A microcomputer program to analyze the CD spectrum of proteins and nucleic acids—Use of LOTUS 1-2-3 spread sheet

A user friendly interactive computer program, CIRDIC, is developed which calculates the molar ellipticity and molar circular dichroic absorption coefficients from the CD spectrum. This, in combination with LOTUS 1-2-3 spread sheet, will give the spectra of above parameters vs wavelength. The code is implemented in MicroSoft FORTRAN 77 which runs on any IBM compatible PC under MSDOS environment.

Optimization and design of energy transport system for solar cooking application

This paper proposes a hybrid solar cooking system where the solar energy is transported to the kitchen. The thermal energy source is used to supplement the Liquefied Petroleum Gas (LPG) that is in common use in kitchens. Solar energy is transferred to the kitchen by means of a circulating fluid. Energy collected from sun is maximized by changing the flow rate dynamically. This paper proposes a concept of maximum power point tracking (MPPT) for the solar thermal collector. The diameter of the pipe is selected to optimize the overall energy transfer. Design and sizing of different components of the system are explained. Concept of MPPT is validated with simulation and experimental results. (C) 2010 Elsevier Ltd. All rights reserved.

Theoretical gain‐optimization studies in CO2–N2 gasdynamic lasers. II. Results of parametric study

Based on a method presented in detail in a previous work by the authors, similar solutions have been obtained for the steady inviscid quasi‐one‐dimensional nonreacting flow in the supersonic nozzle of a CO2–N2 gasdynamic laser system, with either H2O or He as the catalyst. It has been demonstrated how these solutions could be used to optimize the small‐signal gain coefficient on a specified vibrational‐rotational transition. Results presented for a wide range of mixture compositions include optimum values for the small‐signal gain, area ratio, reservoir temperature, and a binary scaling parameter, which is the product of reservoir pressure and nozzle shape factor.

Theoretical gain‐optimization studies in CO2–N2 gasdynamic lasers. I. Theory

Based on a method proposed by Reddy and Daum, the equations governing the steady inviscid nonreacting gasdynamic laser (GDL) flow in a supersonic nozzle are reduced to a universal form so that the solutions depend on a single parameter which combines all the other parameters of the problem. Solutions are obtained for a sample case of available data and compared with existing results to validate the present approach. Also, similar solutions for a sample case are presented.

Optimization of two-dimensional NMR by matched accumulation

It is well known that in the time-domain acquisition of NMR data, signal-to-noise (S/N) improves as the square root of the number of transients accumulated. However, the amplitude of the measured signal varies during the time of detection, having a functional form dependent on the coherence detected. Matching the time spent signal averaging to the expected amplitude of the signal observed should also improve the detected signal-to-noise. Following this reasoning, Barna et al. (J Magn. Reson.75, 384, 1987) demonstrated the utility of exponential sampling in one- and two-dimensional NMR, using maximum-entropy methods to analyze the data. It is proposed here that for two-dimensional experiments the exponential sampling be replaced by exponential averaging. The data thus collected can be analyzed by standard fast-Fourier-transform routines. We demonstrate the utility of exponential averaging in 2D NOESY spectra of the protein ubiquitin, in which an enhanced SIN is observed. It is also shown that the method acquires delayed double-quantum-filtered COSY without phase distortion.

A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

Determining the sequence of amino acid residues in a heteropolymer chain of a protein with a given conformation is a discrete combinatorial problem that is not generally amenable for gradient-based continuous optimization algorithms. In this paper we present a new approach to this problem using continuous models. In this modeling, continuous "state functions" are proposed to designate the type of each residue in the chain. Such a continuous model helps define a continuous sequence space in which a chosen criterion is optimized to find the most appropriate sequence. Searching a continuous sequence space using a deterministic optimization algorithm makes it possible to find the optimal sequences with much less computation than many other approaches. The computational efficiency of this method is further improved by combining it with a graph spectral method, which explicitly takes into account the topology of the desired conformation and also helps make the combined method more robust. The continuous modeling used here appears to have additional advantages in mimicking the folding pathways and in creating the energy landscapes that help find sequences with high stability and kinetic accessibility. To illustrate the new approach, a widely used simplifying assumption is made by considering only two types of residues: hydrophobic (H) and polar (P). Self-avoiding compact lattice models are used to validate the method with known results in the literature and data that can be practically obtained by exhaustive enumeration on a desktop computer. We also present examples of sequence design for the HP models of some real proteins, which are solved in less than five minutes on a single-processor desktop computer Some open issues and future extensions are noted.

Development of a structured program for conversion to prenex normal form

The method of structured programming or program development using a top-down, stepwise refinement technique provides a systematic approach for the development of programs of considerable complexity. The aim of this paper is to present the philosophy of structured programming through a case study of a nonnumeric programming task. The problem of converting a well-formed formula in first-order logic into prenex normal form is considered. The program has been coded in the programming language PASCAL and implemented on a DEC-10 system. The program has about 500 lines of code and comprises 11 procedures.

Filter Optimization for Grid Interactive Voltage Source Inverters

Higher order LCL filters are essential in meeting the interconnection standard requirement for grid-connected voltage source converters. LCL filters offer better harmonic attenuation and better efficiency at a smaller size when compared to the traditional L filters. The focus of this paper is to analyze the LCL filter design procedure from the point of view of power loss and efficiency. The IEEE 1547-2008 specifications for high-frequency current ripple are used as a major constraint early in the design to ensure that all subsequent optimizations are still compliant with the standards. Power loss in each individual filter component is calculated on a per-phase basis. The total inductance per unit of the LCL filter is varied, and LCL parameter values which give the highest efficiency while simultaneously meeting the stringent standard requirements are identified. The power loss and harmonic output spectrum of the grid-connected LCL filter is experimentally verified, and measurements confirm the predicted trends.

