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## 1 Automated Cell Transport in Optical Tweezers-Assisted

Citations: | 3 - 3 self |

### Citations

1612 |
Computer Simulation of Liquids
- Allen, Tildesley
- 1987
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Citation Context ... particle is given by Stokes’ law as 6πηRa, where Ra is the radius of the particle. The scaling constant ζ = √ 2γkBT in (1) is obtained by applying requirements of the fluctuation-dissipation theorem =-=[27]-=-, where kB is the Boltzman’s constant. The acceleration of the particle moving under the influence of the fluid flow at the end of a uniform time step δt can be written in the finite difference form [... |

1493 |
A formal basis for the heuristic determination of minimum cost paths
- Hart, Nilsson, et al.
- 1968
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Citation Context ...on. In both the cases, the underlying state space (also known as a configuration space or C-space) is either discretized and then searched using graph search techniques including heuristic approaches =-=[9]-=-, or sampled using the sampling-based planning algorithms [10]. The explicit representations of the state space include, e.g., a visibility graph [11], road map [10], Voronoi diagram [10,12], or latti... |

1087 | Planning Algorithms
- LaValle
- 2004
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Citation Context ... as a configuration space or C-space) is either discretized and then searched using graph search techniques including heuristic approaches [9], or sampled using the sampling-based planning algorithms =-=[10]-=-. The explicit representations of the state space include, e.g., a visibility graph [11], road map [10], Voronoi diagram [10,12], or lattice-based representations [10]. Chowdhury et al. [13] developed... |

477 | Spatial Planning: A Configuration Space Approach
- Lozano-Perez
- 1983
(Show Context)
Citation Context ...h search techniques including heuristic approaches [9], or sampled using the sampling-based planning algorithms [10]. The explicit representations of the state space include, e.g., a visibility graph =-=[11]-=-, road map [10], Voronoi diagram [10,12], or lattice-based representations [10]. Chowdhury et al. [13] developed A* based path planner with a novel cost function for gripper-based automated indirect m... |

88 |
Forces of a single-beam gradient laser trap on a dielectric sphere in the ray optics regime
- Ashkin
- 1992
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Citation Context ...cs do not provide fine position control over individual cells (e.g., see Fig. 1). Another technology which has become very popular recently in the field of micro-manipulation is optical tweezers (OT) =-=[2,3]-=-. OT has been shown to be a very effective toolfor precise manipulationof individual cells; however, its throughput is significantly lower than the one of microfluidics, and depends on the maximum num... |

53 | Characterization of photodamage to escherichia coli in optical traps
- Neuman, Chadd, et al.
- 1999
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Citation Context ...flow and thus makes the cleaning process less reliable and slower. In addition, exposure to high intensity laser for a longer time due to slow manipulation process may cause photo-damage to the cells =-=[8]-=-. In this paper, we have developed a physics-aware, simulation-assisted planning approach for automated transport of cells. The developed planner enables fast cleaning of microNets inside a microfluid... |

47 |
Dynamic holographic optical tweezers
- Curtis, Koss, et al.
- 2002
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Citation Context ...fted by using a motor-controlled stage. Fast operation: Thecleaningoperationneedstobeveryfasttoutilizethehighthroughput advantage of the microfluidic chamber. Using holographic optical tweezers (HOT) =-=[7]-=-, multiple traps can be created to allow cleaning of multiple nets in parallel. However, man4ual, simultaneous control of multiple traps is very challenging due to the presence of other randomly movi... |

31 | Steering flexible needles under markov motion uncertainty
- Alterovitz, Lim, et al.
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Citation Context ...MDP) and solved using a class of Stochastic Dynamic Programming (SDP) algorithms. A discrete version of the infinite horizon SDP was applied to steer flexible bevel-tip needles inside soft tissues in =-=[18]-=-. Banerjee et al. [19] developed SDP based planner for automated transport of a particle in an environment with obstacles. 5They further extended the planner in [20] for automated transport of multip... |

