43 results on '"Ananthasuresh GK"'
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2. Evaluating Bulk Stiffness of MCF-7 Cells using Micro-scale Composite Compliant Mechanisms
- Author
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Bhargav, Santosh DB, Jorapur, Nikhil, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
Biomechanical assays offer a good alternative to biochemical assays in diagnosing disease states and assessing the efficacy of drugs. In view of this, we have designed, fabricated and tested a miniature compliant tool to estimate the bulk stiffness of cells, particularly MCF-7 (Michigan Cancer Foundation) cells. The compliant tool comprises a gripper and a Displacement-amplifying Compliant Mechanism (DaCM), where the former helps in grasping the cell and the latter enables vision-based sensing of force. A DaCM is necessary because the field of view of a microscope at the required magnification is not large enough to simultaneously observe the cell and a point on the gripper that move sufficiently to estimate the force. Therefore, a DaCM is strategically embedded within an existing gripper design leading to a composite compliant mechanism. The DaCM is designed using the inetoelastostatic map technique to achieve a resolution 42 nN. The gripper, microfabricated with SU-8 polymer using photolithography, is within the footprint of about 10 mm by 10 mm with the smallest feature size of about 5 microns. The gripper was tested in air and was found to be satisfactory in grasping and squeezing objects as small as 15 microns in size. However, testing in aqueous medium encountered an unanticipated problem due to buoyancy, which curled the jaws of the gripper up by as much as 40 microns and thus losing contact with the cell that is to be grasped. A design modification is suggested to fix this problem.
- Published
- 2013
3. A Study of Mechanical Advantage in Compliant Mechanisms
- Author
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Gautam Kumar , R and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
Understanding mechanical advantage of a compliant mechanism is not straightforward for two reasons: (i) it uses a part of the input energy in elastic deformation and (ii) its kinetoelastic behavior depends on the stiffness of the workpiece. In this paper, we study mechanical advantage using non-dimensional analysis of compliant mechanisms. We use parameterized kinetoelastostatic maps that show mechanical advantage against a non-dimensional number that captures geometric and material properties as well as forces. The maps help compare different topologies of compliant mechanisms based on mechanical advantage. The maps also help delineate kinematic and elastic contributions to mechanical advantage. Case studies reveal that while mechanical advantage usually increases with increasing external stiffness and slenderness ratio, but it decreases with increasing gap between the output port and an elastic workpiece. A noteworthy observation in this work is that there can be exceptions to this general trend and that kinematic and elastic contributions can both be positive so that the mechanical advantage of a compliant mechanism can exceed that of a rigid-body counterpart. This work also revisits the fact that it is possible to design a compliant mechanism such that its mechanical advantage is not affected by the stiffness of the workpiece
- Published
- 2013
4. Compact in-plane dual-axis spring-steel accelerometer
- Author
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Khan, Sambuddha, Prasanna, Deepa, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
Presented in this paper is an improvement over a spring-steel dual-axis accelerometer that we had reported earlier.The fabrication process (which entails wire-cut electro discharge machining of easily accessible and inexpensive spring-steelfoil) and the sensing of the displacement (which is done using off-the-shelf Hall-effect sensors) remain the same. Theimprovements reported here are twofold: (i) the footprint of the packaged accelerometer is reduced from 80 mm square to 40mm square, and (ii) almost perfect de-coupling and symmetry are achieved between the two in-plane axes of the packageddevice as opposed to the previous embodiment where this was not the case. Good linearity with about 40 mV/g was measuredalong both the in-plane axes over a range of 0.1 to 1 g. The first two natural frequencies of the devices are at 30 Hz and 100Hz, respectively, as per the experiment. The highlights of this work are cost-effective processing, easy integration of the Hall-effect sensing capability on a customised printed circuit board, and inexpensive packaging without overly compromising eitherthe overall size or the sensitivity of the accelerometer. Through this work, we have reaffirmed the practicability of spring-steelaccelerometers towards the eventual goal of making it compete with micro machined silicon accelerometers in terms of sizeand performance. The cost is likely to be much lower for the spring-steel accelerometers than that of silicon accelerometers, especially when the volume of production is low and the sensor is to be used as a single packaged unit.
