James Caldwell

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We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit(More)
The languages of current dynamic constraint detection techniques are often specified by fixed grammars of universal properties. These properties may not be sufficient to express more subtle facts that describe the essential behavior of a given program. In an effort to make the dynamically recovered specification more expressive and program-specific we(More)
In the constructive setting, membership predicates over recursive types are inhabited by terms indexing the elements that satisfy the criteria for membership. In this paper, we motivate and explore this idea in the concrete setting of lists and trees. We show that the inhabitants of membership predicates are precisely the inhabitants of a generic shape(More)
We present formalized proofs verifying that the first-order unification algorithm defined over lists of satisfiable constraints generates a most general unifier (MGU), which also happens to be idempotent. All of our proofs have been formalized in the Coq theorem prover. Our proofs show that finite maps produced by the unification algorithm provide a model(More)
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