Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

The CAPRI and CASP prediction experiments have demonstrated the power of community wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting there may be important physical chemistry missing in the energy calculations. 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the non-polar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were on average structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a non-binder

Tunisia, 1940-1970: The Spatial Politics of Reconstruction, Decolonization, and Development

This dissertation investigates the dialectical discourses of modernism and the vernacular in Tunisian architectural and urban projects, from the late French protectorate into the period of independence, 1940-1970. With a particular focus on issues of habitation and heritage, this project tracks the reorganization of social space in the reconstruction efforts of the postwar French colonial administration and the architectural and patrimonial discourses of the Tunisian nation-state that came into existence in 1956. In an era that witnessed mass-scale land expropriations, rural-urban migrations, and popular anti-colonial sentiment, this project traces the material effects of Tunisians’ displacements and urban adaptations to their rapidly changing socio-political condition. Underscoring the dialectics intrinsic to the postwar notion of development, namely, tensions between formal and informal settlements, vernacular building traditions and prefabrication methods, and patrimonial preservation and erasure, this dissertation explores the ideological negotiations of architectural progress in the longue durée of decolonization. Throughout this tumultuous period, social housing projects sprouted in parallel with the spread of gourbivilles (earthen dwellings) and bidonvilles (‘tin can’ towns) on the outskirts of Tunisia’s urban centers. Both colonial and postcolonial institutional and state-led reckonings with vernacular architecture forwarded not only modernist building agendas, but promoted primitivizing mythologies of local construction techniques, rooted in racist attitudes towards the purportedly backward indigène. Challenging the predominant historiographical narrative that presents the independence of 1956 as a stark political rupture, this dissertation instead demonstrates that the vestiges of urban and preservationist policy schemes remained ingrained, on an institutional level, from protectorate rule. How the spatial and political processes of decolonization, nation-building, and development intersect with the ethics and economics of habitation undergirds this project

A Coupled Vector-scalar Potential Method For Permanent Magnet Modeling in Large-scale 3d-Fe Magnetic Field Computations

This paper introduces a magnetic scalar potential (MSP) formulation of permanent magnet (PM) modeling. This formulation is suited for use in coupled (combined) vector-scalar magnetic potential (CMVP-MSP) 3D-FE algorithms and computation of large-scale magnetic field problems in elecltric machinery and devices [ 1,2]. This formulation and method facilitate substantially the handling of PM materials, current-carrying conductors, and nonlincar anisotropic laminated iron cores, as adjacent subregions within one global solution region (volume) of a given device

Teaching Electric Machinery and Associated Electromagnetic Fields-A Case for the Benefits of Academic Computing

This paper describes three broad categories of benefits resulting from use of and access to personal computers (PCs) and work stations (WSs) in teaching electric machines and drives. This includes all the electromagnetic field aspects associated with such electromechanical energy conversion devices. The first category concerns benefits from use of computer graphics associated with computational electromagnetics. The second category of benefits involves quantification of machinery parameters and performance characteristics from computational electmmagnetics. Meanwhile, the third category concerns benefits from the use of computer simulations in the study of the now all-important power electronically controlled electric machinery drives, using time domain models in which all significant effects of both time and space harmonics are retained. The material presented here is given at Clarkson University at the senior undergraduate and first-year graduate levels.Scopu