- Published
- 2012
5. Topology optimization-based design of a compliant aircraft compliant aircraft wing for morphing leading and trailing edges
- Author
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Podugu, Pakeeruraju and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
In this paper, we present a methodology for designing a compliant aircraft wing, which can morph from a given airfoil shape to another given shape under the actuation of internal forces and can offer sufficient stiffness in both configurations under the respective aerodynamic loads. The least square error in displacements, Fourier descriptors, geometric moments, and moment invariants are studied to compare candidate shapes and to pose the optimization problem. Their relative merits and demerits are discussed in this paper. The `frame finite element ground structure' approach is used for topology optimization and the resulting solutions are converted to continuum solutions. The introduction of a notch-like feature is the key to the success of the design. It not only gives a good match for the target morphed shape for the leading and trailing edges but also minimizes the extension of the flexible skin that is to be put on the airfoil frame. Even though linear small-displacement elastic analysis is used in optimization, the obtained designs are analysed for large displacement behavior. The methodology developed here is not restricted to aircraft wings; it can be used to solve any shape-morphing requirement in flexible structures and compliant mechanisms.
- Published
- 2012
6. Note on modelling directionality in piezoresistivity
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Balakrishnan, Sreenath, Deshpande, Kaustubh, and Ananthasuresh, GK
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Mechanical Engineering - Abstract
When computing the change in electrical resistivity of a piezoresistive cubic material embedded in a deforming structure, the piezoresistive and the stress tensors should be in the same coordinate system. While the stress tensor is usually calculated in a coordinate system aligned with the principal axes of a regular structure, the specified piezoresistive coefficients may not be in that coordinate system. For instance, piezoresistive coefficients are usually given in an orthogonal cartesian coordinate system aligned with the crystallographic directions and designers sometimes deliberately orient a crystallographic direction other than along the principal directions of the structure to increase the gauge factor. In such structures, it is advantageous to calculate the piezoresistivity tensor in the coordinate system along which the stress tensors are known rather than the other way around. This is because the transformation of stress will have to be done at every point in the structure but piezoresistivity tensor needs to be transformed only once. Here, using tensor transformation relations, we show how to calculate the piezoresistive tensor along any arbitrary Cartesian coordinate system from the piezoresistive coefficients for the coordinate system. Some of the software packages that simulate the piezoresistive effect do not have interfaces for calculation of the entire piezoresistive tensor for arbitrary directions. This warrants additional work for the user because not considering the complete piezoresisitive tensor can lead to large errors. This is illustrated with an example where the error is as high as 33%. Additionally, for elastic analysis, we used hybrid finite element formulation that estimates stresses more accurately than displacement-based formulation. Therefore, as shown in an example where the change in resistance can be calculated analytically, the percentage error of our piezoresistive program is an order of magnitude lower relative to displacement-based finite element method.
- Published
- 2012
7. Simulation of length-preserving motions of flexible one dimensional oObjects using optimization
- Author
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Banerjee, S, Menon, MS, Ananthasuresh, GK, and Ghosal, A
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Mechanical Engineering - Abstract
During the motion of one dimensional flexible objects such as ropes, chains, etc., the assumption of constant length is realistic. Moreover,their motion appears to be naturally minimizing some abstract distance measure, wherein the disturbance at one end gradually dies down along the curve defining the object. This paper presents purely kinematic strategies for deriving length-preserving transformations of flexible objects that minimize appropriate ‘motion’. The strategies involve sequential and overall optimization of the motion derived using variational calculus. Numerical simulations are performed for the motion of a planar curve and results show stable converging behavior for single-step infinitesimal and finite perturbations 1 as well as multi-step perturbations. Additionally, our generalized approach provides different intuitive motions for various problem-specific measures of motion, one of which is shown to converge to the conventional tractrix-based solution. Simulation results for arbitrary shapes and excitations are also included.
- Published
- 2011
8. Micro-mechanical stages with enhanced range
- Author
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Dinesh, M and Ananthasuresh , GK
- Subjects
Mechanical Engineering - Abstract
We present concepts and an optimization-based methodology for the design of micro-mechanical stages that have not only high precision but also an enhanced range. Joint-free distributed compliant designs provide high precision and easy manufacturability at macro and micro scales. The range of motion is enhanced by using displacement-amplifying compliant mechanisms (DaCMs). The main issue addressed in this paper is how to retain the decoupling between the X and Y motions in the stage when it is equipped with DaCMs. The natural frequency of the stage is also not compromised in enhancing the range. The optimized design has 2.5 times more range than the designs reported in the literature. Furthermore, the sensitivity improved by a factor of two when the stage is optimized for an accelerometer.
