Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A

The two protein tyrosine phosphatase (PTP) domains in bi-domain PTPs share high sequence and structural similarity. However, only one of the two PIP domains is catalytically active. Here we describe biochemical studies on the two tandem PTP domains of the bi-domain PTP, PTP99A. Phosphatase activity, monitored using small molecule as well as peptide substrates, revealed that the inactive (D2) domain activates the catalytic (D1) domain. Thermodynamic measurements suggest that the inactive D2 domain stabilizes the bi-domain (D1-D2) protein. The mechanism by which the D2 domain activates and stabilizes the bi-domain protein is governed by few interactions at the inter-domain interface. In particular, mutating Lys990 at the interface attenuates inter-domain communication. This residue is located at a structurally equivalent location to the so-called allosteric site of the canonical single domain PIP, PTP1B. These observations suggest functional optimization in bi-domain PTPs whereby the inactive PTP domain modulates the catalytic activity of the bi-domain enzyme. (C) 2012 Elsevier B.V. All rights reserved.

Sliding-Mode Guidance and Control for All-Aspect Interceptors with Terminal Angle Constraints

In this paper, sliding-mode-control-based guidance laws to intercept stationary, constant-velocity, and maneuvering targets at a desired impact angle are proposed. The desired impact angle, which is defined in terms of a desired line-of-sight angle, is achieved in finite time by selecting the missile's lateral acceleration to enforce terminal sliding mode on a switching surface designed using nonlinear engagement dynamics. The conditions for capturability are also presented. In addition, by considering a three-degree-of-freedom linear-interceptor dynamic model and by following the procedure used to design a dynamic sliding-mode controller, the interceptor autopilot is designed as a simple static controller to track the lateral acceleration generated by the guidance law. Numerical simulation results are presented to validate the proposed guidance laws and the autopilot design for different initial engagement geometries and impact angles.

Seismic Stability and Liquefaction Analysis of Tailings Dam

Proper analysis for safe design of tailings earthen dam is necessary under static loading and more so under earthquake conditions to reduce damages of important geotechnical structure. This paper presents both static and seismic analyses of a typical section of tailings earthen dam constructed by downstream method and located at a site in eastern part India to store non-radioactive nuclear waste material. The entire analysis is performed using geotechnical softwares FLAC(3D) and TALREN 4. Results are obtained for various possible conditions of the reservoir to investigate the stability under both static and seismic loading condition using 1989 Loma Prieta earthquake acceleration-time history. FLAC(3D) analyses indicate the critical maximum displacement at crest of the proposed tailings dam section is 5.5 cm under the static loading but it increases to about 16.24 cm under seismic loading. The slope stability analyses provide the minimum value of factor of safety for seismic loading as 1.5 as compared to 2.31 for static loading. Amplification of base seismic acceleration is also observed. The liquefaction potential analysis in FLAC(3D) indicates considerable loss of shear strength in the tailings portion of the proposed earthen dam section with significantly high values of pore pressure ratio.

Effect of signal peptide on stability and folding of escherichia coli thioredoxin

The signal peptide plays a key role in targeting and membrane insertion of secretory and membrane proteins in both prokaryotes and eukaryotes. In E. coli, recombinant proteins can be targeted to the periplasmic space by fusing naturally occurring signal sequences to their N-terminus. The model protein thioredoxin was fused at its N-terminus with malE and pelB signal sequences. While WT and the pelB fusion are soluble when expressed, the malE fusion was targeted to inclusion bodies and was refolded in vitro to yield a monomeric product with identical secondary structure to WT thioredoxin. The purified recombinant proteins were studied with respect to their thermodynamic stability, aggregation propensity and activity, and compared with wild type thioredoxin, without a signal sequence. The presence of signal sequences leads to thermodynamic destabilization, reduces the activity and increases the aggregation propensity, with malE having much larger effects than pelB. These studies show that besides acting as address labels, signal sequences can modulate protein stability and aggregation in a sequence dependent manner.

Two-axis force sensing and control of a Reorientable scanning probe

This paper presents the design and implementation of a reorientable scanning probe that is capable of two-axis force sensing and control in the 2-D scanning (X-Z) plane. The probe is comprised of three major components, namely a compliant manipulator, laser measurement system, and magnetic actuation system. Control of the position and orientation of the probe tip is realized by means of magnetic actuation combined with a novel structural design. The design of the manipulator's compliance and that of the optical path of the laser measurement system together enable achieving sensitivity to lateral (X) forces that is nearly identical to that of normal (Z) forces. The achieved sensitivity ratio, of about 0.6, is significantly higher than that of conventional scanning probe systems. The theoretical bases for the structural design and the sensitivity of the two-axis force sensing system are presented. Subsequently, fabrication of the manipulator is described and the result of experimental evaluation of the scanning probe's features is discussed. The scanning probe is used to access the vertical and re-entrant features on the two sides of a cylindrical micropipette, which are subsequently scanned by regulating the lateral force of tip-sample interaction.

