## PUBLICATIONS

**A description of the different research subjects and publications can be found under the**

**Research**

**heading, and**

**slides from presentations**

**I have given and some**

**movies**

**are below. Computer codes associated with each paper are also linked below**. I have used the LyX word processor to create my Ph.D. dissertation, papers and presentations, and highly recommend it to everyone!

Here is a

**chronological list**of my publications along with reprints and recent preprints. I generally recommend using these PDFs instead of journal versions since I update these upon finding small mistakes that do not warrant an official erratum.- "
**The hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow**", by O. Maxian, B. Sprinkle, C. S. Peskin, and A. Donev, submitted to*Phys. Rev. Fluids*, 2022 [ArXiv:2201.04187]. Matlab code and examples at SlenderBody repo, and here are some supplementary movies. - "
**Interplay between Brownian motion and cross-linking kinetics controls bundling dynamics in actin networks**" by O. Maxian, A. Donev, and A. Mogilner, submitted to Biophysical J., 2021 [bioRxiv:021.09.17.460819]. Code and examples at SlenderBody repo, and here are some supplementary movies. - "
**Simulations of dynamically cross-linked actin networks: morphology, rheology, and hydrodynamic interactions**" by O. Maxian, R. P. Peláez, A. Mogilner, and A. Donev, PLOS Comp. Bio., 17(12): e1009240, 2021 [bioRxiv.org:2021.07.07.451453]. Code and examples at SlenderBody repo, and here are some supplementary movies. - "
**A fast spectral method for electrostatics in doubly-periodic slit channels**" by O. Maxian, R. P. Peláez, L. Greengard and A. Donev,*J. Chem. Phys.*, 2021 [ArXiv:2101.07088]. Code and examples on DPPoisson github. - "
**Sedimentation of a colloidal monolayer down an inclined plan**e" by B. Sprinkle, S. Wilken, S. Karapetyan, M. Tanaka, Z. Chen, J. R. Cruise, B. Delmotte, M. M. Driscoll, P. Chaikin and A. Donev,*Phys. Rev. Fluids*, 6:034202, 2021 [ArXiv:2011.14472]. Here is a movie of a simulation (see Fig. 1), movie of an experiment (see Fig. 2), and animated versions of Fig. 6 and Fig. 8. - "
**An integral-based spectral method for inextensible slender fibers in Stokes flow**" by O. Maxian, A. Mogilner and A. Donev,*Phys. Rev. Fluids*, 6:014102, 2021 [ArXiv:2007.11728]. Here is a movie of one period of cyclic shearing of a cross-linked fiber suspension (also side view) and more movies and codes and examples by Ondrej Maxian. - "
**A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes**" by D. R. Ladiges, S. P. Carney, A. Nonaka, K. Klymko, G. Moore, A. L. Garcia, S. R. Natesh, A. Donev, and J. B. Bell,*Phys. Rev. Fluids*, 6:044309, 2021 [ArXiv:2007.03036]. - "
**Driven dynamics in dense suspensions of microrollers**" by B. Sprinkle, E. B. van der Wee and Y. Luo and M. Driscoll, and A. Donev,*Soft Matter*, 16, 7982 - 8001, 2020 [ArXiv:2005.06002]. Here is a movie illustrating the two-layer structure of driven uniform suspension of microrollers, corresponding to Fig. 2 in the paper, as well as a movie of a monolayer of colloids (mimicking Quincke rollers), corresponding to Fig. 2 in the paper. Here is also a movie from the experiments. - "
**Reconfigurable microbots folded from simple colloidal chains**" by T. Yang, B. Sprinkle, Y. Guo, J. Qian, D. Hua, A. Donev, D. W.M. Marr, and N. Wu,*PNAS*, 202007255, 2020. Here is a movie of the formation of a helicoidal microbot from a colloidal chain (also see comparison to experimental movie). - "
**Brownian Dynamics of Fully Confined Suspensions of Rigid Particles Without Green's Functions**", by B. Sprinkle, A. Donev, A. Pal Singh Bhalla and N. Patankar,*J. Chem. Phys.*, 150, 164116, 2019 [ArXiv:1901.06427]. Here is a movie for Fig. 5 in section V.B showing defect propagation in a confined colloidal monolayer. - "
**Fluctuating hydrodynamics of electrolytes at electroneutral scales**", by A. Donev, A. J. Nonaka, C. Kim, A. L. Garcia and J. B. Bell,*Phys. Rev. Fluids*, 4(4):043701, 2019 [ArXiv:1809.08163]. - "
**Fluctuating Hydrodynamics and Debye-Hückel-Onsager Theory for Electrolytes**", A. Donev and A. L. Garcia and J.-P. Péraud and A. J. Nonaka and J. B. Bell,*Current Opinion in Electrochemistry*, 13:1-10, 2019 [ArXiv:1808.07799].

