Flexible Object Manipulation

Flexible objects are a challenge to manipulate. Their motions are hard to predict, and the high number of degrees of freedom makes sensing, control, and planning difficult. Additionally, they have more complex friction and contact issues than rigid bodies, and they may stretch and compress. In this thesis, I explore two major types of flexible materials: cloth and string. For rigid bodies, one of the most basic problems in manipulation is the development of immobilizing grasps. The same problem exists for flexible objects. I have shown that a simple polygonal piece of cloth can be fully immobilized by grasping all convex vertices and no more than one third of the concave vertices. I also explored simple manipulation methods that make use of gravity to reduce the number of fingers necessary for grasping. I have built a system for folding a T-shirt using a 4 DOF arm and a fixed-length iron bar which simulates two fingers. The main goal with string manipulation has been to tie knots without the use of any sensing. I have developed single-piece fixtures capable of tying knots in fishing line, solder, and wire, along with a more complex track-based system for autonomously tying a knot in steel wire. I have also developed a series of different fixtures that use compressed air to tie knots in string. Additionally, I have designed four-piece fixtures, which demonstrate a way to fully enclose a knot during the insertion process, while guaranteeing that extraction will always succeed

Geometrical vortex lattice pinning and melting in YBaCuO submicron bridges

Since the discovery of high-temperature superconductors (HTSs), most efforts of researchers have been focused on the fabrication of superconducting devices capable of immobilizing vortices, hence of operating at enhanced temperatures and magnetic fields. Recent findings that geometric restrictions may induce self-arresting hypervortices recovering the dissipation-free state at high fields and temperatures made superconducting strips a mainstream of superconductivity studies. Here we report on the geometrical melting of the vortex lattice in a wide YBCO submicron bridge preceded by magnetoresistance (MR) oscillations fingerprinting the underlying regular vortex structure. Combined magnetoresistance measurements and numerical simulations unambiguously relate the resistance oscillations to the penetration of vortex rows with intermediate geometrical pinning and uncover the details of geometrical melting. Our findings offer a reliable and reproducible pathway for controlling vortices in geometrically restricted nanodevices and introduce a novel technique of geometrical spectroscopy, inferring detailed information of the structure of the vortex system through a combined use of MR curves and large-scale simulations

Interlocking structure design and assembly

Many objects in our life are not manufactured as whole rigid pieces. Instead, smaller components are made to be later assembled into larger structures. Chairs are assembled from wooden pieces, cabins are made of logs, and buildings are constructed from bricks. These components are commonly designed by many iterations of human thinking. In this report, we will look at a few problems related to interlocking components design and assembly. Given an atomic object, how can we design a package that holds the object firmly without a gap in-between? How many pieces should the package be partitioned into? How can we assemble/extract each piece? We will attack this problem by first looking at the lower bound on the number of pieces, then at the upper bound. Afterwards, we will propose a practical algorithm for designing these packages. We also explore a special kind of interlocking structure which has only one or a small number of movable pieces. For example, a burr puzzle. We will design a few blocks with joints whose combination can be assembled into almost any voxelized 3D model. Our blocks require very simple motions to be assembled, enabling robotic assembly. As proof of concept, we also develop a robot system to assemble the blocks. In some extreme conditions where construction components are small, controlling each component individually is impossible. We will discuss an option using global controls. These global controls can be from gravity or magnetic fields. We show that in some special cases where the small units form a rectangular matrix, rearrangement can be done in a small space following a technique similar to bubble sort algorithm

Synergistically enhanced stability of laccase immobilized on synthesized silver nanoparticles with water-soluble polymers