- Published
- 2010
9. A Compliant Mechanism Kit with Flexible Beams and Connectors
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Limaye, P, Ramu, G, Pamulapati, S, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
We present the concept, prototypes, and an optimal design method for a compliant mechanism kit as a parallel to the kits available for rigid-body mechanisms. The kit consists of flexible beams and connectors that can be easily hand-assembled using snap fits. It enables users, using their creativity and mechanics intuition, to quickly realize a compliant mechanism. The mechanisms assembled in this manner accurately capture the essential behavior of the topology, shape, size and material aspects and thereby can lead the way for a real compliant mechanism for practical use. Also described in this paper are the design of the connector to which flexible beams can be added in eight different directions; and prototyping of the spring steel connectors as well as beams using wire-cut electro discharge machining. It is noted in this paper that the concept of the kit also resolves a discrepancy in the finite element (FE) modeling of beam-based compliant mechanisms. The discrepancy arises when two or more beams are joining at one point and thus leading to increased stiffness. After resolving this discrepancy, this work extends the topology optimization to automatically generate designs that can be assembled with the kit. Thus, the kit and the accompanying analysis and optimal synthesis procedures comprise a self-contained educational as well as a research and pragmatic toolset for compliant mechanisms. The paper also illustrates how human creativity finds new ways of using the kit beyond the original intended use and how it is useful even for a novice to design compliant mechanisms.
- Published
- 2009
10. Design and Characterization of a Micromachined Accelerometer with a Mechanical Amplifier for Intrusion Detection
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Khan, S, Bhat, Thejas N, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Published
- 2009
11. A Mechanism with SMA Tendon Actuator for an Aircraft Flap
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Manoj Kumar, R, Ramaiah, KV, Saikrishna, CN, Ravi Kumar, A, Bhaumik, SK, and Ananthasuresh, GK
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Mechanical Engineering - Published
- 2009
12. Miniature Compliant Grippers with Force-Sensing
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Maheswari, N, Reddy, AN, Sahu, DK, and Ananthasuresh, GK
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Mechanical Engineering - Published
- 2009
13. A Flexure-based Deployable Stereo Vision Mechanism and Temperature and Force Sensors for Laparoscopic Tools
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Ramu, G and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
This paper presents concepts, designs, and working prototypes of enhanced laparoscopic surgical tools. The enhancements are in equipping the tool with force and temperature sensing as well as image acquisition for stereo vision. Just as the pupils of our eyes are adequately spaced out and the distance between them is adjustable, two minute cameras mounted on a mechanism in our design can be moved closer or farther apart inside the inflated abdomen during the surgery. The cameras are fitted to a deployable mechanism consisting of flexural joints so that they can be inserted through a small incision and then deployed and moved as needed.A temperature sensor and a force sensor are mounted on either of the gripping faces of the surgical grasping tool to measure the temperature and gripping force, which need to be controlled for safe laparoscopic surgery. The sensors are small enough and hence they do not cause interference during surgery and insertion.Prototyping and working of the enhanced laparoscopic tool are presented with details
- Published
- 2009
14. Haptic Feedback for Injecting Biological Cells using Miniature Compliant Mechanisms
- Author
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Rao, VM and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
We present a real-time haptics-aided injection technique for biological cells using miniature compliant mechanisms. Our system consists of a haptic robot operated by a human hand, an XYZ stage for micro-positioning, a camera for image capture, and a polydimethylsiloxane (PDMS) miniature compliant device that serves the dual purpose of an injecting tool and a force-sensor. In contrast to existing haptics-based micromanipulation techniques where an external force sensor is used, we use visually captured displacements of the compliant mechanism to compute the applied and reaction forces. The human hand can feel the magnified manipulation force through the haptic device in real-time while the motion of the human hand is replicated on the mechanism side. The images are captured using a camera at the rate of 30 frames per second for extracting the displacement data. This is used to compute the forces at the rate of 30 Hz. The force computed in this manner is sent at the rate of 1000 Hz to ensure stable haptic interaction. The haptic cell-manipulation system was tested by injecting into a zebrafish egg cell after validating the technique at a size larger than that of the cell.
- Published
- 2009
15. An Improved Compact Compliant Mechanism for an External Pipe-Crawler
- Author
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Vinod Kumar, BM, Badige, DK, Hegde, S, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
An external pipe-crawling device presented in this paper aids the inspection of pipes in hazardous environments and areas inaccessible to humans. The principal component of our design, which uses inchworm type motion, is a compliant ring mechanism actuated using shape memory alloy (SMA) wire. It was fabricated and tested and was reported in our earlier work. But this device had a drawback of low crawling speed (about 1 mm/min) owing to the delay in heating and cooling of the SMA strips in the linear actuation. Additionally, that design also had the difficulties of mounting on pipes with closed ends, large radial span, and the need for housing for electrical insulation and guiding of the SMA wire. In this paper we present a compact design that overcomes the difficulties of the earlier design. In particular, we present a compact compliant mechanism with two halves so as to enable mounting and un-mounting on any closed or open pipe. Another feature is the presence of insulation and guiding of the SMA wire without housing. This design results in a reduction of the radial span of the ring from 22 mm to 12 mm, and the stiffness of the mechanism and the SMA wire are matched. An SMA helical spring is to used in the place of an SMA strip to increase the crawling speed of the device. A microcontroller-based circuitry is also fitted to cyclically.activate the SMA wires and springs.
