Abstract: A method and apparatus for analyzing molecular systems with reconfigurable special-purpose hardware is provided. An entire molecular mechanics calculation is implemented on a programmable logic device (PLD) integrated circuit (IC) (“single chip”). This single IC accelerator is achieved by run-time reprogramming of the PLD to handle different terms in the molecular mechanics calculation.

Abstract: A general automated method for synthesizing the design of both the topology and parameter values for controllers is described. The automated method automatically makes decisions concerning the total number of signal processing blocks to be employed in the controller, the type of each signal processing block, the topological interconnections between the signal processing blocks, the values of all parameters for the signal processing blocks, and the existence, if any, of internal feedback between the signal processing blocks within the controller. The general automated method can simultaneously optimize prespecified performance metrics (such as minimizing the time required to bring the plant outputs to the desired values as measured by the integral of the time-weighted absolute error or the integral of the squared error), satisfy time-domain constraints (such as overshoot, disturbance rejection, limits on control variables, and limits on state variables), and satisfy frequency domain constraints (bandwidth).

Abstract: Embodiments of the invention provide methods, systems, and articles of manufacture for modeling molecular properties based on information obtained from sources other than direct empirical measurements of the properties. Embodiments of the invention use “virtual data” related to molecular properties to train a molecular properties model. Virtual data about a molecule may include real-valued data (e.g. measurement values falling along a continuous range) or a positive or negative assertion about whether a molecule exhibits a property of interest. Virtual data may be generated using a variety of techniques and may be further characterized by confidence in the accuracy of the virtual data. In addition to virtual data, embodiments of the invention may use “virtual molecules” paired with “virtual data” to train a molecular properties model. The virtual molecules may themselves be generated in a variety of ways.

Abstract: The present invention provides compositions of matter, kits and methods for their use in the treatment of MAP kinase-related conditions and/or HMG-CoA reductase-related conditions. In particular, the invention provides compositions for treating inflammatory and/or cardiovascular conditions in an animal subject by inhibiting p38? MAP kinase and/or HMG-CoA reductase, as well as providing formulations and modes of administering such compositions. The invention further provides methods for the rational design of inhibitors of MAP kinase, HMG-CoA reductase, or both for use in the practice of the present invention.

Abstract: Methods and apparatus for analyzing molecular systems with reconfigurable special-purpose hardware or an ASIC is provided. The present invention provides methods and apparatus to perform a quantum mechanical calculation on a programmable logic device (PLD) integrated circuit (IC) (“single-chip”) or an application specific integrated circuit (ASIC).

Abstract: A general automated method for synthesizing the design of both the topology and parameter values for controllers is described. The automated method automatically makes decisions concerning the total number of signal processing blocks to be employed in the controller, the type of each signal processing block, the topological interconnections between the signal processing blocks, the values of all parameters for the signal processing blocks, and the existence, if any, of internal feedback between the signal processing blocks within the controller. The general automated method can simultaneously optimize prespecified performance metrics (such as minimizing the time required to bring the plant outputs to the desired values as measured by the integral of the time-weighted absolute error or the integral of the squared error), satisfy time-domain constraints (such as overshoot, disturbance rejection, limits on control variables, and limits on state variables), and satisfy frequency domain constraints (bandwidth).

Abstract: A method and apparatus for analyzing molecular systems with reconfigurable special-purpose hardware is provided. An entire molecular mechanics calculation is implemented on a programmable logic device (PLD) integrated circuit (IC) (“single chip”). This single IC accelerator is achieved by run-time reprogramming of the PLD to handle different terms in the molecular mechanics calculation.

Abstract: Method and apparatus for designing a synthesis route for a target molecule is provided. The method for designing a synthesis route for a target molecule comprises: generating a plurality of individuals, wherein each individual encodes a synthesis route; decoding each individual to produce a synthesis route comprising at least one reactant molecules and at least one reaction; and determining how well the synthesis route satisfies a design goal. A computer readable medium containing instructions for a computer program executable by the computer to perform a method for designing a synthesis route for a target molecule is also provided. The apparatus comprises a parallel computer system for executing instructions of a computer program to perform a method for designing a synthesis route for a target molecule.

Abstract: A general automated method for synthesizing the design of both the topology and parameter values for controllers is described. The automated method automatically makes decisions concerning the total number of signal processing blocks to be employed in the controller, the type of each signal processing block, the topological interconnections between the signal processing blocks, the values of all parameters for the signal processing blocks, and the existence, if any, of internal feedback between the signal processing blocks within the controller. The general automated method can simultaneously optimize prespecified performance metrics (such as minimizing the time required to bring the plant outputs to the desired values as measured by the integral of the time-weighted absolute error or the integral of the squared error), satisfy time-domain constraints (such as overshoot, disturbance rejection, limits on control variables, and limits on state variables), and satisfy frequency domain constraints (bandwidth).