"In Press, Accepted Manuscript, Available online 12 March 2017"Silver nanoparticles (AgNPs) were synthesized by citrate reduction method in the presence of polymers, poly(ethylene glycol) (PEG), poly(vinyl alcohol) (PVA) and chitosan, used as stabilizing agents, and an oxidoreductase enzyme, laccase (Lac), with the goal of expanding the NPs antimicrobial action. AgNPs were characterized by UV-visible spectrometry, dynamic light scattering and transmission electron microscopy. As protecting agents, PEG and PVA promoted the formation of spherical uniformly-shaped, small-sized, monodispersed AgNPs (≈ 20 nm). High Mw polymers were established as most effective in producing small-sized NPs. Chitosan's viscosity led to the formation of aggregates. Despite the decrease in Lac activity registered for the hybrid formulation, AgNPs-polymer-Lac, a significant augment in stability over time (up to 13 days, at 50 °C) was observed. This novel formulation displays improved synergistic performance over AgNPs-Lac or polymer-Lac conjugates, since in the former the Lac activity becomes residual at the end of 3 days. By enabling many ionic interactions, chitosan restricted the mass transfer between Lac and substrate and, thus, inhibited the enzymatic activity. These hybrid nanocomposites made up of inorganic NPs, organic polymers and immobilized antimicrobial oxidoreductive enzymes represent a new class of materials with improved synergistic performance. Moreover, the Lac and the AgNPs different antimicrobial action, both in time and mechanism, may also constitute a new alternative to reduce the probability of developing resistance-associated mutations.This work was funded by Portuguese Foundation for Science and TechnologyFCT/MCTES (PIDDAC) and co-financed by European funds (FEDER) through the PT2020 program, research projectM-ERA-NET/0006/2014. A. Zille and H. P. Felgueiras also acknowledge funding from FCT within the scope of the project POCI-01-0145-FEDER-007136 and UID/CTM/00264

Graphene as a Solid-state Ligand for Palladium Catalyzed Cross-coupling Reactions

Palladium-catalyzed carbon-carbon cross-coupling reactions have emerged a broadly useful, selective and widely applicable method to synthesize pharmaceutical active ingredients. As currently practiced in the pharmaceutical industry, homogeneous Pd catalysts are typically used in cross-coupling reactions. The rational development of heterogeneous catalysts for cross-coupling reactions is critical for overcoming the major drawbacks of homogeneous catalysis including difficulties in the separation, purification, and quality control process in drug production. In order to apply heterogeneous catalysis to flow reactors that may overcome this limitation, the catalyst must be strongly bound to a support, highly stable with respect to leaching, and highly active. While the primary role of supports in catalysis has been to anchor metal particles to prevent sintering and leaching, supports can also activate catalytic processes. In this study, by using a xi combined theoretical and experimental method, we probed the effect of graphene as support in the complex reaction cycle of Suzuki reactions. The density functional theory study provides a fundamental understanding of how a graphene support strongly binds the Pd nanoparticles and act as both an efficient charge donor and acceptor in oxidation and reduction reaction steps. Theoretical investigations prove that the Pd-graphene interaction promotes electron flow between the metal cluster and the defected graphene to reduce reaction barrier. The ability for graphene to both accept and donate charge makes graphene an unusually suitable support for multi-step catalytic processes that involve both oxidation and reduction steps. The computer-aided catalyst design with the atomic precise accuracy demonstrates the Pd/graphene catalyst can be further optimized and the first-row transition metal nanoparticles have great potential to replace Pd to catalyze the Suzuki reaction. The corresponding experimental study shows that the method to immobilize the Pd nanoparticles on the graphene is crucial to increasing the reactivity and stability of the resulted catalyst. A comparison of the activation energy and turn over frequency for a series of supported and homogeneous catalysts indicates that exposing palladium-graphene to defect inducing microwave radiation results in dramatically lower activation energies and higher turnover frequencies. Furthermore, the heterogeneity tests demonstrate the Suzuki reactions are carried out on the surface of the immobilized Pd nanoparticle agreeing with the theoretical results. A method to engineer the 2-D graphene support to a 3-D structure to minimize the re-stacking and agglomeration of the graphene lattice will also be introduced in this study

Anomalous Diffusion in Biological Trapping Regions

abstract: Advances in experimental techniques have allowed for investigation of molecular dynamics at ever smaller temporal and spatial scales. There is currently a varied and growing body of literature which demonstrates the phenomenon of \emph{anomalous diffusion} in physics, engineering, and biology. In particular many diffusive type processes in the cell have been observed to follow a power law \left \propto t^\alpha scaling of the mean square displacement of a particle. This contrasts with the expected linear behavior of particles undergoing normal diffusion. \emph{Anomalous sub-diffusion} ($\alpha<1$) has been attributed to factors such as cytoplasmic crowding of macromolecules, and trap-like structures in the subcellular environment non-linearly slowing the diffusion of molecules. Compared to normal diffusion, signaling molecules in these constrained spaces can be more concentrated at the source, and more diffuse at longer distances, potentially effecting the signalling dynamics. As diffusion at the cellular scale is a fundamental mechanism of cellular signaling and additionally is an implicit underlying mathematical assumption of many canonical models, a closer look at models of anomalous diffusion is warranted. Approaches in the literature include derivations of fractional differential diffusion equations (FDE) and continuous time random walks (CTRW). However these approaches are typically based on \emph{ad-hoc} assumptions on time- and space- jump distributions. We apply recent developments in asymptotic techniques on collisional kinetic equations to develop a FDE model of sub-diffusion due to trapping regions and investigate the nature of the space/time probability distributions assosiated with trapping regions. This approach both contrasts and compliments the stochastic CTRW approach by positing more physically realistic underlying assumptions on the motion of particles and their interactions with trapping regions, and additionally allowing varying assumptions to be applied individually to the traps and particle kinetics.Dissertation/ThesisDoctoral Dissertation Mathematics 201

