Papers by Janet Jones-oliveira
We describe the development and use of a hybrid n-dimensional grid generation system called NWGRI... more We describe the development and use of a hybrid n-dimensional grid generation system called NWGRID. The Applied Mathematics Group at Pacific Northwest National Laboratory (PNNL) is developing this tool to support the Laboratory's computational science efforts in chemistry, biology, engineering and environmental (subsurface and atmospheric) modeling. NWGRID is the grid generation system, which is designed for multi-scale, multi-material, multi-physics, time-dependent,
Journal of The Acoustical Society of America, 1996
A transient solution is presented which models the fluidâsolid interaction of a thin elastic prol... more A transient solution is presented which models the fluidâsolid interaction of a thin elastic prolate spheroidal shell loaded end-on by a nonconservative acoustic shock wave. Solutions to the Lagrangian equations of motion are provided for the normal and tangential shell displacement fields, as well as for the incident, scattered, and radiated fluid pressure fields. The explicit analytic solutions converge uniformly
We describe an algorithm for automated blocking of geometry by using the Adaptive Mesh Refinement... more We describe an algorithm for automated blocking of geometry by using the Adaptive Mesh Refinement (AMR) algorithm in NWGRID. NWGRID is PNNL's mesh generation, mesh optimization and dynamic mesh maintenance code. It was originally designed for unstructured grids on massively parallel platforms, and is now being used to build hybrid grids, including unstructured, structured and block structured grids. Our approach
The Journal of the Acoustical Society of America, 1993
The Journal of the Acoustical Society of America, 1992
A transient solution is presented which models the fluidâsolid interaction of a thin elastic prol... more A transient solution is presented which models the fluidâsolid interaction of a thin elastic prolate spheroidal shell loaded end-on by a nonconservative acoustic shock wave. Solutions to the Lagrangian equations of motion are provided for the normal and tangential shell displacement fields, as well as for the incident, scattered, and radiated fluid pressure fields. The explicit analytic solutions converge uniformly
ABSTRACT One embodiment of the present invention includes a computer operable to represent a phys... more ABSTRACT One embodiment of the present invention includes a computer operable to represent a physical system with a graphical data structure corresponding to a matroid. The graphical data structure corresponds to a number of vertices and a number of edges that each correspond to two of the vertices. The computer is further operable to define a closed pathway arrangement with the graphical data structure and identify each different one of a number of fundamental cycles by evaluating a different respective one of the edges with a spanning tree representation. The fundamental cycles each include three or more of the vertices.
We describe the development and use of a hybrid n-dimensional grid generation system called NWGRI... more We describe the development and use of a hybrid n-dimensional grid generation system called NWGRID. The Applied Mathematics Group at Pacific Northwest National Laboratory (PNNL) is developing this tool to support the Laboratory's computational science efforts in chemistry, biology, engineering and environmental (subsurface and atmospheric) modeling. NWGRID is the grid generation system, which is designed for multi-scale, multi-material, multi-physics, time-dependent,
The Journal of the Acoustical Society of America, 1994
The exact series solutions for the transient shell displacement and fluid pressure fields resulti... more The exact series solutions for the transient shell displacement and fluid pressure fields resulting from the axisymmetric acoustic loading of a submerged, thin elastic, spherical shell are well known. Plots of the shell displacements, velocities, accelerations, strains, and strain rates have been published previously. Further investigation for the more general prolate spheroidal geometry has elucidated a complex exchange of energy
Journal of Computational Biology, 2004
We construct an algebraic-combinatorial model of the SOS compartment of the EGFR biochemical netw... more We construct an algebraic-combinatorial model of the SOS compartment of the EGFR biochemical network. A Petri net is used to construct an initial representation of the biochemical decision making network, which in turn defines a hyperdigraph. We observe that the linear algebraic structure of each hyperdigraph admits a canonical set of algebraic-combinatorial invariants that correspond to the information flow conservation laws governing a molecular kinetic reaction network. The linear algebraic structure of the hyperdigraph and its sets of invariants can be generalized to define a discrete algebraic-geometric structure, which is referred to as an oriented matroid. Oriented matroids define a polyhedral optimization geometry that is used to determine optimal subpaths that span the nullspace of a set of kinetic chemical reaction equations. Sets of constrained submodular path optimizations on the hyperdigraph are objectively obtained as a spanning tree of minimum cycle paths. This complete set of subcircuits is used to identify the network pinch points and invariant flow subpaths. We demonstrate that this family of minimal circuits also characteristically identifies additional significant biochemical reaction pattern features. We use the SOS Compartment A of the EGFR biochemical pathway to develop and demonstrate the application of our algebraic-combinatorial mathematical modeling methodology.
Bulletin of Mathematical Biology, 2001
We develop the mathematical machinery for the construction of an algebraic-combinatorial model us... more We develop the mathematical machinery for the construction of an algebraic-combinatorial model using Petri nets to construct an oriented matroid representation of biochemical pathways. For demonstration purposes, we use a model metabolic pathway example from the literature to derive a general biochemical reaction network model. The biomolecular networks define a connectivity matrix that identifies a linear representation of a Petri net. The sub-circuits that span a reaction network are subject to flux conservation laws. The conservation laws correspond to algebraic-combinatorial dual invariants, that are called S- (state) and T- (transition) invariants. Each invariant has an associated minimum support. We show that every minimum support of a Petri net invariant defines a unique signed sub-circuit representation. We prove that the family of signed sub-circuits has an implicit order that defines an oriented matroid. The oriented matroid is then used to identify the feasible sub-circuit pathways that span the biochemical network as the positive cycles in a hyper-digraph.
Advances in Applied Mathematics, 2002
A new orthonormal basis set representation of the prolate spheroidal radial and angular wave func... more A new orthonormal basis set representation of the prolate spheroidal radial and angular wave functions is presented. The embedded series solutions to a fully-coupled fluid-solid interaction continuum physics problem is defined by product sets of Legendre polynomials and modified spherical Bessel functions of the first and third kinds. We prove that the embedded series solutions analytically converge absolutely and uniformly to the exact solutions of the system of coupled continuum equations. The satisfaction of the bilinear concomitant and its utility in establishing the convergence proofs is demonstrated.
Journal of Computational Biology, 2003
We have applied an algorithmic methodology which provably decomposes any complex network into a c... more We have applied an algorithmic methodology which provably decomposes any complex network into a complete family of principal subcircuits to study the minimal circuits that describe the Krebs cycle. Every operational behavior that the network is capable of exhibiting can be represented by some combination of these principal subcircuits and this computational decomposition is linearly efficient. We have developed a computational model that can be applied to biochemical reaction systems which accurately renders pathways of such reactions via directed hypergraphs (Petri nets). We have applied the model to the citric acid cycle (Krebs cycle). The Krebs cycle, which oxidizes the acetyl group of acetyl CoA to CO(2) and reduces NAD and FAD to NADH and FADH(2), is a complex interacting set of nine subreaction networks. The Krebs cycle was selected because of its familiarity to the biological community and because it exhibits enough complexity to be interesting in order to introduce this novel analytic approach. This study validates the algorithmic methodology for the identification of significant biochemical signaling subcircuits, based solely upon the mathematical model and not upon prior biological knowledge. The utility of the algebraic-combinatorial model for identifying the complete set of biochemical subcircuits as a data set is demonstrated for this important metabolic process.
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Papers by Janet Jones-oliveira