Hydrothermal synthesis of CdTe QDs: Their luminescence quenching in the presence of bio-molecules and observation of bistable memory effect in CdTe QD/PEDOT:PSS heterostructure

We report one-pot hydrothermal synthesis of nearly mono-disperse 3-mercaptopropionic acid capped water-soluble cadmium telluride (CdTe) quantum dots (QDs) using an air stable Te source. The optical and electrical characteristics were also studied here. It was shown that the hydrothermal synthesis could be tuned to synthesize nano structures of uniform size close to nanometers. The emissions of the CdTe QDs thus synthesized were in the range of 500-700 nm by varying the duration of synthesis. The full width at half maximum (FWHM) of the emission peaks is relatively narrow (40-90 nm), which indicates a nearly uniform distribution of QD size. The structural and optical properties of the QDs were characterized by transmission electron microscopy (TEM), photoluminescence (PL) and Ultraviolet-visible (UV-Vis) spectroscopy. The photoluminescence quenching of CdTe QDs in the presence of L-cysteine and DNA confirms its biocompatibility and its utility for biosensing applications. The room temperature current-voltage characteristics of QD film on ITO coated glass substrate show an electrically induced switching between states with high and low conductivities. The phenomenon is explained on the basis of charge confinement in quantum dots. (C) 2011 Elsevier B.V. All rights reserved.

On network coding for acyclic networks with delays

Problems related to network coding for acyclic, instantaneous networks (where the edges of the acyclic graph representing the network are assumed to have zero-delay) have been extensively dealt with in the recent past. The most prominent of these problems include (a) the existence of network codes that achieve maximum rate of transmission, (b) efficient network code constructions, and (c) field size issues. In practice, however, networks have transmission delays. In network coding theory, such networks with transmission delays are generally abstracted by assuming that their edges have integer delays. Using enough memory at the nodes of an acyclic network with integer delays can effectively simulate instantaneous behavior, which is probably why only acyclic instantaneous networks have been primarily focused on thus far. However, nulling the effect of the network delays are not always uniformly advantageous, as we will show in this work. Essentially, we elaborate on issues ((a), (b) and (c) above) related to network coding for acyclic networks with integer delays, and show that using the delay network as is (without adding memory) turns out to be advantageous, disadvantageous or immaterial, depending on the topology of the network and the problem considered i.e., (a), (b) or (c).

Acyclic edge coloring of 2-degenerate graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). A graph is called 2-degenerate if any of its induced subgraph has a vertex of degree at most 2. The class of 2-degenerate graphs properly contains seriesparallel graphs, outerplanar graphs, non - regular subcubic graphs, planar graphs of girth at least 6 and circle graphs of girth at least 5 as subclasses. It was conjectured by Alon, Sudakov and Zaks (and much earlier by Fiamcik) that a'(G)<=Delta + 2, where Delta = Delta(G) denotes the maximum degree of the graph. We prove the conjecture for 2-degenerate graphs. In fact we prove a stronger bound: we prove that if G is a 2-degenerate graph with maximum degree ?, then a'(G)<=Delta + 1. (C) 2010 Wiley Periodicals, Inc. J Graph Theory 68:1-27, 2011

Self-Assembling Peptides: From Molecules to Nanobiomaterials

Abstract | Molecular self-assembly plays a vital role in the construction of various nanostructures using the ‘bottom-up’ approach. Peptides have been considered important bio-molecular building blocks for different nanoscale structures as they are biocompatible, biodegradable, generally non-toxic and can be attuned to environmental responses like pH, temperature, salt concentration and others. Peptide based nanostructures can offer various wonderful biological applications in tissue engineering, cell culture, regenerative medicine and drug delivery. In this review, the construction of short peptide-based different nanostructures including nanotubes, nanovesicles and nanofibers, short peptide-based nanoporous materials, short peptide-based nanofibrous hydrogels and nanovesicles for various biological applications has been discussed. Moreover, morphological transformations from one nanoscopic structure to an other type of nanostructure (e.g., nanotubes to nanovesicles) are also clearly discussed in this review.

Utilizing Model Nanostructured Porous Inorganic Compounds Such as Silica to Beneficially Confine “Bio”-Relevant Molecules and Demonstrate their Potential in Therapeutics

Abstract | The importance of well-defined inorganic porous nanostructured materials in the context of biotechnological applications such as drug delivery and biomolecular sensing is reviewed here in detail. Under optimized conditions, the confinement of “bio”-relevant molecules such as pharmaceutical drugs, enzymes or proteins inside such inorganic nanostructures may be remarkably beneficial leading to enhanced molecular stability, activity and performance. From the point of view of basic research, molecular confinement inside nanostructures poses several formidable and intriguing problems of statistical mechanics at the mesoscopic scale. The theoretical comprehension of such non-trivial issues will not only aid in the interpretation of observed phenomena but also help in designing better inorganic nanostructured materials for biotechnological applications.

Carbohydrate-based liquid crystals

The carbohydrate based mesogens have gained an importance in the field of liquid crystals, primarily through the amphiphilic nature of many sugar derivatives. A constitutional requirement for the amphiphilic mesogen is that the molecule consists of distinct regions within the molecule that separately would have different responses to changes in thermal energies and/or solvations. Such molecules can be synthesized by linking one or more alkyl chains of appropriate length to both cyclic and acyclic sugars. A driving force for the mesophase formation in these molecules is the phase segregation, leading to aggregates, possessing distinct lyophilic and hydrophilic regions. In this review, we discuss the thermotropic behavior of the carbohydrate amphiphiles. We discuss the relationship between constitutions, configurations, functionalities of the sugar component and the length of the hydrophobic chains necessary to form the various types of thermotropic phases. The influence of the linking group between the hydrophilic sugar head groups and lyophilic alkyl chains on the transition temperatures and mesophase stabilities are also presented.

