409 research outputs found
Dynamical phase transition of a periodically driven DNA
Replication and transcription are two important processes in living systems.
To execute such processes, various proteins work far away from equilibrium in a
staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA
under a periodic drive in non-equilibrium conditions are studied. A steady
state phase diagram of a driven DNA is proposed which is experimentally
verifiable. As a two state system, we also compare the results of DNA with that
of an Ising magnet under an asymmetrical variation of magnetic field.Comment: 8 pages, 6 figures, Accepted version in PR
Entanglement entropy of a quantum unbinding transition and entropy of DNA
Two significant consequences of quantum fluctuations are entanglement and
criticality. Entangled states may not be critical but a critical state shows
signatures of universality in entanglement. A surprising result found here is
that the entanglement entropy may become arbitrarily large and negative near
the dissociation of a bound pair of quantum particles. Although apparently
counter-intuitive, it is shown to be consistent and essential for the phase
transition, by mapping to a classical problem of DNA melting. We associate the
entanglement entropy to a subextensive part of the entropy of DNA bubbles,
which is responsible for melting. The absence of any extensivity requirement in
time makes this negative entropy an inevitable consequence of quantum mechanics
in continuum. Our results encompass quantum critical points and first-order
transitions in general dimensions.Comment: v2: 6 pages, 3 figures (title modified, more details and figures
added
TYPE II DNA: when the interfacial energy becomes negative
An important step in transcription of a DNA base sequence to a protein is the
initiation from the exact starting point, called promoter region. We propose a
physical mechanism for identification of the promoter region, which relies on a
new classification of DNAs into two types, Type-I and Type-II, like
superconductors, depending on the sign of the energy of the interface
separating the zipped and the unzipped phases. This is determined by the
energies of helical ordering and stretching over two independent length scales.
The negative interfacial energy in Type II DNA leads to domains of helically
ordered state separated by defect regions, or blobs, enclosed by the
interfaces. The defect blobs, pinned by non-coding promoter regions, would be
physically distinct from all other types of bubbles. We also show that the
order of the melting transition under a force is different for Type I and Type
II.Comment: 4 pages, 2 figures, Eq.(4) corrected in 4th versio
Inhomogeneity induced shortcut to adiabaticity in Ising chains with long-range interactions
Driving a homogeneous system across a quantum phase transition in a
quench-time generates excitations on wavelengths longer than the
Kibble-Zurek (KZ) length within the KZ
time window , where and are the
critical exponents. Quenches designed with local time-dependent inhomogeneity
can introduce a gap in the spectrum. For a variety of setups with short-range
interactions, they have been shown to suppress excitations if the spatial
velocity of the inhomogenous front is below the characteristic KZ velocity
. Ising-like models with long-range interactions
can have no sonic horizon, spreading information instantaneously across the
system. Usually, this should imply that inhomogenous transitions will render
the dynamics adiabatic regardless of the front velocity. However, we show that
we get an adiabatic transition with no defects only when the inhomogeneous
front moves slower than a characteristic crossover velocity , where is the slope of the inhomogeneous
front at the critical point. The existence of this crossover velocity and
adiabaticity of the model is a consequence of the energy gap in the
quasiparticle spectrum that is opened by the inhomogeneity. This effect can be
employed for efficient adiabatic quantum state preparation in systems with
long-range interactions.Comment: 12 pages, 10 figures (closed to published version
An integrated and open-ended experiment: study of chemical waves in time and space
In this article we discuss an exciting experiment in non-linear dynamics. This provides an imaginative platform for bringing in chemical, physical, biological, mathematical and computational sciences together. There are implications for earth sciences as well
- …