1,411 research outputs found
Opportunities and limitations of transition voltage spectroscopy: a theoretical analysis
In molecular charge transport, transition voltage spectroscopy (TVS) holds
the promise that molecular energy levels can be explored at bias voltages lower
than required for resonant tunneling. We investigate the theoretical basis of
this novel tool, using a generic model. In particular, we study the length
dependence of the conducting frontier orbital and of the 'transition voltage'
as a function of length. We show that this dependence is influenced by the
amount of screening of the electrons in the molecule, which determines the
voltage drop to be located at the contacts or across the entire molecule. We
observe that the transition voltage depends significantly on the length, but
that the ratio between the transition voltage and the conducting frontier
orbital is approximately constant only in strongly screening (conjugated)
molecules. Uncertainty about the screening within a molecule thus limits the
predictive power of TVS. We furthermore argue that the relative length
independence of the transition voltage for non-conjugated chains is due to
strong localization of the frontier orbitals on the end groups ensuring binding
of the rods to the metallic contacts. Finally, we investigate the
characteristics of TVS in asymmetric molecular junctions. If a single level
dominates the transport properties, TVS can provide a good estimate for both
the level position and the degree of junction asymmetry. If more levels are
involved the applicability of TVS becomes limited.Comment: 8 pages, 12 figure
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Kinetic Uncertainty Relations for the Control of Stochastic Reaction Networks.
Nonequilibrium stochastic reaction networks are commonly found in both biological and nonbiological systems, but have remained hard to analyze because small differences in rate functions or topology can change the dynamics drastically. Here, we conjecture exact quantitative inequalities that relate the extent of fluctuations in connected components, for various network topologies. Specifically, we find that regardless of how two components affect each other's production rates, it is impossible to suppress fluctuations below the uncontrolled equivalents for both components: one must increase its fluctuations for the other to be suppressed. For systems in which components control each other in ringlike structures, it appears that fluctuations can only be suppressed in one component if all other components instead increase fluctuations, compared to the case without control. Even the general N-component system-with arbitrary connections and parameters-must have at least one component with increased fluctuations to reduce fluctuations in others. In connected reaction networks it thus appears impossible to reduce the statistical uncertainty in all components, regardless of the control mechanisms or energy dissipation
Inelastic fingerprints of hydrogen contamination in atomic gold wire systems
We present series of first-principles calculations for both pure and hydrogen
contaminated gold wire systems in order to investigate how such impurities can
be detected. We show how a single H atom or a single H2 molecule in an atomic
gold wire will affect forces and Au-Au atom distances under elongation. We
further determine the corresponding evolution of the low-bias conductance as
well as the inelastic contributions from vibrations. Our results indicate that
the conductance of gold wires is only slightly reduced from the conductance
quantum G0=2e^2/h by the presence of a single hydrogen impurity, hence making
it difficult to use the conductance itself to distinguish between various
configurations. On the other hand, our calculations of the inelastic signals
predict significant differences between pure and hydrogen contaminated wires,
and, importantly, between atomic and molecular forms of the impurity. A
detailed characterization of gold wires with a hydrogen impurity should
therefore be possible from the strain dependence of the inelastic signals in
the conductance.Comment: 5 pages, 3 figures, Contribution to ICN+T2006, Basel, Switzerland,
July-August 200
Constraints on Fluctuations in Sparsely Characterized Biological Systems.
Biochemical processes are inherently stochastic, creating molecular fluctuations in otherwise identical cells. Such "noise" is widespread but has proven difficult to analyze because most systems are sparsely characterized at the single cell level and because nonlinear stochastic models are analytically intractable. Here, we exactly relate average abundances, lifetimes, step sizes, and covariances for any pair of components in complex stochastic reaction systems even when the dynamics of other components are left unspecified. Using basic mathematical inequalities, we then establish bounds for whole classes of systems. These bounds highlight fundamental trade-offs that show how efficient assembly processes must invariably exhibit large fluctuations in subunit levels and how eliminating fluctuations in one cellular component requires creating heterogeneity in another.The work was supported by grant 1137676 from the Division of Mathematical Sciences at the National Science Foundation, and grant GM081563 from the National Institutes of Health.This is the final version of the article. It first appeared from the American Physical Society via http://dx.doi.org/10.1103/PhysRevLett.116.05810
A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number
Motivation: cis-regulatory DNA sequence elements, such as enhancers and silencers, function to control the spatial and temporal expression of their target genes. Although the overall levels of gene expression in large cell populations seem to be precisely controlled, transcription of individual genes in single cells is extremely variable in real time. It is, therefore, important to understand how these cis-regulatory elements function to dynamically control transcription at single-cell resolution. Recently, statistical methods have been proposed to back calculate the rates involved in mRNA transcription using parameter estimation of a mathematical model of transcription and translation. However, a major complication in these approaches is that some of the parameters, particularly those corresponding to the gene copy number and transcription rate, cannot be distinguished; therefore, these methods cannot be used when the copy number is unknown.
