How to accelerate protein search on DNA: Location and dissociation

One of the most important features of biological systems that controls their functioning is the ability of protein molecules to find and recognize quickly specific target sites on DNA. Although these phenomena have been studied extensively, detailed mechanisms of protein-DNA interactions during the search are still not well understood. Experiments suggest that proteins typically find their targets fast by combining three-dimensional and one-dimensional motions, and most of the searching time proteins are non-specifically bound to DNA. However these observations are surprising since proteins diffuse very slowly on DNA, and it seems that the observed fast search cannot be achieved under these conditions for single proteins. Here we propose two simple mechanisms that might explain some of these controversial observations. Using first-passage time analysis, it is shown explicitly that the search can be accelerated by changing the location of the target and by effectively irreversible dissociations of proteins. Our theoretical predictions are supported by Monte Carlo computer simulations

Radiation Pressure Dominate Regime of Relativistic Ion Acceleration

The electromagnetic radiation pressure becomes dominant in the interaction of the ultra-intense electromagnetic wave with a solid material, thus the wave energy can be transformed efficiently into the energy of ions representing the material and the high density ultra-short relativistic ion beam is generated. This regime can be seen even with present-day technology, when an exawatt laser will be built. As an application, we suggest the laser-driven heavy ion collider.Comment: 10 pages, 4 figure

In-Line-Test of Variability and Bit-Error-Rate of HfOx-Based Resistive Memory

Spatial and temporal variability of HfOx-based resistive random access memory (RRAM) are investigated for manufacturing and product designs. Manufacturing variability is characterized at different levels including lots, wafers, and chips. Bit-error-rate (BER) is proposed as a holistic parameter for the write cycle resistance statistics. Using the electrical in-line-test cycle data, a method is developed to derive BERs as functions of the design margin, to provide guidance for technology evaluation and product design. The proposed BER calculation can also be used in the off-line bench test and build-in-self-test (BIST) for adaptive error correction and for the other types of random access memories.Comment: 4 pages. Memory Workshop (IMW), 2015 IEEE Internationa

Iterative graph cuts for image segmentation with a nonlinear statistical shape prior

Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object. When a collection of possible shapes is available, the specification of a shape prior using kernel density estimation is a natural technique. Unfortunately, energy functionals arising from kernel density estimation are of a form that makes them impossible to directly minimize using efficient optimization algorithms such as graph cuts. Our main contribution is to show how one may recast the energy functional into a form that is minimizable iteratively and efficiently using graph cuts.Comment: Revision submitted to JMIV (02/24/13

Nonlinear Lattice Waves in Random Potentials

Localization of waves by disorder is a fundamental physical problem encompassing a diverse spectrum of theoretical, experimental and numerical studies in the context of metal-insulator transition, quantum Hall effect, light propagation in photonic crystals, and dynamics of ultra-cold atoms in optical arrays. Large intensity light can induce nonlinear response, ultracold atomic gases can be tuned into an interacting regime, which leads again to nonlinear wave equations on a mean field level. The interplay between disorder and nonlinearity, their localizing and delocalizing effects is currently an intriguing and challenging issue in the field. We will discuss recent advances in the dynamics of nonlinear lattice waves in random potentials. In the absence of nonlinear terms in the wave equations, Anderson localization is leading to a halt of wave packet spreading. Nonlinearity couples localized eigenstates and, potentially, enables spreading and destruction of Anderson localization due to nonintegrability, chaos and decoherence. The spreading process is characterized by universal subdiffusive laws due to nonlinear diffusion. We review extensive computational studies for one- and two-dimensional systems with tunable nonlinearity power. We also briefly discuss extensions to other cases where the linear wave equation features localization: Aubry-Andre localization with quasiperiodic potentials, Wannier-Stark localization with dc fields, and dynamical localization in momentum space with kicked rotors.Comment: 45 pages, 19 figure

Perturbative analysis of wave interactions in nonlinear systems

This work proposes a new way for handling obstacles to asymptotic integrability in perturbed nonlinear PDEs within the method of Normal Forms - NF - for the case of multi-wave solutions. Instead of including the whole obstacle in the NF, only its resonant part is included, and the remainder is assigned to the homological equation. This leaves the NF intergable and its solutons retain the character of the solutions of the unperturbed equation. We exploit the freedom in the expansion to construct canonical obstacles which are confined to te interaction region of the waves. Fo soliton solutions, e.g., in the KdV equation, the interaction region is a finite domain around the origin; the canonical obstacles then do not generate secular terms in the homological equation. When the interaction region is infifnite, or semi-infinite, e.g., in wave-front solutions of the Burgers equation, the obstacles may contain resonant terms. The obstacles generate waves of a new type, which cannot be written as functionals of the solutions of the NF. When an obstacle contributes a resonant term to the NF, this leads to a non-standard update of th wave velocity.Comment: 13 pages, including 6 figure

Metadevice for intensity modulation with sub-wavelength spatial resolution

Effectively continuous control over propagation of a beam of light requires light modulation with pixelation that is smaller than the optical wavelength. Here we propose a spatial intensity modulator with sub-wavelength resolution in one dimension. The metadevice combines recent advances in reconfigurable nanomembrane metamaterials and coherent all-optical control of metasurfaces. It uses nanomechanical actuation of metasurface absorber strips placed near a mirror in order to control their interaction with light from perfect absorption to negligible loss, promising a path towards dynamic beam diffraction, light focusing and holography without unwanted diffraction artefacts

Wavefront shaping with disorder-engineered metasurfaces

Recently, wavefront shaping with disordered media has demonstrated optical manipulation capabilities beyond those of conventional optics, including extended volume, aberration-free focusing and subwavelength focusing. However, translating these capabilities to useful applications has remained challenging as the input–output characteristics of the disordered media (P variables) need to be exhaustively determined via O(P) measurements. Here, we propose a paradigm shift where the disorder is specifically designed so its exact input–output characteristics are known a priori and can be used with only a few alignment steps. We implement this concept with a disorder-engineered metasurface, which exhibits additional unique features for wavefront shaping such as a large optical memory effect range in combination with a wide angular scattering range, excellent stability, and a tailorable angular scattering profile. Using this designed metasurface with wavefront shaping, we demonstrate high numerical aperture (NA > 0.5) focusing and fluorescence imaging with an estimated ~2.2 × 10^8 addressable points in an ~8 mm field of view

Temperature dependence of plasmonic terahertz absorption in grating-gate gallium-nitride transistor structures

Strong plasmon resonances have been observed in the terahertz transmission spectra (1-5 THz) of large-area slit-grating-gate AlGaN/GaN-based high-electron-mobility transistor (HEMT) structures at temperatures from 10 to 170 K. The resonance frequencies correspond to the excitation of plasmons with wave vectors equal to the reciprocal lattice vectors of the metal grating, which serves both as a gate electrode for the HEMT and a coupler between plasmons and incident terahertz radiation. Wide tunability of the resonances by the applied gate voltage demonstrates potential of these devices for terahertz applications