Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage

Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO ₂ ^— —O— chain changed for —O—PO ₂ ^— —CH₂—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)₁₁ with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The -ggt conformation of the modified linkages is highly preferred, temporary jumps to the -g-gt and ggt conformations were, however, observed.     

Superfield form of discrete gauge states in ĉ = 1 2d supergravity

A general formula for the discrete states (NeveuSchwarz sector) in N = 1 2D super-Liouville theory is written down in the world-sheet supersymmetric form. We then derive a set of gauge states at the discrete momenta. These discrete gauge states are shown to carry the ω_∞ charges and serve as the symmetry parameters in the old covariant quantization of the theory.     

A possibility of parallel and anti-parallel diffraction measurements on neutron diffractometer employing bent perfect crystal monochromator at the monochromatic focusing condition

In a conventional diffractometer having single monochromator, only one position, parallel position, is used for the diffraction experiment (i.e. detection) because the resolution property of the other one, anti-parallel position, is very poor. However, a bent perfect crystal (BPC) monochromator at monochromatic focusing condition can provide a quite flat and equal resolution property at both parallel and anti-parallel positions and thus one can have a chance to use both sides for the diffraction experiment. From the data of the FWHM and the Δd/d measured on three diffraction geometries (symmetric, asymmetric compression and asymmetric expansion), we can conclude that the simultaneous diffraction measurement in both parallel and anti-parallel positions can be achieved.     

RANDOM EDGE can be exponential on abstract cubes

We prove that RANDOM EDGE, the simplex algorithm that always chooses a random improving edge to proceed on, can take a mildly exponential number of steps in the model of abstract objective functions (introduced by Williamson Hoke [Completely unimodal numberings of a simple polytope, Discrete Appl. Math. 20 (1988) 69-81.] and by Kalai [A simple way to tell a simple polytope from its graph, J. Combin. Theory Ser. A 49(2) (1988) 381-383.] under different names). We define an abstract objective function on the n-dimensional cube for which the algorithm, started at a random vertex, needs at least exp(const·n^1/3) steps with high probability. The best previous lower bound was quadratic. So in order for RANDOM EDGE to succeed in polynomial time, geometry must help.     

Generation of 0.2-TW 5.5-fs optical pulses at 1 kHz using a differentially pumped hollow-fiber chirped-mirror compressor

Optical pulses with 1.1-mJ energy and 5.5-fs duration have been generated at 1-kHz repetition rate from a chirped pulse amplification Ti:Sapphire laser incorporating a differentially pumped hollow-fiber chirped-mirror compressor. The effects of self-focusing and multi-photon ionization during the beam propagation were minimized by differentially pumping the hollow fiber filled with neon. The spectral broadening at the hollow-fiber compressor was optimized by adjusting gas pressure, laser intensity, and laser chirp, covering from 540 nm to 950 nm. PACS 42.65.Jx; 42.65.Re     

“Slow” active control of combustion instabilities by modification of liquid fuel spray properties

This paper describes an experimental investigation of the feasibility of using “slow” active control approaches, which “instantaneously” change liquid fuel spray properties, to suppress combustion instabilities. The objective of this control approach was to break up the feedback between the combustion process heat release and combustor pressure oscillations that drive the instability by changing the characteristics of the combustion process (e.g., the characteristic combustion time). To demonstrate the feasibility of such control, this study used a proprietary fuel injector (Nanomiser^TM), which can vary its fuel spray properties, to investigate the dependence of acoustics–combustion process coupling, i.e., the driving of combustion instabilities, upon the fuel spray properties. This study showed that by changing the spray characteristics it is possible to significantly damp combustion instabilities. Furthermore, using combustion zone chemiluminescence distributions, which were obtained by Abel’s deconvolution synchronized with measured acoustic data, it has been shown that the instabilities were mostly driven midway between the combustor centerline and wall, a short distance downstream from the flame holder, where the mean axial flow velocity is approximately zero in the vortex near the flame holder. The results of this study strongly suggest that a “slow” active control system that employs controllable fuel injectors could be effectively used to prevent the onset of detrimental combustion instabilities.     

Stability control of the electrooptic effect with new maleimide copolymers containing photoreactive tricyanopyrrolidene‐based chromophores

New photocrosslinkable maleimide copolymers have been synthesized by the attachment of a tricyanopyrrolidene‐based chromophore. The 2‐(3‐cyano‐4‐(2‐{4‐[hexyl‐(6‐hydroxy‐hexyl)‐amino]‐phenyl}‐vinyl)‐5‐oxo‐1‐{4‐[4‐(3‐oxo‐3‐phenyl‐propenyl)‐ phenoxy]‐butyl}‐1,5‐dihydro‐pyrrol‐2‐ylidene)‐malononitrile chromophore exhibits nonlinear optical activity and contains a chalcone moiety that is sensitive to UV light (λ = 330–360 nm) for crosslink formation. The maleimide monomers have also been functionalized with chalcone moieties. The resultant copolymers exhibit great processability, and one of them shows a maximum electrooptic coefficient of 90 pm/V at 1300 nm. We could control the thermal stability of the electrooptic coefficient with the newly synthesized photoreactive copolymers successfully. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 531–542, 2007     

Bio-Plasmonics: Nano/micro Structure of Surface Plasmon Resonance Devices for Biomedicine

We have reported a novel design of surface plasmon resonance (SPR) device, which uses alternating dielectric layers to enhance the SPR signal quality and modulate its resonant position. Admittance loci method of thin film design has been used in the design of such a device. The use of biomolecular thin film, such as DNAs or Porteins, in this design can result in resonant condition of wavelength changes as well. Bio-plasmonics is proposed for the research and development of novel devices, which use biomolecules as a part of the plasmon oscillation system to actively interact with nano/micro structure.