436 research outputs found
Charge Transport in Polymer Ion Conductors: a Monte Carlo Study
Diffusion of ions through a fluctuating polymeric host is studied both by
Monte Carlo simulation of the complete system dynamics and by dynamic bond
percolation (DBP) theory. Comparison of both methods suggests a multiscale-like
approach for calculating the diffusion coefficients of the ion
Dynamic percolation theory for particle diffusion in a polymer network
Tracer-diffusion of small molecules through dense systems of chain polymers
is studied within an athermal lattice model, where hard core interactions are
taken into account by means of the site exclusion principle. An approximate
mapping of this problem onto dynamic percolation theory is proposed. This
method is shown to yield quantitative results for the tracer correlation factor
of the molecules as a function of density and chain length provided the
non-Poisson character of temporal renewals in the disorder configurations is
properly taken into account
Effects of tunnelling and asymmetry for system-bath models of electron transfer
We apply the newly derived nonadiabatic golden-rule instanton theory to
asymmetric models describing electron-transfer in solution. The models go
beyond the usual spin-boson description and have anharmonic free-energy
surfaces with different values for the reactant and product reorganization
energies. The instanton method gives an excellent description of the behaviour
of the rate constant with respect to asymmetry for the whole range studied. We
derive a general formula for an asymmetric version of Marcus theory based on
the classical limit of the instanton and find that this gives significant
corrections to the standard Marcus theory. A scheme is given to compute this
rate based only on equilibrium simulations. We also compare the rate constants
obtained by the instanton method with its classical limit to study the effect
of tunnelling and other quantum nuclear effects. These quantum effects can
increase the rate constant by orders of magnitude.Comment: 10 pages, 3 figure
A very general rate expression for charge hopping in semiconducting polymers
We propose an expression of the hopping rate between localized states in semiconducting disordered polymers that contains the most used rates in the literature as special cases. We stress that these rates cannot be obtained directly from electron transfer rate theories as it is not possible to define diabatic localized states if the localization is caused by disorder, as in most polymers, rather than nuclear polarization effects. After defining the separate classes of accepting and inducing nuclear modes in the system, we obtain a general expression of the hopping rate. We show that, under the appropriate limits, this expression reduces to (i) single-phonon rate expression or (ii) the Miller-Abrahams rate or (iii) a multi-phonon expression. The description of these limits from a more general expression is useful to interpolate between them, to validate the assumptions of each limiting case, and to define the simplest rate expression that still captures the main features of the charge transport. When the rate expression is fed with a range of realistic parameters the deviation from the Miller-Abrahams rate is large or extremely large, especially for hopping toward lower energy states, due to the energy gap law
Current Profiles of Molecular Nanowires; DFT Green Function Representation
The Liouville-space Green function formalism is used to compute the current
density profile across a single molecule attached to electrodes. Time ordering
is maintained in real, physical, time, avoiding the use of artificial time
loops and backward propagations. Closed expressions for molecular currents,
which only require DFT calculations for the isolated molecule, are derived to
fourth order in the molecule/electrode coupling.Comment: 21 page
Nucleic Acids Res
Cells adapt to environmental changes by efficiently adjusting gene expression programs. Staphylococcus aureus, an opportunistic pathogenic bacterium, switches between defensive and offensive modes in response to quorum sensing signal. We identified and studied the structural characteristics and dynamic properties of the core regulatory circuit governing this switch by deterministic and stochastic computational methods, as well as experimentally. This module, termed here Double Selector Switch (DSS), comprises the RNA regulator RNAIII and the transcription factor Rot, defining a double-layered switch involving both transcriptional and post-transcriptional regulations. It coordinates the inverse expression of two sets of target genes, immuno-modulators and exotoxins, expressed during the defensive and offensive modes, respectively. Our computational and experimental analyses show that the DSS guarantees fine-tuned coordination of the inverse expression of its two gene sets, tight regulation, and filtering of noisy signals. We also identified variants of this circuit in other bacterial systems, suggesting it is used as a molecular switch in various cellular contexts and offering its use as a template for an effective switching device in synthetic biology studies
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