The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Delay and energy optimal two-hop relaying in delay tolerant networks

We study the trade-off between delivery delay and energy consumption in delay tolerant mobile wireless networks that use two-hop relaying. The source may not have perfect knowledge of the delivery status at every instant. We formulate the problem as a stochastic control problem with partial information, and study structural properties of the optimal policy. We also propose a simple suboptimal policy. We then compare the performance of the suboptimal policy against that of the optimal control with perfect information. These are bounds on the performance of the proposed policy with partial information. Several other related open loop policies are also compared with these bounds.

INTACTE: An Interconnect Area, Delay, and Energy Estimation Tool for Microarchitectural Explorations

Prior work on modeling interconnects has focused on optimizing the wire and repeater design for trading off energy and delay, and is largely based on low level circuit parameters. Hence these models are hard to use directly to make high level microarchitectural trade-offs in the initial exploration phase of a design. In this paper, we propose INTACTE, a tool that can be used by architects toget reasonably accurate interconnect area, delay, and power estimates based on a few architecture level parameters for the interconnect such as length, width (in number of bits), frequency, and latency for a specified technology and voltage. The tool uses well known models of interconnect delay and energy taking into account the wire pitch, repeater size, and spacing for a range of voltages and technologies.It then solves an optimization problem of finding the lowest energy interconnect design in terms of the low level circuit parameters, which meets the architectural constraintsgiven as inputs. In addition, the tool also provides the area, energy, and delay for a range of supply voltages and degrees of pipelining, which can be used for micro-architectural exploration of a chip. The delay and energy models used by the tool have been validated against low level circuit simulations. We discuss several potential applications of the tool and present an example of optimizing interconnect design in the context of clustered VLIW architectures. Copyright 2007 ACM.

Enhancement of charge and energy storage in sol-gel derived pure and La-modified PbZrO3 thin films

Antiferroelectric lanthanum-modified PbZrO3 thin films with La contents between 0 and 6 at. % have been deposited on Pt(111)/Ti/SiO2/Si substrate by sol-gel route. On the extent of La-modification, maximum polarization (Pmax) and recoverable energy density (W) have been enhanced followed by their subsequent reduction. A maximum Pmax ( ∼ 0.54 C/m2 at ∼ 60 MV/m) as well as a maximum W ( ∼ 14.9 J/cc at ∼ 60 MV/m) have been achieved on 5% La modification. Both Pmax and W have been found to be strongly dependent on La-induced crystallographic orientations.

Sensitivity of terrestrial water and energy budgets to CO(2)-physiological forcing: an investigation using an offline land model

Increasing concentrations of atmospheric carbon dioxide (CO(2)) influence climate by suppressing canopy transpiration in addition to its well- known greenhouse gas effect. The decrease in plant transpiration is due to changes in plant physiology (reduced opening of plant stomata). Here, we quantify such changes in water flux for various levels of CO(2) concentrations using the National Center for Atmospheric Research's (NCAR) Community Land Model. We find that photosynthesis saturates after 800 ppmv (parts per million, by volume) in this model. However, unlike photosynthesis, canopy transpiration continues to decline at about 5.1% per 100 ppmv increase in CO(2) levels. We also find that the associated reduction in latent heat flux is primarily compensated by increased sensible heat flux. The continued decline in canopy transpiration and subsequent increase in sensible heat flux at elevated CO(2) levels implies that incremental warming associated with the physiological effect of CO(2) will not abate at higher CO(2) concentrations, indicating important consequences for the global water and carbon cycles from anthropogenic CO(2) emissions.

Renewable energy and energy conservation technologies

Energy systems should be consistent with environmental, economic and social sustainability in order to ensure regional sustainable development. This enhances both current and future potential to meet the human needs and aspirations. Sustainable development, a process of change, in which, the exploitation of resources, the direction of investments , the orientation of technological development and institutional change are in harmony. National energy programme should prioritize the development of renewable energy sources, which offer the potentially huge sources of primary energy. The path for sustainability in the next millennium is the low energy path through wise use of energy. Energy conservation and energy efficiency measures would certainly result in meeting the energy demand with as little as half the primary supply at current levels. This requires profound structural changes in socio-economic and institutional arrangements. Environmentally sound, technically and economically viable energy pathways will sustain human progress in the long term future giving a fair and equitable share of the underprivileged and poor of the developing countries. Renewable energy is considered by some as the only hope for the survival of planet yet by others it is viewed as a marginal resource with limited resource. All too often, however, the facts behind the role that renewable energy can, and will, play in the regional energy scene are disguised or ignored as rival camps distort the evidence to suit their own objectives. It was in the light of this confusion that the Energy Research Group at Centre for Ecological Sciences, Indian Institute of Science undertook investigation in Kolar and Uttara Kannada Districts in Karnataka State, India to identify the potential contribution of several types of renewable energy sources: Solar, Wind, Hydro, Bioenergy, etc.

Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein

In Escherichia coli, the filament of RecA formed on single-stranded DNA (ssDNA) is essential for recombinational DNA repair. Although ssDNA-binding protein (SSB) plays a complicated role in RecA reactions in vivo, much of our understanding of the mechanism is based on RecA binding directly to ssDNA. Here we investigate the role of SSB in the regulation of RecA polymerization on ssDNA, based on the differential force responses of a single 576-nucleotide-long ssDNA associated with RecA and SSB. We find that SSB outcompetes higher concentrations of RecA, resulting in inhibition of RecA nucleation. In addition, we find that pre-formed RecA filaments de-polymerize at low force in an ATP hydrolysis- and SSB-dependent manner. At higher forces, re-polymerization takes place, which displaces SSB from ssDNA. These findings provide a physical picture of the competition between RecA and SSB under tension on the scale of the entire nucleoprotein SSB array, which have broad biological implications particularly with regard to competitive molecular binding.

