130,661 research outputs found
Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime
No full textThe data provided here contains experimental results, all Matlab codes for statistical analysis and for generating figures in the paper.DNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for lambda -DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.National Institutes of Health (Grant No. R01-HG006851)Chuang, Hui-Min; Reifenberger, Jeff G.; Bhandari, Aditya Bikram; Dorfman, Kevin D. (2019). Data for: Extension distribution for DNA confined in a nanochannel near the Odijk regime. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/99cv-2243
Data from: The Odijk Regime in Slits
No full textTree, Douglas R; Reinhart, Wesley F; Dorfman, Kevin D. (2014). Data from: The Odijk Regime in Slits. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/163537
Data from: Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel
No full textReifenberger, Jeffrey G; Cao, Han; Dorfman, Kevin D. (2018). Data from: Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/193499
Data from: The backfolded Odijk regime for wormlike chains confined in rectangular nanochannels
No full textMuralidhar, Abhiram; Quevillon, Michael J.; Dorfman, Kevin D.. (2016). Data from: The backfolded Odijk regime for wormlike chains confined in rectangular nanochannels. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/178249
Data from: Resolution Limit for DNA Barcodes in the Odijk Regime
No full textFigs 3 and 5 in matlab .fig files. Figs 4 and 6 as raw data with matlab files to create the figures.Wang, Yanwei; Reinhart, Wes F; Tree, Douglas R; Dorfman, Kevin D. (2013). Data from: Resolution Limit for DNA Barcodes in the Odijk Regime. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/155320
Resolution limit for DNA barcodes in the Odijk regime
No full textWe develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of the DNA, simulations indicate that the theoretical predictions are reasonably accurate for channel widths up to two-thirds of the persistence length. Our results quantify the conjecture that DNA barcoding has kilobase pair resolution—provided the nanochannel lies in the Odijk regime
Application of the optimized Baxter model to the hard-core attractive Yukawa system
No full textWe perform Monte Carlo simulations on the hard-core attractive Yukawa system to test the optimized Baxter model that was introduced by Prinsen and Odijk [J. Chem. Phys. 121, 6525 (2004) ] to study a fluid phase of spherical particles interacting through a short-range pair potential. We compare the chemical potentials and pressures from the simulations with analytical predictions from the optimized Baxter model. We show that the model is accurate to within 10% over a range of volume fractions from 0.1 to 0.4, interaction strengths up to three times the thermal energy, and interaction ranges from 6% to 20% of the particle diameter, and performs even better in most cases. We furthermore establish the consistency of the model by showing that the thermodynamic properties of the Yukawa fluid computed via simulations may be understood on the basis of one similarity variable, the stickiness parameter defined within the optimized Baxter model. Finally, we show that the optimized Baxter model works significantly better than an often used, naive method determining the stickiness parameter by equating the respective second virial coefficients based on the attractive Yukawa and Baxter potentials.Applied Science
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Fast precise GPS positioning in the presence of ionospheric delays
No full textIn many geodetic (surveying) applications positions of points in the terrain need to be determined with high precision (cm-accuracy or even better). The Global Positioning System (GPS) is very suitable for this purpose. High positioning accuracy is in principle feasible when a relative measurement setup is used and in the processing procedure certain systematic errors in the GPS observations are properly taken into account. The largest of these errors is due to the propagation of the GPS signals through the ionosphere, the part of the atmosphere from about 80 km altitude. When the distance between the GPS receivers in the relative measurement setup is sufficiently short (e.g. a few km) it is known that these errors almost cancel, such that the positioning can be conducted using only a short time span of measurements, which is very favorable from an economical point of view. For longer distances the necessary time span increases enormously since unknown parameters for among others the ionospheric errors need to be estimated in the processing. In this thesis a procedure is outlined for the processing of relative GPS observations over medium distances (max. 50 km), while at the same time it should allow a user a short time span of measurements. An important requirement to this procedure is the availability of a permanent network of GPS reference stations. From the observations this permanent network collects, it is possible to generate information about the ionospheric delays, which a user can consequently apply to correct his own GPS observations. Much attention in the thesis is paid to the mathematical modelling aspects of this procedure.Civil Engineering and Geoscience
The Odijk Regime in Slits
No full textDe Gennes’ blob theory has been remarkably successful at describing weakly confined polymers in both slits and channels, and comparable results surround Odijk’s theory of deflection segments for strongly confined wormlike polymers in nanochannels. However, given the success of Odijk’s theory in channels, it is remarkable that there is no comprehensive theory for the simple case of a wormlike polymer strongly confined between two parallel plates. We propose such a theory by drawing inspiration from the existing literature on ideal wormlike chains in slits and Daoud and de Gennes’ idea of mapping a slit-confined chain to a two-dimensional chain. We postulate that the chain can be quantitatively described as a two-dimensional wormlike chain with a weak perturbation in the confining dimension due to deflection segments. By incorporating the effects of real chains, where the variable slit depth adds subtlety due to concomitant changes in the strength of excluded volume interactions, our theory predicts the existence of three distinct subregimes. We investigate the validity of our claims by performing Monte Carlo simulations of a slit-confined wormlike chain using an off-lattice implementation of the pruned–enriched Rosenbluth method. From these simulations, we find strong numerical evidence supporting our predictions, including the existence of subregimes within the Odijk regime
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