Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions

Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators

An approach for real world data modelling with the 3D terrestrial laser scanner for built environment

Capturing and modelling 3D information of the built environment is a big challenge. A number of techniques and technologies are now in use. These include EDM, GPS, and photogrammetric application, remote sensing and traditional building surveying applications. However, use of these technologies cannot be practical and efficient in regard to time, cost and accuracy. Furthermore, a multi disciplinary knowledge base, created from the studies and research about the regeneration aspects is fundamental: historical, architectural, archeologically, environmental, social, economic, etc. In order to have an adequate diagnosis of regeneration, it is necessary to describe buildings and surroundings by means of documentation and plans. However, at this point in time the foregoing is considerably far removed from the real situation, since more often than not it is extremely difficult to obtain full documentation and cartography, of an acceptable quality, since the material, constructive pathologies and systems are often insufficient or deficient (flat that simply reflects levels, isolated photographs,..). Sometimes the information in reality exists, but this fact is not known, or it is not easily accessible, leading to the unnecessary duplication of efforts and resources. In this paper, we discussed 3D laser scanning technology, which can acquire high density point data in an accurate, fast way. Besides, the scanner can digitize all the 3D information concerned with a real world object such as buildings, trees and terrain down to millimetre detail Therefore, it can provide benefits for refurbishment process in regeneration in the Built Environment and it can be the potential solution to overcome the challenges above. The paper introduce an approach for scanning buildings, processing the point cloud raw data, and a modelling approach for CAD extraction and building objects classification by a pattern matching approach in IFC (Industry Foundation Classes) format. The approach presented in this paper from an undertaken research can lead to parametric design and Building Information Modelling (BIM) for existing structures. Two case studies are introduced to demonstrate the use of laser scanner technology in the Built Environment. These case studies are the Jactin House Building in East Manchester and the Peel building in the campus of University Salford. Through these case studies, while use of laser scanners are explained, the integration of it with various technologies and systems are also explored for professionals in Built Environmen

Procedural function-based modelling of volumetric microstructures

We propose a new approach to modelling heterogeneous objects containing internal volumetric structures with size of details orders of magnitude smaller than the overall size of the object. The proposed function-based procedural representation provides compact, precise, and arbitrarily parameterised models of coherent microstructures, which can undergo blending, deformations, and other geometric operations, and can be directly rendered and fabricated without generating any auxiliary representations (such as polygonal meshes and voxel arrays). In particular, modelling of regular lattices and cellular microstructures as well as irregular porous media is discussed and illustrated. We also present a method to estimate parameters of the given model by fitting it to microstructure data obtained with magnetic resonance imaging and other measurements of natural and artificial objects. Examples of rendering and digital fabrication of microstructure models are presented

Towards building information modelling for existing structures

The transformation of cities from the industrial age (unsustainable) to the knowledge age (sustainable) is essentially a ‘whole life cycle’ process consisting of; planning, development, operation, reuse and renewal. During this transformation, a multi-disciplinary knowledge base, created from studies and research about the built environment aspects is fundamental: historical, architectural, archeologically, environmental, social, economic, etc is critical. Although there are a growing number of applications of 3D VR modelling applications, some built environment applications such as disaster management, environmental simulations, computer aided architectural design and planning require more sophisticated models beyond 3D graphical visualization such as multifunctional, interoperable, intelligent, and multi-representational. Advanced digital mapping technologies such as 3D laser scanner technologies can be are enablers for effective e-planning, consultation and communication of users’ views during the planning, design, construction and lifecycle process of the built environment. For example, the 3D laser scanner enables digital documentation of buildings, sites and physical objects for reconstruction and restoration. It also facilitates the creation of educational resources within the built environment, as well as the reconstruction of the built environment. These technologies can be used to drive the productivity gains by promoting a free-flow of information between departments, divisions, offices, and sites; and between themselves, their contractors and partners when the data captured via those technologies are processed and modelled into BIM (Building Information Modelling). The use of these technologies is key enablers to the creation of new approaches to the ‘Whole Life Cycle’ process within the built and human environment for the 21st century. The paper describes the research towards Building Information Modelling for existing structures via the point cloud data captured by the 3D laser scanner technology. A case study building is elaborated to demonstrate how to produce 3D CAD models and BIM models of existing structures based on designated technique