Charles Zhoucheng Zheng

PRIDB: a protein–RNA interface database

The Protein–RNA Interface Database (PRIDB) is a comprehensive database of protein–RNA interfaces extracted from complexes in the Protein Data Bank (PDB). It is designed to facilitate detailed analyses of individual protein–RNA complexes and their interfaces, in addition to automated generation of user-defined data sets of protein–RNA interfaces for statistical analyses and machine learning applications. For any chosen PDB complex or list of complexes, PRIDB rapidly displays interfacial amino acids and ribonucleotides within the primary sequences of the interacting protein and RNA chains. PRIDB also identifies ProSite motifs in protein chains and FR3D motifs in RNA chains and provides links to these external databases, as well as to structure files in the PDB. An integrated JMol applet is provided for visualization of interacting atoms and residues in the context of the 3D complex structures. The current version of PRIDB contains structural information regarding 926 protein–RNA complexes available in the PDB (as of 10 October 2010). Atomic- and residue-level contact information for the entire data set can be downloaded in a simple machine-readable format. Also, several non-redundant benchmark data sets of protein–RNA complexes are provided. The PRIDB database is freely available online at http://bindr.gdcb.iastate.edu/PRIDB.

Collusion Via Resale

The English auction is susceptible to tacit collusion when post-auction inter-bidder resale is allowed. We show this by constructing equilibria where, with positive probability, one bidder wins the auction without any competition and divides the spoils by optimally reselling the good to the other bidders. These equilibria interim Pareto dominate (among bidders) the standard value-bidding equilibrium, without requiring the bidders to make any commitment on bidding behavior or post-bidding spoil-division.

Application of mechanism design to electric power markets

As competition is introduced across the electric power industry around the world, market design for the industry is urgently needed to shape its future structure and performance. When generator companies compete with one another in a deregulated market, they may not be willing to share the information needed to perform an economic dispatch of the generation. Using game theory, this paper designs a new mechanism that achieves efficiency (economic dispatch) in spite of this information problem. In this mechanism, when each company acts in the best of its own interests, the outcome is efficient. The paper demonstrates the merits of the mechanism by simulations including the IEEE 14-bus case.

Application of mechanism design to electric power markets (Republished)

As competition is introduced across the electric power industry around the world, market design for the industry is urgently needed to shape its future structure and performance. When generator companies compete with one another in a deregulated market, they may not be willing to share the information needed to perform an economic dispatch of the generation. Using game theory, this paper designs a new mechanism that achieves efficiency (economic dispatch) in spite of this information problem, In this mechanism, when each company acts in the best of its own interest, the outcome is efficient. The paper demonstrates the merits of the mechanism by simulations including the IEEE 14-bus case. [This paper contained an incorrect graphic when it originally appeared in the IEEE Transactions on Power Systems, vol.16, no.1, p.1-8, 2001. It is republished here with the correct graphic.]

Jump bidding and overconcentration in decentralized simultaneous ascending auctions

A model of English auctions is proposed to incorporate the possibility of jump bidding. When two objects are sold separately via such auctions, bidders signal their willingness to pay via jump bids, thereby forming rational expectations of the prices without relying on any central mediator. Hence a multi-item bidder does not suffer the exposure problem of having to buy an item while he is uncertain about the price of its complement. Single-item bidders, however, free-ride one another in competing against a multi-item bidder. Consequently, the auctions overly concentrate the goods to a multi-item bidder and never overly diffuse them to single-item bidders.

Core equivalence theorem with production

In production economies, the extent to which non-equilibria are blocked depends on the allocation of control rights among shareholders, because a blocking coalitions resources are affected by the firms it jointly owns with outsiders. We formulate a notion of blocking that takes such interdependency problem into account, and we prove an analog of the Debreu-Scarf theorem for replica production economies. Our theorem differs from theirs in using an additional assumption, which we argue is indispensable and is driven by the interdependency problem.

The Default-Prone U.S. Toxic Asset Auction Plan

Abstract Applying auction theory to the toxic-asset rescue plan currently released by the United States Treasury Department, this paper demonstrates an equilibrium where moderately poor bidders outbid rich bidders in such auctions. After defeating their rich rivals and acquiring the toxic assets, such bidders will default on government-provided loans whenever the toxic assets turn out to be unsalvageable. An alternative mechanism is discussed.