@article{stellwagen01a,
        title = {Measuring the translational diffusion coefficients of small DNA molecules
	by capillary electrophoresis},
        author = {N. C. Stellwagen and S. Magnusdottir and C. Gelfi and P. G. Righetti},
        journal = {Biopolymers},
        month = {April},
        number = 4,
        pages = {390--397},
        volume = 58,
        year = 2001,
        timestamp = {2007.06.11},
	de = {DNA; translational diffusion coefficients; capillary electrophoresis},
	sn = {0006-3525},
	owner = {grass},
	ut = {ISI:000167129100004},
	abstract = {The apparent translational diffusion coefficients of four 20 base
	pair (bp) DNA oligonucleotides with different sequences have been
	measured by capillary electrophoresis. using the stopped migration
	method The diffusion coefficients of the four oligomers were equal
	within experimental error, and averaged (120 +/- 10) x 10(-8) cm(2)
	s(-1) in 40 mM Tris-acetate-EDTA buffer at 25 degreesC. Since this
	value is nearly identical to the translational diffusion coefficient
	determined for a different 20-bp oligomer using other methods, the
	stopped migration method can accurately measure the diffusion coefficients
	of small DNA oligomers. The apparent diffusion coefficient of a 118-bp
	DNA restriction fragment was also measured by the stopped migration
	method. However. the observed value was similar to 25% larger than
	expected from other measurements, possibly because the diffusion
	coefficients of larger DNA molecules are somewhat dependent on the
	ionic strength of the solution. (C) 2001 John Wiley & Sons, Inc.
	Biopolymers 58: 390-397, 2001.},
	biburl = {http://www.bibsonomy.org/bibtex/2709c3dfd280810ec232fefd13c170c47/kaigrass},
	keywords = {FREE MODEL; DISPERSION; SALT SOLUTION ZONE LIGHT-SCATTERING; PROTEINS; GEL; MOBILITY; PEPTIDES; DYNAMIC ELECTROPHORESIS; FRAGMENTS;}
}

@article{slater03a,
        title = {The theory of {DNA} separation by capillary electrophoresis},
        author = {G. W. Slater and M. Kenward and L. C. McCormick and M. G. Gauthier},
        journal = {Current Opinion in Biotechnology},
        month = {February},
        number = 1,
        pages = {58--64},
        volume = 14,
        year = 2003,
        timestamp = {2006.11.07},
	pdf = {slater03a.pdf},
	owner = {grass},
	comment = {outstanding},
	abstract = {The Human Genome has been sequenced in large part owing to the invention
	of capillary electrophoresis. Although this technology has matured
	enough to allow such amazing achievements, the physical mechanisms
	at play during separation have yet to be completely understood and
	optimized. Recently, new separation regimes and new physical mechanisms
	have been investigated. The use of free-flow electrophoresis and
	new modes of pulsed-field electrophoresis have been suggested, while
	we have observed a shift towards single nucleotide polymorphism analysis
	and microchip technologies. A strong theoretical basis remains essential
	for the efficient development of new methods.},
	biburl = {http://www.bibsonomy.org/bibtex/216793421ab53a9776c09e0739630d8be/kaigrass},
	keywords = {MODEL; 3-DIMENSIONAL GELS; OGSTON MOLECULES; POLYMER-SOLUTIONS; REPTATION DIFFUSION; GEL-ELECTROPHORESIS; SINGLE-STRANDED-DNA; SOLVABLE MOBILITY; ENTANGLED review, experiment, theory, OBSTRUCTION-SCALING}
}

@article{slater02b,
        title = {Theory of {DNA} electrophoresis (similar to 1999-2002(1)/(2))},
        author = {G. W. Slater and S. Guillouzic and M. G. Gauthier and J. F. Mercier and M. Kenward and L. C. McCormick and F. Tessier},
        journal = {Electrophoresis},
        month = {November},
        number = {22-23},
        pages = {3791--3816},
        volume = 23,
        year = 2002,
        timestamp = {2006.11.07},
	pdf = {slater02b.pdf},
	owner = {grass},
	comment = {outstanding},
	abstract = {Over the last two decades, the introduction of new methods such as
	pulsed-field gel electrophoresis and capillary array electrophoresis
	has made it possible to map and sequence entire genomes, including
	our own. The development-of these experimental methods has been helped
	by the progress of theoretical and computational sciences, and the
	interactions between these three modi operandi of modern science
	are still pushing the limits of our technologies. We now see a clear
	trend towards proteomics and microfluidic (even nanofluidic!) devices.
	In this review, we take a look at the progress of the field over
	the last 3 years using the glasses of the theoretical scientist and
	focusing mostly on new ideas and concepts. About a dozen different
	subfields are discussed and reviewed. We conclude by giving a commented
	list of some of the best review articles published over the last
	2-3 years.},
	biburl = {http://www.bibsonomy.org/bibtex/24fbe0ee292432cb0e68900b2c626d985/kaigrass},
	keywords = {MODEL; METHOD; MOLECULAR BOND CAPILLARY-ELECTROPHORESIS; MONTE-CARLO-SIMULATION SOLUTION OGSTON POLYMER-SOLUTIONS; FLUCTUATION SINGLE-STRANDED-DNA; ULTRADILUTE DIFFUSION-COEFFICIENTS; COMPOSITE PERIODIC EXACT OBJECTS; SOLVABLE BOUNDARY-CONDITIONS; review, experiment, theory, OBSTRUCTION-SCALING}
}

