Multifarious facets of sugar-derived molecular gels: molecular features, mechanisms of self-assembly and emerging applications

The remarkable capability of nature to design and create excellent self-assembled nano-structures, especially in the biological world, has motivated chemists to mimic such systems with synthetic molecular and supramolecular systems. The hierarchically organized self-assembly of low molecular weight gelators (LMWGs) based on non-covalent interactions has been proven to be a useful tool in the development of well-defined nanostructures. Among these, the self-assembly of sugar-derived LMWGs has received immense attention because of their propensity to furnish biocompatible, hierarchical, supramolecular architectures that are macroscopically expressed in gel formation. This review sheds light on various aspects of sugar-derived LMWGs, uncovering their mechanisms of gelation, structural analysis, and tailorable properties, and their diverse applications such as stimuli-responsiveness, sensing, self-healing, environmental problems, and nano and biomaterials synthesis.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Capability approach-based evaluation of a biomass cook-stove design

What is the scope and responsibilities of design? This work partially answers this by employing a normative approach to design of a biomass cook stove. This study debates on the sufficiency of existing design methodologies in the light of a capability approach. A case study of a biomass cook stove Astra Ole has elaborated the theoretical constructs of capability approach, which, in turn, has structured insights from field to evaluate the product. Capability approach based methodology is also prescriptively used to design the mould for rapid dissemination of the Astra Ole.

Ray tracing based path-length calculations for polarized light tomographic imaging

A ray tracing based path length calculation is investigated for polarized light transport in a pixel space. Tomographic imaging using polarized light transport is promising for applications in optical projection tomography of small animal imaging and turbid media with low scattering. Polarized light transport through a medium can have complex effects due to interactions such as optical rotation of linearly polarized light, birefringence, diattenuation and interior refraction. Here we investigate the effects of refraction of polarized light in a non-scattering medium. This step is used to obtain the initial absorption estimate. This estimate can be used as prior in Monte Carlo (MC) program that simulates the transport of polarized light through a scattering medium to assist in faster convergence of the final estimate. The reflectance for p-polarized (parallel) and s-polarized (perpendicular) are different and hence there is a difference in the intensities that reach the detector end. The algorithm computes the length of the ray in each pixel along the refracted path and this is used to build the weight matrix. This weight matrix with corrected ray path length and the resultant intensity reaching the detector for each ray is used in the algebraic reconstruction (ART) method. The proposed method is tested with numerical phantoms for various noise levels. The refraction errors due to regions of different refractive index are discussed, the difference in intensities with polarization is considered. The improvements in reconstruction using the correction so applied is presented. This is achieved by tracking the path of the ray as well as the intensity of the ray as it traverses through the medium.

White light emissive molecular siblings

The design and synthesis of two structurally close and complementarily fluorescent boron based molecular siblings 2 and 3 are reported. The luminescence properties of individual triads are modulated to complement each other by controlling the intramolecular energy transfer in 2 and 3. The binary mixture of 2 and 3 emits white-light.

Minuscule weight percent of graphene oxide and reduced graphene oxide modified Ag3PO4: new insight into improved photocatalytic activity

Designing and fabricating hybrid systems with a visible light active semiconductor as one of its components is an important research area for the development of highly efficient photocatalysts. Herein, we report visible-light driven photocatalytic activity of graphene oxide (GO) and controllably reduced GO (rGO) modified Ag3PO4 composites fabricated by an in situ method. Concentration of graphene derivatives in GO/rGO-Ag3PO4 composites was in the range of 0.13-0.52 wt% which is very minute compared to those reported previously. The optimal concentration of GO in Ag3PO4 with a kinetics (k = 1.23 +/- 0.04 min(-1)) for the degradation of rhodamine B is 0.26 wt%. GO-Ag3PO4 photocatalysts display an improved catalytic activity compared with pristine and rGOs modified Ag3PO4. In line with this, GO/rGO-Ag3PO4 composites show improved photocatalytic activity for the degradation of 2-chlorophenol compared with Degussa P-25. Our experiments with GO reduced to different extents show that, rGO with more polar functional groups exhibits a higher photocatalytic efficiency. The photocatalytic activity in the presence of different scavengers reveals that holes and O-2(-center dot) reactive species play major roles in the degradation phenomenon. In view of our experimental results and reported theoretical studies, a change in conduction band energy level and variation in the contribution of different charge orbitals (C 2p and O 2p) to the conduction band in the composite favours electron flow from graphene derivatives to the semiconductor, enhancing its photocatalytic response.

