1,600 research outputs found
Toward quantum simulations of biological information flow
Recent advances in the spectroscopy of biomolecules have highlighted the
possibility of quantum coherence playing an active role in biological energy
transport. The revelation that quantum coherence can survive in the hot and wet
environment of biology has generated a lively debate across both the physics
and biology communities. In particular, it remains unclear to what extent
non-trivial quantum effects are utilised in biology and what advantage, if any,
they afford. We propose an analogue quantum simulator, based on currently
available techniques in ultra-cold atom physics, to study a model of energy and
electron transport based on the Holstein Hamiltonian By simulating the salient
aspects of a biological system in a tunable laboratory setup, we hope to gain
insight into the validity of several theoretical models of biological quantum
transport in a variety of relevant parameter regimes.Comment: 8 Pages, 2 Figures, Non-technical contributing article for the
Interface Focus Theme Issue `Computability and the Turning centenary'.
Interface Focus
http://rsfs.royalsocietypublishing.org/content/early/2012/03/22/rsfs.2011.0109.shor
Observation and analysis of Fano-like lineshapes in the Raman spectra of molecules adsorbed at metal interfaces
Surface enhanced Raman spectra from molecules (bipyridyl ethylene) adsorbed
on gold dumbells are observed to become increasingly asymmetric (Fano-like) at
higher incident light intensity. The electronic temperature (inferred from the
anti-Stokes (AS) electronic Raman signal increases at the same time while no
vibrational AS scattering is seen. These observations are analyzed by assuming
that the molecule-metal coupling contains an intensity dependent contribution
(resulting from light-induced charge transfer transitions as well as
renormalization of the molecule metal tunneling barrier). We find that
interference between vibrational and electronic inelastic scattering routes is
possible in the presence of strong enough electron-vibrational coupling and can
in principle lead to the observed Fano-like feature in the Raman scattering
profile. However the best fit to the observed results, including the dependence
on incident light intensity and the associated thermal response is obtained
from a model that disregards this coupling and accounts for the structure of
the continuous electronic component of the Raman scattering signal. The
temperatures inferred from the Raman signal are argued to be only of
qualitative value.Comment: 20 pages, 12 figure
Optical properties of current carrying molecular wires
We consider several fundamental optical phenomena involving single molecules
in biased metal-molecule-metal junctions. The molecule is represented by its
highest occupied and lowest unoccupied molecular orbitals, and the analysis
involves the simultaneous consideration of three coupled fluxes: the electronic
current through the molecule, energy flow between the molecule and
electron-hole excitations in the leads and the incident and/or emitted photon
flux. Using a unified theoretical approach based on the non-equilibrium Green
function method we derive expressions for the absorption lineshape (not an
observable but a ueful reference for considering yields of other optical
processes) and for the current induced molecular emission in such junctions. We
also consider conditions under which resonance radiation can induce electronic
current in an unbiased junction. We find that current driven molecular emission
and resonant light induced electronic currents in single molecule junctions can
be of observable magnitude under appropriate realizable conditions. In
particular, light induced current should be observed in junctions involving
molecular bridges that are characterized by strong charge transfer optical
transitions. For observing current induced molecular emission we find that in
addition to the familiar need to control the damping of molecular excitations
into the metal substrate the phenomenon is also sensitive to the way in which
the potential bias si distributed on the junction.Comment: 56 pages, 8 figures; submitted to JC
The projection of a nonlocal mechanical system onto the irreversible generalized Langevin equation, II: Numerical simulations
The irreversible generalized Langevin equation (iGLE) contains a
nonstationary friction kernel that in certain limits reduces to the GLE with
space-dependent friction. For more general forms of the friction kernel, the
iGLE was previously shown to be the projection of a mechanical system with a
time-dependent Hamiltonian. [R. Hernandez, J. Chem. Phys. 110, 7701 (1999)] In
the present work, the corresponding open Hamiltonian system is further
explored. Numerical simulations of this mechanical system illustrate that the
time dependence of the observed total energy and the correlations of the
solvent force are in precise agreement with the projected iGLE.Comment: 8 pages, 9 figures, submitted to J. Chem. Phy
Nonlinear hopping transport in ring systems and open channels
We study the nonlinear hopping transport in one-dimensional rings and open
channels. Analytical results are derived for the stationary current response to
a constant bias without assuming any specific coupling to the external fields.
It is shown that anomalous large effective jump lengths, as observed in recent
experiments by taking the ratio of the third order nonlinear and the linear
conductivity, can occur already in ordered systems. Rectification effects due
to site energy disorder in ring systems are expected to become irrelevant for
large system sizes. In open channels in contrast, rectification effects occur
already for disorder in the jump barriers and do not vanish in the
thermodynamic limit. Numerical solutions for a sinusoidal bias show that the
ring system provides a good description for the transport behavior in the open
channel for intermediate and high frequencies. For low frequencies temporal
variations in the mean particle number have to be taken into account in the
open channel, which cannot be captured in the more simple ring model.Comment: 25 pages, 7 figure
Accurate prediction of gene feedback circuit behavior from component properties
A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology
A mesoscopic ring as a XNOR gate: An exact result
We describe XNOR gate response in a mesoscopic ring threaded by a magnetic
flux . The ring is attached symmetrically to two semi-infinite
one-dimensional metallic electrodes and two gate voltages, viz, and
, are applied in one arm of the ring which are treated as the inputs of
the XNOR gate. The calculations are based on the tight-binding model and the
Green's function method, which numerically compute the conductance-energy and
current-voltage characteristics as functions of the ring-to-electrode coupling
strength, magnetic flux and gate voltages. Our theoretical study shows that,
for a particular value of () (, the elementary
flux-quantum), a high output current (1) (in the logical sense) appears if both
the two inputs to the gate are the same, while if one but not both inputs are
high (1), a low output current (0) results. It clearly exhibits the XNOR gate
behavior and this aspect may be utilized in designing an electronic logic gate.Comment: 8 pages, 5 figure
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