25 |
Controlled microfluidic interfaces
- Atencia, Beebe
(Show Context)
Citation Context ..., we restrict it up to the distance 10Ra from each individual cell. 3.4 Modeling of fluid flow The fluid flow in a microfluidic chamber is laminar since viscosity dominates over inertia at microscale =-=[32]-=-. We carried out computational fluid dynamics (CFD) simulations using FLUENT. We used water (ρf = 998.2 kg/m 3 ) as a working fluid. Hence, fluid flow fields are Newtonian and incompressible in nature... |

17 | A guide to heuristic-based path planning
- Ferguson, Likhachev, et al.
- 2005
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Citation Context .... 4.3.2 Cost function x k+1 = { x k +u k t xj,goal for the linear actions, for the release action The planning algorithm iteratively expands the states from the priority queue Θ with their key values =-=[33,34]-=- computed as (4) key(x) = [key1(x),key2(x)], = [min(g(x),rhs(x))+h(xinit,x), min(g(x),rhs(x))] (5) where g(x) is the optimal cost-to-go from x to xgoal, h(xinit,x) is the heuristic cost estimate ofthe... |

13 | Developing a Stochastic Dynamic Programming Framework for Optical Tweezer based Automated Particle Transport Operations. Accepted for publication
- Banerjee, Pomerance, et al.
(Show Context)
Citation Context ...a class of Stochastic Dynamic Programming (SDP) algorithms. A discrete version of the infinite horizon SDP was applied to steer flexible bevel-tip needles inside soft tissues in [18]. Banerjee et al. =-=[19]-=- developed SDP based planner for automated transport of a particle in an environment with obstacles. 5They further extended the planner in [20] for automated transport of multiple particles. They int... |

8 |
Photon-Atom Interactions
- Weissbluth
- 1989
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Citation Context ...xperiments. �We use the collision engine Box2D [24] to model the collision forces among cells and microNets inside the chamber. �We incorporate all the external forces into Langevin dynamics equation =-=[25]-=- and solve it using Verlet integration scheme to compute the trajectories of the cells. �We simulate the disturbances in the fluid flow by introducing a random Gaussian noise to the fluid force vector... |

8 |
Stochastic Simulations with Graphics Hardware: Characterization of accuracy and performance. Accepted for publication
- Balijepalli, LeBrun, et al.
- 2009
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Citation Context ...on We consider a cell as a particle of a spherical shape. A cell moving in a fluid undergoes the effect of a rapidly fluctuating force generated by fluid molecules, as well as a hydrodynamic dragforce=-=[26]-=-. These forcesareclosely relatedtoeachother. The motionofafreelydiffusing particle can be modeled using Langevin equation [25] as follows: δV(t) δt ζ = −γ V(t)+ Γ(t) (1) m m 6where V(t) is the veloci... |

8 | Indirect Optical Gripping With Triplet Traps - Koss, Chowdhury, et al. - 2011 |

7 | Realtime path planning for coordinated transport of multiple particles using optical tweezers
- Banerjee, Chowdhury, et al.
- 2012
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Citation Context ...ip needles inside soft tissues in [18]. Banerjee et al. [19] developed SDP based planner for automated transport of a particle in an environment with obstacles. 5They further extended the planner in =-=[20]-=- for automated transport of multiple particles. They introduced a time parameter in the convergence loop to enhance the computational speed and accuracy in deriving the safest paths. One of the most s... |

6 |
Dynamics analysis and motion planning for automated cell transportation with optical tweezers
- Wu, Sun, et al.
- 2013
(Show Context)
Citation Context ...such that smooth paths are computed to ensure reliable transport of cells. A sampling RRT based algorithm was developed by Ju et al. [15,16] for automated OT-based transport of cells in 3D. Wu et al. =-=[17]-=- integrated a proportional-integral (PI) controller with A* based planner to achieve a stable and precise transport of cells. The problem of motion planning under uncertainty is usually modeled as a P... |

