Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations

Banana lectin (Banlec) is a homodimeric non-glycosylated protein. It exhibits the b-prism I structure. High-temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter- and intra-subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high-temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability.

Latency, Power and Performance Trade-offs in Network-on-Chips by Link Microarchitecture Exploration

This paper presents a power, latency and throughput trade-off study on NoCs by varying microarchitectural (e.g. pipelining) and circuit level (e.g. frequency and voltage) parameters. We change pipelining depth, operating frequency and supply voltage for 3 example NoCs - 16 node 2D Torus, Tree network and Reduced 2D Torus. We use an in-house NoC exploration framework capable of topology generation and comparison using parameterized models of Routers and links developed in SystemC. The framework utilizes interconnect power and delay models from a low-level modelling tool called Intacte[1]1. We find that increased pipelining can actually reduce latency. We also find that there exists an optimal degree of pipelining which is the most energy efficient in terms of minimizing energy-delay product.

Studies on the purification of banana polyphenoloxidase

Studies on the extractability of polyphenoloxidase (PPO) from the pulp of five banana cultivars revealed a varietal difference in the nature of binding of the PPO in the cell, with the enzyme being entirely in the soluble fraction in one and partly associated with the cell wall in others, necessitating use of a detergent to release it from the latter. Partial purification by acetone precipitation and chromatography using a DEAE-cellulose column yielded two major fractions DE-I and DE-II with purifications of 4- and 16·3-fold and activity recoveries of 38·2 and 43·3% respectively. Further gel filtration of the two fractions on a Sephadex G-100 column improved the purifications to 44- and 50-fold respectively with full activity recovery. Polyacrylamide gel electrophoretic studies showed the two fractions to be composed of isoenzymes differing in pattern. The purified enzyme showed maximum absorption at 275 nm.

On trade-off solution pairs in a special type of transportation problem

Abstract is not available.

The Role of Interface Modification on Thermal Degradation and Crystallization Behavior of Composites from Commingled Polypropylene Fiber and Banana Fiber

The thermal degradation behavior of banana fiber and polypropylene/banana fiber composites has been studied by thermogravimetric analysis. Banana fiber was found to be decomposing in two stages, first one around 320 degrees C and the second one around 450 degrees C. For chemically treated banana fiber, the decomposition process has been at a higher temperature, indicating thermal stability for the treated fiber. Activation energies for thermal degradation were estimated using Coats and Redfern method. Calorific value of the banana fiber was measured using a constant volume isothermal bomb calorimeter. rystallization studies exhibited an increase in the crystallization temperature and crystallinity of polypropylene upon the addition of banana fiber. POLYM. COMPOS., 31:1113-1123, 2010. (C) 2009 Society of Plastics Engineers.

Exploring energy-performance trade-offs for heterogeneous interconnect clustered VLIW processors

Clustered architecture processors are preferred for embedded systems because centralized register file architectures scale poorly in terms of clock rate, chip area, and power consumption. Although clustering helps by improving clock speed, reducing energy consumption of the logic, and making the design simpler, it introduces extra overheads by way of inter-cluster communication. This communication happens over long global wires which leads to delay in execution and significantly high energy consumption.In this paper, we propose a new instruction scheduling algorithm that exploits scheduling slacks of instructions and communication slacks of data values together to achieve better energy-performance trade-offs for clustered architectures with heterogeneous interconnect. Our instruction scheduling algorithm achieves 35% and 40% reduction in communication energy, whereas the overall energy-delay product improves by 4.5% and 6.5% respectively for 2 cluster and 4 cluster machines with marginal increase (1.6% and 1.1%) in execution time. Our test bed uses the Trimaran compiler infrastructure.

