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Finding wide tunnels in protein structures is an important problem in Structural Bioinformatics with applications in various areas such as drug design. Several algorithms have been proposed for finding wide tunnels in a fixed protein conformation. However, to the best of our knowledge, none of the existing work have considered widening the tunnel, i.e., finding a wider tunnel in an alternative conformation of the given structure. In this thesis we initiate this line of research by proposing a tunnel-widening algorithm which aims to make the tunnel wider by a slight local change in the structure of the protein. Given a fixed conformation of a protein with a point located inside it, we first describe an algorithm to identify the widest tunnel from that point to the outside environment of the protein. Then we try to make the tunnel wider by considering various alternative conformations of the protein. We only consider conformations whose energies are not much higher than the energy of the initial conformation. Among these alternative conformations we select the one with the widest tunnel. However, the alternative conformation with the widest tunnel might not be accessible from the initial structure. Thus, in the next step we develop three algorithms for finding a feasible transition pathway from the initial structure to the alternative conformation, i.e., a sequence of intermediate conformations between the initial structure and the alternative conformation such that the energy values of all these intermediate conformations are close to the energy of the initial structure. We evaluate our tunnel-finding and tunnel-widening algorithms on various proteins. Our experiments show that in most cases we can make the tunnel wider in an alternative conformation. However, there are cases in which we find a wider tunnel in an alternative conformation, but the energy value of the alternative conformation is much higher than the energy of the initial structure. We also implemented our three pathway-finding algorithms and tested them on various instances. Our experiments show that although in most cases we can find a feasible transition pathway, there are cases in which the alternative conformation has energy close to the initial structure, but our algorithms cannot find any feasible pathway from the initial structure to the alternative conformation. Furthermore, there is a trade-off between the running time and accuracy of the three pathway-finding algorithms.

Mobile IPv6 supports host mobility by dynamically changing IP addresses while mobile nodes roaming in the Internet. However, there still exist performance problems during handoffs, such as handoff latency, packet loss. When a mobile node increases its mobility, performance degradation induced by frequent handoffs grows drastically. In this thesis, we propose a dual-tunnel with buffering (DTWB) mechanism to reduce packet loss ratio during multiple handoffs. Packet buffering at access routers is initiated by mobile nodes when the received signal strength goes below a predefined threshold. The buffered packets are forwarded through dual tunnels, of which the first tunnel is established between the old access router and the new access router, and the second tunnel is established between the new access router and the mobile nodes. For the purpose of evaluation, we perform experiments on NS-2 simulation. The simulation results demonstrate that our proposed mechanism can minimize the packet loss ratio and increase the throughput during multiple handoffs.

The influence of the surface excavation and loading on the existing tunnels has been investigated using a Finite Element Method program, Plaxis 3D Tunnel. A parametric study has been carried out where the parameters were the depth of the surface excavation, the eccentricity of the excavation with respect to the tunnel axis, the height of the embankment fill and the stiffness of the soil. It is found that, excavations over the existing tunnels have a negative effect on the tunnel lining capacity since the unloading due the excavation reduces the normal forces and increases the bending moments. On the other hand, it is found that surface loading within the limits considered in this study is not critical in terms of the tunnel stability due to the increase in normal forces and decrease in bending moments.

Thèse doctorat : Génie Civil : INSA LYON : 2002. / Titre provenant de l'écran-titre. Bibliogr. p. [147]-152.

Thèse doctorat : Génie Civil : Villeurbanne, INSA : 2003. / Titre provenant de l'écran-titre. Bibliogr. p. 169-174.

The unbalanced traffic flow in the three Road Harbour Crossings (RHCs) connecting Hong Kong Island and Kowloon Peninsula is a very serious transportation problem in Hong Kong. A very important question about the toll structures, i.e. how to set the toll for different vehicle types, is raised during the study of the utilization of the three RHCs. Traditionally, the toll structure is determined according to the cost of maintenance contribution. A per axle pricing system is being adopted in many examples in the world. In transportation economics, the toll charge is studied extensively. However, no study has been done on the methodology to determine the optimum toll structure. This dissertation suggests a new methodology to determine the optimum toll structure. It suggests each type of vehicles should pay the same full cost, i.e. monetary cost plus the time cost. Value of time and occupancy are emphasized during the consideration of the time cost of each type of vehicles. As the time cost of the vehicles varies with the congestion level, the optimum toll structure depends on the congestion level of the road. This dissertation investigates the factors affecting the demand and supply of the RHCs. They are used to predict the total travel time and social welfare under different toll structures. It shows the suggested methodology can maximize the social welfare generated from the tunnel. Optimum toll for CHT is found using the suggested methodology. Optimum toll for EHC and WHC after their franchises expire in 2016 and 2023 are also found. Recommendations are also made in this dissertation to reduce the possible objections from the general public due to the toll adjustments. / published_or_final_version / Transport Policy and Planning / Master / Master of Arts in Transport Policy and Planning

No description available.

Underground tunnels are considered to be a vital infrastructure component in most cities around the world. Careful planning is always necessary to ensure minimum impact on nearby surface and subsurface structures. This thesis describes the experimental and numerical investigations carried out at McGill University to examine the effect of existing pile foundation on the stresses developing in a newly constructed tunnel supported by a flexible lining system. A small scale testing facility was designed and built to simulate the process of tunnel excavation and lining installation in the close vicinity of pre-installed piles. Lining stresses were measured for different separation distances between the tunnel and the existing piles. Significant decrease in circumferential stresses was observed when the lining was installed at a distance that ranges between one to three times the tunnel diameter from the piles. Two-dimensional finite element analyses were also conducted to investigate the different aspects of the pile-soil-lining interaction including lining deformation, axial forces and bending moments. The measured lining stresses agreed with those obtained using finite element analysis. The results presented in this study provided an insight into understanding an important aspect of this soil-structure interaction problem.