Abstract: Systems and methods for computer-aided vaccine design may comprise performing one or more molecular dynamics simulations of a protein assembly having at least one epitope, determining a fluctuation measurement for the at least one epitope using the one or more molecular dynamics simulations, and predicting the immunogenicity of the protein assembly in response to the fluctuation measurement are disclosed.

Abstract: Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Abstract: Virus-like particle (hereinafter sometimes VLP)-based strategies for developing vaccines against human viruses. Computer models of the VLPs are modified by the addition to the computer models of computer models of viral materials of the viruses against which the vaccines are being developed.

Abstract: Virus-like particle (hereinafter sometimes VLP)-based strategies for developing vaccines against human viruses. Computer models of the VLPs are modified by the addition to the computer models of computer models of viral materials of the viruses against which the vaccines are being developed.

Abstract: Systems and methods for computer-aided vaccine design may comprise performing one or more molecular dynamics simulations of a protein assembly having at least one epitope, determining a fluctuation measurement for the at least one epitope using the one or more molecular dynamics simulations, and predicting the immunogenicity of the protein assembly in response to the fluctuation measurement are disclosed.

Abstract: Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Abstract: Disclosed are methods for modeling multi-dimensional domains by merging multiple input data sets into a model, applying multiple dynamic theories to evolve the model, and using information theory to resolve gaps in, and discrepancies among, the data sets and the theories. One example is a three-dimensional geologic basin simulator that integrates seismic inversion techniques with other data to predict fracture location and characteristics. The geologic simulator delineates the effects of regional tectonics, petroleum-derived overpressure, and salt tectonics and constructs maps of high-grading zones of fracture producibility. A second example is a living cell simulator that uses chemical kinetic rate laws of transcription and translation polymerization to compute mRNA and protein populations as they occur autonomously, in response to changes in the surroundings, or from injected viruses or chemical factors. Features such as the eukaryotic nucleus are treated with a novel mesoscopic reaction-transport theory.

Abstract: A three-dimensional, geologic basin simulator for predicting natural resource location and characteristics is disclosed. The simulator integrates seismic inversion techniques with other data to predict fracture location and characteristics. The invention's 3-D finite element basin reaction, transport, mechanical simulator includes a rock rheology that integrates continuous deformation (poroelastic/viscoplastic) with fracture, fault, gouge, and pressure solution. Mechanical processes are used to coevolve deformation with multi-phase flow, petroleum generation, mineral reactions, and heat transfer to predict the location and producibility of fracture sweetspots. The simulator uses these physico-chemical predictions to integrate well log, surface, and core data with the otherwise incomplete seismic data. The simulator delineates the effects of regional tectonics, petroleum-derived overpressure, and salt tectonics and constructs maps of high-grading zones of fracture producibility.