A scalable computational platform for particulate Stokes suspensions

[1]  A. Barnett,et al.  Solution of Stokes flow in complex nonsmooth 2D geometries via a linear-scaling high-order adaptive integral equation scheme , 2019, J. Comput. Phys..

[2]  James W. Swan,et al.  Fast Stokesian dynamics , 2019, Journal of Fluid Mechanics.

[3]  Paramsothy Jayakumar,et al.  Scalable Solvers for Cone Complementarity Problems in Frictional Multibody Dynamics , 2019, 2019 IEEE High Performance Extreme Computing Conference (HPEC).

[4]  Michael J. Shelley,et al.  The odd free surface flows of a colloidal chiral fluid , 2019, Nature Physics.

[5]  David B. Stein,et al.  Fast crystallization of rotating membrane proteins. , 2019, 1903.00940.

[6]  J. Dunkel,et al.  Emergence of three-dimensional order and structure in growing biofilms , 2018, Nature Physics.

[7]  Michael J Shelley,et al.  Computing collision stress in assemblies of active spherocylinders: Applications of a fast and generic geometric method. , 2018, The Journal of chemical physics.

[8]  David Gorsich,et al.  Tensor Train Accelerated Solvers for Nonsmooth Rigid Body Dynamics , 2018, Applied Mechanics Reviews.

[9]  Andreas Klöckner,et al.  A fast algorithm for Quadrature by Expansion in three dimensions , 2018, J. Comput. Phys..

[10]  C. Turc,et al.  Harmonic density interpolation methods for high-order evaluation of Laplace layer potentials in 2D and 3D , 2017, J. Comput. Phys..

[11]  D. Zorin,et al.  Parallel contact-aware simulations of deformable particles in 3D Stokes flow , 2018, 1812.04719.

[12]  W. Li,et al.  RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations , 2017, Comput. Phys. Commun..

[13]  Shravan K. Veerapaneni,et al.  Boundary integral equation analysis for suspension of spheres in Stokes flow , 2017, J. Comput. Phys..

[14]  Michael Siegel,et al.  A local target specific quadrature by expansion method for evaluation of layer potentials in 3D , 2017, J. Comput. Phys..

[15]  Gerhard Gompper,et al.  Active turbulence in a gas of self-assembled spinners , 2017, Proceedings of the National Academy of Sciences.

[16]  Dan Negrut,et al.  Compliant contact versus rigid contact: A comparison in the context of granular dynamics. , 2017, Physical review. E.

[17]  Daniel J. Needleman,et al.  Active matter at the interface between materials science and cell biology , 2017 .

[18]  Dan Negrut,et al.  A comparison of numerical methods for solving multibody dynamics problems with frictional contact modeled via differential variational inequalities , 2017 .

[19]  Lailai Zhu,et al.  Swimming with a cage: low-Reynolds-number locomotion inside a droplet. , 2017, Soft matter.

[20]  Denis Zorin,et al.  Contact-aware simulations of particulate Stokesian suspensions , 2016, J. Comput. Phys..

[21]  Leslie Greengard,et al.  An integral equation formulation for rigid bodies in Stokes flow in three dimensions , 2016, J. Comput. Phys..

[22]  Stuart R. Slattery,et al.  Mesh-free data transfer algorithms for partitioned multiphysics problems: Conservation, accuracy, and parallelism , 2016, J. Comput. Phys..

[23]  Junichiro Makino,et al.  Implementation and performance of FDPS: a framework for developing parallel particle simulation codes , 2016, 1601.03138.

[24]  M. Shelley.  The Dynamics of Microtubule/Motor-Protein Assemblies in Biology and Physics , 2016 .

[25]  Leslie Greengard,et al.  Integral Equation Methods for Elastance and Mobility Problems in Two Dimensions , 2015, SIAM J. Numer. Anal..

[26]  Mu Wang,et al.  Spectral Ewald Acceleration of Stokesian Dynamics for polydisperse suspensions , 2015, J. Comput. Phys..

[27]  G. Biros,et al.  PVFMM: A Parallel Kernel Independent FMM for Particle and Volume Potentials , 2015 .

[28]  Aleksandar Donev,et al.  Brownian dynamics of confined rigid bodies. , 2015, The Journal of chemical physics.

[29]  Hammad Mazhar,et al.  Using Nesterov's Method to Accelerate Multibody Dynamics with Friction and Contact , 2015, ACM Trans. Graph..

[30]  Petia M. Vlahovska,et al.  Periodic and Chaotic Orbits of Plane-Confined Micro-rotors in Creeping Flows , 2015, J. Nonlinear Sci..

[31]  P. Vlahovska,et al.  Collective dynamics in a binary mixture of hydrodynamically coupled microrotors. , 2014, Physical review letters.

[32]  Eligiusz Wajnryb,et al.  The Rotne-Prager-Yamakawa approximation for periodic systems in a shear flow. , 2014, The Journal of chemical physics.

[33]  P. Szymczak,et al.  Rotne–Prager–Yamakawa approximation for different-sized particles in application to macromolecular bead models , 2014, Journal of Fluid Mechanics.

