Related papers: Nonequilibrium effects in DNA microarrays: a multi…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
Development of thermodynamic induction up to second order gives a dynamical bifurcation for thermodynamic variables and allows for the prediction and detailed explanation of nonequilibrium phase transitions with associated spontaneous…
Investigations of the intrinsic electromagnetic nonlinearity of superconductors give insight into the fundamental physics of these materials. Phase-sensitive third-order harmonic voltage data $\tilde{u}_{3f}=|u_{3f}|exp(i\phi_{3f})$ are…
Equilibrium statistical mechanics provides a robust framework for characterizing phase transitions in systems whose microsopic dynamics are time-reversible. Efforts to develop and validate theoretical frameworks for time-irreversible,…
In thermally non-equilibrium plasmas, conventional harmonic models can significantly mispredict superelastic electron heating rates. When the vibrational temperature exceeds the gas temperature ($T_{\rm v}>T_{\rm g}$), these models…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The non-equilibrium relaxational properties of a three dimensional Coulomb glass model are investigated by kinetic Monte Carlo simulations. Our results suggest a transition from stationary to non-stationary dynamics at the equilibrium glass…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Understanding how out-of-equilibrium states thermalize under quantum unitary dynamics is an important problem in many-body physics. In this work, we propose a statistical ansatz for the matrix elements of non-equilibrium initial states in…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused…
We characterize the equation of state for a simple three-dimensional DNA hairpin model using a Metropolis Monte Carlo algorithm. This algorithm was run at constant temperature and fixed separation between the terminal ends of the strand.…
By using the holographic approach, we investigate the interplay between the order parameter and Goldstone modes in the real-time dynamics of the chiral phase transition. By quenching the system to a different thermal bath and obtaining…
We calculate nonequilibrium quasiparticle and phonon distributions for a number of widely-used low transition temperature thin-film superconductors under constant, uniform illumination by sub-gap probe and pair-breaking signal photons…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
Small thermodynamic systems exhibit peculiar behavior different from that observed in long-scale systems. Non-equilibrium processes taking place in those systems are strongly influenced by the presence of fluctuations which can be large.…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
We consider the large-N $\Phi^4$ theory with spontaneously broken symmetry at finite temperature. We study, in the large-N limit, quantum states which are characterized by a time dependent, spatially homogenous expectation value of one of…
Ultrafast laser irradiation of solids leads to a thermodynamic nonequilibrium within and between the electron and phonon subsystems of the material. Due to electron-electron and phonon-phonon collisions, both subsystems relax into…