Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories

An efficient method for simulating continuous-wave electron spin resonance spectra (ESR) of molecules labeled with two dipolar-coupled nitroxides from trajectories of the molecular motion is presented. Two approximate treatments of the dipolar spin evolution, resulting in significantly shorter simulation times, are examined in order to determine their range of applicability. The approach is illustrated in the context of a double-helical B-DNA. ESR spectra for DNA undergoing anisotropic global diffusion and internal stretching dynamics are calculated for three different labeling geometries with the spin labels bracketing, respectively, three, two and one base pairs. While multifrequency spectra of all three labeling schemes are very sensitive to DNA tumbling, the last one is found to be most informative about the local DNA dynamics.     

Metal-Chelating Nanopolymers for Antibody Purification from Human Plasma

The purification of immunoglobulin G (IgG) from human plasma was performed by using a novel metal-chelated adsorbent with nano size. The non-porous nanoparticles were produced by surfactant free emulsion polymerization of ethylene glycol dimethacrylate (EDMA) and 2-methacryloylamidohistidine (MAH). Then, Cu(II) ions were chelated on the nanoparticles. The nano-poly(EDMA-MAH) nanoparticles were characterized by Fourier transform infrared, scanning electron microscope, atomic force microscope and elemental analysis. The non-porous nanoparticles were spherical form and have 100?C250?nm size distribution. The maximum IgG adsorption capacity of the Cu(II) chelated nanoparticles was found to be 463?mg/g polymer at pH 7.0 in HEPES buffer. Desorption of IgG was performed by 1.0?M NaCl and desorption rate was found to be 97?%. IgG was obtained from human plasma with purity of 94?% (up to 578?mg/g polymer). The non-porous nanoparticles allowed one-step purification of IgG from human plasma.     

Crystal Structures of Tetrakis‐(4‐chlorophenylthio)‐butatriene and Tetrakis‐(tert‐butylthio)‐butatriene

Tetrakis‐(4‐chlorophenylthio)‐butatriene (3a) and tetrakis‐(tert‐butylthio)‐butatriene (3b) were synthesized, and their crystal structures were determined. The compound 3a is monoclinic, space group P2₁/c, a=6.9785(8), b=8.6803(9), c=22.884(2) Å, β=93.887(6)^o, V=1383.0(3) ų, Z=2. The compound 3b is monoclinic, space group P2₁/n, a=11.0615(6), b=10.8507(4), c=11.2717(6) Å, β =116.427(2)^o, V=1211.5(1) ų, Z=4. The title compounds 3a and 3b reside on an inversion center so that only half of the molecule is crystallographically unique. Both compounds are not planar. The crystal structures of 3a and 3b have cumulated double bonds. The C7–C8–C8ⁱ and C5–C6–C6ⁱ angles that show the linearity in both structures, respectively, are 176.4(3)° in 3a and 175.6(2)° in 3b.     

Euclidean realizations of Mauldin–Williams graphs

“Graph-directed” fractals are collections of metric spaces, each of which can be expressed as a union of several scaled copies of spaces from the collection. They give rise to weighted, directed graphs where the term comes from. We show in this note that any (finite) weighted, directed graph (with weights between 0 and 1) can be realized in a Euclidean space in the sense that, starting from the graph one can define a system of similitudes (with the similarity ratios being the given weights) on an appropriate Euclidean space. The point is that these maps satisfy a certain property (called the open set condition) so that the theory of Mauldin–Williams can be applied to compute the dimension of the emerging fractals. Additionally, we give a novel example of a system of graph-directed fractals.     

A Bilevel p-median model for the planning and protection of critical facilities

The bilevel p-median problem for the planning and protection of critical facilities involves a static Stackelberg game between a system planner (defender) and a potential attacker. The system planner determines firstly where to open p critical service facilities, and secondly which of them to protect with a limited protection budget. Following this twofold action, the attacker decides which facilities to interdict simultaneously, where the maximum number of interdictions is fixed. Partial protection or interdiction of a facility is not possible. Both the defender’s and the attacker’s actions have deterministic outcome; i.e., once protected, a facility becomes completely immune to interdiction, and an attack on an unprotected facility destroys it beyond repair. Moreover, the attacker has perfect information about the location and protection status of facilities; hence he would never attack a protected facility. We formulate a bilevel integer program (BIP) for this problem, in which the defender takes on the leader’s role and the attacker acts as the follower. We propose and compare three different methods to solve the BIP. The first method is an optimal exhaustive search algorithm with exponential time complexity. The second one is a two-phase tabu search heuristic developed to overcome the first method’s impracticality on large-sized problem instances. Finally, the third one is a sequential solution method in which the defender’s location and protection decisions are separated. The efficiency of these three methods is extensively tested on 75 randomly generated instances each with two budget levels. The results show that protection budget plays a significant role in maintaining the service accessibility of critical facilities in the worst-case interdiction scenario.     

