Abstract

Riboswitches are RNA-based genetic control elements that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket. To facilitate an atomic detail interpretation of experimental investigations on the role of the adenine ligand on the conformational properties and kinetics of folding of the add adenine riboswitch, we performed molecular dynamics simulations in both the presence and the absence of the ligand. In the absence of ligand, structural deviations were observed in the J23 junction and the P1 stem. Destabilization of the P1 stem in the absence of ligand involves the loss of direct stabilizing interactions with the ligand, with additional contributions from the J23 junction region. The J23 junction of the riboswitch is found to be more flexible, and the tertiary contacts among the junction regions are altered in the absence of the adenine ligand; results suggest that the adenine ligand associates and dissociates from the riboswitch in the vicinity of J23. Good agreement was obtained with the experimental data with the results indicating dynamic behavior of the adenine ligand on the nanosecond time scale to be associated with the dynamic behavior of hydrogen bonding with the riboswitch. Results also predict that direct interactions of the adenine ligand with U74 of the riboswitch are not essential for stable binding although it is crucial for its recognition. The possibility of methodological artifacts and force-field inaccuracies impacting the present observations was checked by additional molecular dynamics simulations in the presence of 2,6-diaminopurine and in the crystal environment. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Abstract

Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.

Abstract

The enlarging HIV/AIDS pandemic and the virus’ ability to develop resistance to anti-retroviral therapy requires the development of new drugs based on novel targets. Viruses interact extensively with the host at the cellular and molecular levels, which is necessary for the expression of viral proteins and replication of viral genomes. At another level, these interactions also help the virus evade host immune responses. Besides the prototypic retroviral proteins (Gag, Pol and Env), HIV-1 also expresses two regulatory proteins (Tat and Rev) and four accessory proteins (Nef, Vif, Vpr and Vpu). The accessory proteins are not required for viral replication in vitro, but are critical for pathogenesis and disease development in the host. We have focused our efforts on two of these – Nef and Vpu, with an aim to understand their interactions with host proteins and the functional consequences of these interactions for HIV-1 infection and pathogenesis. The Nef protein binds to multiple host proteins to optimize the host cell environment and to enable infected cells to evade the host immune response. A major property of Nef is to downregulate surface expression of the CD4, MHC I and MHC II proteins, by increasing the endocytosis of these molecules. We also discovered that Nef binds to the cytoplasmic domains of the B7 family of costimulatory proteins – CD80 and CD86; this results in their removal from the cell surface and sequestration to the Golgi compartment (1-3). We have now developed an in vitro screen based on purified recombinant Nef proteins and a 20-mer synthetic peptide from the cytoplasmic domain of CD80 and CD86. A chemical library comprising of 1064 compounds was screened and ~7% compounds were obtained as hits, which inhibited the Nef-CD80/CD86 interaction. These compounds are now being evaluated in a cellbased assay and an independent dose dependent response assay. The top hits will be used in a combinatorial chemical approach to synthesize a large array of new molecules for further screening using the in vitro and cell-based screens. The HIV-1 Vpu protein is required for the release of new virions from the surface of infected cells; for this the transmembrane domain of Vpu is critical. Using the Topology Data Bank of Transmembrane Proteins (TOPDB) database we extracted 13 alpha-helical sequences that closely resemble the Vpu-TM domain. We have taken the top two hits and have constructed recombinant Vpu proteins in which the native TM domain was replaced by the identified sequences. These recombinant proteins were successfully expressed in HEK293 cells, and are now being tested for their effects on virion release as well as their ability to inhibit Vpu activity. We describe here two paradigms to screen for anti-HIV activity based on proteinprotein interactions. Results will be presented for both of these.

Abstract

Distance bounding protocols are used by nodes in wireless networks to calculate upper bounds on their distances to other nodes. However, dishonest nodes in the network can turn the calculations both illegitimate and inaccurate when they participate in protocol executions. It is important to analyze protocols for the possibility of such violations. Past efforts to analyze distance bounding protocols have only been manual. However, automated approaches are important since they are quite likely to find flaws that manual approaches cannot, as witnessed in literature for analysis pertaining to key establishment protocols. In this paper, we use the constraint solver tool to automatically analyze distance bounding protocols. We first formulate a new trace property called Secure Distance Bounding (SDB) that protocol executions must satisfy. We then classify the scenarios in which these protocols can operate considering the (dis) honesty of nodes and location of the attacker in the network. Finally, we extend the constraint solver so that it can be used to test protocols for violations of SDB in these scenarios and illustrate our technique on some published protocols.

Abstract

One important challenge in wireless ad hoc networks is to achieve collision free communication. Many MAC layer protocols have been proposed by considering various communication models of the ad hoc networks. One such protocol is TDMA, which provides for interference free communication while providing some bound on the packet delay. However, most proposed TDMA schemes can perform scheduling transmissions among nodes that are within transmission range. This is due to the simplistic modeling of the underlying network. Recently, more practical network models and overlay construction algorithms have been proposed that consider the interference among nodes as well. Existing TDMA protocols are unsuitable for such models as they will have to consider the interference range of the nodes as well. This requires that the TDMA protocol operate in a global perspective while working as a local-control algorithm. In this work, we describe a novel TDMA protocol that is suitable for such realistic and practical network models. We also extend the TDMA protocol to handle other difficulties such as membership changes within transmission range and interference range. Some networks also have to deal with sleeping nodes that wake up periodically. Our TDMA scheme employs a simple control phase and a data phase to handle such tasks. Some of the benefits of our solution are that no knowledge of the network parameters such as the size or an estimate of the size are used. The overhead of our scheme is also very low and (control) messages exchanged are of small size. Our solution will also be self-stabilizing which is an important property for distributed systems. To the best of our knowledge, our TDMA protocol is the first MAC layer protocol for such realistic network models. Additionally, we report some experimental results of our scheme.