The Relay Selection and Transmission Trade-off in Cooperative Communication Systems

A common and practical paradigm in cooperative communication systems is the use of a dynamically selected `best' relay to decode and forward information from a source to a destination. Such systems use two phases - a relay selection phase, in which the system uses transmission time and energy to select the best relay, and a data transmission phase, in which it uses the spatial diversity benefits of selection to transmit data. In this paper, we derive closed-form expressions for the overall throughput and energy consumption, and study the time and energy trade-off between the selection and data transmission phases. To this end, we analyze a baseline non-adaptive system and several adaptive systems that adapt the selection phase, relay transmission power, or transmission time. Our results show that while selection yields significant benefits, the selection phase's time and energy overhead can be significant. In fact, at the optimal point, the selection can be far from perfect, and depends on the number of relays and the mode of adaptation. The results also provide guidelines about the optimal system operating point for different modes of adaptation. The analysis also sheds new insights on the fast splitting-based algorithm considered in this paper for relay selection.

Influence of glycosidic linkage on the nature of carbohydrate binding in beta-prism I fold lectins: An X-ray and molecular dynamics investigation on banana lectin-carbohydrate complexes

The three crystal structures reported here provide details of the interactions of mannose and the mannosyl-alpha-1,3-mannose component of a pentamannose with banana lectin and evidence for the binding of glucosyl-alpha-1,2-glucose to the lectin. The known structures involving the lectin include a complex with glucosyl-beta-1,3-glucose. Modeling studies on the three disaccharide complexes with the reducing end and the nonreducing end at the primary binding site are also provided here. The results of the Xray and modeling studies show that the disaccharides with an alpha-1,3 linkage prefer to have the nonreducing end at the primary binding site, whereas the reducing end is preferred at the site when the linkage is beta-1,3 in mannose/glucose-specific beta-prism I fold lectins. In the corresponding galactose-specific lectins, however, alpha-1,3-linked disaccharides cannot bind the lectin with the nonreducing end at the primary binding site on account of steric clashes with an aromatic residue that occurs only when the lectin is galactose-specific. Molecular dynamics simulations based on the known structures involving banana lectin enrich the information on lectin-carbohydrate interactions obtained from crystal structures. They demonstrate that conformational selection as well as induced fit operate when carbohydrates bind to banana lectin.

A System-C based Micro architectural Exploration Framework for Latency, Power and Performance Trade-offs of On-Chip Interconnection

We describe a System-C based framework we are developing, to explore the impact of various architectural and microarchitectural level parameters of the on-chip interconnection network elements on its power and performance. The framework enables one to choose from a variety of architectural options like topology, routing policy, etc., as well as allows experimentation with various microarchitectural options for the individual links like length, wire width, pitch, pipelining, supply voltage and frequency. The framework also supports a flexible traffic generation and communication model. We provide preliminary results of using this framework to study the power, latency and throughput of a 4x4 multi-core processing array using mesh, torus and folded torus, for two different communication patterns of dense and sparse linear algebra. The traffic consists of both Request-Response messages (mimicing cache accesses)and One-Way messages. We find that the average latency can be reduced by increasing the pipeline depth, as it enables higher link frequencies. We also find that there exists an optimum degree of pipelining which minimizes energy-delay product.

Trade determination in multi-attribute exchanges

Electronic exchanges are double-sided marketplaces that allow multiple buyers to trade with multiple sellers, with aggregation of demand and supply across the bids to maximize the revenue in the market. Two important issues in the design of exchanges are (1) trade determination (determining the number of goods traded between any buyer-seller pair) and (2) pricing. In this paper we address the trade determination issue for one-shot, multi-attribute exchanges that trade multiple units of the same good. The bids are configurable with separable additive price functions over the attributes and each function is continuous and piecewise linear. We model trade determination as mixed integer programming problems for different possible bid structures and show that even in two-attribute exchanges, trade determination is NP-hard for certain bid structures. We also make some observations on the pricing issues that are closely related to the mixed integer formulations.

