A reactive/deliberative planner using genetic algorithms on tactical primitives

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2006.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 99-102).Unmanned aerial systems are increasingly assisting and replacing humans on so-called dull, dirty, and dangerous missions. In the future such systems will require higher levels of autonomy to effectively use their agile maneuvering capabilities and high-performance weapons and sensors in rapidly evolving, limited-communication combat situations. Most existing vehicle planning methods perform poorly on such realistic scenarios because they do not consider both continuous nonlinear system dynamics and discrete actions and choices. This thesis proposes a flexible framework for forming dynamically realistic, hybrid system plans composed of parametrized tactical primitives using genetic algorithms, which implicitly accommodate hybrid dynamics through a nonlinear fitness function. The framework combines deliberative planning with specially chosen tactical primitives to react to fast changes in the environment, such as pop-up threats. Tactical primitives encapsulate continuous and discrete elements together, using discrete switchings to define the primitive type and both discrete and continuous parameters to capture stylistic variations. This thesis demonstrates the combined reactive/deliberative framework on a problem involving two-dimensional navigation through a field of threats while firing weapons and deploying countermeasures. It also explores the planner's performance with respect to computational resources, problem dimensionality, primitive design, and planner initialization. These explorations can guide further algorithm design and future autonomous tactics research.by Stephen William Thrasher, Jr.S.M

Calibration of Traffic Simulation Models using SPSA

Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) “Γεωπληροφορική

Calibration of Traffic Simulation Models using SPSA

Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) “Γεωπληροφορική

Molecular Dynamics Simulation

Condensed matter systems, ranging from simple fluids and solids to complex multicomponent materials and even biological matter, are governed by well understood laws of physics, within the formal theoretical framework of quantum theory and statistical mechanics. On the relevant scales of length and time, the appropriate ‘first-principles’ description needs only the Schroedinger equation together with Gibbs averaging over the relevant statistical ensemble. However, this program cannot be carried out straightforwardly—dealing with electron correlations is still a challenge for the methods of quantum chemistry. Similarly, standard statistical mechanics makes precise explicit statements only on the properties of systems for which the many-body problem can be effectively reduced to one of independent particles or quasi-particles. [...

Evolution of structure and function in Phenylalanine Hydroxylase. With the regulatory properties in sight

In the post-genomic era, an idea of how similar the genomes of different species actually are is on the horizon. Less than 10 years ago, the human genome was estimated to encode 100000 genes. That was an overestimation, as the real number of human genes is 20000-25000. Most genes are expressed as proteins. The 3D structure of a protein is more conserved than its sequence, and therefore the structural context of protein and gene evolution must not be forgotten. By its structure, the protein can propagate its function. In the early 90’s the estimated number of different protein structure classes, so called folds, was predicted to be about 10000. Today there are slightly above 1000 folds and the discovery of new folds has leveled off, despite an increase in the number of protein structures that have been solved over the last few years. Indeed, some folds are used for more than one function, and found in various functional contexts. Then, if the many components are so similar, how is the biological species divergence from same component genomes achieved? One way to study biological diversity is by dividing it into its smaller components, e.g. by studying protein or gene family evolution. Here the evolution and regulation of the aromatic amino acid hydroxylase (AAAHs) have been under examination. This gene family encodes the proteins phenylalanine hydroxylase (PAH), tyrosine hydroxylase (TH), and tryptophan hydroxylase (TPH). These enzymes are highly physiologically important. PAH, expressed in liver, regulates the homeostasis of L-Phe by hydroxylating it into L-Tyr. TH, expressed in the central nervous system, hydroxylates L-Tyr into L-Dopa. L-Dopa is part of two important pathways i) melanogenesis and ii) dopamine production. In humans, dysfunctions in PAH that cause elevated L-Phe concentration can result in phenylketonuria (PKU). Untreated PKU results in neurological damage. TPH produces a precursor of serotonin from LTrp. The end products of these enzymes are neurotransmitters and hormones with increasingly important functions, from e.g. amoeba to nematode to man. As PAH has evolved in mammals its regulation has become increasingly sophisticated, e.g. homotropic positive cooperativity that shifts the conformational equilibrium from dimeric to tetrameric is seen in the mammalian lineage. Nematode PAH is devoid of positive cooperativity, but resembles the tetrameric high-affinity and high-activity mammalian PAH. TH and TPH are always tetrameric and not allosterically regulated. Each AAAH subunit has a regulatory domain, a catalytic domain, and an oligomerization domain. The promotion of positive cooperativity in PAH has been investigated by comparing mammalian PAH to nematode PAH. The low-affinity and low-activity dimer as well as the high-affinity and high-activity tetramer of PAH were modeled. Sequence analysis on a nematode sequence cluster and a mammalian sequence cluster identified sites with high probability of being involved in functional divergence, e.g. change in regulation. Residue specific electrostatic interaction energies were calculated for all ionizible residues in the models. In general, we note important differences in the substrate binding pocket that aids to explain why the active site in nematode PAH is less dynamic than in mammalian PAH. Our results suggest a pathway for the positive cooperativity from one active site to another, involving various predicted hinge regions from human PAH, where we find the nematode PAH more rigid. The regulatory domain in PAH is part of the ACT domain family. The ACT domains are frequently found regulating metabolic enzymes in an allosteric manner. The allosteric effector is often an amino acid that binds to an interface formed by two ACT domains. No contacts are formed between two ACT domains and the stoichiometry of binding is 1:1 for L-Phe in PAH. Therefore the allosteric effect must originate in the active site when the substrate binds. An alternative pathway for aromatic amino acid biosynthesis is present in e.g. plants and bacteria. This pathway has an L-Phe binding ACT domain, which is homologous to the ACT domain in AAAH. The L-Phe binding motif in this domain is also conserved in PAH. A comparative structural analysis of this area shows why L-Phe may not bind in the AAAH regulatory domain and also indicates why it has remained. The ACT domain has an abundant fold, a superfold. A structural approach was used to identify more potential ACT domains to gain further insights to the functional properties that this domain could perform in general, and in PAH in particular. Here we note e.g. two interesting potential domain families that could be homologous to the ACT domain, namely the GlnB-like domains and heavy metal binding domains. The phylogeny of the AAAH family has not been resolved earlier given the lack of a suitable outgroup. As more genome sequences became available, we identified an outgroup candidate and had it experimentally characterized. The phylogeny was resolved, the ancestral function determined, and by comparing the chromosomal gene locations the order of events in AAAH evolution was envisioned

