Allosteric Communication Mediated by Protein Contact Clusters: A Dynamical Model.

Describing the puzzling phenomenon of long-range communication between distant protein sites, allostery is of paramount importance in biomolecular regulation and signal transduction. It is commonly assumed to arise from a conformational rearrangement of the protein, although the underlying dynamical process has remained largely elusive. This study introduces a dynamical model of allosteric communication based on "contact clusters"─localized groups of highly correlated contacts that facilitate interactions between secondary structures.

Accurate estimation of the normalized mutual information of multidimensional data.

While the linear Pearson correlation coefficient represents a well-established normalized measure to quantify the inter-relation of two stochastic variables X and Y, it fails for multidimensional variables, such as Cartesian coordinates. Avoiding any assumption about the underlying data, the mutual information I(X, Y) does account for multidimensional correlations. However, unlike the normalized Pearson correlation, it has no upper bound (I ∈ [0, ∞)), i.

Time-Dependent Bacterial Contamination of a Surgical Suction Tip.

No in vitro surgical study has evaluated the time-dependent contamination of surgical suction tips compared with controls. Our purpose was to determine the difference in suction tip bacterial contamination rates between suction-positive and suction-negative tips. A matched-pair analysis of the contamination of surgical suction tips over a six-hour period was performed in two clean operating rooms.

Nonadiabatic dynamics of molecules interacting with metal surfaces: A quantum-classical approach based on Langevin dynamics and the hierarchical equations of motion.

A novel mixed quantum-classical approach to simulating nonadiabatic dynamics of molecules at metal surfaces is presented. The method combines the numerically exact hierarchical equations of motion approach for the quantum electronic degrees of freedom with Langevin dynamics for the classical degrees of freedom, namely, low-frequency vibrational modes within the molecule. The approach extends previous mixed quantum-classical methods based on Langevin equations to models containing strong electron-electron or quantum electronic-vibrational interactions, while maintaining a nonperturbative and non-Markovian treatment of the molecule-metal coupling.

Log-periodic oscillations as real-time signatures of hierarchical dynamics in proteins.

The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. D. Sornette [Phys.