681 research outputs found
Inelastic transport theory from first-principles: methodology and applications for nanoscale devices
We describe a first-principles method for calculating electronic structure,
vibrational modes and frequencies, electron-phonon couplings, and inelastic
electron transport properties of an atomic-scale device bridging two metallic
contacts under nonequilibrium conditions. The method extends the
density-functional codes SIESTA and TranSIESTA that use atomic basis sets. The
inelastic conductance characteristics are calculated using the nonequilibrium
Green's function formalism, and the electron-phonon interaction is addressed
with perturbation theory up to the level of the self-consistent Born
approximation. While these calculations often are computationally demanding, we
show how they can be approximated by a simple and efficient lowest order
expansion. Our method also addresses effects of energy dissipation and local
heating of the junction via detailed calculations of the power flow. We
demonstrate the developed procedures by considering inelastic transport through
atomic gold wires of various lengths, thereby extending the results presented
in [Frederiksen et al., Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that
the method applies more generally to molecular devices, we also calculate the
inelastic current through different hydrocarbon molecules between gold
electrodes. Both for the wires and the molecules our theory is in quantitative
agreement with experiments, and characterizes the system-specific mode
selectivity and local heating.Comment: 24 pages, 17 figure
Creation and Reproduction of Model Cells with Semipermeable Membrane
A high activity of reactions can be confined in a model cell with a
semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of
primitive metabolism in a cell. We study two generalized models to understand
the creation of primitive cell systems conceptually from the view point of the
nonlinear-nonequilibrium physics. In the first model, a single-cell system with
a highly active state confined by a semipermeable membrane is spontaneously
created from an inactive homogeneous state by a stochastic jump process. In the
second model, many cell structures are reproduced from a single cell, and a
multicellular system is created.Comment: 11 pages, 7 figure
Bacterial persisters are a stochastically formed subpopulation of low-energy cells.
Persisters represent a small subpopulation of non- or slow-growing bacterial cells that are tolerant to killing by antibiotics. Despite their prominent role in the recalcitrance of chronic infections to antibiotic therapy, the mechanism of their formation has remained elusive. We show that sorted cells of Escherichia coli with low levels of energy-generating enzymes are better able to survive antibiotic killing. Using microfluidics time-lapse microscopy and a fluorescent reporter for in vivo ATP measurements, we find that a subpopulation of cells with a low level of ATP survives killing by ampicillin. We propose that these low ATP cells are formed stochastically as a result of fluctuations in the abundance of energy-generating components. These findings point to a general "low energy" mechanism of persister formation
Experimental Biological Protocols with Formal Semantics
Both experimental and computational biology is becoming increasingly
automated. Laboratory experiments are now performed automatically on
high-throughput machinery, while computational models are synthesized or
inferred automatically from data. However, integration between automated tasks
in the process of biological discovery is still lacking, largely due to
incompatible or missing formal representations. While theories are expressed
formally as computational models, existing languages for encoding and
automating experimental protocols often lack formal semantics. This makes it
challenging to extract novel understanding by identifying when theory and
experimental evidence disagree due to errors in the models or the protocols
used to validate them. To address this, we formalize the syntax of a core
protocol language, which provides a unified description for the models of
biochemical systems being experimented on, together with the discrete events
representing the liquid-handling steps of biological protocols. We present both
a deterministic and a stochastic semantics to this language, both defined in
terms of hybrid processes. In particular, the stochastic semantics captures
uncertainties in equipment tolerances, making it a suitable tool for both
experimental and computational biologists. We illustrate how the proposed
protocol language can be used for automated verification and synthesis of
laboratory experiments on case studies from the fields of chemistry and
molecular programming
Efficiency of Energy Conversion in Thermoelectric Nanojunctions
Using first-principles approaches, this study investigated the efficiency of
energy conversion in nanojunctions, described by the thermoelectric figure of
merit . We obtained the qualitative and quantitative descriptions for the
dependence of on temperatures and lengths. A characteristic temperature:
was observed. When , . When , tends to a saturation value. The dependence of
on the wire length for the metallic atomic chains is opposite to that for
the insulating molecules: for aluminum atomic (conducting) wires, the
saturation value of increases as the length increases; while for
alkanethiol (insulating) chains, the saturation value of decreases as the
length increases. can also be enhanced by choosing low-elasticity bridging
materials or creating poor thermal contacts in nanojunctions. The results of
this study may be of interest to research attempting to increase the efficiency
of energy conversion in nano thermoelectric devices.Comment: 2 figure
Heat dissipation in atomic-scale junctions
Atomic and single-molecule junctions represent the ultimate limit to the
miniaturization of electrical circuits. They are also ideal platforms to test
quantum transport theories that are required to describe charge and energy
transfer in novel functional nanodevices. Recent work has successfully probed
electric and thermoelectric phenomena in atomic-scale junctions. However, heat
dissipation and transport in atomic-scale devices remain poorly characterized
due to experimental challenges. Here, using custom-fabricated scanning probes
with integrated nanoscale thermocouples, we show that heat dissipation in the
electrodes of molecular junctions, whose transmission characteristics are
strongly dependent on energy, is asymmetric, i.e. unequal and dependent on both
the bias polarity and the identity of majority charge carriers (electrons vs.