Correct biological timing in Arabidopsis requires multiple light-signaling pathways.

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control.

The Stability of a Vertical Single-Walled Carbon Nanotube Under Its Own Weight

It has been reported recently that single carbon nanotubes were attached to AFM tips to act as nanotweezers. In order to investigate its stability, a vertical single-walled carbon nanotube (SWCNT) under its own weight is studied in this paper. The lower end of the carbon nanotube is clamped. Firstly the governing dimensionless numbers are derived by dimensional analysis. Then the theoretical analysis based on an elastic column model is carried out. Two ratios, I.e., the ratio of half wall thickness to radius (t=R) and the ratio of gravity to elastic resilience ($\rho$gR=E), and their influences on the ratio of critical length to radius are discussed. It is found that the relationship between the critical ratio of altitude to radius and ratio of half thickness to radius is approximately linear. As the dimensionless number $\rho$gR=E increases, the compressive force per unit length (weight) becomes larger, thus critical ratio of altitude to radius must become smaller to maintain stability. At last the critical length of SWCNT is calculated. The results of this paper will be helpful for the stability design of nanotweezers-like nanostructures.

Evaluación de la eficacia de la técnica de floating system para la producción de radicchio rosso var. di Verona en condiciones controladas

La técnica de producción en Floating system constituye una alternativa económica y veloz de producción en hidroponia. Este sistema permite obtener hojas de vegetales de pequeño tamaño “Baby leaf” listas para consumir (IV Gama), cuyo consumo a nivel mundial muestra una tendencia creciente. Dicha técnica no se encuentra aún muy difundida para la producción de radicchio rosso. El objetivo de este trabajo fue evaluar el efecto del tamaño de celda, del substrato y de la técnica de floating system sobre la producción de radicchio. Los ensayos se realizaron en cámara a 25 ºC con un fotoperíodo de 16 hs de luz y 8 de oscuridad y con una intensidad de luz de 10 000 Lux. Se utilizó un diseño experimental factorial totalmente aleatorizado, con 5 repeticiones y 3 factores, cuyos niveles fueron: 1) Tamaño de celda, (T), con 3 niveles: grande, mediano y pequeño, 2) Técnica de producción, (F), con 2 niveles: floating system y sistema convencional, 3) Sustrato, (S), con 2 niveles: vermiculita y mezcla. Se analizaron las siguientes variables: 1) peso fresco, 2) peso seco, 3) largo de planta, 4) número de hojas y 5) área foliar. Los resultados obtenidos resultan alentadores respecto del empleo de la técnica de floating system. Para la obtención de plántulas con calidad de IV Gama resulta más conveniente el empleo de celdas de 80 cm3 y sustrato mezcla.

Design and Development of a Low-Cost Optical Current Sensor

In this paper we demonstrate the design of a low-cost optical current sensor. The sensor principle is the Faraday rotation of a light beam through a magneto-optical material, SF2, when a magnetic field is present. The prototype has a high sensitivity and a high linearity for currents ranging from 0 up to 800 A. The error of the optical fibre sensor is smaller than 1% for electric currents over 175 A.

Design, synthesis and characterization of sequence-specific DNA-cleaving metalloproteins

This thesis describes research pursued in two areas, both involving the design and synthesis of sequence specific DNA-cleaving proteins. The first involves the use of sequence-specific DNA-cleaving metalloproteins to probe the structure of a protein-DNA complex, and the second seeks to develop cleaving moieties capable of DNA cleavage through the generation of a non-diffusible oxidant under physiological conditions.

Chapter One provides a brief review of the literature concerning sequence-specific DNA-binding proteins. Chapter Two summarizes the results of affinity cleaving experiments using leucine zipper-basic region (bZip) DNA-binding proteins. Specifically, the NH_2-terminal locations of a dimer containing the DNA binding domain of the yeast transcriptional activator GCN4 were mapped on the binding sites 5'-CTGACTAAT-3' and 5'ATGACTCTT- 3' using affinity cleaving. Analysis of the DNA cleavage patterns from Fe•EDTA-GCN4(222-281) and (226-281) dimers reveals that the NH_2-termini are in the major groove nine to ten base pairs apart and symmetrically displaced four to five base pairs from the central C of the recognition site. These data are consistent with structural models put forward for this class of DNA binding proteins. The results of these experiments are evaluated in light of the recently published crystal structure for the GCN4-DNA complex. Preliminary investigations of affinity cleaving proteins based on the DNA-binding domains of the bZip proteins Jun and Fos are also described.