Results: Here, we develop a hierarchical Bayesian model to estimate biokinetic parameters from live cell enhancer–promoter reporter measurements performed on a population of single cells. This allows us to investigate transcriptional dynamics when the copy number is variable across the population. We validate our method using synthetic data and then apply it to quantify the function of two known developmental enhancers in real time and in single cells
Respiration-Induced Intraorgan Deformation of the Liver: Implications for Treatment Planning in Patients Treated With Fiducial Tracking.
Stereotactic body radiation therapy is a well-tolerated modality for the treatment of primary and metastatic liver lesions, and fiducials are often used as surrogates for tumor tracking during treatment. We evaluated respiratory-induced liver deformation by measuring the rigidity of the fiducial configuration during the breathing cycle. Seventeen patients, with 18 distinct treatment courses, were treated with stereotactic body radiosurgery using multiple fiducials. Liver deformation was empirically quantified by measuring the intrafiducial distances at different phases of respiration. Data points were collected at the 0%, 50%, and 100% inspiration points, and the distance between each pair of fiducials was measured at the 3 phases. The rigid body error was calculated as the maximum difference in the intrafiducial distances. Liver disease was calculated with Child-Pugh score using laboratory values within 3 months of initiation of treatment. A peripheral fiducial was defined as within 1.5 cm of the liver edge, and all other fiducials were classified as central. For 5 patients with only peripheral fiducials, the fiducial configuration had more deformation (average maximum rigid body error 7.11 mm, range: 1.89-11.35 mm) when compared to patients with both central and peripheral and central fiducials only (average maximum rigid body error 3.36 mm, range: 0.5-9.09 mm, P = .037). The largest rigid body errors (11.3 and 10.6 mm) were in 2 patients with Child-Pugh class A liver disease and multiple peripheral fiducials. The liver experiences internal deformation, and the fiducial configuration should not be assumed to act as a static structure. We observed greater deformation at the periphery than at the center of the liver. In our small data set, we were not able to identify cirrhosis, which is associated with greater rigidity of the liver, as predictive for deformation. Treatment planning based only on fiducial localization must take potential intraorgan deformation into account
Inelastic Scattering in Metal-H2-Metal Junctions
We present first-principles calculations of the dI/dV characteristics of an
H2 molecule sandwiched between Au and Pt electrodes in the presence of
electron-phonon interactions. The conductance is found to decrease by a few
percentage at threshold voltages corresponding to the excitation energy of
longitudinal vibrations of the H2 molecule. In the case of Pt electrodes, the
transverse vibrations can mediate transport through otherwise non-transmitting
Pt -channels leading to an increase in the differential conductance even
though the hydrogen junction is characterized predominately by a single almost
fully open transport channel. In the case of Au, the transverse modes do not
affect the dI/dV because the Au d-states are too far below the Fermi level. A
simple explanation of the first-principles results is given using scattering
theory. Finally, we compare and discuss our results in relation to experimental
data.Comment: Accepted in Phys. Rev.
Stochastic Simulations of the Repressilator Circuit
The genetic repressilator circuit consists of three transcription factors, or
repressors, which negatively regulate each other in a cyclic manner. This
circuit was synthetically constructed on plasmids in {\it Escherichia coli} and
was found to exhibit oscillations in the concentrations of the three
repressors. Since the repressors and their binding sites often appear in low
copy numbers, the oscillations are noisy and irregular. Therefore, the
repressilator circuit cannot be fully analyzed using deterministic methods such
as rate-equations. Here we perform stochastic analysis of the repressilator
circuit using the master equation and Monte Carlo simulations. It is found that
fluctuations modify the range of conditions in which oscillations appear as
well as their amplitude and period, compared to the deterministic equations.
The deterministic and stochastic approaches coincide only in the limit in which
all the relevant components, including free proteins, plasmids and bound
proteins, appear in high copy numbers. We also find that subtle features such
as cooperative binding and bound-repressor degradation strongly affect the
existence and properties of the oscillations.Comment: Accepted to PR
Charging induced asymmetry in molecular conductors
We investigate the origin of asymmetry in various measured current-voltage
(I-V) characteristics of molecules with no inherent spatial asymmetry, with
particular focus on a recent break junction measurement. We argue that such
asymmetry arises due to unequal coupling with the contacts and a consequent
difference in charging effects, which can only be captured in a self-consistent
model for molecular conduction. The direction of the asymmetry depends on the
sign of the majority carriers in the molecule. For conduction through highest
occupied molecular orbitals (i.e. HOMO or p-type conduction), the current is
smaller for positive voltage on the stronger contact, while for conduction
through lowest unoccupied molecular orbitals (i.e. LUMO or n-type conduction),
the sense of the asymmetry is reversed. Within an extended Huckel description
of the molecular chemistry and the contact microstructure (with two adjustable
parameters, the position of the Fermi energy and the sulphur-gold bond length),
an appropriate description of Poisson's equation, and a self-consistently
coupled non-equilibrium Green's function (NEGF) description of transport, we
achieve good agreement between theoretical and experimental I-V
characteristics, both in shape as well as overall magnitude.Comment: length of the paper has been extended (4 pages to 6 pages), two new
figures have been added (3 figures to 5 figures), has been accepted for PR
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