Triple helix conformation of botryosphaeran, a (1 -> 3;1 -> 6)-beta-D-glucan produced by Botryosphaeria rhodina MAMB-05

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Molecular Dynamics Simulations of the d(TAT) Triple Helix

Molecular dynamics (MD) simulations have been used to study the dynamical and time-averaged characteristics of the DNA triple helix d(T)10âd(A)10âd(T)10. The structures sampled during the trajectory resemble closely the B-type model for the DNA triplex proposed on the basis of NMR data, although there are some subtle differences. Alternative P- and A-type conformations for the triplex, suggested from X-ray experiments, are not predicted to contribute significantly to the structure of the DNA triplex in solution. Comparison with the best available experimental data supports the correctnes of the MD-generated structures. The analysis of the collected data gives a detailed picture of the characteristics of triple-helix DNA. A new and interesting pattern of hydration, specific for triplex DNA, is an important observation. The results suggest that molecular dynamics can be useful for the study of novel nucleic acid structures.

Micro and Macro Causes of Violence

The dominant emotion in violence-threatening situations is confrontational tension/fear (ct/f), which causes most violence to abort, or to be carried out inaccurately and incompetently. For violence to be successful, there must be a pathway around the barrier of ct/f. These pathways include: attacking the weak; audience-oriented staged and controlled fair fights; confrontation-avoiding remote violence; confrontation-avoiding by deception; confrontation-avoiding by absorption in technique. Successfully violent persons, on both sides of the law, are those who have developed these skilled interactional techniques. Since successful violence involves dominating the emotional attention space, only a small proportion of persons can belong to the elite which does most of each type of violence. Macro-violence, including victory and defeat in war, and in struggles of paramilitaries and social movements, is shaped by both material resources and social/emotional resources for maintaining violent organizations and forcing their opponents into organizational breakdown. Social and emotional destruction generally precedes physical destruction.

DNA triple-helix formation at pyrimidine-purine inversion sites

A systematic investigation of a series of triplex forming oligonucleotides (TFOs) containing alpha- and beta-thymidine, alpha- and beta-N7-hypoxanthine, and alpha- and beta- N7 and N9 aminopurine nucleosides, designed to bind to T-A inversion sites in DNA target sequences was performed. Data obtained from gel mobility assays indicate that t-A recognition in the antiparallel triple-helical binding motif is possible if the nucleoside alpha N9-aminopurine is used opposite to the inversion site in the TFO.

Detection of competing DNA structures by thermal gradient gel electrophoresis: from self-association to triple helix formation by (G,A)-containing oligonucleotides

Sequence-specific recognition of DNA can be achieved by triple helix-forming oligonucleotides that bind to the major groove of double-helical DNA. These oligonucleotides have been used as sequence-specific DNA ligands for various purposes, including sequence-specific gene regulation in the so-called ‘antigene strategy’. In particular, (G,A)-containing oligonucleotides can form stable triple helices under physiological conditions. However, triplex formation may be in competition with self-association of these oligonucleotides. For biological applications it would be interesting to identify the conditions under which one structure is favoured as compared to the other(s). Here we have directly studied competition between formation of a parallel (G,A) homoduplex and that of a triple helix by a 13 nt (G,A)-containing oligonucleotide. Temperature gradient gel electrophoresis allows simultaneous detection of competition between the two structures, because of their different temperature dependencies and gel electrophoretic mobilities, and characterisation of this competition.

SMEs and Level 2 BIM, the Way Forward

The UK construction industry comprises a very high proportion of SMEs that is companies employing up to 250. A Department for Business, Innovation and Skills research paper, found that SMEs had a 71.2% share of work in the construction industry. Micro and small firms (i.e. those employing up to 50) had a share of 46.7% of work (Ive and Murray 2013). The Government has high ambitions for UK construction. Having been found by successive government commissioned studies to be inefficient and highly fragmented, ambitious targets have been set for the industry to achieve 33% reduction in costs and 50% faster delivery by 2025. As a significant construction client, the Government has mandated the use of Level 2 BIM from 2016 on publicly funded projects over £5 million. The adoption of BIM plays a key role in the 2025 vision but a lack of clarity persists in the industry over BIM and significant barriers are perceived to its implementation, particularly amongst SMEs. However, industry wide transformation will be challenging without serious consideration of the capabilities of this large majority. Many larger firms, having implemented Level 2 BIM are now working towards Level 3 BIM while many of the smaller firms in the industry have not even heard of BIM. It would seem that fears of a ‘two tier’ industry are perhaps being realised. This paper builds on an earlier one (Mellon & Kouider 2014) and investigates, through field work, the level of Level 2 BIM implementation amongst SMEs compared to a large organisation. Challenges and innovative solutions identified through collected data are fully discussed and compared. It is suggested that where the SME perceives barriers towards adoption of the technologies which underpin BIM, they may consider collaborative methods of working as an interim step in order to work towards realising the efficiencies and benefits that these methods can yield. While the barriers to adoption of BIM are significant, it is suggested that they are not insurmountable for the SME and some recommendations for possible solutions are made.

What determines innovation activity in Chinese state-owned enterprises? The role of foreign direct investment

We investigate whether inward foreign direct investment (FDI), either at the firm or industry level, has any impact on product innovation by Chinese state-owned enterprises (SOEs). We use a comprehensive firm-level panel data set of some 20,000 SOEs during 1999-2005. Our results show that foreign capital participation at the firm level is associated with higher innovative activity. Inward FDI in the sector, by contrast, has a negative effect on innovative activity in SOEs on average. However, there is a positive effect of sector-level FDI on SOEs that export, invest in human capital, or undertake R&D. © 2008 Elsevier Ltd. All rights reserved.

