Topological origin of the phase transition in a model of DNA denaturation

The hypothesis that phase transitions originate from some topological change of the critical level hypersurface of the potential energy receives direct evident support by our study of the Bishop-Peyrard model of DNA thermal denaturation.     

Statistical mechanics of thermal denaturation of DNA oligomers

Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.     

Sharpness of the phase transition in percolation models

The equality of two critical points — the percolation thresholdp _H and the pointp _T where the cluster size distribution ceases to decay exponentially — is proven for all translation invariant independent percolation models on homogeneousd-dimensional lattices (d1). The analysis is based on a pair of new nonlinear partial differential inequalities for an order parameterM(,h), which forh=0 reduces to the percolation densityP — at the bond densityp=1–e ^– in the single parameter case. These are: (1)MhM/h+M ²+MM/, and (2) M/|J|MM/h. Inequality (1) is intriguing in that its derivation provides yet another hint of a ³ structure in percolation models. Moreover, through the elimination of one of its derivatives, (1) yields a pair of ordinary differential inequalities which provide information on the critical exponents and . One of these resembles an Ising model inequality of Fröhlich and Sokal and yields the mean field bound 2, and the other implies the result of Chayes and Chayes that . An inequality identical to (2) is known for Ising models, where it provides the basis for Newman's universal relation and for certain extrapolation principles, which are now made applicable also to independent percolation. These results apply to both finite and long range models, with or without orientation, and extend to periodic and weakly inhomogeneous systems.Research supported in part by the NSF Grant PHY-8605164Also in the Physics Department     

Constrained thermal denaturation of DNA under fixed linking number

A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation transition upon heating. However, in circular DNA chains and some experimental setups that manipulate single DNA molecules, the total number of turns (linking number) is constant at all times. The consequences of this additional topological invariant on the melting behaviour are nontrivial. Below, we investigate the melting characteristics of a homogeneous DNA where the linking number along the melting curve is preserved by supercoil formation in duplex portions. We obtain the mass fraction and the number of loops and supercoils below and above the melting temperature. We also argue that a macroscopic loop appears at T _c and calculate its size as a function of temperature.     

Direct observation of large temperature fluctuations during DNA thermal denaturation

In this Letter, we report direct measurement of large low frequency temperature fluctuations in double stranded DNA when it undergoes a denaturation transition. The fluctuation, which occurs only in the temperature range where the denaturation occurs, is several orders more than the expected equilibrium fluctuation. It is absent in single stranded DNA of the same sequence. The fluctuation at a given temperature also depends on the wait time and vanishes in a scale of a few hours. It is suggested that the large fluctuation occurs due to coexisting denaturated and closed base pairs that are in dynamic equilibrium due to the transition through a potential barrier in the scale of 25-30kBT0 (T0=300 K).     

Order of the phase transition of a twodimensional rotor system

A twodimensional rigid lattice of rotors with one rotational degree of freedom is studied in molecular field approximation and by molecular dynamics. The system undergoes a phase transition from an orientationally ordered low temperature structure to the orientationally disordered crystal (ODIC) also called the plastic high temperature phase. As a parameter of the interaction is varied the MFA-solution shows a changeover from a continuous to a discontinuous transition. I have deliberately performed a computer simulation of the system in the microcanonical ensemble where it is possible to fix the energy at an arbitrary level — even right within the step occuring at a first order transition- and to measure the temperature. The surprising result is a smaller derivative of the energy versus temperature relation than expected for a first order phase transition.     

Absorbing phase transition in energy exchange models

We study energy exchange models with dissipation (λ) and noise (of amplitude σ) and show that in presence of a threshold these models undergo an absorbing phase transition when either dissipation or noise strength or both are varied. Using Monte Carlo simulations we find that the behaviour along the critical line, which separates the active phase from the absorbing one, belongs to directed percolation (DP) universality class. We claim that the conserved version with λ = 1 and σ = 0 also shows a DP transition; the apparent non-DP behaviour observed earlier is an artifact of undershooting in the decay of activity density starting from a random initial condition.     

元胞自动机交通流模型的相变特性研究

系统地研究 VDR模型和T²模型在不同车流密度时车辆位置的相关性. 通过VDR模型、BJH模型和T²模型的序参量计算，确定在这三个模型中车流从自由流动到阻塞的相变特性，结果发现引入慢启动规则后，在不同的延迟概率和最大速度情况下，将引起交通相变特性的改变. 关键词： 交通流 元胞自动机 相关函数 序参量     

Order to disorder optical phase transition in random photonic crystals

Transition process of optical modal properties induced by the introduction of randomness into random photonic crystals is investigated by a computational method. We analyze an impulse response of two-dimensional triangular photonic crystals, in which the positions of the air holes are slightly deviated to random directions. It is shown that the appropriate degree of random departure from a perfect crystal state gives rise to multiple scattering of low group velocity band-edge modes and supports their strong Anderson localization. The achieved confinement efficiency of light exceeds the one obtained in the perfect photonic crystal state.     

