Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

Ab initio simulation of charged slabs at constant chemical potential

We present a practical scheme for performing ab initio supercell calculations of charged slabs at constant electron chemical potential mu, rather than at constant number of electrons N-e. To this end, we define the chemical potential relative to a plane (or "reference electrode") at a finite distance from the slab (the distance should reflect the particular geometry of the situation being modeled). To avoid a net charge in the supercell, and thus make possible a standard supercell calculation, we restore the electroneutrality of the periodically repeated unit by means of a compensating charge, whose contribution to the total energy and potential is subtracted afterwards. The "constant mu" mode enables one to perform supercell calculation on slabs, where the slab is kept at a fixed potential relative to the reference electrode. We expect this to be useful in modeling many experimental situations, especially in electro-chemistry. (C) 2001 American Institute of Physics.

Simulation of the surface structure of butylmethylimidazolium ionic liquids

Molecular dynamics simulations of the liquid/vacuum surfaces of the room temperature ionic liquids [bmim][PF6], [bmim][BF4] and [bmim][Cl] have been carried out at various temperatures. The surfaces are structured with a top monolayer containing oriented cations and anions. The butyl side chains tend to face the vacuum and the methyl side chains the liquid. However, as the butyl chains are not densely packed, both anions and rings are visible from the vacuum phase. The effects of temperature and the anion on the degree of cation orientation is small, but the potential drop from the vacuum to the interior of the liquid is greater for liquids with smaller anions. We compare the simulation results with a range of experimental observations and suggest that neutron reflection from samples with protiated butyl groups would be a sensitive probe of the structure.

A Maxwell relation for current-induced forces

A Maxwell relation is presented involving current-induced forces. It provides a new physical picture of the origin of current-induced forces and in the small-voltage limit it enables the identification of a simple thermodynamic potential which drives electromigration. The question of whether current-induced forces are conservative or non-conservative is discussed briefly in the light of these insights.

Molecular conduction: Do time-dependent simulations tell you more than the Landauer approach?

A dynamical method for simulating steady-state conduction in atomic and molecular wires is presented which is both computationally and conceptually simple. The method is tested by calculating the current-voltage spectrum of a simple diatomic molecular junction, for which the static Landauer approach produces multiple steady-state solutions. The dynamical method quantitatively reproduces the static results and provides information on the stability of the different solutions. (c) 2006 American Institute of Physics.

'Superluminal' tunnelling as a weak measurement effect

We exploit the analogy between the transfer of a pulse across a scattering medium and Aharonov's weak measurements to resolve the long standing paradox between the impossibility to exceed the speed of light and the seemingly "superluminal" behavior of a tunneling particle in the barrier or a photon in a "fast-light" medium. We demonstrate that superluminality occurs when the value of the duration tau spent in the barrier is uncertain, whereas when tau is known accurately, no superluminal behavior is observed. In all cases only subluminal durations contribute to the transmission which precludes faster-than-light information transfer, as observed in a recent experiment.

Nature of quantum measurement for quantities not represented by Hermitian operators

In the case of a simple quantum system, we investigate the possibility of defining meaningful probabilities for a quantity that cannot be represented by a Hermitian operator. We find that the consistent-histories approach, recently applied to the case of quantum traversal time [N. Yamada, Phys. Rev. Lett. 83, 3350 (1999)], does not provide a suitable criterion and we dispute Yamada's claim of finding a simple solution to the tunneling-time problem. Rather, we define the probabilities for certain types of generally nonorthogonal decomposition of the system's quantum state. These relate to the interaction between the system and its environment, can be observed in a generalized von Neumann measurement, and are consistent with a particular class of positive-operator-valued measures.

Geometrical dependence in photoionization of H-2(+) in high-intensity, high-frequency, ultrashort laser pulses

The ionization dynamics of H2 + exposed to high-intensity, high-frequency, ultrashort laser pulses is investigated with two theoretical approaches. The time-dependent Schrödinger equation is solved by a direct numerical method, and a simple two-center interference-diffraction model is studied. The energy and angular distributions of the photoelectron for various internuclear distances and relative orientations between the internuclear axis of the molecule and the polarization of the field are calculated. The main features of the photoelectron spectrum pattern are described well by the interference-diffraction model, and excellent quantitative agreement between the two methods is found. The effect of quantal vibration on the photoelectron spectrum is also calculated. We find that vibrational average produces some broadening of the main features, but that the patterns remain clearly distinguishable.

Phase-resolved emission spectroscopy of a hydrogen rf discharge for the determination of quenching coefficients

Collisional effects can have strong influences on the population densities of excited states in gas discharges at elevated pressure. The knowledge of the pertinent collisional coefficient describing the depopulation of a specific level (quenching coefficient) is, therefore, important for plasma diagnostics and simulations. Phase resolved optical emission spectroscopy (PROES) applied to a capacitively coupled rf discharge excited with a frequency of 13.56 MHz in hydrogen allows the measurement of quenching coefficients for emitting states of various species, particularly of noble gases, with molecular hydrogen as a collision partner. Quenching coefficients can be determined subsequent to electron-impact excitation during the short field reversal phase within the sheath region from the time behavior of the fluorescence. The PROES technique based on electron-impact excitation is not limited â?? in contrast to laser techniques â?? by optical selection rules and the energy gap between the ground state and the upper level of the observed transition. Measurements of quenching coefficients and natural fluorescence lifetimes are presented for several helium (3 1S,4 1S,3 3S,3 3P,4 3S), neon (2p1 ,2p2 ,2p4 ,2p6), argon (3d2 ,3d4 ,3d18 and 3d3), and krypton (2p1 ,2p5) states as well as for some states of the triplet system of molecular hydrogen.

Dielectronic recombination of He-like to C-like iodine ions

KLL dielectronic recombination resonances, where a free electron is captured into the L shell and at the same time a K shell electron is excited into the L shell, have been measured for open shell iodine ions by measuring the detected yield of escaping ions of various charge states and modeling the charge balance in an electron beam ion trap. In the modeling, the escape from the trap and multiple charge exchange were considered. Extracted ions were used to measure the charge balance in the trap. The different charge states were clearly separated, which along with the correction for artifacts connected with ion escape and multiple charge exchange made the open shell highly charged ion measurements of this type possible for the first time. From the measured spectra resonant strengths were obtained. The results were 4.27(39)x10(-19) cm(2) eV, 2.91(26)x10(-19) cm(2) eV, 2.39(22)x10(-19) cm(2) eV, 1.49(14)x10(-19) cm(2) eV and 7.64(76)x10(-20) cm(2) eV for the iodine ions from He-like to C-like, respectively.