Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (similar to 80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

Bilinear tension softening diagrams of concrete mixes corresponding to their size-independent specific fracture energy

The study of the fracture behaviour of concrete structures using the fictitious crack model requires two fracture properties of the concrete mix, namely, the size-independent specific fracture energy G(F). and the corresponding tension softening relation sigma(w) between the residual stress carrying capacity sigma and the crack opening w in the fracture process zone ahead of a real crack. In this paper, bi-linear tension softening diagrams of three different concrete mixes, ranging in compressive strength from 57 to 122 MPa whose size-independent specific fracture energy has been previously determined, have been constructed in an inverse manner based on the concept of a non-linear hinge from the load-crack mouth opening plots of notched three-point bend beams. (C) 2013 Elsevier Ltd. All rights reserved.

An insight into real-time performance assessment of a building integrated photovoltaic (BIPV) installation in Bangalore (India)

Building integrated photovoltaic (BIPV) applications are gaining widespread popularity. The performance of any given BIPV system is dependent on prevalent meteorological factors, site conditions and system characteristics. Investigations pertaining to the performance assessment of photovoltaic (PV) systems are generally confined to either controlled environment-chambers or computer-based simulation studies. Such investigations fall short of providing a realistic insight into how a PV system actually performs real-time. Solar radiation and the PV cell temperature are amongst the most crucial parameters affecting PV output. The current paper deals with the real-time performance assessment of a recently commissioned 5.25 kW, BIPV system installed at the Center for Sustainable Technologies, Indian Institute of Science, Bangalore. The overall average system efficiency was found to be 6% for the period May 2011-April 2012. This paper provides a critical appraisal of PV system performance based on ground realities, particularly characteristic to tropical (moderate) regions such as Bangalore, India. (C) 2013 International Energy Initiative. Published by Elsevier Inc. All rights reserved.

Cell (module) temperature regulated performance of a building integrated photovoltaic system in tropical conditions

The performance of a building integrated photovoltaic system (BIPV) has to be commendable, not only on the electrical front but also on the thermal comfort front, thereby fulfilling the true responsibility of an energy providing shelter. Given the low thermal mass of BIPV systems, unintended and undesired outcomes of harnessing solar energy - such as heat gain into the building, especially in tropical regions - have to be adequately addressed. Cell (module) temperature is one critical factor that affects both the electrical and the thermal performance of such installations. The current paper discusses the impact of cell (module) temperature on both the electrical efficiency and thermal comfort by investigating the holistic performance of one such system (5.25 kW(p)) installed at the Centre for Sustainable Technologies in the Indian Institute of Science, Bangalore. Some recommendations (passive techniques) for improving the performance and making BIPV structures thermally comfortable have been listed out. (C) 2014 Elsevier Ltd. All rights reserved.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Collective eigenstates of emission in an N-entity heterostructure and the evaluation of its Green tensors and self-energy components

Optical emission from emitters strongly interacting among themselves and also with other polarizable matter in close proximity has been approximated by emission from independent emitters. This is primarily due to our inability to evaluate the self-energy matrices and radiative properties of the collective eigenstates of emitters in heterogeneous ensembles. A method to evaluate self-energy matrices that is not limited by the geometry and material composition is presented to understand and exploit such collective excitations. Numerical evaluations using this method are used to highlight the significant differences between independent and the collective modes of emission in nanoscale heterostructures. A set of N Lorentz emitters and other polarizable entities is used to represent the coupled system of a generalized geometry in a volume integral approach. Closed form relations between the Green tensors of entity pairs in free space and their correspondents in a heterostructure are derived concisely. This is made possible for general geometries because the global matrices consisting of all free-space Green dyads are subject to conservation laws. The self-energy matrix can then be assembled using the evaluated Green tensors of the heterostructure, but a decomposition of its components into their radiative and nonradiative decay contributions is nontrivial. The relations to compute the observables of the eigenstates (such as quantum efficiency, power/energy of emission, radiative and nonradiative decay rates) are presented. A note on extension of this method to collective excitations, which also includes strong interactions with a surface in the near-field, is added. (C) 2014 Optical Society of America

Assessing impact of material transition and thermal comfort models on embodied and operational energy in vernacular dwellings (India)