Laboratory Directed Research and Development FY2010 Annual Report

A premier applied-science laboratory, Lawrence Livermore National Laboratory (LLNL) has at its core a primary national security mission - to ensure the safety, security, and reliability of the nation's nuclear weapons stockpile without nuclear testing, and to prevent and counter the spread and use of weapons of mass destruction: nuclear, chemical, and biological. The Laboratory uses the scientific and engineering expertise and facilities developed for its primary mission to pursue advanced technologies to meet other important national security needs - homeland defense, military operations, and missile defense, for example - that evolve in response to emerging threats. For broader national needs, LLNL executes programs in energy security, climate change and long-term energy needs, environmental assessment and management, bioscience and technology to improve human health, and for breakthroughs in fundamental science and technology. With this multidisciplinary expertise, the Laboratory serves as a science and technology resource to the U.S. government and as a partner with industry and academia. This annual report discusses the following topics: (1) Advanced Sensors and Instrumentation; (2) Biological Sciences; (3) Chemistry; (4) Earth and Space Sciences; (5) Energy Supply and Use; (6) Engineering and Manufacturing Processes; (7) Materials Science and Technology; Mathematics and Computing Science; (8) Nuclear Science and Engineering; and (9) Physics

Computational investigation of the photochemistry and spectroscopy of cyclic aromatic hydrocarbons in interstellar ice analogs

This thesis describes the photochemistry and ultraviolet (UV) spectroscopy of cyclic aromatic hydrocarbons such as benzene and naphthalene, along with small water clusters and crystalline water ice clusters. Firstly, benzene and naphthalene interactions with small water hexamer (W6) clusters, and then benzene interactions with crystalline water ice clusters are investigated. This thesis primarily focuses on the applications of a range of computational chemistry techniques to investigate and characterize excited states of these complex systems, which are generated following one-photon absorption. Benzene and naphthalene, as prototypical polycyclic aromatic hydrocarbons (PAHs), and water and crystalline ice clusters, taken as representative of interstellar ices, could also be considered as useful model systems to replicate polycyclic aromatic hydrocarbons (PAHs) in interstellar ices, and to study their behaviour under UV processing. From coupled cluster (CC) benchmark studies on small water clusters up to water the pentamer, it is shown that that highly correlated linear-response coupled cluster methods such as CCSD and CC3 are important to consider while studying electronic excitations, as electron correlation effects play an important role in such systems, with double excitations playing a dominant role. However, triple excitations contributions calculated are negligible with CCSD and CC3 methods converging monotonically to similar results. The aggregation effect on water at CCSD level has shown a blue shift of ~ 0.7 eV in the central water molecule of water pentamer (C2v) relative to water monomer (C2v), and is in good agreement with the experimental blue shift of ~ 1 eV in condensed phase. For both benzene- and naphthalene-bound water W6 clusters, we have calculated interesting features of benzene- and naphthalene-mediated electronic excitations of the water W6 cluster at wavelengths where photon absorption cross section of water is negligible i.e., above 170 nm. These excitations were originally absent in the isolated water W6 cluster. Similar features are calculated for benzene-bound crystalline ice clusters, which also illustrate the effect of cyclic aromatic hydrocarbons on electronic excitations of ice clusters, and are also observed experimentally. The brightest → ∗ electronic transition of benzene and naphthalene is calculated to be red-shifted in wavelength and occurs with lower intensities after interacting with the water W6 and ice clusters. The degeneracy of this transition is also slightly broken in benzene. We have observed new electronic transition features such as charge transfer (CT), and locally diffuse Rydberg type excitation in these complexes. We have found a good performance of hybrid DFT functionals i.e. M06-2X and CAM-B3LYP in calculating vertical excitation energies of these complexes using time dependent density functional theory (TD-DFT). Further, diffusion studies of the deuterium (D) atom have shown the importance of surface morphology in generating different potential sites and hopping characteristics of the D atom on crystalline and amorphous ice surfaces. D2 formation is found to be efficient on the amorphous ice surface, with longer residence times of the D atom indicating a possibility of the deuterium atom getting trapped in such sites. There is then a further possibility of the diffusing D atom to recombine with the trapped D atom to form a D2 molecule. However, such D atom trapping is a rare possibility on crystalline surface, as hopping is fast and thus the recombination process is not efficient on crystalline ice surface