Research Outputs
Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
Browse
51 results
Filters
Advanced Search
Filter by
Settings
Search Results
Publication Restricted A Finite-volumefront-tracking method for computations of multiphase flows in complex geometries(Koç University, 2004) Kayaalp, Arif Doruk; Muradoğlu, Metin; 0000-0002-1758-5418; Koç University Graduate School of Sciences and Engineering; Mechanical Engineering; 46561Publication Open Access A note on a strongly damped wave equation with fast growing nonlinearities(American Institute of Physics (AIP) Publishing, 2015) Zelik, Sergey; Department of Mathematics; Kalantarov, Varga; Faculty Member; Department of Mathematics; College of Sciences; 117655A strongly damped wave equation including the displacement depending nonlinear damping term and nonlinear interaction function is considered. The main aim of the note is to show that under the standard dissipativity restrictions on the nonlinearities involved, the initial boundary value problem for the considered equation is globally well-posed in the class of sufficiently regular solutions and the semigroup generated by the problem possesses a global attractor in the corresponding phase space. These results are obtained for the nonlinearities of an arbitrary polynomial growth and without the assumption that the considered problem has a global Lyapunov function. (C) 2015 AIP Publishing LLCPublication Restricted Application of pseudo-hermitian theory to the PT-Symetric delta function potential with continuous real spectrum(Koç University, 2007) Batal, Ahmet; Mostafazadeh, Ali; 0000-0002-0739-4060; Koç University Graduate School of Sciences and Engineering; Mathematics; 4231Publication Open Access Blume-Emery-Griffiths spin glass and inverted tricritical points(American Physical Society (APS), 2008) Özçelik, V. Ongun; Department of Physics; Berker, Ahmet Nihat; Faculty Member; Department of Physics; College of SciencesThe Blume-Emery-Griffiths spin glass is studied by renormalization-group theory in d=3. The boundary between the ferromagnetic and paramagnetic phases has first-order and two types of second-order segments. This topology includes an inverted tricritical point, first-order transitions replacing second-order transitions as temperature is lowered. The phase diagrams show disconnected spin-glass regions, spin-glass and paramagnetic reentrances, and complete reentrance, where the spin-glass phase replaces the ferromagnet as temperature is lowered for all chemical potentials.Publication Open Access Buckling of stiff polymers: influence of thermal fluctuations(American Physical Society (APS), 2007) Emanuel, Marc; Mohrbach, Herve; Schiessel, Helmut; Kulic, Igor M.; Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; Department of Mechanical Engineering; College of Engineering; 109820The buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuations on the buckling transition is, however, often ignored and not completely understood. A quantitative theory of the buckling of a wormlike chain based on a semiclassical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows one to go beyond the classical Euler buckling is derived in the linear and nonlinear regimes as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to two dimensions as opposed to the three-dimensional case. The transition to a buckled state softens at finite temperature. We derive the scaling behavior of the transition shift with increasing ratio of contour length versus persistence length.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; Reşat, Haluk; Faculty Member; Department of Chemical and Biological Engineering; 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 Restricted Construction of a consistent quantum mechanical system with non-hermitian set of opeartors(Koç University, 2006) Özçelik, Seher; Mostafazadeh, Ali; 0000-0002-0739-4060; Koç University Graduate School of Sciences and Engineering; Mathematics; 4231Publication Open Access Deep spin-glass hysteresis-area collapse and scaling in the three-dimensional +/- J Ising model(American Physical Society (APS), 2012) Berker, A. Nihat; Department of Physics; Sarıyer, Ozan; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; N/A; 49854We investigate the dissipative loss in the +/- J Ising spin glass in three dimensions through the scaling of the hysteresis area, for a maximum magnetic field that is equal to the saturation field. We perform a systematic analysis for the whole range of the bond randomness as a function of the sweep rate by means of frustration-preserving hard-spin mean-field theory. Data collapse within the entirety of the spin-glass phase driven adiabatically (i.e., infinitely slow field variation) is found, revealing a power-law scaling of the hysteresis area as a function of the antiferromagnetic bond fraction and the temperature. Two dynamic regimes separated by a threshold frequency omega(c) characterize the dependence on the sweep rate of the oscillating field. For omega < omega(c), the hysteresis area is equal to its value in the adiabatic limit omega = 0, while for omega > omega(c) it increases with the frequency through another randomness-dependent power law.Publication Open Access Denaturation of circular DNA: supercoil mechanism 2011(American Physical Society (APS), 2011) Bar, Amir; Mukamel, David; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854The denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga (PS) model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double-stranded helix, released by a loop denaturation, is absorbed by supercoils. We find that as in the case of linear DNA, the order of the transition is determined by the loop exponent c. However the first-order transition displayed by the PS model for c > 2 in linear DNA is replaced by a continuous transition with arbitrarily high order as c approaches 2, while the second-order transition found in the linear case in the regime 1 < c <= 2 disappears. In addition, our analysis reveals that melting under fixed linking number is a condensation transition, where the condensate is a macroscopic loop which appears above the critical temperature.Publication Open Access Denaturation of circular DNA: supercoils and overtwist(American Physical Society (APS), 2012) Bar, Amir; Mukamel, David; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854The denaturation transition of circular DNA is studied within a Poland-Scheraga-type approach, generalized to account for the fact that the total linking number (LK), which measures the number of windings of one strand around the other, is conserved. In the model the LK conservation is maintained by invoking both overtwisting and writhing (supercoiling) mechanisms. This generalizes previous studies, which considered each mechanism separately. The phase diagram of the model is analyzed as a function of the temperature and the elastic constant κ associated with the overtwisting energy for any given loop entropy exponent c. As in the case where the two mechanisms apply separately, the model exhibits no denaturation transition for c 2. For c > 2 and κ = 0 we find that the model exhibits a first-order transition. The transition becomes of higher order for any κ > 0. We also calculate the contribution of the two mechanisms separately in maintaining the conservation of the linking number and find that it is weakly dependent on the loop exponent c.