Miniature Compliant Grippers With Vision-Based Force Sensing

This paper is concerned with grasping biological cells in aqueous medium with miniature grippers that can also help estimate forces using vision-based displacement measurement and computation. We present the design, fabrication, and testing of three single-piece, compliant miniature grippers with parallel and angular jaw motions. Two grippers were designed using experience and intuition, while the third one was designed using topology optimization with implicit manufacturing constraints. These grippers were fabricated using different manufacturing techniques using spring steel and polydimethylsiloxane ( PDMS). The grippers also serve the purpose of a force sensor. Toward this, we present a vision-based force-sensing technique by solving Cauchy's problem in elasticity using an improved algorithm. We validated this technique at the macroscale, where there was an independent method to estimate the force. In this study, the gripper was used to hold a yeast ball and a zebrafish egg cell of less than 1 mm in diameter. The forces involved were estimated to be about 30 and 10 mN for the yeast ball and the zebrafish egg cell, respectively.

A DC-to-Three-Phase-AC High-Frequency Link Converter With Compensation for Nonlinear Distortion

This paper focuses on a new high-frequency (HF) link dc-to-three-phase-ac power converter. The least number of switching devices among other HF link dc-to-three-phase-ac converters, improved power density due to the absence of devices of bidirectional voltage-blocking capability, simple commutation requirements, and isolation between input and output are the integral features of this topology. The commutation process of the converter requires zero portions in the link voltage. This causes a nonlinear distortion in the output three-phase voltages. The mathematical analysis is carried out to investigate the problem, and suitable compensation in modulating signal is proposed for different types of carrier. Along with the modified modulator structure, a synchronously rotating reference-frame-based control scheme is adopted for the three-phase ac side in order to achieve high dynamic performance. The effectiveness of the proposed scheme has been investigated and verified through computer simulations and experimental results with 1-kVA prototype.

Playing Games on Sets and Models

The most prominent objective of the thesis is the development of the generalized descriptive set theory, as we call it. There, we study the space of all functions from a fixed uncountable cardinal to itself, or to a finite set of size two. These correspond to generalized notions of the universal Baire space (functions from natural numbers to themselves with the product topology) and the Cantor space (functions from natural numbers to the {0,1}-set) respectively. We generalize the notion of Borel sets in three different ways and study the corresponding Borel structures with the aims of generalizing classical theorems of descriptive set theory or providing counter examples. In particular we are interested in equivalence relations on these spaces and their Borel reducibility to each other. The last chapter shows, using game-theoretic techniques, that the order of Borel equivalence relations under Borel reduciblity has very high complexity. The techniques in the above described set theoretical side of the thesis include forcing, general topological notions such as meager sets and combinatorial games of infinite length. By coding uncountable models to functions, we are able to apply the understanding of the generalized descriptive set theory to the model theory of uncountable models. The links between the theorems of model theory (including Shelah's classification theory) and the theorems in pure set theory are provided using game theoretic techniques from Ehrenfeucht-Fraïssé games in model theory to cub-games in set theory. The bottom line of the research declairs that the descriptive (set theoretic) complexity of an isomorphism relation of a first-order definable model class goes in synch with the stability theoretical complexity of the corresponding first-order theory. The first chapter of the thesis has slightly different focus and is purely concerned with a certain modification of the well known Ehrenfeucht-Fraïssé games. There we (me and my supervisor Tapani Hyttinen) answer some natural questions about that game mainly concerning determinacy and its relation to the standard EF-game

