128 research outputs found
Quantum modeling of bioconjugated nanomaterials
In recent years, the bio-conjugated nanostructured materials have emerged as a new class of materials for the bio-sensing and medical diagnostics applications. In spite of their multi-directional applications, interfacing nanomaterials with bio-molecules has been a challenge due to somewhat limited knowledge about the underlying physics and chemistry behind these interactions and also for the complexity of biomolecules.
The main objective of this dissertation is to provide such a detailed knowledge on bioconjugated nanomaterials toward their applications in designing the next generation of sensing devices. Specifically, we investigate the changes in the electronic properties of a boron nitride nanotube (BNNT) due to the adsorption of different bio-molecules, ranging from neutral (DNA/RNA nucleobases) to polar (amino acid molecules).
BNNT is a typical member of III-V compounds semiconductors with morphology similar to that of carbon nanotubes (CNTs) but with its own distinct properties. More specifically, the natural affinity of BNNTs toward living cells with no apparent toxicity instigates the applications of BNNTs in drug delivery and cell therapy.
Our results predict that the adsorption of DNA/RNA nucleobases on BNNTs amounts to different degrees of modulation in the band gap of BNNTs, which can be exploited for distinguishing these nucleobases from each other. Interestingly, for the polar amino acid molecules, the nature of interaction appeared to vary ranging from Coulombic, van der Waals and covalent depending on the polarity of the individual molecules, each with a different binding strength and amount of charge transfer involved in the interaction.
The strong binding of amino acid molecules on the BNNTs explains the observed protein wrapping onto BNNTs without any linkers, unlike carbon nanotubes (CNTs). Additionally, the widely varying binding energies corresponding to different amino acid molecules toward BNNTs indicate to the suitability of BNNTs for the biosensing applications, as compared to the metallic CNTs.
The calculated I-V characteristics in these bioconjugated nanotubes predict notable changes in the conductivity of BNNTs due to the physisorption of DNA/RNA nucleobases. This is not the case with metallic CNTs whose transport properties remained unaltered in their conjugated systems with the nucleobases. Collectively, the bioconjugated BNNTs are found to be an excellent system for the next generation sensing devices
The tubby family proteins
The tubby mouse shows a tripartite syndrome characterized by maturity-onset obesity, blindness and deafness. The causative gene Tub is the founding member of a family of related proteins present throughout the animal and plant kingdoms, each characterized by a signature carboxy-terminal tubby domain. This domain consists of a β barrel enclosing a central α helix and binds selectively to specific membrane phosphoinositides. The vertebrate family of tubby-like proteins (TULPs) includes the founding member TUB and the related TULPs, TULP1 to TULP4. Tulp1 is expressed in the retina and mutations in TULP1 cause retinitis pigmentosa in humans; Tulp3 is expressed ubiquitously in the mouse embryo and is important in sonic hedgehog (Shh)-mediated dorso-ventral patterning of the spinal cord. The amino terminus of these proteins is diverse and directs distinct functions. In the best-characterized example, the TULP3 amino terminus binds to the IFT-A complex, a complex important in intraflagellar transport in the primary cilia, through a short conserved domain. Thus, the tubby family proteins seem to serve as bipartite bridges through their phosphoinositide-binding tubby and unique amino-terminal functional domains, coordinating multiple signaling pathways, including ciliary G-protein-coupled receptor trafficking and Shh signaling. Molecular studies on this functionally diverse protein family are beginning to provide us with remarkable insights into the tubby-mouse syndrome and other related diseases
A Theoretical Analysis of Deep Neural Networks for Texture Classification
We investigate the use of Deep Neural Networks for the classification of
image datasets where texture features are important for generating
class-conditional discriminative representations. To this end, we first derive
the size of the feature space for some standard textural features extracted
from the input dataset and then use the theory of Vapnik-Chervonenkis dimension
to show that hand-crafted feature extraction creates low-dimensional
representations which help in reducing the overall excess error rate. As a
corollary to this analysis, we derive for the first time upper bounds on the VC
dimension of Convolutional Neural Network as well as Dropout and Dropconnect
networks and the relation between excess error rate of Dropout and Dropconnect
networks. The concept of intrinsic dimension is used to validate the intuition
that texture-based datasets are inherently higher dimensional as compared to
handwritten digits or other object recognition datasets and hence more
difficult to be shattered by neural networks. We then derive the mean distance
from the centroid to the nearest and farthest sampling points in an
n-dimensional manifold and show that the Relative Contrast of the sample data
vanishes as dimensionality of the underlying vector space tends to infinity.Comment: Accepted in International Joint Conference on Neural Networks, IJCNN
201
A detailed investigation to study the pattern of the interplay of Cyclic AMP Receptor Protein (CRP) of E. coli with its different classes of promoters