- Published
- 2009
16. On computing the forces from the noisy displacement data of an elastic body
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Reddy, A Narayana and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
This Study is concerned with the accurate computation of the unknown forces applied on the boundary of an elastic body using its measured displacement data with noise. Vision-based minimally intrusive force-sensing using elastically deformable grasping tools is the motivation for undertaking this problem. Since this problem involves incomplete and inconsistent displacement/force of ail elastic body, it leads to an ill-posed problem known as Cauchy's problem in elasticity. Vision-based displacement measurement necessitates large displacements of the elastic body for reasonable accuracy. Therefore, We use geometrically non-linear modelling of the elastic body, which was not considered by others who attempted to solve Cauchy's elasticity problem before. We present two methods to solve the problem. The first method uses the pseudo-inverse of an over-constrained system of equations. This method is shown to be not effective when the noise in the measured displacement data is high. We attribute this to the appearance of spurious forces at regions where there should not be any forces. The second method focuses on minimizing the spurious forces by varying the measured displacements within the known accuracy of the measurement technique. Both continuum and frame elements are used in the finite element modelling of the elastic bodies considered in the numerical examples. The performance of the two methods is compared using seven numerical examples, all of which show that the second method estimates the forces with an error that is not more than the noise in the measured displacements. An experiment was also conducted to demonstrate the effectiveness of the second method in accurately estimating the applied forces.
- Published
- 2008
17. An SMA-actuated, Compliant Mechanism-based Pipe-crawler
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Balaji, G, Biradar, P, Saikrishna, CN, Ramaiah, Venkata K, Bhaumik, SK, Haruray, A, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Published
- 2008
18. Optimal Design of a Meso-scale Gripper and its Prototyping with Spring Steel and PDMS
- Author
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Sahu, DK and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Published
- 2008
19. A Comparative Study of the Formulations for Topology Optimization of Compliant Mechanisms
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Deepak, Sangamesh R, Dinesh, M, and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
The topology optimization problem for the synthesis of compliant mechanisms has been formulated in many different ways in the last 15 years, but there is not yet a definitive formulation that is universally accepted. Furthermore, there are two unresolved issues in this problem. In this paper, we present a comparative study of five distinctly different formulations that are reported in the literature. Three benchmark examples are solved with these formulations using the same input and output specifications and the same numerical optimization algorithm. A total of 35 different synthesis examples are implemented. The examples are limited to desired instantaneous output direction for prescribed input force direction. Hence, this study is limited to linear elastic modeling with small deformations. Two design parameterizations, namely, the frame element based ground structure and the density approach using continuum elements, are used. The obtained designs are evaluated with all other objective functions and are compared with each other. The checkerboard patterns, point flexures, the ability to converge from an unbiased uniform initial guess, and the computation time are analyzed. Some observations are noted based on the extensive implementation done in this study. Complete details of the benchmark problems and the results are included. The computer codes related to this study are made available on the internet for ready access.
- Published
- 2008
20. Topology Optimization of Microsystems Devices Including Micromachining Constraints
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Ananthasuresh, GK
- Subjects
Mechanical Engineering - Published
- 2007
21. On Including Manufacturing Constraints in the Topology Optimization of Surface-Micromachined Structures
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Agrawal, M and Ananthasuresh, GK
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Mechanical Engineering - Published
- 2007
22. Shape Memory Alloy Actuation for a Novel Spring-Steel Compliant XY Stage
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Dinesh, M and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Published
- 2007
23. Topology Optimization of Compliant Micromechnisms with Manufaturing Constraints Imposed by the Wet Ecthing of (110) Silicon
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Hegde, S and Ananthasuresh, GK
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Mechanical Engineering - Published
- 2007
24. Size-Optimization of a Beam under Deformation Dependent Loads
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Sivanagendra, P and Ananthasuresh, GK
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Mechanical Engineering - Published
- 2007
25. Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types
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Ananthasuresh, GK
- Subjects
Mechanical Engineering - Abstract
The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.