Vernacular dwellings are well-suited climate-responsive designs that adopt local materials and skills to support comfortable indoor environments in response to local climatic conditions. These naturally-ventilated passive dwellings have enabled civilizations to sustain even in extreme climatic conditions. The design and physiological resilience of the inhabitants have coevolved to be attuned to local climatic and environmental conditions. Such adaptations have perplexed modern theories in human thermal-comfort that have evolved in the era of electricity and air-conditioned buildings. Vernacular local building elements like rubble walls and mud roofs are given way to burnt brick walls and reinforced cement concrete tin roofs. Over 60% of Indian population is rural, and implications of such transitions on thermal comfort and energy in buildings are crucial to understand. Types of energy use associated with a buildings life cycle include its embodied energy, operational and maintenance energy, demolition and disposal energy. Embodied Energy (EE) represents total energy consumption for construction of building, i.e., embodied energy of building materials, material transportation energy and building construction energy. Embodied energy of building materials forms major contribution to embodied energy in buildings. Operational energy (OE) in buildings mainly contributed by space conditioning and lighting requirements, depends on the climatic conditions of the region and comfort requirements of the building occupants. Less energy intensive natural materials are used for traditional buildings and the EE of traditional buildings is low. Transition in use of materials causes significant impact on embodied energy of vernacular dwellings. Use of manufactured, energy intensive materials like brick, cement, steel, glass etc. contributes to high embodied energy in these dwellings. This paper studies the increase in EE of the dwelling attributed to change in wall materials. Climatic location significantly influences operational energy in dwellings. Buildings located in regions experiencing extreme climatic conditions would require more operational energy to satisfy the heating and cooling energy demands throughout the year. Traditional buildings adopt passive techniques or non-mechanical methods for space conditioning to overcome the vagaries of extreme climatic variations and hence less operational energy. This study assesses operational energy in traditional dwelling with regard to change in wall material and climatic location. OE in the dwellings has been assessed for hot-dry, warm humid and moderate climatic zones. Choice of thermal comfort models is yet another factor which greatly influences operational energy assessment in buildings. The paper adopts two popular thermal-comfort models, viz., ASHRAE comfort standards and TSI by Sharma and Ali to investigate thermal comfort aspects and impact of these comfort models on OE assessment in traditional dwellings. A naturally ventilated vernacular dwelling in Sugganahalli, a village close to Bangalore (India), set in warm - humid climate is considered for present investigations on impact of transition in building materials, change in climatic location and choice of thermal comfort models on energy in buildings. The study includes a rigorous real time monitoring of the thermal performance of the dwelling. Dynamic simulation models validated by measured data have also been adopted to determine the impact of the transition from vernacular to modern material-configurations. Results of the study and appraisal for appropriate thermal comfort standards for computing operational energy has been presented and discussed in this paper. (c) 2014 K.I. Praseeda. Published by Elsevier Ltd.

Discerning heat transfer in building materials

The function of a building is to ensure safety and thermal comfort for healthy living conditions. Buildings primarily comprise an envelope, which acts as an interface separating the external environment from the indoors environment. The building envelope is primarily responsible for regulating indoor thermal comfort in response to external climatic conditions. It usually comprises a configuration of building materials to thus far provide requisite structural performance. However, studies into building-envelope configurations to provide a particular thermal performance are limited. As the building envelope is exposed to the external environment there will be heat and moisture transfer to the indoor environment through it. The overall phenomenon of heat and moisture transfer depends on the microstructure and configuration within the building material. Further, thermal property of a material is generally dependent on its microstructure, which comprises a network of pores and particles arranged in a definite structure. Thermal behaviour of a building material thus depends on the thermal conductivities of the solid particles, pore micro-structure and its constituent fluid (air and/or moisture). The thermal response of a building envelope is determined by the thermal characteristics of the individual building materials and its configuration. Understanding the heat transfer influenced by the complex networks of pores and particles is a relatively new study in the area of building climatic-response. The current study reviews the heat-transfer mechanisms that determine the thermal performance of a building material attributed to its micro-structure. A theoretical basis for the same is being evolved and its relevance in regulating heat-transfer through building envelopes, walls in particular, is reviewed in this paper. (C) 2014 N.C. Balaji. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Conservation Properties of the Trapezoidal Rule in Linear Time Domain Analysis of Acoustics and Structures

The trapezoidal rule, which is a special case of the Newmark family of algorithms, is one of the most widely used methods for transient hyperbolic problems. In this work, we show that this rule conserves linear and angular momenta and energy in the case of undamped linear elastodynamics problems, and an ``energy-like measure'' in the case of undamped acoustic problems. These conservation properties, thus, provide a rational basis for using this algorithm. In linear elastodynamics problems, variants of the trapezoidal rule that incorporate ``high-frequency'' dissipation are often used, since the higher frequencies, which are not approximated properly by the standard displacement-based approach, often result in unphysical behavior. Instead of modifying the trapezoidal algorithm, we propose using a hybrid finite element framework for constructing the stiffness matrix. Hybrid finite elements, which are based on a two-field variational formulation involving displacement and stresses, are known to approximate the eigenvalues much more accurately than the standard displacement-based approach, thereby either bypassing or reducing the need for high-frequency dissipation. We show this by means of several examples, where we compare the numerical solutions obtained using the displacement-based and hybrid approaches against analytical solutions.

Embodied and operational energy of urban residential buildings in India

Globally, buildings consume nearly half of the total energy produced, and consequently responsible for a large share of CO2 emissions. A building's life cycle energy (LCE) comprises its embodied energy (EE) and operational energy (OE). The building design, prevalent climatic conditions and occupant behaviour primarily determines its LCE. Thus, for the identification of appropriate emission-reduction strategies, studies into building LCE are crucial. While OE reflects the energy utilized in operating a, EE comprises the initial capital energy involved in its construction (material and burden associated with material consumption in buildings. Assessment of EE and OE in buildings is crucial towards identifying appropriate design and operational strategies for reduction of the building's life cycle energy. This paper discusses EE and OE assessment of a few residential buildings in different climatic locations in India. The study shows that share of OE and EE in LCE greatly depends upon the types of materials used in construction and extent of space conditioning adopted. In some cases EE can exceed life cycle OE. Buildings with reinforced concrete frame and monolithic reinforced concrete walls have very high EE. (C) 2015 Elsevier B.V. All rights reserved.