Showing papers by "Hans-Peter Lenhof published in 1999"

q-gram based database searching using a suffix array (QUASAR)

Abstract: Multi-purpose, adjustable stabilizing cleats which can be attached to various types of transmission and/or drive shaft tunnel or hump mounted trays with adjustment of the cleats enabling them to be positioned for effective engagement with surface areas of transmission humps or tunnels of different shapes and configurations. The cleats can also be attached to other objects for engaging carpeted surfaces, upholstered furniture and the like.

An exact solution for the segment-to-segment multiple sequence alignment problem

Abstract: Motivation: In molecular biology, sequence alignment is a crucial tool in studying the structure and function of molecules, as well as the evolution of species. In the segment-to-segment variation of the multiple alignment problem, the input can be seen as a set of non-gapped segment pairs (diagonals). Given a weight function that assigns a weight score to every possible diagonal, the goal is to choose a consistent set of diagonals of maximum weight. We show that the segment-to-segment multiple alignment problem is equivalent to a novel formulation ofthe Maximum Trace problem: the Generalized Maximum Trace (GMT) problem. Solving this problem to optimality, therefore, may improve upon the previous greedy strategies that are used for solving the segment-to-segment multiple sequence alignment problem. We show that the GMT can be stated in terms ofan integer linear program and then solve the integer linear program using methods from polyhedral combinatorics. This leads to a branch-and-cut algorithm for segment-to-segment multiple sequence alignment. Results: We report on our first computational experiences with this novel method and show that the program is able to find optimal solutions for real-world test examples.

BALL: Biochemical Algorithms Library

Abstract: In the next century, virtual laboratories will play a key role in biotechnology Computer experiments will not only replace time-consuming and expensive real-world experiments, but they will also provide insights that cannot be obtained using "wet" experiments The field that deals with the modeling of atoms, molecules, and their reactions is called Molecular Modeling The advent of Life Sciences gave rise to numerous new developments in this area However, the implementation of new simulation tools is extremely time-consuming This is mainly due to the large amount of supporting code that is required in addition to the code necessary to implement the new idea The only way to reduce the development time is to reuse reliable code, preferably using object-oriented approaches We have designed and implemented BALL, the first object-oriented application framework for rapid prototyping inMolecular Modeling By the use of the composite design pattern and polymorphism we were able to model the multitude of complex biochemical concepts in a well-structured and comprehensible class hierarchy, the BALL kernel classes The isomorphism between the biochemical structures and the kernel classes leads to an intuitive interface Since BALL was designed for rapid software prototyping, ease of use, extensibility, and robustness were our principal design goals Besides the kernel classes, BALL provides fundamental components for import/export of data in various file formats, Molecular Mechanics simulations, three-dimensional visualization, and more complex ones like a numerical solver for the Poisson-Boltzmann equation

BALL: Biochemical Algorithms Library

Abstract: In the next century, virtual laboratories will play a key role in biotechnology. Computer experiments will not only replace time-consuming and expensive real-world experiments, but they will also provide insights that cannot be obtained using "wet" experiments. The field that deals with the modeling of atoms, molecules, and their reactions is called Molecular Modeling. The advent of Life Sciences gave rise to numerous new developments in this area. However, the implementation of new simulation tools is extremely time-consuming. This is mainly due to the large amount of supporting code that is required in addition to the code necessary to implement the new idea. The only way to reduce the development time is to reuse reliable code, preferably using object-oriented approaches. We have designed and implemented BALL, the first object-oriented application framework for rapid prototyping inMolecular Modeling. By the use of the composite design pattern and polymorphism we were able to model the multitude of complex biochemical concepts in a well-structured and comprehensible class hierarchy, the BALL kernel classes. The isomorphism between the biochemical structures and the kernel classes leads to an intuitive interface. Since BALL was designed for rapid software prototyping, ease of use, extensibility, and robustness were our principal design goals. Besides the kernel classes, BALL provides fundamental components for import/export of data in various file formats, Molecular Mechanics simulations, three-dimensional visualization, and more complex ones like a numerical solver for the Poisson-Boltzmann equation.

Simulating Synthetic Polymer Chains in Parallel

Abstract: We have investigated algorithms that are particularly suited for the parallel MD simulations of synthetic polymers. These algorithms distribute the atoms of the polymer among the processors. Dynamic non-bonded interactions, which are the difficult part of an MD simulation, are realised with the help of a special coarse-grained representation of the chain structure. We have devised and compared a master version and a distributed version of the algorithm. Surprisingly, the master version is competitive for a relatively large number of processors. We also investigated methods to improve load balancing. The resulting simulation package will be made available in the near future.

Simulating synthetic polymer chains in parallel

Abstract: We have investigated algorithms that are particularly suited for the parallel MD simulations of synthetic polymers. These algorithms distribute the atoms of the polymer among the processors. Dynamic nonbonded interactions, which are the difficult part of an MD simulation, are realised with the help of a special coarse-grained representation of the chain structure. We have devised and compared a master version and a distributed version of the algorithm. Surprisingly, the master version is competitive for a relatively large number of processors. We also investigated methods to improve load balancing. The resulting simulation package will be made available in the near future.