The activity of most of the promoters in Escherichia coli, involved in the metabolism of sugars other than glucose, is controlled by a CRP (cAMP receptor protein) or CAP (catabolite activator protein). CRP-dependent promoters are differentiated into various classes (Class I, Class II, and Class III) based on its cognate binding site’s position on DNA. The promoters regulated by CAP are differentially regulated by this transcriptional factor and it is also imperative to mention that these promoters vary greatly in respect to the binding site of CAP to its cognate binding site, it has also been reported that either it overlaps with the binding site of RNA polymerase or it present upstream to it. In Class I CAP-dependent promoters, a particular CAP molecule makes protein-protein interaction for the start of transcription. In Class II CAP-dependent promoters, a particular CAP molecule makes multiple interactions for the start of transcription. At last, in Class III-CAP dependent promoters, more than one CAP molecule is involved and activation of transcription is done synergistically. It has also been documented that CAP shows a kind of biphasic behavior in some promoters. So, the main focus of this work is to find out whether this biphasic behavior is true for other E. coli promoters as well. Experiments have been performed to know more about this biphasic nature and the various patterns of interactions of catabolite activator protein (CAP) of E. coli with its different classes of promoters
Novel spherical boron clusters and structural transition from 2D quasi-planar structures to 3D double-rings
Based on ab initio quantum-chemical and density functional methods we determined the geometry, electronic and structural properties of three cluster-families: boron spheres, double-rings and quasi-planars up to a cluster size of 122 atoms. The most stable structure is the B100 sphere showing similar shape but more stability than the B80 cage recently proposed by Yakobson et al [PRL 98, 166804 (2007)]. In addition we compared the stability of the three cluster families to each other, and reported the structural transition from 2D quasiplanar clusters to 3D double-rings. This transition occurs between the B16 and B19 clusters
Applicability of carbon and boron nitride nanotubes as biosensors: Effect of biomolecular adsorption on the transport properties of carbon and boron nitride nanotubes
The effect of molecular adsorption on the transport properties of single walled carbon and boron nitride nanotubes (CNTs and BNNTs) is investigated using density functional theory and nonequilibrium Green’s function methods. The calculated I-V characteristics predict noticeable changes in the conductivity of semiconducting BNNTs due to physisorption of nucleic acid base molecules. Specifically, guanine which binds to the side wall of BNNT significantly enhances its conductivity by introducing conduction channels near the Fermi energy of the bioconjugated system. For metallic CNTs, a large background current masks relatively small changes in current due to the biomolecular adsorption. The results therefore suggest the suitability of BNNTs for biosensing applications
Competing covalent and ionic bonding in Ge-Sb-Te phase change materials
Ge2Sb2Te5 and related phase change materials are highly unusual in that they
can be readily transformed between amorphous and crystalline states using very
fast melt, quench, anneal cycles, although the resulting states are extremely
long lived at ambient temperature. These states have remarkably different
physical properties including very different optical constants in the visible
in strong contrast to common glass formers such as silicates or phosphates.
This behavior has been described in terms of resonant bonding, but puzzles
remain, particularly regarding different physical properties of crystalline and
amorphous phases. Here we show that there is a strong competition between ionic
and covalent bonding in cubic phase providing a link between the chemical basis
of phase change memory property and origins of giant responses of piezoelectric
materials (PbTiO3, BiFeO3). This has important consequences for dynamical
behavior in particular leading to a simultaneous hardening of acoustic modes
and softening of high frequency optic modes in crystalline phase relative to
amorphous. This different bonding in amorphous and crystalline phases provides
a direct explanation for different physical properties and understanding of the
combination of long time stability and rapid switching and may be useful in
finding new phase change compositions with superior properties
Theoretical Study of Physisorption of Nucleobases on Boron Nitride Nanotubes: A New Class of Hybrid Nano-Bio Materials
We investigate the adsorption of the nucleic acid bases, adenine (A), guanine
(G), cytosine (C), thymine (T) and uracil (U) on the outer wall of a high
curvature semiconducting single-walled boron nitride nanotube (BNNT) by first
principles density functional theory calculations. The calculated binding
energy shows the order: G>A\approxC\approxT\approxU implying that the
interaction strength of the (high-curvature) BNNT with the nucleobases, G being
an exception, is nearly the same. A higher binding energy for the G-BNNT
conjugate appears to result from a stronger hybridization of the molecular
orbitals of G and BNNT, since the charge transfer involved in the physisorption
process is insignificant. A smaller energy gap predicted for the G-BNNT
conjugate relative to that of the pristine BNNT may be useful in application of
this class of biofunctional materials to the design of the next generation
sensing devices.Comment: 17 pages 6 figure
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