- Published
- 2006
26. Kinematics of Planar, Radially Foldable Mechanisms using Algebraic Loci
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Patel, J and Ananthasuresh, GK
- Subjects
Mechanical Engineering - Published
- 2006
27. Mechanical Design of Compliant Microsystems-A Perspective and Prospects
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Ananthasuresh, GK and Howell, Larry L
- Subjects
Mechanical Engineering - Abstract
The field of microsystems, or microelectromechanical systems (MEMS) as it is popularly known, is a truly multidisciplinary area of research. It combines a wide variety of physical, chemical, and biological phenomena into an integrated system on a chip. This unprecedented integration naturally calls for new systems design approaches as well as efficient ways to analyze a single system or a component that is governed by many types of partial and ordinary differential equations from different physical and chemical domains. The key component of almost all MEMS devices, with the exception of microfluidic systems, is a movable mechanical structure of micron dimensions. Since the early works in this area dating back to the late sixties of the 20th Century, simple mechanical structures such as beams and diaphragms have dominated MEMS. Thus, the mechanical design in MEMS is mainly concerned with the design of such elastically deforming structures subjected to a variety of forces ranging from electrostatic, thermal, magnetic, piezoelectric, radiation pressure, etc. In addition to these unconventional forces and the accompanying complex equations that govern them, micromachining brings additional difficulties in microsystem design.
- Published
- 2005
28. Design-encoded dual shape-morphing and shape-memory in 4D printed polymer parts toward cellularized vascular grafts.
- Author
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Choudhury S, Joshi A, Baghel VS, Ananthasuresh GK, Asthana S, Homer-Vanniasinkam S, and Chatterjee K
- Subjects
- Humans, Polymers chemistry, Biocompatible Materials chemistry, Biocompatible Materials pharmacology, Finite Element Analysis, Tissue Engineering, Human Umbilical Vein Endothelial Cells, Smart Materials chemistry, Printing, Three-Dimensional, Blood Vessel Prosthesis
- Abstract
Current additive manufacturing technologies wherein as-printed simple two-dimensional (2D) structures morph into complex tissue mimetic three-dimensional (3D) shapes are limited to multi-material hydrogel systems, which necessitates multiple fabrication steps and specific materials. This work utilizes a single shape memory thermoplastic polymer (SMP), PLMC (polylactide- co -trimethylene carbonate), to achieve programmable shape deformation through anisotropic design and infill angles encoded during 3D printing. The shape changes were first computationally predicted through finite element analysis (FEA) simulations and then experimentally validated through quantitative correlation. Rectangular 2D sheets could self-roll into complete hollow tubes of specific diameters (ranging from ≈6 mm to ≈10 mm) and lengths (as long as 40 mm), as quantitatively predicted from FEA simulations within one minute at relatively lower temperatures (≈80 °C). Furthermore, shape memory properties were demonstrated post-shape change to exhibit dual shape morphing at temperatures close to physiological levels. The tubes (retained as the permanent shape) were deformed into flat sheets (temporary shape), seeded with endothelial cells (at T < T
g ), and thereafter triggered at ≈37 °C back into tubes (permanent shape), utilizing the shape memory properties to yield bioresorbable tubes with cellularized lumens for potential use as vascular grafts with improved long-term patency. Additionally, out-of-plane bending and twisting deformation were demonstrated in complex structures by careful control of infill angles that can unprecedently expand the scope of cellularized biomimetic 3D shapes. This work demonstrates the potential of the combination of shape morphing and SMP behaviors at physiological temperatures to yield next-generation smart implants with precise control over dimensions for tissue repair and regeneration.- Published
- 2024
- Full Text
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29. 4D Printed Programmable Shape-Morphing Hydrogels as Intraoperative Self-Folding Nerve Conduits for Sutureless Neurorrhaphy.
- Author
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Joshi A, Choudhury S, Baghel VS, Ghosh S, Gupta S, Lahiri D, Ananthasuresh GK, and Chatterjee K
- Subjects
- Rats, Animals, Hydrogels pharmacology, Hydrogels chemistry, Biocompatible Materials pharmacology, Biocompatible Materials chemistry, Sciatic Nerve surgery, Sciatic Nerve physiology, Gelatin pharmacology, Gelatin chemistry, Printing, Three-Dimensional, Tissue Engineering, Tissue Scaffolds chemistry, Peripheral Nerve Injuries
- Abstract
There are only a few reports of implantable 4D printed biomaterials, most of which exhibit slow deformations rendering them unsuitable for in situ surgical deployment. In this study, a hydrogel system is engineered with defined swelling behaviors, which demonstrated excellent printability in extrusion-based 3D printing and programmed shape deformations post-printing. Shape deformations of the spatially patterned hydrogels with defined infill angles are computationally predicted for a variety of 3D printed structures, which are subsequently validated experimentally. The gels are coated with gelatin-rich nanofibers to augment cell growth. 3D-printed hydrogel sheets with pre-programmed infill patterns rapidly self-rolled into tubes in vivo to serve as nerve-guiding conduits for repairing sciatic nerve defects in a rat model. These 4D-printed hydrogels minimized the complexity of surgeries by tightly clamping the resected ends of the nerves to assist in the healing of peripheral nerve damage, as revealed by histological evaluation and functional assessments for up to 45 days. This work demonstrates that 3D-printed hydrogels can be designed for programmed shape changes by swelling in vivo to yield 4D-printed tissue constructs for the repair of peripheral nerve damage with the potential to be extended in other areas of regenerative medicine., (© 2023 Wiley-VCH GmbH.)
