▪ Abstract Soft lithography, a set of techniques for microfabrication, is based on printing and molding using elastomeric stamps with the patterns of interest in bas-relief. As a technique for fabricating microstructures for biological applications, soft lithography overcomes many of the shortcomings of photolithography. In particular, soft lithography offers the ability to control the molecular structure of surfaces and to pattern the complex molecules relevant to biology, to fabricate channel structures appropriate for microfluidics, and to pattern and manipulate cells. For the relatively large feature sizes used in biology (≥50 μm), production of prototype patterns and structures is convenient, inexpensive, and rapid. Self-assembled monolayers of alkanethiolates on gold are particularly easy to pattern by soft lithography, and they provide exquisite control over surface biochemistry.

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Soft Lithography in Biology and Biochemistry

This Account summarizes techniques for fabrication and applications in biomedicine of microfluidic devices fabricated in poly(dimethylsiloxane) (PDMS). The methods and applications described focus on the exploitation of the physical and chemical properties of PDMS in the fabrication or actuation of the devices. Fabrication of channels in PDMS is simple, and it can be used to incorporate other materials and structures through encapsulation or sealing (both reversible and irreversible).

Poly(dimethylsiloxane) as a material for fabricating microfluidic devices.

https://www-sop.inria.fr/asclepios/Publications/Tom.Vercauteren/Eval14NonlinearRegistration-Klein-NeuroImage09.pdf

Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration.

PART I: FOUNDATIONS 1. Introduction to Fixed-Parameter Algorithms 2. Preliminaries and Agreements 3. Parameterized Complexity Theory - A Primer 4. Vertex Cover - An Illustrative Example 5. The Art of Problem Parameterization 6. Summary and Concluding Remarks PART II: ALGORITHMIC METHODS 7. Data Reduction and Problem Kernels 8. Depth-Bounded Search Trees 9. Dynamic Programming 10. Tree Decompositions of Graphs 11. Further Advanced Techniques 12. Summary and Concluding Remarks PART III: SOME THEORY, SOME CASE STUDIES 13. Parameterized Complexity Theory 14. Connections to Approximation Algorithms 15. Selected Case Studies 16. Zukunftsmusik References Index

Invitation to fixed-parameter algorithms

■ Abstract Fluid flow at the microscale exhibits unique phenomena that can be leveraged to fabricate devices and components capable of performing functions useful for biological studies. The physics of importance to microfluidics are reviewed. Common methods of fabricating microfluidic devices and systems are described. Components, including valves, mixers, and pumps, capable of controlling fluid flow by utilizing the physics of the microscale are presented. Techniques for sensing flow characteristics are described and examples of devices and systems that perform bioanalysis are presented. The focus of this review is microscale phenomena and the use of the physics of the scale to create devices and systems that provide functionality useful to the life sciences.

https://www.researchgate.net/profile/Glennys_Mensing/publication/11260597_Physics_and_applications_of_microfluidics_in_biology/links/5437f5160cf2027cbb206767.pdf

Physics and applications of microfluidics in biology.

This paper describes a procedure for making topologically complex three-dimensional microfluidic channel systems in poly(dimethylsiloxane) (PDMS). This procedure is called the “membrane sandwich” method to suggest the structure of the final system:  a thin membrane having channel structures molded on each face (and with connections between the faces) sandwiched between two thicker, flat slabs that provide structural support. Two “masters” are fabricated by rapid prototyping using two-level photolithography and replica molding. They are aligned face to face, under pressure, with PDMS prepolymer between them. The PDMS is cured thermally. The masters have complementary alignment tracks, so registration is straightforward. The resulting, thin PDMS membrane can be transferred and sealed to another membrane or slab of PDMS by a sequence of steps in which the two masters are removed one at a time; these steps take place without distortion of the features. This method can fabricate a membrane containing a channel...

/pdf/fabrication-of-topologically-complex-three-dimensional-5f4z92zag2.pdf

Fabrication of topologically complex three-dimensional microfluidic systems in PDMS by rapid prototyping.

https://www.cs.mcgill.ca/~sue/papers/tuning.pdf

Tuning and comparing spatial normalization methods.

This report describes the spontaneous folding of flat elastomeric sheets, patterned with magnetic dipoles, into free-standing, 3D objects that are the topological equivalents of spherical shells. The path of the self-assembly is determined by a competition between mechanical and magnetic interactions. The potential of this strategy for the fabrication of 3D electronic devices is demonstrated by generating a simple electrical circuit surrounding a spherical cavity.

/pdf/magnetic-self-assembly-of-three-dimensional-surfaces-from-3gbsj4w6f9.pdf

Magnetic self-assembly of three-dimensional surfaces from planar sheets

We present new lowest energy configurations for several large benchmark problems for the two-dimensional hydrophobic-hydrophilic model. We found these solutions with a generic implementation of tabu search using an apparently novel set of transformations that we call pull moves. Our experiments show that our algorithm can find these best solutions in 3 to 14 hours, on average. Pull moves appear quite effective and may also be useful for other local search algorithms for the problem. Additionally, we prove that pull moves are complete; that is, any pair of valid configurations are mutually reachable through a sequence of pull moves. Our implementation was developed with the Human-Guided Search (HuGS) middleware, which allows rapid development of interactive optimization systems.

/pdf/a-complete-and-effective-move-set-for-simplified-protein-y1z6dxat07.pdf

A complete and effective move set for simplified protein folding

This paper is motivated by questions concerning the planning of motion in robotics. In particular, it is concerned with the motion of planar linkages from the complexity point of view. There are two main results. First, a planar linkage can be constrained to stay inside a bounded region whose boundary consists of straight lines by the addition of a polynomial number of new links. Second, the question of whether a planar linkage in some initial configuration can be moved so that a designated joint reaches a given point in the plane is PSPACE-hard.

/pdf/movement-problems-for-2-dimensional-linkages-5fgrmknzfy.pdf

Sue Whitesides

Papers

Fabrication of topologically complex three-dimensional microfluidic systems in PDMS by rapid prototyping.

Tuning and comparing spatial normalization methods.

Magnetic self-assembly of three-dimensional surfaces from planar sheets

A complete and effective move set for simplified protein folding

Movement problems for 2-dimensional linkages