[34]  Sarah Niebe,et al.  Numerical methods for linear complementarity problems in physics-based animation , 2015, SIGGRAPH '13.

[35]  Mihai Anitescu,et al.  Using Krylov subspace and spectral methods for solving complementarity problems in many‐body contact dynamics simulation , 2013 .

[36]  Hammad Mazhar,et al.  Chrono: A Parallel Physics Library for Rigid-Body, Flexible-Body, and Fluid Dynamics , 2013 .

[37]  Eligiusz Wajnryb,et al.  Generalization of the Rotne–Prager–Yamakawa mobility and shear disturbance tensors , 2013, Journal of Fluid Mechanics.

[38]  S. Ramaswamy,et al.  Hydrodynamics of soft active matter , 2013 .

[39]  Helen J. Wilson,et al.  Stokes flow past three spheres , 2013, J. Comput. Phys..

[40]  Daniel P. Robinson,et al.  Subspace Accelerated Matrix Splitting Algorithms for Asymmetric and Symmetric Linear Complementarity Problems , 2013, SIAM J. Optim..

[41]  Mihai Anitescu,et al.  A compliant visco-plastic particle contact model based on differential variational inequalities , 2013 .

[42]  Michael Shelley,et al.  Active suspensions and their nonlinear models , 2013 .

[43]  Jingfang Huang,et al.  A fast algorithm for Brownian dynamics simulation with hydrodynamic interactions , 2013, Math. Comput..

[44]  Hammad Mazhar,et al.  CHRONO: a parallel multi-physics library for rigid-body, flexible-body, and fluid dynamics , 2013 .

[45]  Zydrunas Gimbutas,et al.  A fast multipole method for the Rotne-Prager-Yamakawa tensor and its applications , 2013, J. Comput. Phys..

[46]  Mihai Anitescu,et al.  A complementarity-based rolling friction model for rigid contacts , 2013 .

[47]  Daniel T. N. Chen,et al.  Spontaneous motion in hierarchically assembled active matter , 2012, Nature.

[48]  M. Kuimova.  Mapping viscosity in cells using molecular rotors. , 2012, Physical chemistry chemical physics : PCCP.

[49]  Hammad Mazhar,et al.  Leveraging parallel computing in multibody dynamics , 2012 .

[50]  M. Anitescu,et al.  A matrix-free cone complementarity approach for solving large-scale, nonsmooth, rigid body dynamics , 2011 .

[51]  Mihai Anitescu,et al.  GPU-Based Parallel Computing for the Simulation of Complex Multibody Systems with Unilateral and Bilateral Constraints: An Overview , 2011 .

[52]  Mihai Anitescu,et al.  An iterative approach for cone complementarity problems for nonsmooth dynamics , 2010, Comput. Optim. Appl..

[53]  M. Anitescu,et al.  A Convex Complementarity Approach for Simulating Large Granular Flows , 2010 .

[54]  Joontaek Park,et al.  A cloud of rigid fibres sedimenting in a viscous fluid , 2010, Journal of Fluid Mechanics.

[55]  Anna-Karin Tornberg,et al.  Gravity induced sedimentation of slender fibers , 2009 .

[56]  N. Wagner,et al.  Shear thickening in colloidal dispersions , 2009 .

[57]  M. Anitescu,et al.  A Fast NCP Solver for Large Rigid-Body Problems with Contacts, Friction, and Joints , 2009 .

[58]  M. Anitescu,et al.  Large-scale parallel multi-body dynamics with frictional contact on the graphical processing unit , 2008 .

[59]  Dietmar Fey,et al.  LibGeoDecomp: A Grid-Enabled Library for Geometric Decomposition Codes , 2008, PVM/MPI.

[60]  M. Shelley,et al.  Instabilities and pattern formation in active particle suspensions: kinetic theory and continuum simulations. , 2008, Physical review letters.

[61]  Takuji Ishikawa,et al.  Coherent structures in monolayers of swimming particles. , 2008, Physical review letters.

[62]  É. Guazzelli,et al.  Sedimentation of small particles : how can such a simple problem be so difficult? , 2006 .

[63]  W. Hager,et al.  The cyclic Barzilai-–Borwein method for unconstrained optimization , 2006 .

[64]  Katarina Gustavsson,et al.  A numerical method for simulations of rigid fiber suspensions , 2006, J. Comput. Phys..

[65]  Bertrand Maury,et al.  A time-stepping scheme for inelastic collisions , 2006, Numerische Mathematik.

[66]  John F. Brady,et al.  STOKESIAN DYNAMICS , 2006 .

[67]  Mihai Anitescu,et al.  Optimization-based simulation of nonsmooth rigid multibody dynamics , 2006, Math. Program..

[68]  J. F. Brady,et al.  Chaos and threshold for irreversibility in sheared suspensions , 2005, Nature.

[69]  B. Maury,et al.  A PENALTY METHOD FOR THE SIMULATION OF FLUID - RIGID BODY INTERACTION , 2005 .

[70]  Roger Fletcher,et al.  Projected Barzilai-Borwein methods for large-scale box-constrained quadratic programming , 2005, Numerische Mathematik.