- "
**Fluctuating hydrodynamics of reactive liquid mixtures**", C. Kim and A. J. Nonaka and A. L. Garcia and J. B. Bell and A. Donev,*J. Chem. Phys.*, 149, 084113, 2018 [ArXiv:1806.03389].

- "
**Hydrodynamic fluctuations in quasi-two dimensional diffusion**", R. P. Peláez, F. Balboa Usabiaga, S. Panzuela, Q. Xiao, R. Delgado-Buscalioni and A. Donev,*J. Stat. Mech.*, 063207, 2018 [ArXiv:1802.07356]. See the fluam github repo for particle codes and our FHDq2D github repo for the fluctuating hydrodynamics codes. - "
**Efficient Reactive Brownian Dynamics**", A. Donev, C.-Y. Yang and C. Kim,*J. Chem. Phys.*, 148, 034103, 2018 [ArXiv:1710.02232]. See our SRBD github repo for codes. - "
**Large Scale Brownian Dynamics of Confined Suspensions of Rigid Particles**", B. Sprinkle, F. Balboa Usabiaga, N. A. Patankar and A. Donev,*J. Chem. Phys.*, 147, 244103, 2017 [ArXiv:1709.02410]. See our RigidMultiblobsWall github for codes. Here is an animated Fig. 6 (gif), as well as an animated bottom panel of Fig. 2. - "
**A fluctuating boundary integral method for Brownian suspensions**", Y. Bao, M. Rachh, E. Keaveny, L. Greengard and A. Donev,*J. Comp. Phys.*, 374:1094–1119, 2018 [ArXiv:1709.01480 ]. See the**FBIM code**written by Bill Bao. - "
**Minimal model for a hydrodynamic fingering instability in active suspensions**", B. Delmotte, M. Driscoll, P. Chaikin, A. Donev,*Phys. Rev. Fluids*, 2(11):114301, 2017 [ArXiv:1706.07330]. - "
**Fluctuation-enhanced electric conductivity in electrolyte solutions**", J.-P. Peraud, A. Nonaka, A. Chaudhri, J. B. Bell, A. Donev and A. L. Garcia, PNAS, 114(41):10829-10833, 2017 [ArXiv:1706.06227].

- "
**An Immersed Boundary Method with Divergence-Free Velocity Interpolation**", Y. Bao, A. Donev, B. E. Griffith, D. M. McQueen and C. S. Peskin,*J. Comp. Phys.*, 347:183-206, 2017 [ArXiv:1701.07169]. See the**DFIB code**written by Bill Bao. - "
**Hydrodynamic shocks in microroller suspensions**", B. Delmotte, M. Driscoll, P. Chaikin, A. Donev,*Phys. Rev. Fluids*, 2(9):092301, 2017 [ArXiv:1702.03350].

- "
**Stochastic Simulation of Reaction-Diffusion Systems: A Fluctuating-Hydrodynamics Approach**", C. Kim, A. Nonaka, J. B. Bell, A. Garcia and A. Donev,*J. Chem. Phys.*, 146, 124110, 2017 [ArXiv:1612.07238 ]. See our FHD_ReactDiff github repo for codes. Here is an animated Fig. 8 (avi), and an animation of the formation of a Turing pattern in the BPM model with FHD or RDME (section V.B) - "
**Brownian Dynamics of Confined Suspensions of Active Microrollers**", F. Balboa Usabiaga, B. Delmotte and A. Donev,*J. Chem. Phys.*, 146, 134104, 2017 [ArXiv:1612.00474]. See our RigidMultiblobsWall github for codes, and this directory for Supplementary Material Movies. - "
**Rapid Sampling of Stochastic Displacements in Brownian Dynamics Simulations**", by A. M. Fiore, F. Balboa Usabiaga, A. Donev and J. W. Swan,*J. Chem. Phys.*, 146, 124116, 2017 [Arxiv:1611.09322]. See our PSE github for codes based on HOOMD, or the easy to-use python interface in UAMMD. - "
**Unstable fronts and motile structures formed by microrollers**", M. Driscoll, B. Delmotte, M. Youssef, S. Sacanna, A. Donev and P. Chaikin,*Nature Physics*, 13, 375-379, 2017, [ArXiv:1609.08673]. See also the News & Views associated with the paper. These simulations predicted the existence of critters, seen in this movie. - "
**The NEUF-DIX Space Project - Non-Equilibrium Fluctuations during DIffusion in compleX liquids**", P. Baaske and H. Bataller and M. Braibanti and M. Carpineti and R. Cerbino and F. Croccolo and A. Donev and W. Kohler and J.~M. Ortiz de Zarate and Alberto Vailati,*Eur. Phys. J. E*, 39:119, 2016. - "
**Low Mach Number Fluctuating Hydrodynamics for Electrolytes**", J.-P. Peraud, A. Nonaka, A. Chaudhri, J. B. Bell, A. Donev and A. L. Garcia, