1,173 research outputs found
Feasibility study into a computational approach for marine propeller noise and cavitation modelling
Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles
We investigate unfolding/folding force kinetics in DNA hairpins exhibiting
two and three states with newly designed short dsDNA handles (29 bp) using
optical tweezers. We show how the higher stiffness of the molecular setup
moderately enhances the signal-to-noise ratio (SNR) in hopping experiments as
compared to conventional long handles constructs (approximately 700 bp). The
shorter construct results in a signal of higher SNR and slower
folding/unfolding kinetics, thereby facilitating the detection of otherwise
fast structural transitions. A novel analysis of the elastic properties of the
molecular setup, based on high-bandwidth measurements of force fluctuations
along the folded branch, reveals that the highest SNR that can be achieved with
short handles is potentially limited by the marked reduction of the effective
persistence length and stretch modulus of the short linker complex.Comment: Main paper: 20 pages and 6 figures. Supplementary Material: 25 page
Analysis of and workarounds for element reversal for a finite element-based algorithm for warping triangular and tetrahedral meshes
We consider an algorithm called FEMWARP for warping triangular and
tetrahedral finite element meshes that computes the warping using the finite
element method itself. The algorithm takes as input a two- or three-dimensional
domain defined by a boundary mesh (segments in one dimension or triangles in
two dimensions) that has a volume mesh (triangles in two dimensions or
tetrahedra in three dimensions) in its interior. It also takes as input a
prescribed movement of the boundary mesh. It computes as output updated
positions of the vertices of the volume mesh. The first step of the algorithm
is to determine from the initial mesh a set of local weights for each interior
vertex that describes each interior vertex in terms of the positions of its
neighbors. These weights are computed using a finite element stiffness matrix.
After a boundary transformation is applied, a linear system of equations based
upon the weights is solved to determine the final positions of the interior
vertices. The FEMWARP algorithm has been considered in the previous literature
(e.g., in a 2001 paper by Baker). FEMWARP has been succesful in computing
deformed meshes for certain applications. However, sometimes FEMWARP reverses
elements; this is our main concern in this paper. We analyze the causes for
this undesirable behavior and propose several techniques to make the method
more robust against reversals. The most successful of the proposed methods
includes combining FEMWARP with an optimization-based untangler.Comment: Revision of earlier version of paper. Submitted for publication in
BIT Numerical Mathematics on 27 April 2010. Accepted for publication on 7
September 2010. Published online on 9 October 2010. The final publication is
available at http://www.springerlink.co
Corepressors: custom tailoring and alterations while you wait
A diverse cadre of metazoan transcription factors mediate repression by recruiting protein complexes containing the SMRT (silencing mediator of retinoid and thyroid hormone receptor) or N-CoR (nuclear receptor corepressor) corepressors. SMRT and N-CoR nucleate the assembly of still larger corepressor complexes that perform the specific molecular incantations necessary to confer transcriptional repression. Although SMRT and N-CoR are paralogs and possess similar molecular architectures and mechanistic strategies, they nonetheless exhibit distinct molecular and biological properties. It is now clear that the functions of both SMRT and N-CoR are further diversified through alternative mRNA splicing, yielding a series of corepressor protein variants that participate in distinctive transcription factor partnerships and display distinguishable repression properties. This review will discuss what is known about the structure and actions of SMRT, N-CoR, and their splicing variants, and how alternative splicing may allow the functions of these corepressors to be adapted and tailored to different cells and to different developmental stages
The effect of layer number and substrate on the stability of graphene under MeV proton beam irradiation
The use of graphene electronics in space will depend on the radiation
hardness of graphene. The damage threshold of graphene samples, subjected to 2
MeV proton irradiation, was found to increase with layer number and also when
the graphene layer was supported by a substrate. The thermal properties of
graphene as a function of the number of layers or as influenced by the
substrate argue against a thermal model for the production of damage by the ion
beam. We propose a model of intense electronically-stimulated surface
desorption of the atoms as the most likely process for this damage mechanism.Comment: 20 pages, 5 figure
Measuring Temperature Gradients over Nanometer Length Scales
When a quantum dot is subjected to a thermal gradient, the temperature of
