Abstract

DNA molecules tagged to metal nanoparticles, especially gold nanoparticles (AuNPs), have been shown to have potential applications in the design and fabrication of novel electronic nano-devices, but the binding mechanism between gold nanoparticles and DNA bases and its implications are not completely understood. In this work, a comprehensive study to examine the effect of structural perturbations caused to DNA base pairs in terms of size expansion and adsorption on a gold cluster (Au3) has been carried out using density functional theory. The geometric and electronic features of these complexes provide evidence for the distortion of certain base pairs depending on the binding site of the cluster. This is further substantiated via normal mode, natural bond orbital (NBO) and atoms in molecules (AIM) analyses. The natural population analysis (NPA) and NBO analysis indicate that complexation greatly affects …

Abstract

Bacillus halodurans (Bh) ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids. Long timescale molecular dynamics simulations have been performed on the BhRNase H-DNA-RNA hybrid complex and the respective monomers to understand the recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation. Several structural and energetic analyses were performed and significant structural changes are observed in enzyme and hybrid duplex during complex formation. Hybrid molecule binding to RNase H enzyme leads to conformational changes in the DNA strand. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and …

Abstract

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2–G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (Rg), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound …

Abstract

3a is an accessory protein from SARS coronavirus that is known to play a significant role in the proliferation of the virus by forming tetrameric ion channels. Although the monomeric units are known to consist of three transmembrane (TM) domains, there are no solved structures available for the complete monomer. The present study proposes a structural model for the transmembrane region of the monomer by employing our previously tested approach, which predicts potential orientations of TM α-helices by minimizing the unfavorable contact surfaces between the different TM domains. The best model structure comprising all three α-helices has been subjected to MD simulations to examine its quality. The TM bundle was found to form a compact and stable structure with significant intermolecular interactions. The structural features of the proposed model of 3a account for observations from previous …

Abstract

Silent information regulator 2 (Sir2), the founding member of the conserved sirtuin family of NAD+-dependent histone deacetylase, regulates several physiological processes including genome stability, gene silencing, metabolism and life span in yeast. Within the nucleus, Sir2 is associated with telomere clusters in the nuclear periphery and rDNA in the nucleolus and regulates gene silencing at these genomic sites. How distribution of Sir2 between telomere and rDNA is regulated is not known. Here we show that Sir2 is sumoylated and this modification modulates the intra-nuclear distribution of Sir2. We identify Siz2 as the key SUMO ligase and show that multiple lysines in Sir2 are subject to this sumoylation activity. Mutating K215 alone counteracts the inhibitory effect of Siz2 on telomeric silencing. SUMO modification of Sir2 impairs interaction with Sir4 but not Net1 and, furthermore, SUMO modified Sir2 shows …

Abstract

The laboratory is an indispensable component of learning in engineering education. In this paper, we examine the impact of Advanced VLSI Virtual Lab, which is a part of the Government of India's suite of Virtual Labs, in improving the understanding and learning of students at a small sized university in India. The Advanced VLSI Virtual Lab includes ten simulated interactive experiments in the area of design and application development. Over a hundred Virtual Labs have been proposed and built, but, so far, few have been subject to systematic investigation of their effectiveness in helping the student learn. Our work is one of the first efforts to statistically study the effectiveness of the Virtual Lab. To this end, we designed and conducted pre- and post-tests, and feedback surveys on the lab. The tests and the survey, on analysis, reveal that the lab is effective in enhancing student learning. Our results are encouraging to …

Abstract

Generation of problem sets and quizzes forms an important part of education technologies. Although some systems have been built for quiz generation, they mostly focus on abstract logic and mathematical constructs. Knowledge in other domains is relational rather than propositional, and many systems use dedicated knowledge databases. We present a method to present this knowledge in the form of objective question sets and drills. We implement a four-fold approach - ontologies, propositional logic, similarity finding, and hierarchies - as a way to generate quizzes as well as to solve human generated problems of a similar nature. The architecture of this system is such that any knowledgebase can be turned into a vast number of diverse, complex questions. We build this system for an ontology of North Indian Ragas, and also test it on a smaller ontology of animals. We demonstrate an approach to solving human

Abstract

In CMOS radio frequency integrated circuits, inductors are a barrier in achieving better monolithic solutions because of the large area occupied and the associated parasitics. For better performance of on-chip inductors, soft magnetic materials are incorporated with them. In an earlier work, it was shown that by tailoring the shape and size of the permalloy patterns, formation of magnetic domains can be controlled. When such domain patterns are incorporated with inductors, they have varied effects on inductor performance. In this paper, it is demonstrated that by depositing 60 nm thick domain-controlled permalloy patterns, better performance of inductors can be obtained at higher frequencies (>5 GHz). About 2× increment in inductance and 7× increment in quality factor is obtained at frequencies >5 GHz by incorporating appropriate domain-controlled permalloy patterns with inductors.

Abstract

This brief relates to communication established through high-speed serial links. A serial communication channel can be formed by grouping multiple high-speed serial communication lanes to achieve greater serial bandwidth. Such channels require circuitry to eliminate relative skew across multiple lanes to ensure data integrity in the receiver. Channel bonding is a mechanism used to synchronize serial communication channels in larger data rate and bandwidth applications. This brief presents an approach to channel bonding that optimizes area, power, and initialization time and yields better performance. The ideas discussed here use a delay-based model and explore the possibility of performing channel bonding in a centralized way. The methodology is deployed in the Aurora Protocol Solution Suite, and a comparative analysis with another state-of-the-art approach is performed.

Abstract

We propose an alternate method to sense inertial rotation using semiconductor ring laser gyroscope (SRLG). We show that inertial rotation causes change in the magnitude of voltage across the terminals of semiconductor gain medium which can be measured externally to determine angular rotation velocity. The resonant oscillating frequency of the counter-traveling waves are not involved in the measurement which leads to elimination of lock-in in the gyro. The mathematical analysis and simulation results of the proposed method are also shown.