The interaction of halogen molecules with SWNTs and graphene

The interaction of halogen molecules of varying electron affinity, such as iodine monochloride (ICl), bromine (Br(2)), iodine monobromide (IBr) and iodine (I(2)) with single-walled carbon nanotubes (SWNTs) and graphene has been investigated in detail. Halogen doping of the two nanocarbons has been examined using Raman spectroscopy in conjunction with electronic absorption spectroscopy and extensive theoretical calculations. The halogen molecules, being electron withdrawing in nature, induce distinct changes in the electronic states of both the SWNTs and graphene, which manifests with a change in the spectroscopic signatures. Stiffening of the Raman G-bands of the nanocarbons upon treatment with the different halogen molecules and the emergence of new bands in the electronic absorption spectra, both point to the fact that the halogen molecules are involved in molecular charge-transfer with the nanocarbons. The experimental findings have been explained through density functional theory (DFT) calculations, which suggest that the extent of charge-transfer depends on the electron affinities of the different halogens, which determines the overall spectroscopic properties. The magnitude of the molecular charge-transfer between the halogens and the nanocarbons generally varies in the order ICl > Br(2) > IBr > I(2), which is consistent with the expected order of electron affinities.

Chemistry and biology of DNA-binding small molecules

Regulation of the transcription machinery is one of the many ways to achieve control of gene expression. This has been done either at the transcription initiation stage or at the elongation stage. Different methodologies are known to inhibit transcription initiation via targeting of double-stranded (ds) DNA by: (i) synthetic oligonucleotides, (ii) ds-DNA-specific, sequenceselective minor-groove binders (distamycin A), intercalators (daunomycin) combilexins and (iii) small molecule (peptide or intercalator)-oligonucleotide conjugates. In some cases, instead of ds-DNA, higher order G-quadruplex structures are formed at the start site of transcription. In this regard G-quadruplex DNA-specific small molecules play a significant role towards inhibition of the transcription machinery. Different types of designer DNA-binding agents act as powerful sequence-specific gene modulators, by exerting their effect from transcription regulation to gene modification. But most of these chemotherapeutic agents have serious side effects. Accordingly, there is always a challenge to design such DNA-binding molecules that should not only achieve maximum specific DNA-binding affinity, and cellular and nuclear transport activity, but also would not interfere with the functions of normal cells.

Cation-templated 2-D Mn(II)-oxalate framework with an acyclic tetrameric water cluster

The single-crystal X-ray structure of a cation-templated manganese-oxalate coordination polymer [NH(C2H5)(3)][Mn-2(ox)(3)]center dot(5H(2)O)] (1) is reported. In 1, triethylammonium cation is entrapped between the cavities of 2-D honeycomb layers constructed by oxalate and water. The acyclic tetrameric water clusters and discrete water assemble the parallel 2-D honeycomb oxalate layers via an intricate array of hydrogen bonds into an overall 3-D network. The magnetic susceptibility, with and without the water cluster, are reported with infrared and EPR studies.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Excitation energy transfer from dye molecules to doped graphene

Recently, we have reported theoretical studies on the rate of energy transfer from an electronically excited molecule to graphene. It was found that graphene is a very efficient quencher of the electronically excited states and that the rate infinity z(-4). The process was found to be effective up to 30 nm which is well beyond the traditional FRET limit. In this report, we study the transfer of an amount of energy (h) over bar Omega from a dye molecule to doped graphene. We find a crossover of the distance dependence of the rate from z(-4) to exponential as the Fermi level is increasingly shifted into the conduction band, with the crossover occurring at a shift of the Fermi level by an amount (h) over bar Omega/2.

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

Use of Vertex Index in Structure-Activity Analysis and Design of Molecules

The last few decades have witnessed application of graph theory and topological indices derived from molecular graph in structure-activity analysis. Such applications are based on regression and various multivariate analyses. Most of the topological indices are computed for the whole molecule and used as descriptors for explaining properties/activities of chemical compounds. However, some substructural descriptors in the form of topological distance based vertex indices have been found to be useful in identifying activity related substructures and in predicting pharmacological and toxicological activities of bioactive compounds. Another important aspect of drug discovery e. g. designing novel pharmaceutical candidates could also be done from the distance distribution associated with such vertex indices. In this article, we will review the development and applications of this approach both in activity prediction as well as in designing novel compounds.

Cyclodextrin functionalized magnetic iron oxide nanocrystals: a host-carrier for magnetic separation of non-polar molecules and arsenic from aqueous media

A single-step magnetic separation procedure that can remove both organic pollutants and arsenic from contaminated water is clearly a desirable goal. Here we show that water dispersible magnetite nanoparticles prepared by anchoring carboxymethyl-beta-cyclodextrin (CMCD) cavities to the surface of magnetic nanoparticles are suitable host carriers for such a process. Monodisperse, 10 nm, spherical magnetite, Fe3O4, nanocrystals were prepared by the thermal decomposition of FeOOH. Trace amounts of antiferromagnet, FeO, present in the particles provides an exchange bias field that results in a high superparamagnetic blocking temperature and appreciable magnetization values that facilitate easy separation of the nanocrystals from aqueous dispersions on application of modest magnetic fields. We show here that small molecules like naphthalene and naphthol can be removed from aqueous media by forming inclusion complexes with the anchored cavities of the CMCD-Fe3O4 nanocrystals followed by separation of the nanocrystals by application of a magnetic field. The adsorption properties of the iron oxide surface towards As ions are unaffected by the CMCD capping so it too can be simultaneously removed in the separation process. The CMCD-Fe3O4 nanocrystals provide a versatile platform for magnetic separation with potential applications in water remediation.