electrons entering the dot can be determined from the dot's thermocurrent if
the conductance spectrum and background temperature are known. We demonstrate
this technique by measuring the temperature difference across a 15 nm quantum
dot embedded in a nanowire. This technique can be used when the dot's energy
states are separated by many kT and will enable future quantitative
investigations of electron-phonon interaction, nonlinear thermoelectric
effects, and the effciency of thermoelectric energy conversion in quantum dots.Comment: 6 pages, 5 figure
Theory of biopolymer stretching at high forces
We provide a unified theory for the high force elasticity of biopolymers
solely in terms of the persistence length, , and the monomer spacing,
. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely
Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the
Worm-like Chain (WLC) is a better model. We show that can be estimated
from the force extension curve (FEC) at the extension
(normalized by the contour length of the biopolymer). After validating the
theory using simulations, we provide a quantitative analysis of the FECs for a
diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and
unstructured PEVK domain of titin) for . The success of a specific
polymer model (FJC or WLC) to describe the FEC of a given biopolymer is
naturally explained by the theory. Only by probing the response of biopolymers
over a wide range of forces can the -dependent elasticity be fully
described.Comment: 20 pages, 4 figure
Change in hardness of an as-cast and softening heat-treated low-gold-content alloy for bonding porcelain by simulated porcelain firing and its mechanism
Co-production of hydrogen and ethanol from glucose in Escherichia coli by activation of pentose-phosphate pathway through deletion of phosphoglucose isomerase (pgi) and overexpression of glucose-6-phosphate dehydrogenase (zwf) and 6-phosphogluconate dehydrogenase (gnd)
Background: Biologically, hydrogen (H-2) can be produced through dark fermentation and photofermentation. Dark fermentation is fast in rate and simple in reactor design, but H-2 production yield is unsatisfactorily low as < 4 mol H-2/ mol glucose. To address this challenge, simultaneous production of H-2 and ethanol has been suggested. Co-production of ethanol andH(2) requires enhanced formation of NAD(P) H during catabolism of glucose, which can be accomplished by diversion of glycolytic flux from the Embden-Meyerh-of-Parnas (EMP) pathway to the pentose-phosphate (PP) pathway in Escherichia coli. However, the disruption of pgi (phosphoglucose isomerase) for complete diversion of carbon flux to the PP pathway made E. coli unable to grow on glucose under anaerobic condition. Results: Here, we demonstrate that, when glucose-6-phosphate dehydrogenase (Zwf) and 6-phosphogluconate dehydrogenase (Gnd), two major enzymes of the PP pathway, are homologously overexpressed, E. coli.pgi can recover its anaerobic growth capability on glucose. Further, with additional deletions of Delta hycA,Delta hyaAB,Delta hybBC,Delta ldhA, and Delta frdAB, the recombinant.pgi mutant could produce 1.69 mol H-2 and 1.50 mol ethanol from 1 mol glucose. However, acetate was produced at 0.18 mol mol(-1) glucose, indicating that some carbon is metabolized through the Entner-Doudoroff (ED) pathway. To further improve the flux via the PP pathway, heterologous zwf and gnd from Leuconostoc mesenteroides and Gluconobacter oxydans, respectively, which are less inhibited by NADPH, were overexpressed. The new recombinant produced more ethanol at 1.62 mol mol(-1) glucose along with 1.74 mol H-2 mol(-1) glucose, which are close to the theoretically maximal yields, 1.67 mol mol(-1) each for ethanol andH(2). However, the attempt to delete the ED pathway in the.pgi mutant to operate the PP pathway as the sole glycolytic route, was unsuccessful. Conclusions: By deletion of pgi and overexpression of heterologous zwf and gnd in E. coli Delta hycA Delta hyaAB Delta hybBC Delta ldhA Delta frdAB, two important biofuels, ethanol andH(2), could be successfully co-produced at high yields close to their theoretical maximums. The strains developed in this study should be applicable for the production of other biofuels and biochemicals, which requires supply of excessive reducing power under anaerobic conditions
Negative Thermal Expansion Coefficient of Graphene Measured by Raman Spectroscopy
The thermal expansion coefficient (TEC) of single-layer graphene is estimated
with temperature-dependent Raman spectroscopy in the temperature range between
200 and 400 K. It is found to be strongly dependent on temperature but remains
negative in the whole temperature range, with a room temperature value of
-8.0x10^{-6} K^{-1}. The strain caused by the TEC mismatch between graphene and
the substrate plays a crucial role in determining the physical properties of
graphene, and hence its effect must be accounted for in the interpretation of
experimental data taken at cryogenic or elevated temperatures.Comment: 17 pagese, 3 figures, and supporting information (4 pages, 3
figures); Nano Letters, 201
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