysis that the current on these wires was less chiral, and no direct correlation between the numbers of conduction channels and helical strands was found.Item Open Access Directed polymers on a disordered tree with a defect subtree(Institute of Physics Publishing, 2018) Madras, N.; Yıldırım, GökhanWe study the question of how the competition between bulk disorder and a localized microscopic defect affects the macroscopic behavior of a system in the directed polymer context at the free energy level. We consider the directed polymer model on a disordered d-ary tree and represent the localized microscopic defect by modifying the disorder distribution at each vertex in a single path (branch), or in a subtree, of the tree. The polymer must choose between following the microscopic defect and finding the best branches through the bulk disorder. We describe three possible phases, called the fully pinned, partially pinned and depinned phases. When the microscopic defect is associated only with a single branch, we compute the free energy and the critical curve of the model, and show that the partially pinned phase does not occur. When the localized microscopic defect is associated with a non-disordered regular subtree of the disordered tree, the picture is more complicated. We prove that all three phases are non-empty below a critical temperature, and that the partially pinned phase disappears above the critical temperature.Item Open Access Investigation of multi-objective optimization criteria for RNA design(IEEE, 2017-12) Hampson, D. J. D.; Sav, Sinem; Tsang, H. H.RNA design is the inverse of RNA folding and it appears to be NP-hard. In RNA design, a secondary structure is given and the goal is to find a nucleotide sequence that will fold into this structure. To find such sequence(s) involves exploring the exponentially large sequence space. In literature, heuristic algorithms are the standard technique for tackling the RNA design. Heuristic algorithms enable effective and efficient exploration of the high-dimensional sequence-structure space when searching for candidates that fold into a given target structure. The main goal of this paper is to investigate the use of multi-objective criteria in SIMARD and Quality Pre-selection Strategy (QPS). The objectives that we optimize are Hamming distance (between designed structure and target structure) and thermodynamic free energy. We examine the different combinations of optimization criteria, and attempt to draw conclusions about the relationships between them. We find that energy is a poor primary objective but makes an excellent secondary objective. We also find that using multi-objective pre-selection produces viable solutions in far fewer steps than was previously possible with SIMARD. © 2016 IEEE.Item Open Access Protein folding rates correlate with heterogeneity of folding mechanism(American Physical Society, 2004) Öztop, B.; Ejtehadi, M. R.; Plotkin, S. S.The folding rates of protein were shown to correlate with the degree of heterogeneity in the formation of native contacts. It was shown that both experimental rates and simulated free energy barriers for 2-state proteins depend on the degree of heterogeneity present in the folding process. Heterogeneity due to variance in the distribution of native loop lengths, and variance in the distribution of φ values, were observed to increase folding rates and reduce folding barriers. The observed effect due to φ variance was found to be the most statistically significant, because φ variance captures both heterogeneity arising from native topology and that arising from energetics.Item Open Access SIMARD: a simulated annealing based RNA design algorithm with quality pre-selection strategies(IEEE, 2017-12) Sav, Sinem; Hampson, D. J. D.; Tsang, H. H.Most of the biological processes including expression levels of genes and translation of DNA to produce proteins within cells depend on RNA sequences, and the structure of the RNA plays vital role for its function. RNA design problem refers to the design of an RNA sequence that folds into given secondary structure. However, vast number of possible nucleotide combinations make this an NP-Hard problem. To solve the RNA design problem, a number of researchers have tried to implement algorithms using local stochastic search, context-free grammars, global sampling or evolutionary programming approaches. In this paper, we examine SIMARD, an RNA design algorithm that implements simulated annealing techniques. We also propose QPS, a mutation operator for SIMARD that pre-selects high quality sequences. Furthermore, we present experiment results of SIMARD compared to eight other RNA design algorithms using the Rfam datset. The experiment results indicate that SIMARD shows promising results in terms of Hamming distance between designed sequence and the target structure, and outperforms ERD in terms of free energy. © 2016 IEEE.Item Open Access Sorption of Cs+ and Ba2+ on magnesite(Cambridge University Press, 1998) Shahwan, Talal; Süzer, Şefik; Erten, Hasan N.Sorption behavior of Cs and Ba ions on magnesite was studied using the radiotracer method complemented by X-ray photoelectron spectroscopy. Cs and Ba were used as radiotracers. The sorption of Cs is seen to be temperature dependent, whereas Ba sorption is not much affected by temperature changes. It was found that Freundlich type isotherms provide an adequate description of the sorption process. The magnitude of the free energy of sorption are seen to be within the 8-16 kj/mol range. It can be remarked that the sorption of Cs and Ba on magnesite is a fast process suggesting an ion exchange type mechanism, mainly taking place at the surface of mineral particles.Item Open Access Theories of nanoparticle and nanostructure formation in liquid phase(Elsevier, 2018) Karatutlu, A.; Barhoum, A.; Sapelkin, A.Nanoparticles (NPs) and nanostructured materials exhibit shape- and size-dependent properties that are desired for a wide variety of applications, such as catalysis, sensing, drug delivery, energy production, and storage. In view of this, it is essential to produce well-defined NPs and nanostructures with desired characteristics, to understand their formation and growth mechanisms, and to define the critical size below which they act differently from bulk materials in order to develop synthetic strategies. For example, quantum dots (below 20nm) are mainly single nanocrystals characterized by a single-domain crystalline lattice without grain boundaries. These tiny individual crystals differ drastically from bulk polycrystalline materials. In fact, existing investigations indicated that ordered polycrystalline particles are preferably formed at high supersaturations, where rapid nucleation generates many NPs, which subsequently tend to aggregate randomly at high NP concentrations. Single crystals, such as quantum dots, form at low supersaturations. The reduction of the supersaturation to a level at which primary NPs are still formed in solution yields mesocrystals. This chapter discusses the advanced nucleation and growth theories that are used to explain the growth of the obtained nanoparticles and nanostructures to the desired structures.