Aptamers as Theranostic Agents: Modifications, Serum Stability and Functionalisation

Aptamers, and the selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX) used to generate them, were first described more than twenty years ago. Since then, there have been numerous modifications to the selection procedures. This review discusses the use of modified bases as a means of enhancing serum stability and producing effective therapeutic tools, as well as functionalising these nucleic acids to be used as potential diagnostic agents.

Partially integrated guidance and control of an air-dropped guided munition with explicit trajectory fixing

An innovative partially integrated guidance and control (PIGC) technique is developed for trajectory fixing by considering six degree-of-freedom (Six-DOF) nonlinear engagement dynamics for successful interception of ground targets by guided munitions. This trajectory fixing algorithm gives closed form solution, where two different trajectories are designed in x - h and x - y planes separately using simple quadratic equations. In order to follow designed trajectories commanded pitch and yaw rates are generated in outer loop using dynamic inversion technique. In inner loop these body rates are tracked using faster dynamic inversion loop by generating the necessary control surface deflections. Simulation studies with actuator dynamics have been carried out to account for three dimensional (3D) engagement geometry to demonstrate the usefulness of PIGC technique.

Constrained 3D sketching with haptics and active motion annotation

The aim of this work is to enable seamless transformation of product concepts to CAD models. This necessitates availability of 3D product sketches. The present work concerns intuitive generation of 3D strokes and intrinsic support for space sharing and articulation for the components of the product being sketched. Direct creation of 3D strokes in air lacks in precision, stability and control. The inadequacy of proprioceptive feedback for the task is complimented in this work with stereo vision and haptics. Three novel methods based on pencil-paper interaction analogy for haptic rendering of strokes have been investigated. The pen-tilt based rendering is simpler and found to be more effective. For the spatial conformity, two modes of constraints for the stylus movements, corresponding to the motions on a control surface and in a control volume have been studied using novel reactive and field based haptic rendering schemes. The field based haptics, which in effect creates an attractive force field near a surface, though non-realistic, provided highly effective support for the control-surface constraints. The efficacy of the reactive haptic rendering scheme for the constrained environments has been demonstrated using scribble strokes. This can enable distributed collaborative 3D concept development. The notion of motion constraints, defined through sketch strokes enables intuitive generation of articulated 3D sketches and direct exploration of motion annotations found in most product concepts. The work, thus, establishes that modeling of the constraints is a central issue in 3D sketching.

Partial Integrated Guidance and Control of Interceptors for High-Speed Ballistic Targets

A new partial integrated guidance and control design approach is proposed in this paper, which combines the benefits of both integrated guidance and control as well as the conventional guidance and control design philosophies. The proposed technique essentially operates in a two-loop structure. In the outer loop, an optimal guidance problem is formulated considering the nonlinear six degrees-of-freedom equation of motion of the interceptor. From this loop, the required pitch and yaw rates are generated by solving a nonlinear suboptimal guidance formulation in a computationally efficient manner while simultaneously assuring roll stabilization. Next, the inner loop tracks these outer loop body rate commands. This manipulation of the six degrees-of-freedom dynamics in both loops preserves the inherent time scale separation property between the translational and rotational dynamics, while retaining the philosophy of integrated guidance and control design as well. Because of this, the tuning process is quite straightforward and nontedious as well. Extensive six degrees-of-freedom simulations studies have been carried out, considering three-dimensional engagement geometry, to demonstrate the effectiveness of the proposed new design approach engaging high-speed ballistic targets. A variety of comparison studies have also been carried out to demonstrate the effectiveness of the proposed approach.

Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing

Multiple methods currently exist for rapid construction and screening of single-site saturation mutagenesis (SSM) libraries in which every codon or nucleotide in a DNA fragment is individually randomized. Nucleotide sequences of each library member before and after screening or selection can be obtained through deep sequencing. The relative enrichment of each mutant at each position provides information on its contribution to protein activity or ligand-binding under the conditions of the screen. Such saturation scans have been applied to diverse proteins to delineate hot-spot residues, stability determinants, and for comprehensive fitness estimates. The data have been used to design proteins with enhanced stability, activity and altered specificity relative to wild-type, to test computational predictions of binding affinity, and for protein model discrimination. Future improvements in deep sequencing read lengths and accuracy should allow comprehensive studies of epistatic effects, of combinational variation at multiple sites, and identification of spatially proximate residues.

