Herbert J. Bernstein

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This paper documents the discovery of a new, better-than-classical quantum algorithm for the depth-two AND/OR tree problem. We describe the genetic programming system that was constructed specifically for this work, the quantum computer simulator that is used to evaluate the fitness of evolving quantum algorithms, and the newly discovered algorithm.
Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL, for Bravais lattice(More)
The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function.(More)
Transmitting quantum information between two remote parties is a requirement for many quantum applications; however, direct transmission of states is often impossible because of noise and loss in the communication channel. Entanglement-enhanced state communication can be used to avoid this issue, but current techniques require extensive experimental(More)
Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500(More)
NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The(More)
ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters(More)
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