4 |
Automated Indirect Optical Micromanipulation of Biological Cells Using Indirect Pushing for Minimizing Photo-Damage
- Thakur, Chowdhury, et al.
- 2012
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Citation Context ...ectly trapped to be transported to their nearby unfilled microNets, which may affect their viability. Hence, another future direction of this research is to use optical grippers [13,35–37] or pushers =-=[38]-=- made of optically trapped beads to indirectly trap and transport cells to the desired microNets. The planner will need to generate paths for the entire ensembles, which will require detailed modeling... |

3 |
Manipulation of biological samples using micro and nano techniques
- Castillo, Dimaki, et al.
(Show Context)
Citation Context ...ately placing cells in an array for biological experiments. 1 Introduction Cell localization, transport, sorting, and characterization are crucial in many emerging medical and biological applications =-=[1]-=-. We will refer to these types of operations as cell manipulation. In medicine, for example, diagnosis, therapy, and drug delivery may be significantly improved by deploying specialized robotics techn... |

2 |
Macro to nano: a simple method for transporting cultured cells from milliliter scale to nanoliter scale,” Exp
- Seale, Faley, et al.
- 2010
(Show Context)
Citation Context ... by combining them into a single hybrid system. In our hybrid system, we integrated a microfluidic chamber [4] (see Fig. 1) into our OT system. The microfluidic chamber contains about 10000 microNets =-=[5]-=- (previously, they have been termed traps, but to avoid confusion with the laser traps, herein we term them MicroNets or nets) that are created intentionally to direct the fluid flow in a certain dire... |

2 |
Cell shape dynamics: From waves to migration,” PLoS
- Driscoll, McCann, et al.
- 2012
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Citation Context ...ting the fluid flow. This results in statistical variations in the number of cells inside each microNet, which is not desirable for certain biological experiments, e.g., cell-cell interaction studies =-=[6]-=-, where each microNet should contain the same number of cells. OT provides fine manipulation control and thus can be used for moving the excess of cells from crowded microNets to the nets with the ins... |

2 |
Force and motion analysis for automated cell transportation with optical tweezers”, Proceeding of the 8th World Congress on Intelligent Control and Automation
- Wu, Sun, et al.
(Show Context)
Citation Context ... or lattice-based representations [10]. Chowdhury et al. [13] developed A* based path planner with a novel cost function for gripper-based automated indirect manipulation of cells using OT. Wu et al. =-=[14]-=- developed a similar A* based approach for automated transport of directly trapped cells using OT. In that approach, the cost function is designed such that smooth paths are computed to ensure reliabl... |

2 |
Automated transportation of single cells using robot-tweezer manipulation system
- Hu, Sun
- 2011
(Show Context)
Citation Context ...rease of computational time with the increase in the dimensionality of the state space. In addition to the planning approaches developed in OT domain, closed-loop control techniques were developed in =-=[21,22]-=- for automated transport of biological cells. 3 Simulations of Cell Motion in Microfluidic Chamber 3.1 Overview Given a cell C and its corresponding state x = [x,y] T in a microfluidic chamber with th... |

2 |
Building a better cell trap: Applying Lagrangian modeling to the design of microfluidic devices for cell biology
- Kim, Wang, et al.
(Show Context)
Citation Context ... it in a look-up table ∆ (see Fig. 1). We adopt the following approach to simulate the cell motion. �We use FLUENT (ANSYS, Inc. version 13.0.0) to model the fluid flow inside the microfluidic chamber =-=[23]-=-. The quality of the fluid flow vectors is validated using physical experiments. �We use the collision engine Box2D [24] to model the collision forces among cells and microNets inside the chamber. �We... |

2 | Using GPUs for realtime prediction of optical forces on microsphere ensembles - Bista, Chowdhury, et al. |

