Solid phase extraction of DNA from biological samples in a post-based, high surface area poly(methyl methacrylate) (PMMA) microdevice

This work describes the performance of poly(methyl methacrylate) (PMMA) microfluidic DNA purification devices with embedded microfabricated posts, functionalized with chitosan. PMMA is attractive as a substrate for creating high surface area (SA) posts for DNA capture because X-ray lithography can be exploited for extremely reproducible fabrication of high SA structures. However, this advantage is offset by the delicate nature of the posts when attempting bonding to create a closed system, and by the challenge of functionalizing the PMMA surface with a group that invokes DNA binding. Methods are described for covalent functionalization of the post surfaces with chitosan that binds DNA in a pH-dependent manner, as well as for bonding methods that avoid damaging the underlying post structure. A number of geometric posts designs are explored, with the goal of identifying post structures that provide the requisite surface area without a concurrent rise in fluidic resistance that promotes device failure. Initial proof-of-principle is shown by recovery of prepurified human genomic DNA (hgDNA), with real-world utility illustrated by purifying hgDNA from whole blood and demonstrating it to be PCR-amplifiable.     

The steady boundary value problem for charged incompressible fluids: PNP/Navier–Stokes systems

The initial-boundary value problem for the Poisson–Nernst–Planck/Navier–Stokes model was investigated in [J.W. Jerome, R. Sacco, Global weak solutions for an incompressible charged fluid with multi-scale couplings: initial-boundary-value problem, Nonlinear Anal. 71 (2009) e2487–e2497], where an existence theory was demonstrated, based upon Rothe’s method of horizontal lines. In this article, the steady case is considered, and the existence of a weak solution is established for the boundary-value problem. This solution satisfies a weak maximum principle for the concentrations relative to the boundary values. As noted in the above-mentioned citation, the model assumes significance because of its connection to the electrophysiology of the cell, including neuronal cell monitoring and microfluidic devices in biochip technology. The model has also been used in other applications, including electro-osmosis. The steady model is especially important in ion channel modeling, because the channel remains open for milliseconds, and the transients appear to decay on the scale of tens of nanoseconds.     

The N4 molecule and the N3 + ion

The possibility of the nitrogen molecule forming a stable dimer is investigated. Through ab initio calculations in an extended contracted-gaussian basis, it is demonstrated that N₄ in tetrahedral geometry and N₃ ⁺ in D _3h geometry are local minimum points on their respective internuclear potential energy surfaces. The N₄ molecule is considerably higher in energy than two ground-state N₂ molecules and some study of the barrier for N₄ decomposition has been made. The bond lengths and force constants for the two systems are shown to be similar to their hydrocarbon counterparts, C₄H₄ and C₃H₃ ⁺, tetrahedrane and cyclopropenyl cation. Other related systems are discussed as well.     

Towards conformationally dependent redox-responsive molecular switches. New polyferrocene bis benzo crown ether receptors

New polyferrocene bis benzo-15-crown-5 ligands have been prepared and shown to form 1:1 intramolecular sandwich complexes with the potassium cation. Electrochemical investigations reveal that both receptors undergo small anodic perturbations of the respective ferrocene-ferrocenium redox couples in the presence of alkali metal cations.     

Kernel energy method: Basis functions and quantum methods

The kernel energy method (KEM) has been illustrated with peptides and has been shown to reduce the computational difficulty associated with obtaining ab initio quality quantum chemistry results for large biological compounds. In a recent paper, the method was illustrated by application to 15 different peptides, ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate Hartree–Fock (HF) molecular energies within the model, using Slater‐type orbital (STO)‐3G basis functions. A question arises concerning whether the results obtained from the use of KEM are wholly dependent on the STO‐3G basis functions that were employed, because of their relative simplicity, in the first applications. In the present work, it is shown that the accuracy of KEM does not depend on a particular choice of basis functions. This is done by calculating the ground‐state energy of a representative peptide, ADPGV7B, containing seven amino acid residues, using seven different commonly employed basis function sets, ranging in size from small to medium to large. It is shown that the accuracy of the KEM does not vary in any systematic way with the size or mathematical completeness of the basis set used, and good accuracy is maintained over the entire variety of basis sets that have been tested. Both approximate HF and density functional theory (DFT) calculations are made. We conclude that the accuracy inherent in the KEM is not dependent on a particular choice of basis functions. The first application, to 15 different peptides mentioned above, employed only HF calculations. A second question that arises is whether the results obtained with the use of KEM will be accurate only within the HF approximation. Therefore, in the present work we also study whether KEM is applicable across a variety of quantum computational methods, characterized by differing levels of accuracy. The peptide, Zaib4, containing 74 atoms, was used to calculate its energy at seven different levels of accuracy. These include the semi‐empirical methods, AM1 and PM5, a DFT B3LYP model, and ab initio HF, MP2, CID, and CCSD calculations. KEM was found to be widely applicable across the spectrum of quantum methods tested. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

An analysis of carrier-mediated photodiffusion membranes

Reversible photochromic reactions can be combined with carrier-mediated transport in partially illuminated membranes to achieve very high degrees of flux enhancement. Transport across these membranes can be achieved even against a concentration gradient. Coupled systems of non-linear diffusion-reaction equations for these membranes were solved using the technique of orthogonal collocation on finite elements to study and optimize the transport across them. The results indicate that the efficiency of light utilization is maximum for thin membranes at low degrees of illumination. Carrier-mediated photodiffusion membranes in combination with a fuel cell can be used for the storage of solar energy.     

Molecular dynamics calculations of the hard-sphere equation of state

The equation of state of the hard-sphere fluid is studied by a Monte Carlomolecular dynamics method for volumes ranging from 25V ₀ to 1.6V ₀ , whereV ₀ is the close-packed volume, and for system sizes from 108 to 4000 particles. TheN dependence of the equation of state is compared to the theoretical dependence given by Salsburg for theNPT ensemble, after correction for the ensemble difference, in order to obtain estimates for the thermodynamic limit. The observed values of the pressure are compared with both the [3/2] and the [2/3] Padé approximants to the virial series, using Kratky's value for the fifth virial coefficientB ₅ and choosingB ₆ andB ₇, to obtain a least-squares fit. The resulting values ofB ₆ andB ₇ lie within the uncertainties of the Ree-Hoover-Kratky Monte Carlo estimates for these virial coefficients. The values ofB ₈,B ₉, andB ₁₀ predicted by our optimal [3/2] approximant are also reported. Finally, the Monte Carlo-molecular dynamics equation of state is compared with a number of analytic expressions for the hard-sphere equation of state.Work supported by the Office of Basic Energy Sciences, U.S. Department of Energy.     

Amperometric bienzyme electrode for l-carnitine

An electrochemical sensor with two soluble enzymes allows assay of 0.1–10 mM, l- carnitine with an accuracy of 2%. The assay takes about 2 min. The first enzyme, carnitine dehydrogenase, catalyzes the oxidation of l-carnitine by NAD⁺. The NADH formed is oxidized by hexacyanoferrate(III) in a reaction catalyzed by diaphorase, and the hexacyanoferrate(II) produced is oxidized by electrolysis at 0.3 V. The sensor can be used for several days.