@article{slater00a,
        title = {Theory of {DNA} electrophoresis: {A} look at some current challenges},
        author = {G. W. Slater and C. Desrulsseaux and S. J. Hubert and J. F. Mercier and J. Labrie and J. Boileau and F. Tessier and M. P. Pepin},
        journal = {Electrophoresis},
        month = {December},
        number = 18,
        pages = {3873--3887},
        volume = 21,
        year = 2000,
        timestamp = {2006.11.07},
	pdf = {slater00a.pdf},
	owner = {grass},
	comment = {outstanding},
	abstract = {Although electrophoresis is one of the basic methods of the modern
	molecular biology laboratory, new ideas are being suggested at an
	accelerated rate, in large part because of the pressing demands of
	the biomedical community. Although we now have, at least for some
	methods, a fairly good theoretical understanding of the physical
	mechanisms that lead to the observed peak spacings, widths and shapes,
	this knowledge is often too qualitative to be used to guide further
	technical developments and improvements. In this article, we review
	some selected elements of the current state of our theoretical ignorance,
	focusing mostly on DNA electrophoresis, and we offer several suggestions
	for further theoretical investigations.},
	biburl = {http://www.bibsonomy.org/bibtex/20649bd7b2ed120342a4698f20bbd7d05/kaigrass},
	keywords = {MODEL; AGAROSE CAPILLARY-ELECTROPHORESIS; OGSTON POLYMER-SOLUTIONS; GEL-ELECTROPHORESIS; SINGLE-STRANDED-DNA; DNA; ULTRADILUTE POLYMER; END-LABELED PULSED-FIELD TRAPPING LOW-VISCOSITY SOLVABLE GELS ELECTROPHORESIS; review, experiment, theory,}
}

@article{jendrejack02a,
        title = {Stochastic simulations of DNA in flow: Dynamics and the effects of
	hydrodynamic interactions},
        author = {R. M. Jendrejack and J. J. de Pablo and M. D. Graham},
        journal = {Journal Of Chemical Physics},
        month = {May},
        number = 17,
        pages = {7752--7759},
        volume = 116,
        year = 2002,
        timestamp = {2007.06.11},
	sn = {0021-9606},
	owner = {grass},
	ut = {ISI:000175068800046},
	abstract = {We present a fully parametrized bead-spring chain model for stained
	lambda-phage DNA. The model accounts for the finite extensibility
	of the molecule, excluded volume effects, and fluctuating hydrodynamic
	interactions (HI). Parameters are determined from equilibrium experimental
	data for 21 mum stained lambda-phage DNA, and are shown to quantitatively
	predict the non-equilibrium behavior of the molecule. The model is
	then used to predict the equilibrium and nonequilibrium behavior
	of DNA molecules up to 126 mum. In particular, the HI model gives
	results that are in quantitative agreement with experimental diffusivity
	data over a wide range of molecular weights. When the bead friction
	coefficient is fit to the experimental relaxation time at a particular
	molecular weight, the stretch in shear and extensional flows is adequately
	predicted by either a free-draining or HI model at that molecular
	weight, although the fitted bead friction coefficients for the two
	models differ significantly. In shear flow, we find two regimes at
	high shear rate (gamma) that follow different scaling behavior. In
	the first, the viscosity and first normal stress coefficient scale
	roughly as gamma(-6/11) and gamma(-14/11), respectively. At higher
	shear rates, these become gamma(-2/3) and gamma(-4/3). These regimes
	are found for both free-draining and HI models and can be understood
	based on scaling arguments for the diffusion of chain ends. (C) 2002
	American Institute of Physics.},
	biburl = {http://www.bibsonomy.org/bibtex/27d3b84c93752a744c1cc952a5b3671bd/kaigrass},
	keywords = {MODEL; POLYMERS; FLEXIBLE MOTION; FLOW; MOLECULES; SHEAR-FLOW; CHAIN; FIELD ELASTICITY; DYNAMICS; ELONGATIONAL SINGLE-POLYMER}
}