- Published
- 2023
- Full Text
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30. Self-offloading therapeutic footwear using compliant snap-through arches.
- Author
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Maharana P, Sonawane J, Belehalli P, and Ananthasuresh GK
- Abstract
In diabetic peripheral neuropathy, offloading high-plantar-pressure areas using statically offloaded customized insoles or expensive sensors and actuators are commonly-followed treatment procedures. In this article, we propose the concept of dynamically self-offloading therapeutic footwear that operates mechanically without using sensors and actuators. We achieve this by using an array of snapping arches. When a load higher than a bespoke value is applied, these arches enter negative-stiffness regime and offload the high-pressure region by snapping to a different shape. They again return to their initial shape when the load disappears. Thus, they serve as both sensors and actuators that get actuated by person's body weight. We present an analytical method to compute the switching load and the switchback time of such arches and use them to customize the footwear according to the person's body weight, gait speed, and foot size. We identify the high-pressure regions from the clinical data and place the arches such that these high-pressure regions get dynamically offloaded, and the pressure gets redistributed to other regions. We considered 200 kPa as a limiting pressure to prevent the prolonged effects of high plantar pressure. To check the efficacy of the concept, a complete 3D-printed prototype made of thermoplastic polyurethane was tested and compared with barefoot and in-shoe plantar pressure for subjects recruited at a clinical facility. We notice that the self-offloading insole shows the plantar pressure reduction at all the foot regions, and significant offloading of 57% is observed at the forefoot region., Competing Interests: The authors declare no competing interests exist., (© The Author(s) 2022.)
- Published
- 2022
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31. Editor's Desk.
- Author
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Ananthasuresh GK
- Published
- 2022
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32. Two nondimensional parameters for characterizing the nuclear morphology.
- Author
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Balakrishnan S, Raju SR, Barua A, Pradeep RP, and Ananthasuresh GK
- Subjects
- Actins, Cell Nucleus Shape, Cytoplasm, Nuclear Envelope, Cell Nucleus, Cytoskeleton
- Abstract
Nuclear morphology is an important indicator of cell function. It is regulated by a variety of factors such as the osmotic pressure difference between the nucleoplasm and cytoplasm, cytoskeletal forces, elasticity of the nuclear envelope and chromosomes. Nucleus shape and size are typically quantified using multiple geometrical quantities that are not necessarily independent of one another. This interdependence makes it difficult to decipher the implications of changes in nuclear morphology. We resolved this by analyzing nucleus shapes of populations for multiple cell lines using a mechanics-based model. We deduced two independent nondimensional parameters, namely, flatness index and isometric scale factor. We show that nuclei in a cell population have similar flatness but variable scale factor. Furthermore, nuclei of different cell lines segregate according to flatness. Cellular perturbations using biochemical and biomechanical techniques suggest that the flatness index correlates with actin tension and the scale factor anticorrelates with elastic modulus of nuclear envelope. We argue that nuclear morphology measures such as volume, projected area, height etc., are subsumed by flatness and scale factor, which can unambiguously characterize nuclear morphology., (Copyright © 2021 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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33. Editor's Desk.
- Author
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Ananthasuresh GK
- Published
- 2021
- Full Text
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34. Editor's Desk.
- Author
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Ananthasuresh GK
- Published
- 2020
- Full Text
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35. Analytical modelling of spatial deformation pathways in planar and spatial shallow bistable arches.
- Author
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Palathingal S and Ananthasuresh GK
- Abstract
We analyse spatial bistable arches and present an analytical model incorporating axial, two transverse bending and torsion energy components. We extend the St. Venant and Michell relationship used in flexural-torsional buckling of planar arches and use it in modelling spatial arches. We study deformation pathways in spatial arches and their effect on critical characteristics of bistability such as back and forth switching forces, and the distance travelled by a point of the arch. We show that not considering spatial deformation leads to incorrect inferences concerning the bistability of planar arches too. Thus, this model serves as a generalized framework for the existing analysis on planar arches since they belong to a subset of spatial arches. Additionally, the effects of eccentric loading on spatial deformations are explored for arches with a range of as-fabricated shapes and boundary conditions, and the results are validated with finite-element analysis., Competing Interests: We declare we have no competing interests.
- Published
- 2019
- Full Text
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36. A Nondimensional Model Reveals Alterations in Nuclear Mechanics upon Hepatitis C Virus Replication.