[71]  Steven G. Johnson,et al.  The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.

[72]  David Baraff,et al.  Issues in computing contact forces for non-penetrating rigid bodies , 1993, Algorithmica.

[73]  J. Brady,et al.  Suspensions of prolate spheroids in Stokes flow , 2005 .

[74]  Roger Fletcher,et al.  On the Barzilai-Borwein Method , 2005 .

[75]  R. Goldstein,et al.  Self-concentration and large-scale coherence in bacterial dynamics. , 2004, Physical review letters.

[76]  Mihai Anitescu,et al.  A constraint‐stabilized time‐stepping approach for rigid multibody dynamics with joints, contact and friction , 2004 .

[77]  Eric D. Wetzel,et al.  The ballistic impact characteristics of Kevlar® woven fabrics impregnated with a colloidal shear thickening fluid , 2003 .

[78]  M. Anitescu,et al.  A Time-stepping Method for Stii Multibody Dynamics with Contact and Friction ‡ , 2022 .

[79]  John F. Brady,et al.  Rheology and microstructure in concentrated noncolloidal suspensions , 2002 .

[80]  H. Lekkerkerker,et al.  Insights into phase transition kinetics from colloid science , 2002, Nature.

[81]  John F. Brady,et al.  Accelerated Stokesian Dynamics simulations , 2001, Journal of Fluid Mechanics.

[82]  L. Cipelletti,et al.  Jamming phase diagram for attractive particles , 2001, Nature.

[83]  John F. Brady,et al.  Brownian Dynamics simulation of hard-sphere colloidal dispersions , 2000 .

[84]  David E. Stewart,et al.  Rigid-Body Dynamics with Friction and Impact , 2000, SIAM Rev..

[85]  D. Stewart,et al.  Time-stepping for three-dimensional rigid body dynamics , 1999 .

[86]  D. Stewart.  Convergence of a Time‐Stepping Scheme for Rigid‐Body Dynamics and Resolution of Painlevé's Problem , 1998 .

[87]  M. Anitescu,et al.  Formulating Dynamic Multi-Rigid-Body Contact Problems with Friction as Solvable Linear Complementarity Problems , 1997 .

[88]  D. Stewart,et al.  AN IMPLICIT TIME-STEPPING SCHEME FOR RIGID BODY DYNAMICS WITH INELASTIC COLLISIONS AND COULOMB FRICTION , 1996 .

[89]  J. Brady,et al.  Stokesian Dynamics simulation of Brownian suspensions , 1996, Journal of Fluid Mechanics.

[90]  M. Anitescu,et al.  Formulating Three-Dimensional Contact Dynamics Problems , 1996 .

[91]  John F. Brady,et al.  Suspensions of prolate spheroids in Stokes flow. Part 1. Dynamics of a finite number of particles in an unbounded fluid , 1993, Journal of Fluid Mechanics.

[92]  C. Pozrikidis.  Boundary Integral and Singularity Methods for Linearized Viscous Flow: Index , 1992 .

[93]  J. Brady,et al.  Dynamic simulation of an electrorheological fluid , 1992 .

[94]  Roger T. Bonnecaze,et al.  Yield stresses in electrorheological fluids , 1992 .

[95]  Sangtae Kim,et al.  Microhydrodynamics: Principles and Selected Applications , 1991 .

[96]  M. Shelley,et al.  On the connection between thin vortex layers and vortex sheets , 1990, Journal of Fluid Mechanics.

[97]  David J. Montana,et al.  The Kinematics of Contact and Grasp , 1988, Int. J. Robotics Res..

[98]  H. Power,et al.  Second kind integral equation formulation of Stokes' flows past a particle of arbitary shape , 1987 .

[99]  Louis J. Durlofsky,et al.  Dynamic simulation of hydrodynamically interacting particles , 1987, Journal of Fluid Mechanics.

[100]  J. Pang,et al.  Iterative methods for large convex quadratic programs: a survey , 1987 .

[101]  Bernard Roth,et al.  On the spatial motion of a rigid body with point contact , 1987, Proceedings. 1987 IEEE International Conference on Robotics and Automation.

[102]  Olvi L. Mangasarian,et al.  Error bounds for monotone linear complementarity problems , 1986, Math. Program..

[103]  C. Beenakker.  Ewald sum of the Rotne-Prager tensor , 1986 .

[104]  R. Krasny.  Desingularization of periodic vortex sheet roll-up , 1986 .

[105]  Per Lötstedt.  Mechanical Systems of Rigid Bodies Subject to Unilateral Constraints , 1982 .

[106]  P. Cundall,et al.  A discrete numerical model for granular assemblies , 1979 .

[107]  J. Blake,et al.  A spherical envelope approach to ciliary propulsion , 1971, Journal of Fluid Mechanics.

[108]  Hiromi Yamakawa,et al.  Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction , 1970 .

[109]  S. Prager,et al.  Variational Treatment of Hydrodynamic Interaction in Polymers , 1969 .

[110]  H. Brinkman.  A calculation of the viscous force exerted by a flowing fluid on a dense swarm of particles , 1949 .