In-cylinder investigations and analysis of a SI gas engine fuelled with H-2 and CO rich syngas fuel: Sensitivity analysis of combustion descriptors for engine diagnostics and control

The sensitivity of combustion phasing and combustion descriptors to ignition timing, load and mixture quality on fuelling a multi-cylinder natural gas engine with bio-derived H-2 and CO rich syngas is addressed. While the descriptors for conventional fuels are well established and are in use for closed loop engine control, presence of H-2 in syngas potentially alters the mixture properties and hence combustion phasing, necessitating the current study. The ability of the descriptors to predict abnormal combustion, hitherto missing in the literature, is also addressed. Results from experiments using multi-cylinder engines and numerical studies using zero dimensional Wiebe function based simulation models are reported. For syngas with 20% H-2 and CO and 2% CH4 (producer gas), an ignition retard of 5 +/- 1 degrees was required compared to natural gas ignition timing to achieve peak load of 72.8 kWe. It is found that, for syngas, whose flammability limits are 0.42-1.93, the optimal engine operation was at an equivalence ratio of 1.12. The same methodology is extended to a two cylinder engine towards addressing the influence of syngas composition, especially H-2 fraction (varying from 13% to 37%), on the combustion phasing. The study confirms the utility of pressure trace derived combustion descriptors, except for the pressure trace first derivative, in describing the MBT operating condition of the engine when fuelled with an alternative fuel. Both experiments and analysis suggest most of the combustion descriptors to be independent of the engine load and mixture quality. A near linear relationship with ignition angle is observed. The general trend(s) of the combustion descriptors for syngas fuelled operation are similar to those of conventional fuels; the differences in sensitivity of the descriptors for syngas fuelled engine operation requires re-calibration of control logic for MBT conditions. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Structure, stability and elasticity of DNA nanotubes

DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for the construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix, 8-helix and tri-tubes with different sequences and lengths. We have used fully atomistic molecular dynamics simulations to study the structure, stability and elasticity of these structures. Several nanosecond long MD simulations give the microscopic details about DNA nanotubes. Based on the structural analysis of simulation data, we show that 6-helix nanotubes are stable and maintain their tubular structure; while 8-helix nanotubes are flattened to stabilize themselves. We also comment on the sequence dependence and the effect of overhangs. These structures are approximately four times more rigid having a stretch modulus of similar to 4000 pN compared to the stretch modulus of 1000 pN of a DNA double helix molecule of the same length and sequence. The stretch moduli of these nanotubes are also three times larger than those of PX/JX crossover DNA molecules which have stretch moduli in the range of 1500-2000 pN. The calculated persistence length is in the range of a few microns which is close to the reported experimental results on certain classes of DNA nanotubes.

Experimental Characterization and Control of Miniaturized Pneumatic Artificial Muscle

Robotic surgical tools used in minimally invasive surgeries (MIS) require miniaturized and reliable actuators for precise positioning and control of the end-effector. Miniature pneumatic artificial muscles (MPAMs) are a good choice due to their inert nature, high force to weight ratio, and fast actuation. In this paper, we present the development of miniaturized braided pneumatic muscles with an outer diameter of similar to 1.2 mm, a high contraction ratio of about 18%, and capable of providing a pull force in excess of 4 N at a supply pressure of 0.8 MPa. We present the details of the developed experimental setup, experimental data on contraction and force as a function of applied pressure, and characterization of the MPAM. We also present a simple kinematics and experimental data based model of the braided pneumatic muscle and show that the model predicts contraction in length to within 20% of the measured value. Finally, a robust controller for the MPAMs is developed and validated with experiments and it is shown that the MPAMs have a time constant of similar to 10 ms thereby making them suitable for actuating endoscopic and robotic surgical tools.

Electrospun SnSb Crystalline Nanoparticles inside Porous Carbon Fibers as a High Stability and Rate Capability Anode for Rechargeable Batteries

In an electrochemical alloying reaction, the electroactive particles become mechanically unstable owing to large volume changes occurring as a result of high amounts of lithium intake. This is detrimental for long-term battery performance. Herein, a novel synthesis approach to minimize such mechanical instabilities in tin particles is presented. An optimal one-dimensional assembly of crystalline single-phase tin-antimony (SnSb) alloy nanoparticles inside porous carbon fibers (abbreviated SnSb-C) is synthesized for the first time by using the electrospinning technique (employing non-oxide precursors) in combination with a sintering protocol. The ability of antimony to alloy independently with lithium is beneficial as it buffers the unfavorable volume changes occurring during successive alloying/dealloying cycles in Sn. The SnSb-C assembly provides nontortuous (tortuosity coefficient, =1) fast conducting pathways for both electrons and ions. The presence of carbon in SnSb-C completely nullifies the conventional requirement of other carbon forms during cell electrode assembly. The SnSb-C exhibited remarkably high electrochemical lithium stability and high specific capacities over a wide range of currents (0.2-5Ag(-1)). In addition to lithium-ion batteries, it is envisaged that SnSb-C also has potential as a noncarbonaceous anode for other battery chemistries, such as sodium-ion batteries.