Spectral-interferometric study of nonlinear-spectronic similariton

By means of spectral interferometry we study properties of similaritons formed in a single-mode optical fiber without gain. Nonlinear-spectronic character of such similaritons leads to linearization of their chirp and spectral-temporal similarity, which may be useful for applications in ultrafast optics.     

Preparation and characterization of polyion-complexed Langmuir-Blodgett films containing an NLO chromophore

Polyion complexes formed by monolayers of quaternary ammonium amphiphiles containing the 4-nitro-4'-alkoxy azobenzene chromophore spread at the surface of aqueous solutions of a number of anionic polyelectrolytes were investigated. In general, pi-A isotherms were found to depend on the nature of the polyion present in the subphase, with monolayers of complexes involving polycarboxylates tending to exhibit larger limiting areas than those formed with polysulfonates or polysulfates. Monolayers of the polyion complexes can be transferred to hydrophilic solid substrates to yield Z-type LB films, although some peeling off for more than 10 layers is an impediment. X-ray reflectivity measurements indicate that relatively smooth and uniform films are obtained up to about 10 layers. Average layer thicknesses are, however, significantly smaller than extended molecular lengths, implying that the amphiphiles are strongly inclined from the surface normal. Polarized FT-IR measurements also indicate poor molecular orientation perpendicular to the surface. Preliminary SHG measurements for LB films of two systems, 12Q/CMC-Na and 12Q/PAA, confirm the presence of noncentrosymmetric out-of-plane chromophore ordering. Stable signals are observed for elevated temperatures up to 130 degrees C and for a period of 4 months at room temperature. To the best of our knowledge, this represents the first report of stable SHG in LB films of polyion complexes.     

Diagnostics of femtosecond laser pulses based on generation of nonlinear-dispersive similariton

We propose and test experimentally a method, alternative to the autocorrelation technique, for determination of the duration of femtosecond laser pulses. The method is based on generation of nonlinear-dispersive similariton in a passive optical fiber (without gain) and measuring its spectral width (or duration) determined by the power of the initial pulse.     

Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers

We address the question of what are the molecular mechanisms providing discrimination between seemingly similar counterions binding to various biomolecular surfaces. In the case of protein association with Na (+) and K (+) ions, recent works proposed that specificity of carboxylate functional groups interacting with these mobile ions rationalizes the observed ionic discrimination. We probe in this work whether similar arguments may be used to explain higher propensity of Na (+) ions to associate with DNA compared with K (+) ions, which was suggested by our simulations and some experiments. By comparing our extensive molecular dynamics simulations of Na (+) and K (+) distributions around a 16-base-pair DNA oligomer, [(CGAGGTTTAAACCTCG)] 2, with additional simulations where DNA is replaced by a "soup" of monomers (dimethylphosphate anion), we conclude that DNA specificity toward Na (+)/K (+) is not determined by the underlying functional group specificity. Instead, the collective effect of DNA charges drives larger Na (+) association. To gain additional microscopic insights into the mechanisms of specificity on ionic associations in these systems, we carried out energetic analysis of the association between Na (+) and K (+) with chloride and dimethylphosphate anions. The insights gained from our computational work shed light on a number of experiments on electrolyte solutions of monovalent salts and DNA.     

Character of similaritons formed in a single-mode fiber without gain

Based on the numerical and experimental studies, a nonlinear-spectronic character of similaritons formed in a single-mode optical fiber without gain is demonstrated. It is shown that the combined action of the Kerr-type nonlinearity and normal dispersion of the fiber leads to the formation of similaritons. The temporal envelop, spectral and phase profiles of such similaritons have a nearly parabolic shape in their central energy-carrying parts.     

A variational approach to the stochastic aspects of cellular signal transduction

Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process noisy signals. The essential difficulty associated with the master equation approach to solving the stochastic chemical kinetics problem is the enormous number of ordinary differential equations involved. In this work, we show how to achieve tremendous reduction in the dimensionality of specific reaction cascade dynamics by solving variationally an equivalent quantum field theoretic formulation of stochastic chemical kinetics. The present formulation avoids cumbersome commutator computations in the derivation of evolution equations, making the physical significance of the variational method more transparent. We propose novel time-dependent basis functions which work well over a wide range of rate parameters. We apply the new basis functions to describe stochastic signaling in several enzymatic cascades and compare the results so obtained with those from alternative solution techniques. The variational Ansatz gives probability distributions that agree well with the exact ones, even when fluctuations are large and discreteness and nonlinearity are important. A numerical implementation of our technique is many orders of magnitude more efficient computationally compared with the traditional Monte Carlo simulation algorithms or the Langevin simulations.     

Self-Bending of a Laser Beam in Photorefractive Crystals with Variable Nonlinearity Coefficient

The self-bending of a laser beam in photorefractive crystal is considered in the case in which the coefficient of photorefractive diffusion nonlinearity changes along deflection path. The bent trajectory is calculated analytically and the obtained result is compared with those reported before.     

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out ～3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms β-hairpins, H3 and H2B adopt α-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy.