Macroscopic loop formation in circular DNA denaturation

The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed in expense of 1) overtwist, 2) supercoils. Recent work has shown that the supercoiling mechanism results in a BEC-like picture where a macroscopic loop appears at Tc 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 Tc, with a cusp at the critical point.Comment: 5 pages, 3 figures, submitted for publicatio

Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model

Here 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.Comment: 21 pages, 7 figures, 1 tabl

Phase transitions in tetrahedral Ising lattices

Ankara : Department of Physics and Institute of Engineering and Sciences, Bilkent Univ., 1993.Thesis (Master's) -- Bilkent University, 1993.Includes bibliographical references leaves 38-40After a review of the Renormalization CJroup theory, the phase diagram of unisotro])ic tetrahedral Ising lattice is explored l)y the motivation gained through the recent experimental findings about SiGe alloys. Renormalization Group approcich and the mean-field R(J approximation previously pro])osed by Kinzel ¿ire used. Four different ordered pluises are olxserved. The critical expoiKMit // is Ciih’uhited using the liiUNirized t.ra.nsform<ition ¿iround the fixed points and ('om|)fii’ed with previous works. It is ('oiu'luded tluit the newly observed orderings in Si(!e superlattices are induced by surface effects.Kabakçıoğlu, AlkanM.S

A Quantum Otto Engine with Shortcuts to Thermalization and Adiabaticity

We investigate the energetic advantage of accelerating a quantum harmonic oscillator Otto engine by use of shortcuts to adiabaticity (for the power and compression strokes) and to equilibrium (for the hot isochore), by means of counter-diabatic (CD) driving. By comparing various protocols with and without CD driving, we find that, applying both type of shortcuts leads to enhanced power and efficiency even after the driving costs are taken into account. The hybrid protocol not only retains its advantage in the limit cycle, but also recovers engine functionality (i.e., a positive power output) in parameter regimes where an uncontrolled, finite-time Otto cycle fails. We show that controlling three strokes of the cycle leads to an overall improvement of the performance metrics compared with controlling only the two adiabatic strokes. Moreover, we numerically calculate the limit cycle behavior of the engine and show that the engines with accelerated isochoric and adiabatic strokes display a superior power output in this mode of operation.Comment: 12 pages, 7 figure

Machine learning in and out of equilibrium

The algorithms used to train neural networks, like stochastic gradient descent (SGD), have close parallels to natural processes that navigate a high-dimensional parameter space -- for example protein folding or evolution. Our study uses a Fokker-Planck approach, adapted from statistical physics, to explore these parallels in a single, unified framework. We focus in particular on the stationary state of the system in the long-time limit, which in conventional SGD is out of equilibrium, exhibiting persistent currents in the space of network parameters. As in its physical analogues, the current is associated with an entropy production rate for any given training trajectory. The stationary distribution of these rates obeys the integral and detailed fluctuation theorems -- nonequilibrium generalizations of the second law of thermodynamics. We validate these relations in two numerical examples, a nonlinear regression network and MNIST digit classification. While the fluctuation theorems are universal, there are other aspects of the stationary state that are highly sensitive to the training details. Surprisingly, the effective loss landscape and diffusion matrix that determine the shape of the stationary distribution vary depending on the simple choice of minibatching done with or without replacement. We can take advantage of this nonequilibrium sensitivity to engineer an equilibrium stationary state for a particular application: sampling from a posterior distribution of network weights in Bayesian machine learning. We propose a new variation of stochastic gradient Langevin dynamics (SGLD) that harnesses without replacement minibatching. In an example system where the posterior is exactly known, this SGWORLD algorithm outperforms SGLD, converging to the posterior orders of magnitude faster as a function of the learning rate.Comment: 24 pages, 6 figure

Deep Spin-Glass Hysteresis Area Collapse and Scaling in the d=3d=3 ±J\pm J Ising Model

We investigate the dissipative loss in the $\pm J$ 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.Comment: 6 pages, 6 figure

Denaturation of Circular DNA: Supercoils and Overtwist

The 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 $\kappa$ associated with the overtwisting energy for any given loop entropy exponent, $c$. As is the case where the two mechanisms apply separately, the model exhibits no denaturation transition for $c \le 2$. For $c>2$ and $\kappa=0$ we find that the model exhibits a first order transition. The transition becomes of higher order for any $\kappa>0$. 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 $c$.Comment: 10 pages, 6 figure

Strongly Asymmetric Tricriticality of Quenched Random-Field Systems

In view of the recently seen dramatic effect of quenched random bonds on tricritical systems, we have conducted a renormalization-group study on the effect of quenched random fields on the tricritical phase diagram of the spin-1 Ising model in $d=3$. We find that random fields convert first-order phase transitions into second-order, in fact more effectively than random bonds. The coexistence region is extremely flat, attesting to an unusually small tricritical exponent $\beta_u$; moreover, an extreme asymmetry of the phase diagram is very striking. To accomodate this asymmetry, the second-order boundary exhibits reentrance.Comment: revtex, 4 pages, 2 figs, submitted to PR

Delocalization Transition of a Rough Adsorption-Reaction Interface

We introduce a new kinetic interface model suitable for simulating adsorption-reaction processes which take place preferentially at surface defects such as steps and vacancies. As the average interface velocity is taken to zero, the self- affine interface with Kardar-Parisi-Zhang like scaling behaviour undergoes a delocalization transition with critical exponents that fall into a novel universality class. As the critical point is approached, the interface becomes a multi-valued, multiply connected self-similar fractal set. The scaling behaviour and critical exponents of the relevant correlation functions are determined from Monte Carlo simulations and scaling arguments.Comment: 4 pages with 6 figures, new comment