| Patent application number | Description | Published |
|---|
| 20090024347 | Thermal Simulation Using Adaptive 3D and Hierarchical Grid Mechanisms - A thermally aware design automation suite integrates system-level thermal awareness into design of semiconductor chips, performing fine-grain static and/or transient thermal simulations of the chips based on thermal models and boundary conditions. The thermal simulations are performed in accordance with one or more grids, with boundaries and/or resolutions being determined by adaptive and/or hierarchical multi-dimensional techniques. The adaptive grid techniques include material-boundary, rate-of-change, and convergence-information heuristics. For example, a finer grid is used in a region having higher temperature gradients compared to a region having lower temperature gradients. The hierarchical grid techniques are based on critical, intermediate, and boundary regions specified manually or automatically, each region having a respective grid resolution. For example, a critical region is analyzed according to a grid that is finer than a grid of an intermediate region, and resolution of a grid of a boundary region is adapted to boundary conditions. | 01-22-2009 |
| 20090299647 | METHOD, SYSTEM, AND COMPUTER PROGRAM PRODUCT FOR IDENTIFYING BINDING CONFORMATIONS OF CHEMICAL FRAGMENTS AND BIOLOGICAL MOLECULES - A new approach to identifying binding conformations of chemical fragments and biological molecules is presented, in which fragment poses are explored in a systematic fashion. In an embodiment, for each pose, a fast computation is performed of the fragment interaction with the biological molecule using interpolation on a grid. Once the energies of fragment poses are computed, thermodynamical quantities such as binding affinity, binding enthalpy, and binding entropy are computed by direct sum over fragment poses. Using the present invention, it is possible to navigate fragment configuration space to identify separate binding modes. The present invention can be used to scan an entire biological molecule to identify possible binding pockets, or it can be used for localized explorations limited to interesting areas of known binding pockets. | 12-03-2009 |
| 20110004413 | METHOD AND SYSTEM FOR CALLING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE WITH RESPECT TO A REFERENCE POLYNUCLEOTIDE SEQUENCE - Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence. | 01-06-2011 |