Fast fluorescence switching within hydrophilic supramolecular assemblies

We designed a supramolecular strategy to modulate fluorescence in water under optical control. It is based on the entrapment of fluorophore-photochrome dyads within the hydrophobic interior of an amphiphilic polymer. The polymeric envelope around the dyads protects them from the aqueous environment, while imposing hydrophilic character on the overall supramolecular construct. In the resulting assemblies, the photochromic component can be operated reversibly on a microsecond timescale under the influence of ultraviolet stimulations. In turn, the reversible transformations control the emission intensity of the adjacent fluorophore. As a result, the fluorescence of such nanostructured constructs can be photomodulated for hundreds of cycles in water with microsecond switching speeds. Thus, our protocol for fast fluorescence switching in aqueous solutions can eventually lead to the realization of functional probes for the investigation of biological samples.     

Form-stable electrospun nanofibrous mats as a potential phase change material

A series of Poly vinyl butyral–Poly (acrylic acid) (PVB-PAA) based form-stable phase change materials (PCMs) have been prepared for the use of thermal energy storage applications. Six types of formulations containing five different fatty alcohols were prepared by adding PVB to PAA. Using electrospinning to fabricate nanofibrous mats, our aim was to investigate their properties as form-stable PCMs. Fatty alcohols, 1-Tetradecanol, 1-Hexadecanol, 1-Octadecanol, 1-Eicosanol and 1-Docosanol, were added separately to base formulation. The structural characterization tests were performed by ATR-FTIR spectroscopy. Morphological tests were conducted using Scanning Electron Microscope (SEM). Thermal performances and phase change behaviors were tested by thermogravimetric analysis system (TGA) and differential scanning calorimetry (DSC). The heating cycle phase change enthalpy is measured between 223 and 241?J/g, and the freezing cycle phase change enthalpy is found between 215 and 239?J/g. The main decomposition PVB-PAA based PCMs started at 220?°C. This study suggested that PVB-PAA based PCMs possess well phase change properties and they were found to have an applicable temperature range. With the presented results these materials promise a great potential in thermal energy storage applications.     

Site‐Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater

Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site‐selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site‐specific incorporation of the non‐canonical amino acid β‐(1‐azulenyl)‐l ‐alanine (AzAla) through genetic code expansion. As an exception to Kasha's rule, AzAla undergoes ultrafast internal conversion and heating after S₁ excitation while upon S₂ excitation, it serves as a fluorescent label. We equipped PDZ3, a protein interaction domain of postsynaptic density protein 95, with this ultrafast heater at two distinct positions. We indeed observed VET from the incorporation sites in the protein to a bound peptide ligand on the picosecond timescale by ultrafast IR spectroscopy. This approach based on genetically encoded AzAla paves the way for detailed studies of VET and its role in a wide range of proteins.     

Scattering of plane-waves by an impedance half-plane at the interface between isorefractive media

The scattering of plane waves by an impedance half-plane located at the interface of two isorefractive media is investigated. The scattered field, in addition to the diffracted and geometrical optics fields, is analyzed numerically and compared to the scattered field of perfectly conducting half-plane. The effect of the isorefractive media on the scattered field is also examined.     

Modeling of Tarsus-Adana-Gaziantep highway-induced noise pollution within the scope of Adana city and estimated the affected population

The purpose of this study is, via employing SoundPLAN 7.3 software, to model the noise pollution that Tarsus-Adana-Gaziantep (TAG) Highway passing through Adana city induces in Adana city center and to designate the ratio of population exposed to the noise. The study was executed in an area extending from a 17 km-route of TAG Highway passing through Adana city center and 1900.62 ha area that surrounding 500 m north and 500 m south directions of this particular route.