Training for Antenna Selection in Time-Varying Channels: Optimal Selection, Energy Allocation, and Energy Efficiency Evaluation

Single receive antenna selection (AS) is a popular method for obtaining diversity benefits without the additional costs of multiple radio receiver chains. Since only one antenna receives at any time, the transmitter sends a pilot multiple times to enable the receiver to estimate the channel gains of its N antennas to the transmitter and select an antenna. In time-varying channels, the channel estimates of different antennas are outdated to different extents. We analyze the symbol error probability (SEP) in time-varying channels of the N-pilot and (N+1)-pilot AS training schemes. In the former, the transmitter sends one pilot for each receive antenna. In the latter, the transmitter sends one additional pilot that helps sample the channel fading process of the selected antenna twice. We present several new results about the SEP, optimal energy allocation across pilots and data, and optimal selection rule in time-varying channels for the two schemes. We show that due to the unique nature of AS, the (N+1)-pilot scheme, despite its longer training duration, is much more energy-efficient than the conventional N-pilot scheme. An extension to a practical scenario where all data symbols of a packet are received by the same antenna is also investigated.

The effect of cell size and channel density on neuronal information encoding and energy efficiency

Identifying the determinants of neuronal energy consumption and their relationship to information coding is critical to understanding neuronal function and evolution. Three of the main determinants are cell size, ion channel density, and stimulus statistics. Here we investigate their impact on neuronal energy consumption and information coding by comparing single-compartment spiking neuron models of different sizes with different densities of stochastic voltage-gated Na+ and K+ channels and different statistics of synaptic inputs. The largest compartments have the highest information rates but the lowest energy efficiency for a given voltage-gated ion channel density, and the highest signaling efficiency (bits spike(-1)) for a given firing rate. For a given cell size, our models revealed that the ion channel density that maximizes energy efficiency is lower than that maximizing information rate. Low rates of small synaptic inputs improve energy efficiency but the highest information rates occur with higher rates and larger inputs. These relationships produce a Law of Diminishing Returns that penalizes costly excess information coding capacity, promoting the reduction of cell size, channel density, and input stimuli to the minimum possible, suggesting that the trade-off between energy and information has influenced all aspects of neuronal anatomy and physiology.

Multiple sub-row buffers in DRAM: unlocking performance and energy improvement opportunities

The twin demands of energy-efficiency and higher performance on DRAM are highly emphasized in multicore architectures. A variety of schemes have been proposed to address either the latency or the energy consumption of DRAMs. These schemes typically require non-trivial hardware changes and end up improving latency at the cost of energy or vice-versa. One specific DRAM performance problem in multicores is that interleaved accesses from different cores can potentially degrade row-buffer locality. In this paper, based on the temporal and spatial locality characteristics of memory accesses, we propose a reorganization of the existing single large row-buffer in a DRAM bank into multiple sub-row buffers (MSRB). This re-organization not only improves row hit rates, and hence the average memory latency, but also brings down the energy consumed by the DRAM. The first major contribution of this work is proposing such a reorganization without requiring any significant changes to the existing widely accepted DRAM specifications. Our proposed reorganization improves weighted speedup by 35.8%, 14.5% and 21.6% in quad, eight and sixteen core workloads along with a 42%, 28% and 31% reduction in DRAM energy. The proposed MSRB organization enables opportunities for the management of multiple row-buffers at the memory controller level. As the memory controller is aware of the behaviour of individual cores it allows us to implement coordinated buffer allocation schemes for different cores that take into account program behaviour. We demonstrate two such schemes, namely Fairness Oriented Allocation and Performance Oriented Allocation, which show the flexibility that memory controllers can now exploit in our MSRB organization to improve overall performance and/or fairness. Further, the MSRB organization enables additional opportunities for DRAM intra-bank parallelism and selective early precharging of the LRU row-buffer to further improve memory access latencies. These two optimizations together provide an additional 5.9% performance improvement.

Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency

Information is encoded in neural circuits using both graded and action potentials, converting between them within single neurons and successive processing layers. This conversion is accompanied by information loss and a drop in energy efficiency. We investigate the biophysical causes of this loss of information and efficiency by comparing spiking neuron models, containing stochastic voltage-gated Na+ and K+ channels, with generator potential and graded potential models lacking voltage-gated Na+ channels. We identify three causes of information loss in the generator potential that are the by-product of action potential generation: (1) the voltage-gated Na+ channels necessary for action potential generation increase intrinsic noise and (2) introduce non-linearities, and (3) the finite duration of the action potential creates a `footprint' in the generator potential that obscures incoming signals. These three processes reduce information rates by similar to 50% in generator potentials, to similar to 3 times that of spike trains. Both generator potentials and graded potentials consume almost an order of magnitude less energy per second than spike trains. Because of the lower information rates of generator potentials they are substantially less energy efficient than graded potentials. However, both are an order of magnitude more efficient than spike trains due to the higher energy costs and low information content of spikes, emphasizing that there is a two-fold cost of converting analogue to digital; information loss and cost inflation.

A Discussion on Modeling Shape Memory Alloy Embedded in A Composite Laminate as Axial Force and Elastic Foundation

In this paper, the possible error sources of the composite natural frequencies due to modeling the shape memory alloy (SMA) wire as an axial force or an elastic foundation and anisotropy are discussed. The great benefit of modeling the SMA wire as an axial force and an elastic foundation is that the complex constitutive relation of SMA can be avoided. But as the SMA wire and graphite-epoxy are rigidly bonded together, such constraint causes the re-distribution of the stress in the composite. This, together with anisotropy, which also reduces the structural stiffness can cause the relatively large error between the experimental data and theoretical results.