The best available descriptions of systems often come at a fine level (atomistic, stochastic, microscopic, agent based), whereas the questions asked and the tasks required by the modeler (prediction, parametric analysis, optimization, and control) are at a much coarser, macroscopic level. Traditional modeling approaches start by deriving macroscopic evolution equations from microscopic models, ...

Sec. S1 describes in more detail the protein redesign algorithms and the computational protocol, including computational experiment design and supporting data, used to redesign GrsA-PheA. Sec. S2 gives details about the structural analysis of the predicted mutants (Sec. S2.1) and the comparison to other methods and evolution (Sec. S2.2). Sec. S3 gives additional details about the experimental p...

The TeraGyroid experiment[1] addressed a large scale problem of genuine scientific interest and showed how intercontinental Grids enable new paradigms for collaborative computational science that can dramatically reduce the time to insight. TeraGyroid used computational steering over a Grid to study the self-assembly and dynamics of gyroid mesophases (found in novel materials and living cells) ...

Coprocessing involves running a visualization process concurrently with a simulation, and making intermediate simulation results visible during the course of the run. Through computational monitoring, a researcher can watch the progress of a run, perhaps ending the run if it looks unproductive. In this report, we experiment with applying two software packages designed to support computational m...

We present an empirical study of the accuracy{cost tradeoos of Anderson's method. The various parameters that control the degree of approximation of the computational elements and the separateness of interacting computational elements govern both the arithmetic complexity and the accuracy of the method. Our experiment shows that for a given error requirement, using a near{{eld containing only n...

Universe operates in pure principle only, wherefrom we can choose to view Universe as an emergent computation. The proposed method for this most basic of computations is the computational cosmography, wherein a system of interacting deformable polyhedra utilizing the geometric prim-itives of R.B. Fuller's synergetic geometry coordinate and evolve within an isotropic vector matrix. A gedanken ex...

The genomic data available to computational biologists represents the product of the complex processes of evolution. In particular, the forces of mutation, duplication, and selection have acted to sculpt modern protein sequence and structure in the context of changing functional requirements. Just as crystallographers are able to determine protein structures through an analysis of X-ray diffrac...

The problem of scheduling workflow applications in a grid environment is considered. The problem is divided into two stages: (i) resource allocation, which consists in allocating distributed grid resources to tasks of a workflow in such a way that the resource demands of each task are satisfied, and (ii) scheduling performed by local grid schedulers. Grid resources are divided into computationa...

We introduce computational systems to formalise the notion of rewriting directed by user defined strategies. This provides a semantics for ELAN, an environment dedicated to prototype, experiment and study the combination of different deduction systems for constraint solving, theorem proving and logic programming paradigms. Formally, a computational system can be represented as a rewrite theory ...