A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

Determining the sequence of amino acid residues in a heteropolymer chain of a protein with a given conformation is a discrete combinatorial problem that is not generally amenable for gradient-based continuous optimization algorithms. In this paper we present a new approach to this problem using continuous models. In this modeling, continuous "state functions" are proposed to designate the type of each residue in the chain. Such a continuous model helps define a continuous sequence space in which a chosen criterion is optimized to find the most appropriate sequence. Searching a continuous sequence space using a deterministic optimization algorithm makes it possible to find the optimal sequences with much less computation than many other approaches. The computational efficiency of this method is further improved by combining it with a graph spectral method, which explicitly takes into account the topology of the desired conformation and also helps make the combined method more robust. The continuous modeling used here appears to have additional advantages in mimicking the folding pathways and in creating the energy landscapes that help find sequences with high stability and kinetic accessibility. To illustrate the new approach, a widely used simplifying assumption is made by considering only two types of residues: hydrophobic (H) and polar (P). Self-avoiding compact lattice models are used to validate the method with known results in the literature and data that can be practically obtained by exhaustive enumeration on a desktop computer. We also present examples of sequence design for the HP models of some real proteins, which are solved in less than five minutes on a single-processor desktop computer Some open issues and future extensions are noted.

An optimal parallel algorithm for sparse matrix bandwidth reduction on a linear array

A simple and efficient algorithm for the bandwidth reduction of sparse symmetric matrices is proposed. It involves column-row permutations and is well-suited to map onto the linear array topology of the SIMD architectures. The efficiency of the algorithm is compared with the other existing algorithms. The interconnectivity and the memory requirement of the linear array are discussed and the complexity of its layout area is derived. The parallel version of the algorithm mapped onto the linear array is then introduced and is explained with the help of an example. The optimality of the parallel algorithm is proved by deriving the time complexities of the algorithm on a single processor and the linear array.

Stability of synchronization in a multi-cellular system

Networks of biochemical reactions regulated by positive-and negative-feedback processes underlie functional dynamics in single cells. Synchronization of dynamics in the constituent cells is a hallmark of collective behavior in multi-cellular biological systems. Stability of the synchronized state is required for robust functioning of the multi-cell system in the face of noise and perturbation. Yet, the ability to respond to signals and change functional dynamics are also important features during development, disease, and evolution in living systems. In this paper, using a coupled multi-cell system model, we investigate the role of system size, coupling strength and its topology on the synchronization of the collective dynamics and its stability. Even though different coupling topologies lead to synchronization of collective dynamics, diffusive coupling through the end product of the pathway does not confer stability to the synchronized state. The results are discussed with a view to their prevalence in biological systems. Copyright (C) EPLA, 2010

Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates

Beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.

Identification of Critical Residues of the Mycobacterial Dephosphocoenzyme A Kinase by Site-Directed Mutagenesis

Dephosphocoenzyme A kinase performs the transfer of the c-phosphate of ATP to dephosphocoenzyme A, catalyzing the last step of coenzyme A biosynthesis. This enzyme belongs to the P-loop-containing NTP hydrolase superfamily, all members of which posses a three domain topology consisting of a CoA domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. Differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have pointed out the tubercular CoaE as a high confidence drug target (HAMAP database). Unfortunately the absence of a three-dimensional crystal structure of the enzyme, either alone or complexed with either of its substrates/regulators, leaves both the reaction mechanism unidentified and the chief players involved in substrate binding, stabilization and catalysis unknown. Based on homology modeling and sequence analysis, we chose residues in the three functional domains of the enzyme to assess their contributions to ligand binding and catalysis using site-directed mutagenesis. Systematically mutating the residues from the P-loop and the nucleotide-binding site identified Lys14 and Arg140 in ATP binding and the stabilization of the phosphoryl intermediate during the phosphotransfer reaction. Mutagenesis of Asp32 and Arg140 showed catalytic efficiencies less than 5-10% of the wild type, indicating the pivotal roles played by these residues in catalysis. Non-conservative substitution of the Leu114 residue identifies this leucine as the critical residue from the hydrophobic cleft involved in leading substrate, DCoA binding. We show that the mycobacterial enzyme requires the Mg2+ for its catalytic activity. The binding energetics of the interactions of the mutant enzymes with the substrates were characterized in terms of their enthalpic and entropic contributions by ITC, providing a complete picture of the effects of the mutations on activity. The properties of mutants defective in substrate recognition were consistent with the ordered sequential mechanism of substrate addition for CoaE.