holes). In contrast, atomic junctions whose transmission characteristics show
weak energy dependence do not exhibit appreciable asymmetry. Our results
unambiguously relate the electronic transmission characteristics of
atomic-scale junctions to their heat dissipation properties establishing a
framework for understanding heat dissipation in a range of mesoscopic systems
where transport is elastic. We anticipate that the techniques established here
will enable the study of Peltier effects at the atomic scale, a field that has
been barely explored experimentally despite interesting theoretical
predictions. Furthermore, the experimental advances described here are also
expected to enable the study of heat transport in atomic and molecular
junctions, which is an important and challenging scientific and technological
goal that has remained elusive.Comment: supporting information available in the journal web site or upon
reques
Effect of Thermoelectric Cooling in Nanoscale Junctions
We propose a thermoelectric cooling device based on an atomic-sized junction.
Using first-principles approaches, we investigate the working conditions and
the coefficient of performance (COP) of an atomic-scale electronic refrigerator
where the effects of phonon's thermal current and local heating are included.
It is observed that the functioning of the thermoelectric nano-refrigerator is
restricted to a narrow range of driving voltages. Compared with the bulk
thermoelectric system with the overwhelmingly irreversible Joule heating, the
4-Al atomic refrigerator has a higher efficiency than a bulk thermoelectric
refrigerator with the same due to suppressed local heating via the
quasi-ballistic electron transport and small driving voltages. Quantum nature
due to the size minimization offered by atomic-level control of properties
facilitates electron cooling beyond the expectation of the conventional
thermoelectric device theory.Comment: 8 figure
Deterministic and stochastic descriptions of gene expression dynamics
A key goal of systems biology is the predictive mathematical description of
gene regulatory circuits. Different approaches are used such as deterministic
and stochastic models, models that describe cell growth and division explicitly
or implicitly etc. Here we consider simple systems of unregulated
(constitutive) gene expression and compare different mathematical descriptions
systematically to obtain insight into the errors that are introduced by various
common approximations such as describing cell growth and division by an
effective protein degradation term. In particular, we show that the population
average of protein content of a cell exhibits a subtle dependence on the
dynamics of growth and division, the specific model for volume growth and the
age structure of the population. Nevertheless, the error made by models with
implicit cell growth and division is quite small. Furthermore, we compare
various models that are partially stochastic to investigate the impact of
different sources of (intrinsic) noise. This comparison indicates that
different sources of noise (protein synthesis, partitioning in cell division)
contribute comparable amounts of noise if protein synthesis is not or only
weakly bursty. If protein synthesis is very bursty, the burstiness is the
dominant noise source, independent of other details of the model. Finally, we
discuss two sources of extrinsic noise: cell-to-cell variations in protein
content due to cells being at different stages in the division cycles, which we
show to be small (for the protein concentration and, surprisingly, also for the
protein copy number per cell) and fluctuations in the growth rate, which can
have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012
The Influence of Molecular Adsorption on Elongating Gold Nanowires
Using molecular dynamics simulations, we study the impact of physisorbing
adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs)
undergoing elongation. We used various adsorbate models in our simulations,
with each model giving rise to a different surface coverage and mobility of the
adsorbed phase. We find that the local structure and mobility of the adsorbed
phase remains relatively uniform across all segments of an elongating AuNW,
except for the thinning region of the wire where the high mobility of Au atoms
disrupts the monolayer structure, giving rise to higher solvent mobility. We
analyzed the AuNW trajectories by measuring the ductile elongation of the wires
and detecting the presence of characteristic structural motifs that appeared
during elongation. Our findings indicate that adsorbates facilitate the
formation of high-energy structural motifs and lead to significantly higher
ductile elongations. In particular, our simulations result in a large number of
monatomic chains and helical structures possessing mechanical stability in
excess of what we observe in vacuum. Conversely, we find that a molecular
species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the
mechanical stability of monatomic chains.Comment: To appear in Journal of Physical Chemistry
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