Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics

It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.     

Structure Features of 1,3,5-Tris(Diphenylphosphinoxidemethylene)Ben zene in Crystal and Solution on the Base of X-Ray,Dipole Moments and Quantum Chemical Analysis

Abstract

The molecular structure, polarity and conformations in solution of 1,3,5-tris(diphenylphosphinoxidemethy1ene)benzene 1,3,5-[Ph₂P(0)CH₂]₃C₆H₃ have been studied by X-ray, dipole moments and quantum chemistry methods. It have been shown, that in crystal molecule has the conformation in which two diphenylphosphinoxide fragments dispose on one and the same side, but the third - on the other side of central benzene ring plane with torsion angles C_SP2-C_SP2-C_SP3-P 60–80° and C_SP2-C_SP3-P=O about 50–70°. In solution conformational picture is more rich: side by side with the structures realized in crystal, conformations with all three diphenylphosphinoxide fragments disposed on one and the same side of central benzene ring plane with torsion angles C_SP2-C_SP2-C_SP3-P 70-90° and C_SP2-C_SP3-P=O about 70–75° become preferable.     

Optical detection of attosecond ionization induced by a few-cycle laser field in a transparent dielectric material

We observe an optical signature induced by the modulation of electron density inside a bulk transparent solid that is quasiperiodically ionized on an attosecond time scale by electric field peaks of a focused few-cycle laser pulse. The emitted optical signal resulting from the attosecond ionization dynamics is spatially, temporally and spectrally isolated from concomitant optical responses through the use of a noncollinear pump-probe technique. The method holds promise for developing an attosecond metrology for bulk solids, in which, unlike in the established attosecond metrology of gases and surfaces, direct detection of charged particles is unfeasible.     

Very-large-mode-area photonic bandgap Bragg fiber polarizing in a wide spectral range

A design of a polarizing all-glass Bragg fiber with a microstructure core has been proposed for the first time. This design provides suppression of high-order modes and of one of the polarization states of the fundamental mode. The polarizing fiber was fabricated by a new, simple method based on a combination of the modified chemical vapor deposition (MCVD) process and the rod-in-tube technique. The mode field area has been found to be about 870 μm2 near λ=1064 nm. The polarization extinction ratio better than 13 dB has been observed over a 33% wavelength range (from 1 to 1.4 μm) after propagation in a 1.7 m fiber piece bent to a radius of 70 cm.     

Compressibility of Gas Hydrates

Experimental data on the pressure dependence of unit cell parameters for the gas hydrates of ethane (cubic structure I, pressure range 0–2 GPa), xenon (cubic structure I, pressure range 0–1.5 GPa) and the double hydrate of tetrahydrofuran+xenon (cubic structure II, pressure range 0–3 GPa) are presented. Approximation of the data using the cubic Birch–Murnaghan equation, P=1.5B₀[(V₀/V)^7/3?(V₀/V)^5/3], gave the following results: for ethane hydrate V₀=1781 ų, B₀=11.2 GPa; for xenon hydrate V₀=1726 ų, B₀=9.3 GPa; for the double hydrate of tetrahydrofuran+xenon V₀=5323 ų, B₀=8.8 GPa. In the last case, the approximation was performed within the pressure range 0–1.5 GPa; it is impossible to describe the results within a broader pressure range using the cubic Birch–Murnaghan equation. At the maximum pressure of the existence of the double hydrate of tetrahydrofuran+xenon (3.1 GPa), the unit cell volume was 86 % of the unit cell volume at zero pressure. Analysis of the experimental data obtained by us and data available from the literature showed that 1) the bulk modulus of gas hydrates with classical polyhedral structures, in most cases, are close to each other and 2) the bulk modulus is mainly determined by the elasticity of the hydrogen‐bonded water framework. Variable filling of the cavities with guest molecules also has a substantial effect on the bulk modulus. On the basis of the obtained results, we concluded that the bulk modulus of gas hydrates with classical polyhedral structures and existing at pressures up to 1.5 GPa was equal to (9±2) GPa. In cases when data on the equations of state for the hydrates were unavailable, the indicated values may be recommended as the most probable ones.     

Synthesis of difurazanyl ethers from 4,4′‐dinitroazoxyfurazan

Nonselective attacks at the carbon bonded to a nitro group and carbon bonded to the N(O) atom of the azoxy group were observed in the reactions of 4,4′‐dinitroazoxyfurazan with bases and nucleophiles. A mechanism is presented to account for both of the pathways to products. A series of new difurazanyl ether derivatives was synthesized. © 2000 John Wiley & Sons, Inc. Heteroatom Chem 11:48–56, 2000