Chapter Three describes experiments demonstrating the simultaneous binding of GCN4(226-281) and 1-Methylimidazole-2-carboxamide-netropsin (2-ImN), a designed synthetic peptide which binds in the minor groove of DNA at 5'-TGACT-3' sites as an antiparallel, side-by-side dimer. Through the use of Fe•EDTA-GCN4(226-281) as a sequence-specific footprinting agent, it is shown that the dimeric protein GCN4(226-281) and the dimeric peptide 2- ImN can simultaneously occupy their common binding site in the major and minor grooves of DNA, respectively. The association constants for 2-ImN in the presence and in the absence of Fe•EDTA-GCN4(226-281) are found to be similar, suggesting that the binding of the two dimers is not cooperative.

Chapter Four describes the synthesis and characterization of PBA-β-OH-His- Hin(139-190), a hybrid protein containing the DNA-binding domain of Hin recombinase and the putative iron-binding and oxygen-activating domain of the antitumor antibiotic bleomycin. This 54-residue protein, comprising residues 139-190 of Hin recombinase with the dipeptide pyrimidoblamic acid-β-hydroxy-L-histidine (PBA-β-OH-His) at the NH2 terminus, was synthesized by solid phase methods. PBA-β-OH-His-Hin(139- 190) binds specifically to DNA at four distinct Hin binding sites with affinities comparable to those of the unmodified Hin(139-190). In the presence of dithiothreitol (DTT), Fe•PB-β-OH-His-Hin(139-190) cleaves DNA with specificity remarkably similar to that of Fe•EDTA-Hin(139-190), although with lower efficiency. Analysis of the cleavage pattern suggests that DNA cleavage is mediated through a diffusible species, in contrast with cleavage by bleomycin, which occurs through a non-diffusible oxidant.

Rational design of zinc phosphide heterojunction photovoltaics

The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an "earth-abundant" solar absorber, we find zinc phosphide (α-Zn₃P₂) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>10⁴ cm^-1), and long minority-carrier diffusion length (>5 μm), Zn₃P₂ is composed of abundant Zn and P elements and has excellent physical properties for scalable thin-film deposition. However, to date, a Zn₃P₂ device of sufficient efficiency for commercial applications has not been demonstrated. Record efficiencies of 6.0% for multicrystalline and 4.3% for thin-film cells have been reported, respectively. Performance has been limited by the intrinsic p-type conductivity of Zn₃P₂ which restricts us to Schottky and heterojunction device designs. Due to our poor understanding of Zn₃P₂ interfaces, an ideal heterojunction partner has not yet been found.

The goal of this thesis is to explore the upper limit of solar conversion efficiency achievable with a Zn₃P₂ absorber through the design of an optimal heterojunction PV device. To do so, we investigate three key aspects of material growth, interface energetics, and device design. First, the growth of Zn₃P₂ on GaAs(001) is studied using compound-source molecular-beam epitaxy (MBE). We successfully demonstrate the pseudomorphic growth of Zn₃P₂ epilayers of controlled orientation and optoelectronic properties. Next, the energy-band alignments of epitaxial Zn₃P₂ and II-VI and III-V semiconductor interfaces are measured via high-resolution x-ray photoelectron spectroscopy in order to determine the most appropriate heterojunction partner. From this work, we identify ZnSe as a nearly ideal n-type emitter for a Zn₃P₂ PV device. Finally, various II-VI/Zn₃P₂ heterojunction solar cells designs are fabricated, including substrate and superstrate architectures, and evaluated based on their solar conversion efficiency.

Design of antenna-coupled lumped-element titanium nitride KIDs for long-wavelength multi-band continuum imaging

Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional "RF" structures such as hybrids, switches, and lumped-element or microstrip band-defining filters.

Simultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A KID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector of light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.

However, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID design that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to the fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.

Excess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we derive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.