Bridging large and small scales of water models using hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework

This thesis presents a two-dimensional water model investigation and development of a multiscale method for the modelling of large systems, such as virus in water or peptide immersed in the solvent. We have implemented a two-dimensional ‘Mercedes Benz’ (MB) or BN2D water model using Molecular Dynamics. We have studied its dynamical and structural properties dependence on the model’s parameters. For the first time we derived formulas to calculate thermodynamic properties of the MB model in the microcanonical (NVE) ensemble. We also derived equations of motion in the isothermal–isobaric (NPT) ensemble. We have analysed the rotational degree of freedom of the model in both ensembles. We have developed and implemented a self-consistent multiscale method, which is able to communicate micro- and macro- scales. This multiscale method assumes, that matter consists of the two phases. One phase is related to micro- and the other to macroscale. We simulate the macro scale using Landau Lifshitz-Fluctuating Hydrodynamics, while we describe the microscale using Molecular Dynamics. We have demonstrated that the communication between the disparate scales is possible without introduction of fictitious interface or approximations which reduce the accuracy of the information exchange between the scales. We have investigated control parameters, which were introduced to control the contribution of each phases to the matter behaviour. We have shown, that microscales inherit dynamical properties of the macroscales and vice versa, depending on the concentration of each phase. We have shown, that Radial Distribution Function is not altered and velocity autocorrelation functions are gradually transformed, from Molecular Dynamics to Fluctuating Hydrodynamics description, when phase balance is changed. In this work we test our multiscale method for the liquid argon, BN2D and SPC/E water models. For the SPC/E water model we investigate microscale fluctuations which are computed using advanced mapping technique of the small scales to the large scales, which was developed by Voulgarakisand et. al.

Classification of Maximal Optical Orthogonal Codes of Weight 3 and Small Lengths

Dedicated to the memory of the late professor Stefan Dodunekov on the occasion of his 70th anniversary. We classify up to multiplier equivalence maximal (v, 3, 1) optical orthogonal codes (OOCs) with v ≤ 61 and maximal (v, 3, 2, 1) OOCs with v ≤ 99. There is a one-to-one correspondence between maximal (v, 3, 1) OOCs, maximal cyclic binary constant weight codes of weight 3 and minimum dis tance 4, (v, 3; ⌊(v − 1)/6⌋) difference packings, and maximal (v, 3, 1) binary cyclically permutable constant weight codes. Therefore the classification of (v, 3, 1) OOCs holds for them too. Some of the classified (v, 3, 1) OOCs are perfect and they are equivalent to cyclic Steiner triple systems of order v and (v, 3, 1) cyclic difference families.

Noninvasive imaging of three-dimensional micro and nanostructures by topological methods

We present topological derivative and energy based procedures for the imaging of micro and nano structures using one beam of visible light of a single wavelength. Objects with diameters as small as 10 nm can be located and their position tracked with nanometer precision. Multiple objects dis-tributed either on planes perpendicular to the incidence direction or along axial lines in the incidence direction are distinguishable. More precisely, the shape and size of plane sections perpendicular to the incidence direction can be clearly determined, even for asymmetric and nonconvex scatterers. Axial resolution improves as the size of the objects decreases. Initial reconstructions may proceed by gluing together two-dimensional horizontal slices between axial peaks or by locating objects at three-dimensional peaks of topological energies, depending on the effective wavenumber. Below a threshold size, topological derivative based iterative schemes improve initial predictions of the lo-cation, size, and shape of objects by postprocessing fixed measured data. For larger sizes, tracking the peaks of topological energy fields that average information from additional incident light beams seems to be more effective.

How nonprofit boards monitor, judge and influence organisational performance

The law and popular opinion expect boards of directors will actively monitor their organisations. Further, public opinion is that boards should have a positive impact on organisational performance. However, the processes of board monitoring and judgment are poorly understood, and board influence on organisational performance needs to be better understood. This thesis responds to the repeated calls to open the ‘black box’ linking board practices and organisational performance by investigating the processual behaviours of boards. The work of four boards1 of micro and small-sized nonprofit organisations were studied for periods of at least one year, using a processual research approach, drawing on observations of board meetings, interviews with directors, and the documents of the boards. The research shows that director turnover, the difficulty recruiting and engaging directors, and the administration of reporting, had strong impacts upon board monitoring, judging and/or influence. In addition, board monitoring of organisational performance was adversely affected by directors’ limited awareness of their legal responsibilities and directors’ limited financial literacy. Directors on average found all sources of information about their organisation’s work useful. Board judgments about the financial aspects of organisational performance were regulated by the routines of financial reporting. However, there were no comparable routines facilitating judgments about non-financial performance, and such judgments tended to be limited to specific aspects of performance and were ad hoc, largely in response to new information or the repackaging of existing information in a new form. The thesis argues that Weick’s theory of sensemaking offers insight into the way boards went about the task of understanding organisational performance. Board influence on organisational performance was demonstrated in the areas of: compliance; instrumental influence through service and through discussion and decision-making; and by symbolic, legitimating and protective means. The degree of instrumental influence achieved by boards depended on director competency, access to networks of influence, and understandings of board roles, and by the agency demonstrated by directors. The thesis concludes that there is a crowding out effect whereby CEO competence and capability limits board influence. The thesis also suggests that there is a second ‘agency problem’, a problem of director volition. The research potentially has profound implications for the work of nonprofit boards. Rather than purporting to establish a general theory of board governance, the thesis embraces calls to build situation-specific mini-theories about board behaviour.