General, PDB-based collective variables for protein folding

New, automated forms of data-analysis are required in order to understand the high-dimensional trajectories that are obtained from molecular dynamics simulations on proteins. Dimensionality reduction algorithms are particularly appealing in this regard as they allow one to construct unbiased, low-dimensional representations of the trajectory using only the information encoded in the trajectory. The downside of this approach is that different sets of coordinates are required for each different chemical systems under study precisely because the coordinates are constructed using information from the trajectory. In this paper we show how one can resolve this problem by using the sketch-map algorithm that we recently proposed to construct a low-dimensional representation of the structures contained in the protein data bank (PDB). We show that the resulting coordinates are as useful for analysing trajectory data as coordinates constructed using landmark configurations taken from the trajectory and that these coordinates can thus be used for understanding protein folding across a range of systems.

Entanglement between collective operators in a linear harmonic chain

We investigate entanglement between collective operators of two blocks of oscillators in an infinite linear harmonic chain. These operators are defined as averages over local operators (individual oscillators) in the blocks. On the one hand, this approach of "physical blocks" meets realistic experimental conditions, where measurement apparatuses do not interact with single oscillators but rather with a whole bunch of them, i.e., where in contrast to usually studied "mathematical blocks" not every possible measurement is allowed. On the other, this formalism naturally allows the generalization to blocks which may consist of several noncontiguous regions. We quantify entanglement between the collective operators by a measure based on the Peres-Horodecki criterion and show how it can be extracted and transferred to two qubits. Entanglement between two blocks is found even in the case where none of the oscillators from one block is entangled with an oscillator from the other, showing genuine bipartite entanglement between collective operators. Allowing the blocks to consist of a periodic sequence of subblocks, we verify that entanglement scales at most with the total boundary region. We also apply the approach of collective operators to scalar quantum field theory.

Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure. (C) 2001 American Institute of Physics.

Ultrafast Probing of Collective Electron Dynamics Driven by Dielectronic Repulsion

We use the time-dependent R-matrix approach to investigate an ultrashort pump-probe scheme to observe collective electron dynamics in C(+). The ionization probability of a coherent superposition of the 2s2p(2) (2)D and (2)S states shows rapid modulation due to collective dynamics of the two equivalent 2p electrons, with the modulation frequency linked to the dielectronic repulsion. The best insight into this collective dynamics is achieved by a transformation from LS symmetry to the uncoupled basis. Such dynamics may be important in high-harmonic generation using open-shell atoms and ions.