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 $\chi^{(2)}$ nonlinearity. In particular, we demonstrate that the cascading of nonresonant wave interaction processes generates an effective $\chi^{(3)}$ 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