2 |
Computer Experiments on Classical Fluids.I. Thermodynamical Properties of Lennard-Jones Molecules
- Verlet
- 1967
(Show Context)
Citation Context ...orce due to collisions between the particles and microNets, and other surrounding particles. Once we calculate the acceleration A(t+δt), we use the velocity form of the second order Verlet integrator =-=[31]-=- to calculate the position and velocity of the particle [26,28,29]. The simulation time step is taken as the closest multiple as described in [26]. of 10 smaller than m γ Prior to modeling the externa... |

1 |
Microfluidicplatformforreal-timesignaling analysis of multiple single T cells in parallel
- Faley, Seale, et al.
- 2008
(Show Context)
Citation Context ...s that can be created. The advantages of these two manipulation technologies can be exploited by combining them into a single hybrid system. In our hybrid system, we integrated a microfluidic chamber =-=[4]-=- (see Fig. 1) into our OT system. The microfluidic chamber contains about 10000 microNets [5] (previously, they have been termed traps, but to avoid confusion with the laser traps, herein we term them... |

1 |
Automated transport of biological cells with optical tweezers using planar gripper formations
- Chowdhury, Thakur, et al.
- 2012
(Show Context)
Citation Context ...lgorithms [10]. The explicit representations of the state space include, e.g., a visibility graph [11], road map [10], Voronoi diagram [10,12], or lattice-based representations [10]. Chowdhury et al. =-=[13]-=- developed A* based path planner with a novel cost function for gripper-based automated indirect manipulation of cells using OT. Wu et al. [14] developed a similar A* based approach for automated tran... |

1 |
rrt-based path planning to robotic manipulation of biological cells with optical tweezer
- “Apply
(Show Context)
Citation Context ...ed cells using OT. In that approach, the cost function is designed such that smooth paths are computed to ensure reliable transport of cells. A sampling RRT based algorithm was developed by Ju et al. =-=[15,16]-=- for automated OT-based transport of cells in 3D. Wu et al. [17] integrated a proportional-integral (PI) controller with A* based planner to achieve a stable and precise transport of cells. The proble... |

1 |
checked date: Dec.20
- org
- 2012
(Show Context)
Citation Context ...S, Inc. version 13.0.0) to model the fluid flow inside the microfluidic chamber [23]. The quality of the fluid flow vectors is validated using physical experiments. �We use the collision engine Box2D =-=[24]-=- to model the collision forces among cells and microNets inside the chamber. �We incorporate all the external forces into Langevin dynamics equation [25] and solve it using Verlet integration scheme t... |

1 |
Generating Simplified TrappingProbabilityModelsFromSimulationofOpticalTweezers System
- Banerjee, Balijepalli, et al.
- 2009
(Show Context)
Citation Context ...and other surrounding particles. Once we calculate the acceleration A(t+δt), we use the velocity form of the second order Verlet integrator [31] to calculate the position and velocity of the particle =-=[26,28,29]-=-. The simulation time step is taken as the closest multiple as described in [26]. of 10 smaller than m γ Prior to modeling the external forces (i.e., the collision and fluid forces), we evaluate the B... |

1 |
Robustgrippersynthesis forindirect manipulationofcells using holographicoptical tweezers
- Chowdhury, Wang, et al.
- 2012
(Show Context)
Citation Context ...0; prelease,T = 0.65, (i) w = 0; prelease,T = 0.5 Fig. 1). We demonstrate the usefulness of the developed planner using BioRyx 200 (Arryx, Inc., Chicago, IL) holographic laser tweezer as described in =-=[35]-=-. Cells are identified by thresholding the image and calculating the center of mass of all the remaining blobs (see Fig. 3). Yeast cells used in this experiment are cultivated from a fast growing yeas... |

1 | Survey on indirect optical manipulationof cells, nucleic acids, andmotor proteins - Banerjee, Chowdhury, et al. - 2011 |