Nature inspired optimization techniques for the design optimization of laminated composite structures using failure criteria

The design optimization of laminated composites using naturally inspired optimization techniques such as vector evaluated particle swarm optimization (VEPSO) and genetic algorithms (GA) are used in this paper. The design optimization of minimum weight of the laminated composite is evaluated using different failure criteria. The failure criteria considered are maximum stress (MS), Tsai-Wu (TW) and failure mechanism based (FMB) failure criteria. Minimum weight of the laminates are obtained for different failure criteria using VEPSO and GA for different combinations of loading. From the study it is evident that VEPSO and GA predict almost the same minimum weight of the laminate for the given loading. Comparison of minimum weight of the laminates by different failure criteria differ for some loading combinations. The comparison shows that FMBFC provide better results for all combinations of loading. (C) 2010 Elsevier Ltd. All rights reserved.

HELANAL: A program to characterise helix geometry in proteins,

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their C-alpha atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Compiler-assisted power optimization for clustered VLIW architectures

Clustered VLIW architectures solve the scalability problem associated with flat VLIW architectures by partitioning the register file and connecting only a subset of the functional units to a register file. However, inter-cluster communication in clustered architectures leads to increased leakage in functional components and a high number of register accesses. In this paper, we propose compiler scheduling algorithms targeting two previously ignored power-hungry components in clustered VLIW architectures, viz., instruction decoder and register file. We consider a split decoder design and propose a new energy-aware instruction scheduling algorithm that provides 14.5% and 17.3% benefit in the decoder power consumption on an average over a purely hardware based scheme in the context of 2-clustered and 4-clustered VLIW machines. In the case of register files, we propose two new scheduling algorithms that exploit limited register snooping capability to reduce extra register file accesses. The proposed algorithms reduce register file power consumption on an average by 6.85% and 11.90% (10.39% and 17.78%), respectively, along with performance improvement of 4.81% and 5.34% (9.39% and 11.16%) over a traditional greedy algorithm for 2-clustered (4-clustered) VLIW machine. (C) 2010 Elsevier B.V. All rights reserved.

Coupled electrostatic-elastic analysis for topology optimization using material interpolation

In this paper, we present a novel analytical formulation for the coupled partial differential equations governing electrostatically actuated constrained elastic structures of inhomogeneous material composition. We also present a computationally efficient numerical framework for solving the coupled equations over a reference domain with a fixed finite-element mesh. This serves two purposes: (i) a series of problems with varying geometries and piece-wise homogeneous and/or inhomogeneous material distribution can be solved with a single pre-processing step, (ii) topology optimization methods can be easily implemented by interpolating the material at each point in the reference domain from a void to a dielectric or a conductor. This is attained by considering the steady-state electrical current conduction equation with a `leaky capacitor' model instead of the usual electrostatic equation. This formulation is amenable for both static and transient problems in the elastic domain coupled with the quasi-electrostatic electric field. The procedure is numerically implemented on the COMSOL Multiphysics (R) platform using the weak variational form of the governing equations. Examples have been presented to show the accuracy and versatility of the scheme. The accuracy of the scheme is validated for the special case of piece-wise homogeneous material in the limit of the leaky-capacitor model approaching the ideal case.

Indian Nanoelectronics Users Program An Outreach Vehicle to Expedite Nanoelectronics Research in India

The worldwide research in nanoelectronics is motivated by the fact that scaling of MOSFETs by conventional top down approach will not continue for ever due to fundamental limits imposed by physics even if it is delayed for some more years. The research community in this domain has largely become multidisciplinary trying to discover novel transistor structures built with novel materials so that semiconductor industry can continue to follow its projected roadmap. However, setting up and running a nanoelectronics facility for research is hugely expensive. Therefore it is a common model to setup a central networked facility that can be shared with large number of users across the research community. The Centres for Excellence in Nanoelectronics (CEN) at Indian Institute of Science, Bangalore (IISc) and Indian Institute of Technology, Bombay (IITB) are such central networked facilities setup with funding of about USD 20 million from the Department of Information Technology (DIT), Ministry of Communications and Information Technology (MCIT), Government of India, in 2005. Indian Nanoelectronics Users Program (INUP) is a missionary program not only to spread awareness and provide training in nanoelectronics but also to provide easy access to the latest facilities at CEN in IISc and at IITB for the wider nanoelectronics research community in India. This program, also funded by MCIT, aims to train researchers by conducting workshops, hands-on training programs, and providing access to CEN facilities. This is a unique program aiming to expedite nanoelectronics research in the country, as the funding for projects required for projects proposed by researchers from around India has prior financial approval from the government and requires only technical approval by the IISc/ IITB team. This paper discusses the objectives of INUP, gives brief descriptions of CEN facilities, the training programs conducted by INUP and list various research activities currently under way in the program.

Stochastic Approximation Algorithms for Constrained Optimization via Simulation

We develop four algorithms for simulation-based optimization under multiple inequality constraints. Both the cost and the constraint functions are considered to be long-run averages of certain state-dependent single-stage functions. We pose the problem in the simulation optimization framework by using the Lagrange multiplier method. Two of our algorithms estimate only the gradient of the Lagrangian, while the other two estimate both the gradient and the Hessian of it. In the process, we also develop various new estimators for the gradient and Hessian. All our algorithms use two simulations each. Two of these algorithms are based on the smoothed functional (SF) technique, while the other two are based on the simultaneous perturbation stochastic approximation (SPSA) method. We prove the convergence of our algorithms and show numerical experiments on a setting involving an open Jackson network. The Newton-based SF algorithm is seen to show the best overall performance.