Proposed visible emission line space solar coronagraph

The outer atmosphere of the sun called the corona has been observed during total solar eclipse for short periods (typically <6 min), from as early as the eighteenth century. In the recent past, space-based instruments have permitted us to study the corona uninterruptedly. In spite of these developments, the dynamic corona and its high temperature (1-2 million K) are yet to be Ally understood. It is conjectured that their dynamic nature and associated energetic events are possible reasons behind the high temperature. In order to study these in detail, a visible emission line space solar coronagraph is being proposed as a payload under the small-satellite programme of the Indian Space Research Organisation. The satellite is named as Aditya-1 and the scientific objectives of this payload are to study: (i) the existence of intensity oscillations for the study of wave-driven coronal heating; (ii) the dynamics and formation of coronal loops and temperature structure of the coronal features; (iii) the origin, cause and acceleration of coronal mass ejections (CMEs) and other solar active features, and (iv) coronal magnetic field topology and three-dimensional structures of CMEs using polarization information. The uniqueness of this payload compared to previously flown space instruments is as follows: (a) observations in the visible wavelength closer to the disk (down to 1.05 solar radii); (b) high time cadence capability (better than two-images per second), and (c) simultaneous observations of at least two spectral windows all the time and three spectral windows for short durations.

Studies on Compact Discharge Plasma Source for NOX Treatment in Engine Exhaust

This paper proposes a compact electric discharge plasma source for controlling NOX emission in diesel engine exhaust. An automobile ignition coil was used to generate the high voltage pulse using flyback topology. This design is aimed at retrofitting the existing catalytic converters with pulse assisted cleaning technique. In this paper we bring out a relative comparison of discharge plasma and plasma-adsorbent process at different gas flow rates. Activated alumina was used as adsorbent. The main emphasis is laid on the development of a compact pulse source from a DC supply for the removal of NOX from the filtered diesel engine exhaust.

Role of organic fluorine in crystal engineering

The design of compounds with novel and improved physico-chemical properties as advanced functional materials with a specific application spectrum requires the knowledge about possible supramolecular packing motifs and their experimental control in crystalline lattice. Besides the structure of the individual molecule, non-covalent interactions play a significant role in the determination of molecular conformation, along with the formation of three-dimensional supramolecular architecture in a crystal as a requirement for molecular recognition processes, and the related bioactivity. Involvement of functional groups will contribute to the formation of a predefined packing motif due to their well-defined interactions. The strength and directionality of these interactions create characteristic packing motifs, which can be used for the design of supramolecular arrangements by the development of appropriate strategies for the precise control of their topology. Most relevant of these non-covalent interactions are stacking interactions and hydrogen bonds, which have been subjects of extensive study in the last two decades. In recent literature, substantial efforts have been put in by various researchers towards the understanding of interactions involving organic fluorine and the role they play in generating different packing motifs which guides assembling of molecules in the crystal lattice.

Design of logical topologies for wavelength-routed optical networks

his paper studies the problem of designing a logical topology over a wavelength-routed all-optical network (AON) physical topology, The physical topology consists of the nodes and fiber links in the network, On an AON physical topology, we can set up lightpaths between pairs of nodes, where a lightpath represents a direct optical connection without any intermediate electronics, The set of lightpaths along with the nodes constitutes the logical topology, For a given network physical topology and traffic pattern (relative traffic distribution among the source-destination pairs), our objective is to design the logical topology and the routing algorithm on that topology so as to minimize the network congestion while constraining the average delay seen by a source-destination pair and the amount of processing required at the nodes (degree of the logical topology), We will see that ignoring the delay constraints can result in fairly convoluted logical topologies with very long delays, On the other hand, in all our examples, imposing it results in a minimal increase in congestion, While the number of wavelengths required to imbed the resulting logical topology on the physical all optical topology is also a constraint in general, we find that in many cases of interest this number can be quite small, We formulate the combined logical topology design and routing problem described above (ignoring the constraint on the number of available wavelengths) as a mixed integer linear programming problem which we then solve for a number of cases of a six-node network, Since this programming problem is computationally intractable for larger networks, we split it into two subproblems: logical topology design, which is computationally hard and will probably require heuristic algorithms, and routing, which can be solved by a linear program, We then compare the performance of several heuristic topology design algorithms (that do take wavelength assignment constraints into account) against that of randomly generated topologies, as well as lower bounds derived in the paper.