The fate of arsenic in soil-plant systems

The final publication is available at Springer via http://dx.doi.org/10.1007/978-1-4614-1463-6_1Arsenic (As) is an element belonging to the group V-A, and it demonstrates characteristics of a metalloid. Because arsenic more easily forms anions, its non-metal properties dominate. When arsenic is in an oxidation state of +5, it acts similar to phosphorus, a fact that has many implications for the way in which it reacts in soil, as well as its potential toxicity in plants. The most common oxidation states of As are -3, 0, +3, and +5. Arsines and metal arsines are those in which As has an oxidation state of -3, and these forms are very unstable under oxidizing conditions. Under aerobic conditions, the oxidation state of As tends to be +5, and when this occurs at a pH between 2 and 3, arsenic acid (H3AsO4) is formed. When the pH rises to values between 3 and 11, this compound disassociates to H2AsO4 - and HAsO4 2- (Smedley and Kinninburgh 2002). Under anaerobic conditions, the predominant As species is H3AsO3This study was supported by the Spanish Ministry of Education and Science, project CTM 2010-21922-CO2-02, and by Comunidad de Madrid, project S2009/AMB- 147

Diversity of soil invertebrates associated to six spatially aggregated plant species in the Yasuní National Park, Amazonian Ecuador.

Amazonian tropical rainforests harbor the largest biodiversity on Earth. Over the past decade, there has been increasing interest in understanding how such diversity can coexist in small areas. One broadly accepted explanation is the Negative Density Dependence hypothesis (NDD) that promotes species coexistence through a spacing mechanism that prevents species from becoming locally abundant. This may happen due to seedling mortality caused by intraspecific competition, or the attack of natural enemies. However, there are organisms such as particular plant tree species that are adapted to live in aggregation. How does this particular group of plants cope with the above mentioned survival constraints? A potential mechanism would be the efficient use of nutrients mainly coming from their own litter resources that are invested by plants in growing and defense. If that is so, one would expect detritivore communities within the sites of plants aggregation to be different from what is found outside these microhabitats. Here, using two different sampling methodologies, we provide a detailed description of soil fauna community diversity in areas of aggregation of six common tree species in the Yasuní National Park (Amazonian Ecuador). We hypothesized that (i) both capture methodologies used in our survey (i.e. Winkler extraction and pitfall traps) are complementary between them in terms of species composition; (ii) the ‘litter transformers’ guild represents the largest portion of the soil invertebrate fauna in both, the number of species and abundance; and (iii) soil fauna communities in areas of plants aggregation are significantly different in terms of the number of species, composition, abundance and functionality, compared to the sites where the focal plant species are absent. Agreeing with our hypotheses, our results showed that Amazonian soil fauna are predominantly represented by species included within the litter transformers functional group (65 % of total collection), and they are clustered in small-scale patches and specific to the areas of aggregation of our focal plant species. This suggests that plant species living in aggregation may create microhabitats that promote the association of particular soil fauna species that may be adapted to exploit specific combinations of nutrients in the Yasuní forest floor

Modeling of a permeable reactive barrier

The focus of the presentstudy was centered on the modeling analysis to support the Permeable Reactive Barrier (PRB) design. The flow model formulated to simulate the Permeable Reactive Barrier System integrated the available geologic, hydro geologic and geo-chemical data from numerous recent installations to simulate a subsurface ground water scenario. Different generic cases that a PRB system would fall into were identified based on its utility and aquifer conditions and then employed to produce different model adaptations. The different simulation codes and interfaces were evaluated, and the most expedient of them was used to simulate the Model. The simulations were then used to study the sensitivity of different parameters and identify those that were critical to the design of the system. Design curves, devised to aid the design of a barrier, were verified with the residence time curves mapped for the same parameters. The results of the sensitivity analysis and the developed design curves were used to arrive at a uniform procedure for the design of a Continuous Configuration Barrier System. The procedure was appraised by working through the design of a Permeable Reactive Barrier at a GW contaminated site located in the Piedmont Province of the Appalachian Highlands in New Jersey