Order of phase transition between the Meissner state and the mixed state

The critical value of the Ginzburg-Landau parameter which separates type-II/1 from type-II/2 superconductors is computed by means of the boson formulation of superconductivity. By taking into account the tail effect of the function c(k), which describes the electrodynamics of the superconducting state, it is shown that the attractive part of the interaction energy between two flux lines indeed vanishes for a critical value of κ. The dependence on Λ = VN(O) is also discussed.     

Thermal phase transition for some spin-boson models

In this work we study two different spin-boson models. Such models are generalizations of the Dicke model, it means they describe systems of N$N$ identical two-level atoms coupled to a single-mode quantized bosonic field, assuming the rotating wave approximation. In the first model, we consider the wavelength of the bosonic field to be of the order of the linear dimension of the material composed of the atoms, therefore we consider the spatial sinusoidal form of the bosonic field. The second model is the Thompson model, where we consider the presence of phonons in the material composed of the atoms. We study finite temperature properties of the models using the path integral approach and functional methods. In the thermodynamic limit, N→∞$N\to \infty$, the systems exhibit phase transitions from normal to superradiant phase at some critical values of temperature and coupling constant. We find the asymptotic behavior of the partition functions and the collective spectrums of the systems in the normal and the superradiant phases. We observe that the collective spectrums have zero energy values in the superradiant phases, corresponding to the Goldstone mode associated to the continuous symmetry breaking of the models. Our analysis and results are valid in the limit of zero temperature β→∞$\beta \to \infty$, where the models exhibit quantum phase transitions.     

Spherical models with a Gates-Penrose-type phase transition

Gates and Penrose have given criteria under which classical gases with weak long-range interactions fail to be described by the van der Waals equation with Maxwell's rule. Unfortunately, examples of equations of state for such systems have not yet been produced. This paper examines the Gates-Penrose class of interactions-i.e.,U (r)=q(r)+(r), in the limit0, where the Fourier transform (p) has a minimum at a nonzero value ofp-for the spherical model on a one-dimensional lattice. Free energy and magnetization isotherms are computed; it is seen that there is a phase transition, but that the zero-field spontaneous magnetization is always zero (a parahelicoidal phase). However, the pair-correlation function may exhibit either long-range order or the appearance of oscillation.     

Disorder induced phase transition in kinetic models of opinion dynamics

We propose a model of continuous opinion dynamics, where mutual interactions can be both positive and negative. Different types of distributions for the interactions, all characterized by a single parameter p$p$ denoting the fraction of negative interactions, are considered. Results from exact calculation of a discrete version and numerical simulations of the continuous version of the model indicate the existence of a universal continuous phase transition at p=_pc$p=p_c$ below which a consensus is reached. Although the order–disorder transition is analogous to a ferromagnetic–paramagnetic phase transition with comparable critical exponents, the model is characterized by some distinctive features relevant to a social system.     

Dynamical first-order phase transition in kinetically constrained models of glasses

We show that the dynamics of kinetically constrained models of glass formers takes place at a first-order coexistence line between active and inactive dynamical phases. We prove this by computing the large-deviation functions of suitable space-time observables, such as the number of configuration changes in a trajectory. We present analytic results for dynamic facilitated models in a mean-field approximation, and numerical results for the Fredrickson-Andersen model, the East model, and constrained lattice gases, in various dimensions. This dynamical first-order transition is generic in kinetically constrained models, and we expect it to be present in systems with fully jammed states.     

The existence of a phase transition in classical antiferromagnetic models

For a wide class of antiferromagnetic models we prove the existence of a phase transition using an extended Peierls argument, taking into account a result of Dobrushin [R. L. Dobrushin,Funct. Anal. Appl. 2:44 (1968); in English,2:302 (1968)] for an antiferromagnetic Ising model and the results of Malyshev [V. Malyshev,Comm. Math. Phys. 40:75–82 (1975)] for ferromagnetic models (such as the anisotropic rotator). In particular we review a result of Fröhlich, Israel, Lieb, and Simon [J. Fröhlichet al., J. Stat. Phys. 22(3):297–347 (198)] obtained when reflection positivity holds.