Pipelined ring algorithm for matrix multiplication on transputer networks: performance analysis and estimation

A parallel matrix multiplication algorithm is presented, and studies of its performance and estimation are discussed. The algorithm is implemented on a network of transputers connected in a ring topology. An efficient scheme for partitioning the input matrices is introduced which enables overlapping computation with communication. This makes the algorithm achieve near-ideal speed-up for reasonably large matrices. Analytical expressions for the execution time of the algorithm have been derived by analysing its computation and communication characteristics. These expressions are validated by comparing the theoretical results of the performance with the experimental values obtained on a four-transputer network for both square and irregular matrices. The analytical model is also used to estimate the performance of the algorithm for a varying number of transputers and varying problem sizes. Although the algorithm is implemented on transputers, the methodology and the partitioning scheme presented in this paper are quite general and can be implemented on other processors which have the capability of overlapping computation with communication. The equations for performance prediction can also be extended to other multiprocessor systems.

Diffusion Anomaly in Silicalite and VPI-5 from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations on rigid and flexible framework models of silicalite and a rigid framework model of the aluminophosphate VPI-5 for different sorbate diameters are reported. The sorbate-host interactions are modeled in terms of simple atom-atom Lennard-Jones interactions. The results suggest that the diffusion coefficient exhibits an anomaly as gamma approaches unity. The MD results confirm the existence of a linear regime for sorbate diameters significantly smaller than the channel diameter and an anomalous regime observed for sorbate diameters comparable to the channel diameter. The power spectra obtained by Fourier transformation of the velocity autocorrelation function indicate that there is an increase in the intensity of the low-frequency component for the velocity component parallel to the direction of motion for the sorbate diameter in the anomalous regime. The present results suggest that the diffusion anomaly is observed irrespective of (1) the geometry and topology of the pore structure and (2) the nature of the host material. The results are compared with the work of Derouane and co-workers, who have suggested the existence of ''floating molecules'' on the basis of earlier theoretical and computational approaches.

The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin

Bacteriorhodopsin (bR) continues to be a proven testing ground for the study of integral membrane proteins (IMPs). It is important to study the stability of the individual helices of bR, as they are postulated to exist as independently stable transmembmne helices (TMHs) and also for their utility as templates for modeling other IMPs with the postulated seven-helix bundle topology. Toward this purpose, the seven helices of bR have been studied by molecular dynamics simulation in this study. The suitability of using the backbone-dependent rotamer library of side-chain conformations arrived at from the data base of globular protein structures in the case TMHs has been tested by another set of ? helix simulations with the side-chain orientations taken from this library. The influence of the residue's net charge oil the helix stability was examined by simulating the helices III, IV, and VI (from both of the above sets of helices) with zero net charge on the side chains. The results of these 20 simulations demonstrate in general the stability of the isolated helices of bR in conformity with the two-stage hypothesis of IMP folding. However, the helices I, II, V, and VII are more stable than the other three helices. The helical nature of certain regions of III, IV, and VI are influenced by factors such as the net charge and orientation of several residues. It is seen that the residues Arg, Lys, Asp, and Glu (charged residues), and Ser, Thr, Gly, and Pro, play a crucial role in the stability of the helices of bR. The backbone-dependent rotamer library for the side chains is found to be suitable for the study of TMHs in IMP. (C) 1996 John Wiley & Sons, Inc.