Abstract

Heritage structures bears a valuable testimony of ancient cultural heritage of any country. Among these structures statues, iconic emblems plays significant role. In the proposed to study the vulnerability of monolithic statues to earthquake ground motions. Initially we used the equations developed by Housner for studying the dynamics of rigid blocks. Parametric study was conducted to study the inuence of size of the block and input parameters such as amplitude and frequency on the behaviour of the block. The study was extended to generate safe surface for the block of given dimensions. This surface gives the information that with any combination of parameters such as amplitude of vibration, frequency of vibration and duration of vibration, if the point lies outside the surface then block overturns otherwise it is safe. To verify the above formulation we selected four statues, viz, Gomateswara statue, Christ the Redeemer, Statue of Liberty, Guinyin Statue for case study. Initially all the statues were idealized like rigid blocks and later safe surfaces were developed for each statue. Since each statue is having different dimensions, surfaces were are also of different nature. Later, eighteen earthquake records were selected and strong ground motion parameters were estimated. Finally every statue was tested for the safety during the earthquake events. It was found that as the height of the statue is increasing its vulnerability is increasing. However, for all the given ground motions, none of the statue overturned.

Abstract

Many countries have become victims of terrorism on a large scale. Bombs have exploded in and around buildings in many countries causing civilian causalities and structural damage. A bomb explosion with in or around a building can have catastrophic effects, damaging and destroying internal or external portions of the building. Bomb damage to buildings depends on the type and layout of the structure, material used, range of the located explosive device and the charge weight. The impact from the blast causes debris, fire and smoke and hence can result in injury and death of occupants. Escape of the occupants and protection of the valuable documents, equipments, property is possible only when there is minimum damage to structures. This may be achieved by designing the building structures for blast loading. This attempt gives basic idea to all the consultants in estimating the blast loads over the building structures.

Abstract

Bhuj earthquake of 26 January 2001 caused 14,000 casualties. Main reason for such huge casualties is low earthquake awareness and poor construction practices. Based on the technology advancement and knowledge gained after earthquake occurrences, the seismic code is usually revised. Last revision of IS 1893 (Criteria for earthquake resistant design of structures) was done in 2002 after a long gap of about 18 years. Some new clauses were included and some old provisions were updated. Assuming that concerned authorities will take enough steps for code compliance and the structures that are being constructed are earthquake resistant. In this light, what will happen to the safety of pre-code revision structures? These structures carry major percentage of vulnerable structure stock. Even if we have a very good disaster response system, it is impossible to reduce earthquake damage without considering the safety of pre-code revision structures. In this regard, a comprehensive study of seismic risk assessment of Gujarat is necessary. As a pilot study, government of Gujarat selected Gandhidham and Adipur cities. Rapid Visual Screening (RVS) was conducted on 16000 buildings in Gandhidham and Adipur cities. Initial results reveal that there are large variety of construction practices, however, predominantly RCC and masonry structure were found. RVS score of these structures reveal that in general buildings are of low quality and further evaluation and strengthening of buildings is recommended. Keywords: RVS, performance score, preliminary assessment and detailed assessment Earthquake Vulnerability Assessment of Existing Buildings in Gandhidham and Adipur Cities Kachchh, Gujarat (India)

Abstract

Heritage could be something which is acquired from one’s ancestors. It could be natural heritage, cultural heritage, food heritage, built monumental heritage; or it could be the virtue of vernacular architectural & construction techniques which people from many different communities have secured from their ancestors through generations. But, with the advent of modernism, vernacular architecture, construction techniques and skills are fast disappearing as there is simply no demand for them anymore. Similar to the case with many of our traditional crafts, we are facing the risk of extinction of skills for buildings. As more and more constructions in villages are turning towards cement and steel, the traditional and sophisticated art of construction will fade away sooner rather than later. The preservation of such skills and, in fact their propagation must be an important priority for stakeholders and policy makers. This paper not only the presents the risks of extinction which these heritage construction techniques & skills are facing from modern mind-set, but it also presents some of the vernacular building typologies in seismic zones IV & V showing, their uniqueness in intertwining the culture and resistance to natural forces of the region.

Abstract

A multi-robotic exploration with the requirement of communication link to a fixed base station is presented in this paper. The robots organize themselves into roles of maintainers of communication (hinged robots or robot nodes) or explorers of the environment ensuring that every robot is in contact with the base station directly or through the hinged robots. A two phased strategy for the same is presented. The first phase is characterized by a recursive growth of trees that starts from the root node or the base station and then repeated from other nodes of the hitherto grown tree in a depth first fashion. The second phase constitutes the recursive tree growth invoked repeatedly from the frontier nodes. While the first phase rapidly explores areas around the base station in a concentric fashion, the second phase extends the depth of the explored area to increase the limits of coverage. The strategy is consistent in that none of the robots loose contact with the base station. Extensive simulations confirm the efficacy of the method and comparisons portray performance gain in terms of exploration time and absence of deadlocks vis-a-vis the few methods previously reported in the literature.