699 research outputs found
Differential Cyclic Voltammetry - a Novel Technique for Selective and Simultaneous Detection using Redox Cycling Based Sensors
Redox cycling (RC) is an effect that is used to amplify electrochemical signals. However, traditional techniques such as cyclic voltammetry (CV) do not provide clear insight for a mixture of multiple redox couples while RC is applied. Thus, we have developed a new measurement technique which delivers electrochemical spectra of all reversible redox couples present based on concentrations and standard potentials. This technique has been named differential cyclic voltammetry (DCV). We have fabricated micrometer-sized interdigitated electrode (IDE) sensors to conduct DCV measurements in mixtures of 1mM catechol and 4mM [Ru(NH3)6]Cl3. To simulate the electrochemical behavior of these sensors we have also developed a finite element model (FEM) in Comsol®. The\ud
experimental data corresponds to the calculated spectra obtained from simulations. Additionally, the measured spectra can be used to easily derive standard potentials and concentrations simultaneously and selectively.\u
Scaling theory of DNA confined in nanochannels and nanoslits
A scaling analysis is presented of the statistics of long DNA confined in
nanochannels and nanoslits. It is argued that there are several regimes in
between the de Gennes and Odijk limits introduced long ago. The DNA chain folds
back on itself giving rise to a global persistence length which may be very
large owing to entropic deflection. Moreover, there is an orientational
excluded-volume effect between the DNA segments imposed solely by the
nanoconfinement. These two effects cause the chain statistics to be intricate
leading to nontrivial power laws for the chain extension in the intermediate
regimes. It is stressed that DNA confinement within nanochannels differs from
that in nanoslits because the respective orientational excluded-volume effects
are not the same.Comment: 5 pages, 1 figure Several corrections, some minor changes in the text
and replacement of one referenc
Forces During Bacteriophage DNA Packaging and Ejection
The conjunction of insights from structural biology, solution biochemistry,
genetics and single molecule biophysics has provided a renewed impetus for the
construction of quantitative models of biological processes. One area that has
been a beneficiary of these experimental techniques is the study of viruses. In
this paper we describe how the insights obtained from such experiments can be
utilized to construct physical models of processes in the viral life cycle. We
focus on dsDNA bacteriophages and show that the bending elasticity of DNA and
its electrostatics in solution can be combined to determine the forces
experienced during packaging and ejection of the viral genome. Furthermore, we
quantitatively analyze the effect of fluid viscosity and capsid expansion on
the forces experienced during packaging. Finally, we present a model for DNA
ejection from bacteriophages based on the hypothesis that the energy stored in
the tightly packed genome within the capsid leads to its forceful ejection. The
predictions of our model can be tested through experiments in vitro where DNA
ejection is inhibited by the application of external osmotic pressure
A closed form for the electrostatic interaction between two rod-like charged objects
We have calculated the electrostatic interaction between two rod-like charged
objects with arbitrary orientations in three dimensions. we obtained a closed
form formula expressing the interaction energy in terms of the separation
distance between the centers of the two rod-like objects, , their lengths
(denoted by and ), and their relative orientations (indicated by
and ). When the objects have the same length (),
for particular values of separations, i.e for , two types of
minimum are appeared in the interaction energy with respect to . By
employing the closed form formula and introducing a scaled temperature , we
have also studied the thermodynamic properties of a one dimensional system of
rod-like charged objects. For different separation distances, the dependence of
the specific heat of the system to the scaled temperature has been studied. It
is found that for , the specific heat has a maximum.Comment: 10 pages, 9 figures, 1 table, Accepted by J. Phys.: Condens. Matte
Buckling instability for a charged and fluctuating semiflexible polymer
In this article we address the problem of Euler's buckling instability in a
charged semi-flexible polymer that is under the action of a compressive force.
We consider this instability as a phase transition and investigate the role of
thermal fluctuations in the buckling critical force. By performing molecular
dynamic simulations, we show that the critical force decreases when the
temperature increases. Repulsive electrostatic interaction in the finite
temperature is in competition with thermal fluctuations to increase the
buckling threshold
Dynamics of DNA Ejection From Bacteriophage
The ejection of DNA from a bacterial virus (``phage'') into its host cell is
a biologically important example of the translocation of a macromolecular chain
along its length through a membrane. The simplest mechanism for this motion is
diffusion, but in the case of phage ejection a significant driving force
derives from the high degree of stress to which the DNA is subjected in the
viral capsid. The translocation is further sped up by the ratcheting and
entropic forces associated with proteins that bind to the viral DNA in the host
cell cytoplasm. We formulate a generalized diffusion equation that includes
these various pushing and pulling effects and make estimates of the
corresponding speed-ups in the overall translocation process. Stress in the
capsid is the dominant factor throughout early ejection, with the pull due to
binding particles taking over at later stages. Confinement effects are also
investigated, in the case where the phage injects its DNA into a volume
comparable to the capsid size. Our results suggest a series of in vitro
experiments involving the ejection of DNA into vesicles filled with varying
amounts of binding proteins from phage whose state of stress is controlled by
ambient salt conditions or by tuning genome length.Comment: 17 pages, 5 figure
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