Anaerobic retting of banana and arecanut wastes in a plug flow digester for recovery of fiber, biogas and compost

Leaves and leaf sheath of banana and areca husk (Areca catechu) constitute an important component of urban solid waste (USW) in India which are difficult to degrade under normal windrow composting conditions. A successful method of anaerobic digestion built around the fermentation properties of these feedstock has been evolved which uses no moving parts, pretreatment or energy input while enabling recovery of four products: fiber, biogas, compost and pest repellent. An SRT of 27 d and 35 d was found to be optimum for fiber recovery for banana leaf and areca husk, respectively. Banana leaf showed a degradation pattern different from other leaves with slow pectin-1 degradation (80%) and 40% lignin removal in 27 d SRT. Areca husk however, showed a degradation pattern similar to other plant biomass. Mass recovery levels for banana leaf were fiber-20%, biogas-70% (400 ml/g TS) and compost-10%. For areca husk recovery was fiber-50%, biogas-45% (250 ml/g TS) and compost-5%. (C) 2012 Elsevier Inc. All rights reserved.

Performance and variability trade-off with gate-to-source/drain overlap length

The impact of gate-to-source/drain overlap length on performance and variability of 65 nm CMOS is presented. The device and circuit variability is investigated as a function of three significant process parameters, namely gate length, gate oxide thickness, and halo dose. The comparison is made with three different values of gate-to-source/drain overlap length namely 5 nm, 0 nm, and -5 nm and at two different leakage currents of 10 nA and 100 nA. The Worst-Case-Analysis approach is used to study the inverter delay fluctuations at the process corners. The drive current of the device for device robustness and stage delay of an inverter for circuit robustness are taken as performance metrics. The design trade-off between performance and variability is demonstrated both at the device level and circuit level. It is shown that larger overlap length leads to better performance, while smaller overlap length results in better variability. Performance trades with variability as overlap length is varied. An optimal value of overlap length of 0 nm is recommended at 65 nm gate length, for a reasonable combination of performance and variability.

Diversity-Rate Trade-off for Fading Channels with Power Control

We consider a complex, additive, white Gaussian noise channel with flat fading. We study its diversity order vs transmission rate for some known power allocation schemes. The capacity region is divided into three regions. For one power allocation scheme, the diversity order is exponential throughout the capacity region. For selective channel inversion (SCI) scheme, the diversity order is exponential in low and high rate region but polynomial in mid rate region. For fast fading case we also provide a new upper bound on block error probability and a power allocation scheme that minimizes it. The diversity order behaviour of this scheme is same as for SCI but provides lower BER than the other policies.

Threats and trade-fffs in resource critical crowdsourcing tasks over networks

In recent times, crowdsourcing over social networks has emerged as an active tool for complex task execution. In this paper, we address the problem faced by a planner to incen-tivize agents in the network to execute a task and also help in recruiting other agents for this purpose. We study this mecha-nism design problem under two natural resource optimization settings: (1) cost critical tasks, where the planner’s goal is to minimize the total cost, and (2) time critical tasks, where the goal is to minimize the total time elapsed before the task is executed. We define a set of fairness properties that should beideally satisfied by a crowdsourcing mechanism. We prove that no mechanism can satisfy all these properties simultane-ously. We relax some of these properties and define their ap-proximate counterparts. Under appropriate approximate fair-ness criteria, we obtain a non-trivial family of payment mech-anisms. Moreover, we provide precise characterizations of cost critical and time critical mechanisms.

Regenerating codes: A reformulated storage-bandwidth trade-off and a new construction

In this paper, the storage-repair-bandwidth (SRB) trade-off curve of regenerating codes is reformulated to yield a tradeoff between two global parameters of practical relevance, namely information rate and repair rate. The new information-repair-rate (IRR) tradeoff provides a different and insightful perspective on regenerating codes. For example, it provides a new motivation for seeking to investigate constructions corresponding to the interior of the SRB tradeoff. Interestingly, each point on the SRB tradeoff corresponds to a curve in the IRR tradeoff setup. We characterize completely, functional repair under the IRR framework, while for exact repair, an achievable region is presented. In the second part of this paper, a rate-half regenerating code for the minimum storage regenerating point is constructed that draws upon the theory of invariant subspaces. While the parameters of this rate-half code are the same as those of the MISER code, the construction itself is quite different.