7 research outputs found
Characterization of the low temperature properties of a simplified protein model
Prompted by results that showed that a simple protein model, the frustrated
G\=o model, appears to exhibit a transition reminiscent of the protein
dynamical transition, we examine the validity of this model to describe the
low-temperature properties of proteins. First, we examine equilibrium
fluctuations. We calculate its incoherent neutron-scattering structure factor
and show that it can be well described by a theory using the one-phonon
approximation. By performing an inherent structure analysis, we assess the
transitions among energy states at low temperatures. Then, we examine
non-equilibrium fluctuations after a sudden cooling of the protein. We
investigate the violation of the fluctuation--dissipation theorem in order to
analyze the protein glass transition. We find that the effective temperature of
the quenched protein deviates from the temperature of the thermostat, however
it relaxes towards the actual temperature with an Arrhenius behavior as the
waiting time increases. These results of the equilibrium and non-equilibrium
studies converge to the conclusion that the apparent dynamical transition of
this coarse-grained model cannot be attributed to a glassy behavior
On 4-point correlation functions in simple polymer models
We derive an exact formula for the covariance of cartesian distances in two
simple polymer models, the freely-jointed chain and a discrete flexible model
with nearest-neighbor interaction. We show that even in the interaction-free
case correlations exist as long as the two distances at least partially share
the same segments. For the interacting case, we demonstrate that the naive
expectation of increasing correlations with increasing interaction strength
only holds in a finite range of values. Some suggestions for future
single-molecule experiments are made
Can one predict DNA Transcription Start Sites by studying bubbles?
It has been speculated that bubble formation of several base-pairs due to
thermal fluctuations is indicatory for biological active sites. Recent
evidence, based on experiments and molecular dynamics (MD) simulations using
the Peyrard-Bishop-Dauxois model, seems to point in this direction. However,
sufficiently large bubbles appear only seldom which makes an accurate
calculation difficult even for minimal models. In this letter, we introduce a
new method that is orders of magnitude faster than MD. Using this method we
show that the present evidence is unsubstantiated.Comment: 4 pages, 3 figures, accepted for publication in physical review
letter
Comment on "A generalized Langevin formalism of complete DNA melting transition"
We show that the calculated DNA denaturation curves for finite
(Peyrard-Bishop-Dauxois (PBD) chains are intrinsically undefined.Comment: 2 pages. Accepted for EP
Far-off-resonant wave interaction in one-dimensional photonic crystals with quadratic nonlinearity
We extend a recently developed Hamiltonian formalism for nonlinear wave
interaction processes in spatially periodic dielectric structures to the
far-off-resonant regime, and investigate numerically the three-wave resonance
conditions in a one-dimensional optical medium with nonlinearity.
In particular, we demonstrate that the cascading of nonresonant wave
interaction processes generates an effective nonlinear response in
these systems. We obtain the corresponding coupling coefficients through
appropriate normal form transformations that formally lead to the Zakharov
equation for spatially periodic optical media.Comment: 14 pages, 4 figure