of a doctoral dissertation at the University of Miami.Dissertation supervised by Professor Victor J. Milenkovic. No. of pages in text: 162A new paradigm for rigid body simulation is presented and analyzed. Current techniques for rigid body simulation run slowly on scenes with many bodies in close proximity. Each time two bodies collide or make or break a static contact, the simulator must interrupt the numerical integration of velocities and accelerations. Even for simple scenes, the number of discontinuities per frame time can rise to the millions. An efficient optimization-based animation (OBA) algorithm is presented which can simulate scenes with many convex threedimensional bodies settling into stacks and other "crowded" arrangements. This algorithm simulates Newtonian (second order) physics and Coulomb friction, and it uses quadratic programming (QP) to calculate new positions, momenta, and accelerations strictly at frame times. The extremely small integration steps inherent to traditional simulation techniques are avoided.Contact points are synchronized at the end of each frame. Resolving contacts with friction is known to be a difficult problem. Analytic force calculation can have ambiguous or non-existing solutions. Purely impulsive techniques avoid these ambiguous cases, but still require an excessive and computationally expensive number of updates in the case of many simultaneous contacts. It is shown informally that even taking into account advances in stiff integration techniques, penalty force methods cannot overcome this issue of running time in highly crowded scenes. New algorithms are presented that calculate simultaneous impulses to resolve collisions and static contacts under the Coulomb friction model. The simultaneous impulses are the solution to a QP.In addition, the algorithms apply "bouncing at distance" and "freezing of bodies" to further speed up the simulation. These new QP algorithms are hybridized with a traditional priority queue momentum update scheme to allow sequential impulses when they are required for realism, such as in the office toy pendulum. When added to the implementation of OBA, these new algorithms increase the speed of the simulation by a factor of up to 30.The position update has been hybridized with retroactive detection (RD) to prevent fast and thin bodies from passing through each other. Due to the modular design of the OBA simulator, the described techniques can be used as components in any existing simulator that follows a modular design of position update, finding contacts, and resolving contacts. Non-convex bodies are simulated as unions of convex bodies. Links and joints are simulated with bi-directional constraints. Analysis of the algorithm and discussion of example simulations are provided. DedicationIn loving memory of my father.iii
A long-standing paradigm in B cell immunology is that effective somatic hypermutation and affinity maturation require cycling between the dark zone and light zone of the germinal center. The cyclic re-entry hypothesis was first proposed based on considerations of the efficiency of affinity maturation using an ordinary differential equations model for B cell population dynamics. More recently, two-photon microscopy studies of B cell motility within lymph nodes in situ have revealed the complex migration patterns of B lymphocytes both in the preactivation follicle and post-activation germinal center. There is strong evidence that chemokines secreted by stromal cells and the regulation of cognate G-protein coupled receptors by these chemokines are necessary for the observed spatial cell distributions. For example, the distribution of B cells within the light and dark zones of the germinal center appears to be determined by the reciprocal interaction between the level of the CXCR4 and CXCR5 receptors and the spatial distribution of their respective chemokines CXCL12 and CXCL13. Computer simulations of individual-based models have been used to study the complex biophysical and mechanistic processes at the individual cell level, but such simulations can be challenging to parameterize and analyze. In contrast, ordinary differential equations are more tractable, but traditional compartment model formalizations ignore the spatial chemokine distribution that drives B cell redistribution. Motivated by the desire to understand the motility patterns observed in an individual-based simulation of B cell migration in the lymph node, we propose and analyze the dynamics of an ordinary differential equation model incorporating explicit chemokine spatial distributions. While there is experimental evidence that B cell migration patterns in the germinal center are driven by extrinsically regulated differentiation programs, the model shows, perhaps surprisingly, that feedback from receptor down-regulation induced by external chemokine fields can give rise to spontaneous interzonal and intrazonal oscillations in the absence of any extrinsic regulation. While the extent to which such simple feedback mechanisms contributes to B cell migration patterns in the germinal center is unknown, the model provides an alternative hypothesis for how complex B cell migration patterns might arise from very simple mechanisms.Electronic Supplementary MaterialThe online version of this article (doi:10.1007/s11538-012-9799-9) contains supplementary material, which is available to authorized users.
A suite of algorithms is presented for contact resolution in rigid body simulation under the Coulomb friction model: Given a set of rigid bodies with many contacts among them, resolve dynamic contacts (collisions) and static (persistent) contacts. The suite consists of four algorithms: 1) partial sequential collision resolution, 2) final resolution of collisions through the solution of a single convex QP (positive semidefinite quadratic program), 3) resolution of static contacts through the solution of a single convex QP, 4) freezing of "stationary" bodies. This suite can generate realistic-looking results for simple examples yet, for the first time, can also tractably resolve contacts for a simulation as large as 1,000 cubes in an "hourglass." Freezing speeds up this simulation by more than 25 times. Thanks to excellent commercial QP technology, the contact resolution suite is simple to implement and can be "plugged into" any simulation algorithm to provide fast and realistic-looking animations of rigid bodies.
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