- Author
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Balakrishnan S, Mathad SS, Sharma G, Raju SR, Reddy UB, Das S, and Ananthasuresh GK
- Subjects
- Actins chemistry, Actins metabolism, Cell Line, Tumor, Hepatocytes metabolism, Hepatocytes virology, Humans, Lamin Type A chemistry, Lamin Type A metabolism, Nuclear Envelope virology, Elastic Modulus, Hepacivirus physiology, Models, Theoretical, Nuclear Envelope chemistry, Virus Replication
- Abstract
Morphology of the nucleus is an important regulator of gene expression. Nuclear morphology is in turn a function of the forces acting on it and the mechanical properties of the nuclear envelope. Here, we present a two-parameter, nondimensional mechanical model of the nucleus that reveals a relationship among nuclear shape parameters, such as projected area, surface area, and volume. Our model fits the morphology of individual nuclei and predicts the ratio between forces and modulus in each nucleus. We analyzed the changes in nuclear morphology of liver cells due to hepatitis C virus (HCV) infection using this model. The model predicted a decrease in the elastic modulus of the nuclear envelope and an increase in the pre-tension in cortical actin as the causes for the change in nuclear morphology. These predictions were validated biomechanically by showing that liver cells expressing HCV proteins possessed enhanced cellular stiffness and reduced nuclear stiffness. Concomitantly, cells expressing HCV proteins showed downregulation of lamin-A,C and upregulation of β-actin, corroborating the predictions of the model. Our modeling assumptions are broadly applicable to adherent, monolayer cell cultures, making the model amenable to investigate changes in nuclear mechanics due to other stimuli by merely measuring nuclear morphology. Toward this, we present two techniques, graphical and numerical, to use our model for predicting physical changes in the nucleus., (Copyright © 2019 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
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37. Single-photon-multi-layer-interference lithography for high-aspect-ratio and three-dimensional SU-8 micro-/nanostructures.
- Author
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Ghosh S and Ananthasuresh GK
- Abstract
We report microstructures of SU-8 photo-sensitive polymer with high-aspect-ratio, which is defined as the ratio of height to in-plane feature size. The highest aspect ratio achieved in this work exceeds 250. A multi-layer and single-photon lithography approach is used in this work to expose SU-8 photoresist of thickness up to 100 μm. Here, multi-layer and time-lapsed writing is the key concept that enables nanometer localised controlled photo-induced polymerisation. We use a converging monochromatic laser beam of 405 nm wavelength with a controllable aperture. The reflection of the converging optics from the silicon substrate underneath is responsible for a trapezoidal edge profile of SU-8 microstructure. The reflection induced interfered point-spread-function and multi-layer-single-photon exposure helps to achieve sub-wavelength feature sizes. We obtained a 75 nm tip diameter on a pyramid shaped microstructure. The converging beam profile determines the number of multiple optical focal planes along the depth of field. These focal planes are scanned and exposed non-concurrently with varying energy dosage. It is notable that an un-automated height axis control is sufficient for this method. All of these contribute to realising super-high-aspect-ratio and 3D micro-/nanostructures using SU-8. Finally, we also address the critical problems of photoresist-based micro-/nanofabrication and their solutions.
- Published
- 2016
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38. A Scalable Perfusion Culture System with Miniature Peristaltic Pumps for Live-Cell Imaging Assays with Provision for Microfabricated Scaffolds.
- Author
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Balakrishnan S, Suma MS, Raju SR, Bhargav SD, Arunima S, Das S, and Ananthasuresh GK
- Abstract
We present a perfusion culture system with miniature bioreactors and peristaltic pumps. The bioreactors are designed for perfusion, live-cell imaging studies, easy incorporation of microfabricated scaffolds, and convenience of operation in standard cell culture techniques. By combining with miniature peristaltic pumps-one for each bioreactor to avoid cross-contamination and to maintain desired flow rate in each-we have made a culture system that facilitates perfusion culture inside standard incubators. This scalable system can support multiple parallel perfusion experiments. The major components are fabricated by three-dimensional printing using VeroWhite, which we show to be amenable to ex vivo cell culture. Furthermore, the components of the system can be reused, thus making it economical. We validate the system and illustrate its versatility by culturing primary rat hepatocytes, live imaging the growth of mouse fibroblasts (NIH 3T3) on microfabricated ring-scaffolds inserted into the bioreactor, performing perfusion culture of breast cancer cells (MCF7), and high-magnification imaging of hepatocarcinoma cells (HuH7).
- Published
- 2015
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39. A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization.
