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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Macroscopic loop formation in circular DNA denaturation(American Physical Society (APS), 2012) Bar, Amir; Mukamel, David; Department of Physics; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; College of Sciences; 49854The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T-c and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T-c, with a cusp at the critical point.Publication Open Access Finite-size effects in the dynamics and thermodynamics of two-dimensional Coulomb clusters(American Physical Society (APS), 2005) Calvo, F.; Wales, D. J.; Department of Chemistry; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; College of Sciences; 7129The dynamics and thermodynamics of melting in two-dimensional Coulomb clusters is revisited using molecular dynamics and Monte Carlo simulations. Several parameters are considered, including the Lindemann index, the largest Lyapunov exponent, and the diffusion constant. In addition to the orientational and radial melting processes, isomerizations and complex size effects are seen to occur in a very similar way to atomic and molecular clusters. The results are discussed in terms of the energy landscape represented through disconnectivity graphs, with proper attention paid to the broken ergodicity problems in simulations. Clusters bound by 1/r(3) and e(-kappa r)/r forces, and heterogeneous clusters made of singly and doubly charged species, are also studied, as well as the evolution toward larger systems.Publication Open Access Quantum correlated heat engine with spin squeezing(American Physical Society (APS), 2014) Altıntaş, Ferdi; Department of Physics; Department of Physics; Hardal, Ali Ümit Cemal; Müstecaplıoğlu, Özgür Esat; Faculty Member; Graduate School of Sciences and Engineering; College of Sciences; N/A; 1674We propose a four-level quantum heat engine in an Otto cycle with a working substance of two spins subject to an external magnetic field and coupled to each other by a one-axis twisting spin squeezing nonlinear interaction. We calculate the positive work and the efficiency of the engine for different parameter regimes. In particular, we investigate the effects of quantum correlations at the end of the two isochoric processes of the Otto cycle, as measured by the entanglement of formation and quantum discord, on the work extraction and efficiency. The regimes where the quantum correlations could enhance the efficiency and work extraction are characterized.Publication Open Access Calculating the local solvent chemical potential in crystal hydrates(American Physical Society (APS), 2000) Mezei, M.; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Reşat, Haluk; Faculty Member; College of EngineeringDetermining solvation patterns in biological systems is crucial in investigating the functional role water may play in structural stabilization and molecular recognition. Determining whether a particular position would be occupied by a solvent molecule requires the local thermodynamics to be known. In this work we introduce a simple and inexpensive approach based on grand canonical molecular simulations to determine the occupancy factors of the cavities. The method is applied to the test case of the sodium salt of hyaluronic acid. The results agree very well with experimental results and demonstrate the success of the method.Publication Open Access Twist-writhe partitioning in a coarse-grained DNA minicircle model(American Physical Society (APS), 2010) Department of Mechanical Engineering; Department of Physics; Department of Mechanical Engineering; Department of Physics; Sayar, Mehmet; Avşaroğlu, Barış; Kabakçıoğlu, Alkan; Faculty Member; Faculty Member; College of Engineering; College of Sciences; 109820; N/A; 49854Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.Publication Open Access Junction formation during desiccation cracking(American Physical Society (APS), 2006) Toga, K. B.; Department of Mechanical Engineering; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Faculty Member; College of Engineering; 115108In order to provide a sound physical basis for the understanding of the formation of desiccation crack networks, an experimental study is presented addressing junction formation. Focusing on junctions, basic features of the network determining the final pattern, provides an elemental approach and imparts conceptual clarity to the rather complicated problem of the evolution of crack patterns. Using coffee-water mixtures a clear distinction between junction formation during nucleation and propagation is achieved. It is shown that for the same drying suspension, one can switch from the well-known symmetric triple junctions that are unique to the nucleation phase to propagation junctions that are purely dictated by the variations of the stress state. In the latter case, one can even manipulate the path of a propagating crack in a deterministic fashion by changing the stress state within the suspension. Clear microscopic evidence is provided for the formation of propagation junctions, and material inhomogeneity is observed to be reflected by a broad distribution of angles, in stark contrast to shrinkage cracks in homogeneous solid films.Publication Open Access Rotationally induced transitions in small clusters(American Physical Society (APS), 2001) Department of Chemistry; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; College of Sciences; 7129The dynamics of an Ar-6 cluster held together by Lennard-Jones forces is studied classically. The development of chaotic dynamics is mainly followed by a calculation of the maximum Lyapunov exponent (MLE). Initial momentum vectors are chosen from the eigenvectors of the Hessian of the potential energy so that rotating and nonrotating clusters can be studied systematically. It is found that the dependence of MLE on the total energy is considerably different for rotational and vibrational excitations. As the magnitude of the angular momentum increases, sharp transitions in MLE are observed. These transitions are explained in terms of the changes of the topology of the effective rovibrational potential energy surface and the dynamic equilibration between the global and local minima.Publication Open Access Scale-free network hidden in a collapsing polymer(American Physical Society (APS), 2005) Stella, A. L.; Department of Physics; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; College of Sciences; 49854We show that the collapsed globular phase of a polymer accommodates a scale-free incompatibility graph of its contacts. The degree distribution of this network is found to decay with the exponent gamma=1/(2-c) up to a cutoff degree d(c)proportional to L2-c, where c is the loop exponent for dense polymers (c=11/8 in two dimensions) and L is the length of the polymer. Our results exemplify how a scale-free network can emerge from standard criticality.Publication Open Access Recovering smooth dynamics from time series with the aid of recurrence plots(American Physical Society (APS), 1999) Atay, F. M.; Department of Mathematics; Department of Mathematics; College of SciencesA graphical method based on recurrence plots is used in the reconstruction of the phase space from a time series of measurements. It is demonstrated that if the embedding delay and dimension are correctly chosen, the recurrence plot of a smooth dynamical system has a particularly simple form. It is shown how to use recurrence plots to determine the correct embedding parameters so that reliable quantitative information can be drawn about the system generating the time series. The average line length in the plot is shown to be directly related to the prediction horizon. Furthermore, it is a numerical characteristic of the embedded series independent of the threshold used in the plot. [S1063-651X(99)04206-3].Publication Open Access Equilibrium polyelectrolyte bundles with different multivalent counterion concentrations(American Physical Society (APS), 2010) Holm, Christian; Department of Mechanical Engineering; Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; College of Engineering; 109820We present the results of molecular-dynamics simulations on the salt concentration dependence of the formation of polyelectrolyte bundles in thermodynamic equilibrium. Extending our results on salt-free systems we investigate here deficiency or excess of trivalent counterions in solution. Our results reveal that the trivalent counterion concentration significantly alters the bundle size and size distribution. The onset of bundle formation takes place at earlier Bjerrum length values with increasing trivalent counterion concentration. For the cases of 80%, 95%, and 100% charge compensation via trivalent counterions, the net charge of the bundles decreases with increasing size. We suggest that competition among two different mechanisms, counterion condensation and merger of bundles, leads to a nonmonotonic change in line-charge density with increasing Bjerrum length. The investigated case of having an abundance of trivalent counterions by 200% prohibits such a behavior. In this case, we find that the difference in effective line-charge density of different size bundles diminishes. In fact, the system displays an isoelectric point, where all bundles become charge neutral.