Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach

We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic Gillespie scheme with the denaturation zones in double stranded DNA studied as a single molecule time series. Simulated Annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data.Comment: 9 pages, 4 figures, iop article package include

Master equation approach to DNA-breathing in heteropolymer DNA

After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent single-stranded bubbles. Their unzipping and zipping dynamics can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure

Cooling of Dark-Matter Admixed Neutron Stars with density-dependent Equation of State

We propose a dark-matter (DM) admixed density-dependent equation of state where the fermionic DM interacts with the nucleons via Higgs portal. Presence of DM can hardly influence the particle distribution inside neutron star (NS) but can significantly affect the structure as well as equation of state (EOS) of NS. Introduction of DM inside NS softens the equation of state. We explored the effect of variation of DM mass and DM Fermi momentum on the NS EOS. Moreover, DM-Higgs coupling is constrained using dark matter direct detection experiments. Then, we studied cooling of normal NSs using APR and DD2 EOSs and DM admixed NSs using dark-matter modified DD2 with varying DM mass and Fermi momentum. We have done our analysis by considering different NS masses. Also DM mass and DM Fermi momentum are varied for fixed NS mass and DM-Higgs coupling. We calculated the variations of luminosity and temperature of NS with time for all EOSs considered in our work and then compared our calculations with the observed astronomical cooling data of pulsars namely Cas A, RX J0822-43, 1E 1207-52, RX J0002+62, XMMU J17328, PSR B1706-44, Vela, PSR B2334+61, PSR B0656+14, Geminga, PSR B1055-52 and RX J0720.4-3125. It is found that APR EOS agrees well with the pulsar data for lighter and medium mass NSs but cooling is very fast for heavier NS. For DM admixed DD2 EOS, it is found that for all considered NS masses, all chosen DM masses and Fermi momenta agree well with the observational data of PSR B0656+14, Geminga, Vela, PSR B1706-44 and PSR B2334+61. Cooling becomes faster as compared to normal NSs in case of increasing DM mass and Fermi momenta. It is infered from the calculations that if low mass super cold NSs are observed in future that may support the fact that heavier WIMP can be present inside neutron stars.Comment: 24 Pages, 15 Figures and 2 Tables. Version accepted in The European Physical Journal

Magnetoresistance behavior of a ferromagnetic shape memory alloy: Ni_1.75Mn_1.25Ga

A negative-positive-negative switching behavior of magnetoresistance (MR) with temperature is observed in a ferromagnetic shape memory alloy Ni_1.75Mn_1.25Ga. In the austenitic phase between 300 and 120 K, MR is negative due to s-d scattering. Curiously, below 120K MR is positive, while at still lower temperatures in the martensitic phase, MR is negative again. The positive MR cannot be explained by Lorentz contribution and is related to a magnetic transition. Evidence for this is obtained from ab initio density functional theory, a decrease in magnetization and resistivity upturn at 120 K. Theory shows that a ferrimagnetic state with anti-ferromagnetic alignment between the local magnetic moments of the Mn atoms is the energetically favoured ground state. In the martensitic phase, there are two competing factors that govern the MR behavior: a dominant negative trend up to the saturation field due to the decrease of electron scattering at twin and domain boundaries; and a weaker positive trend due to the ferrimagnetic nature of the magnetic state. MR exhibits a hysteresis between heating and cooling that is related to the first order nature of the martensitic phase transition.Comment: 17 pages, 5 figures. Accepted in Phys. Rev.

FPGA-based Assessment of Midori and GIFT Lightweight Block Ciphers

Lightweight block ciphers are today of paramount importance to provide security services in constrained environments. Recent studies have questioned the security properties of PRESENT, which makes it evident the need to study alternative ciphers. In this work we provide hardware architectures for Midori and GIFT, and compare them against implementations for PRESENT and GIMLI under fair conditions. The hardware description for our designs is made publicly available

Theory of Adiabatic fluctuations : third-order noise

We consider the response of a dynamical system driven by external adiabatic fluctuations. Based on the `adiabatic following approximation' we have made a systematic separation of time-scales to carry out an expansion in $\alpha |\mu|^{-1}$, where $\alpha$ is the strength of fluctuations and $|\mu|$ is the damping rate. We show that probability distribution functions obey the differential equations of motion which contain third order terms (beyond the usual Fokker-Planck terms) leading to non-Gaussian noise. The problem of adiabatic fluctuations in velocity space which is the counterpart of Brownian motion for fast fluctuations, has been solved exactly. The characteristic function and the associated probability distribution function are shown to be of stable form. The linear dissipation leads to a steady state which is stable and the variances and higher moments are shown to be finite.Comment: Plain Latex, no figures, 28 pages; to appear in J. Phys.

Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.Comment: 7 pages, 4 figure

Exotic phases in compact stars

We discuss how the co-existence of hyperons, antikaon condensate and color superconducting quark matter in neutron star interior influences the gross properties of compact stars such as, the equation of state and mass-radius relationship. We compare our results with the recent observations. We also discuss about superdense stars in the third family branch which may contain a pure color-flavor-locked (CFL) core.Comment: 6 pages, presented in "Strange Quarks in Matter" (SQM2003) conference, Atlantic Beach, NC, USA, March 12-17, 2003 and to be published in J. Phys.

Dynamics of a metastable state nonlinearly coupled to a heat bath driven by an external noise

Based on a system-reservoir model, where the system is nonlinearly coupled to a heat bath and the heat bath is modulated by an external stationary Gaussian noise, we derive the generalized Langevin equation with space dependent friction and multiplicative noise and construct the corresponding Fokker-Planck equation, valid for short correlation time, with space dependent diffusion coefficient to study the escape rate from a metastable state in the moderate to large damping regime. By considering the dynamics in a model cubic potential we analyze the result numerically which are in good agreement with the theoretical prediction. It has been shown numerically that the enhancement of rate is possible by properly tuning the correlation time of the external noise.Comment: 13 pages, 5 figures, Revtex4. To appear in Physical Review