- Author
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Rakshit S and Ananthasuresh GK
- Subjects
- Algorithms, Databases, Protein, Muramidase chemistry, Oligopeptides chemistry, Oligopeptides metabolism, Protein Structure, Secondary, Thermodynamics, Ubiquitin chemistry, Models, Molecular, Peptides chemistry, Peptides metabolism, Protein Folding
- Abstract
We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.
- Published
- 2010
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40. A search for energy minimized sequences of proteins.
- Author
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Jha AN, Ananthasuresh GK, and Vishveshwara S
- Subjects
- Amino Acid Sequence, Databases, Protein, Models, Molecular, Protein Conformation, Proteins chemistry
- Abstract
In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10(-7). In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.
- Published
- 2009
- Full Text
- View/download PDF
41. An amino acid map of inter-residue contact energies using metric multi-dimensional scaling.
- Author
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Rakshit S and Ananthasuresh GK
- Subjects
- Amino Acid Sequence, Chemical Phenomena, Chemistry, Physical, Cluster Analysis, Computational Biology methods, Hydrophobic and Hydrophilic Interactions, Peptide Mapping, Amino Acids chemistry
- Abstract
We present an amino map based on their inter-residue contact energies using the Miyazawa-Jernigan matrix. This work is based on the method of metric multi-dimensional scaling (MMDS). The MMDS map shows, among other things, that the MJ contact energies imply the hydrophobic-hydrophilic nature of the amino acid residues. With the help of the map we are able to compare and draw inferences from uncorrelated data sets such as BLOSUM and PAM with MJ methods. We also use a hierarchical clustering method on our MMDS distance matrix to group the amino acids and arrive at an optimum number of groups for simplifying the amino acid set.
- Published
- 2008
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42. Protein sequence design based on the topology of the native state structure.
- Author
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Jha AN, Ananthasuresh GK, and Vishveshwara S
- Subjects
- Animals, Models, Biological, Protein Folding, Computer Simulation, Models, Molecular, Protein Structure, Secondary
- Abstract
Computational design of sequences for a given structure is generally studied by exhaustively enumerating the sequence space or by searching in such a large space, which is prohibitively expensive. However, we point out that the protein topology has a wealth of information, which can be exploited to design sequences for a chosen structure. In this paper, we present a computationally efficient method for ranking the residue sites in a given native-state structure, which enables us to design sequences for a chosen structure. The premise for the method is that the topology of the graph representing the energetically interacting neighbours in a protein plays an important role in the inverse-folding problem. While our previous work (which was also based on topology) used eigenspectral analysis of the adjacency matrix of interactions for ranking the residue sites in a given chain, here we use a simple but effective way of assigning weights to the nodes on the basis of secondary connections, along with primary connections. This indirectly accounts for the edge weight in the graph and removes degeneracy in the degree. The new scheme needs only a few multiplications and additions to compute the preferred ranking of the residue sites even for structures of real proteins of sizes of a few hundred amino acid residues. We use HP lattice model examples (for which exhaustive enumeration of sequences is practical) to validate our ranking approach in obtaining sequences of lowest energy for any H-P residue composition for a given native-state structure. Some examples of native structures of real proteins are also included. Quantitative comparison of the efficacy of the new scheme with the earlier schemes is made. The new scheme consistently performs better and with much lower computational cost. An optimization procedure is added to work with the new scheme in a few rare cases wherein the new scheme fails to provide the best sequence, an optimization procedure is added to work with the new scheme.
- Published
- 2007
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43. A method for computing the inter-residue interaction potentials for reduced amino acid alphabet.
- Author
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Luthra A, Jha AN, Ananthasuresh GK, and Vishveswara S
- Subjects
- Amino Acids chemistry, Peptide Mapping, Predictive Value of Tests, Proteins chemistry, Proteins genetics, Thermodynamics, Amino Acids metabolism, Computational Biology methods, Proteins metabolism, Sequence Analysis, Protein
- Abstract
Inter-residue potentials are extensively used in the design and evaluation of protein structures. However,dealing with all (20 x 20) interactions becomes computationally difficult in extensive investigations. Hence, it is desirable to reduce the alphabet of 20 amino acids to a smaller number. Currently, several methods of reducing the residue types exist; however a critical assessment of these methods is not available. Towards this goal,here we review and evaluate different methods by comparing with the complete (20 x 20) matrix of Miyazawa-Jernigan potential, including a method of grouping adopted by us, based on multi dimensional scaling (MDS). The second goal of this paper is the computation of inter-residue interaction energies for the reduced amino acid alphabet, which has not been explicitly addressed in the literature until now. By using a least squares technique, we present a systematic method of obtaining the interaction energy values for any type of grouping scheme that reduces the amino acid alphabet. This can be valuable in designing the protein structures.
- Published
- 2007
- Full Text
- View/download PDF
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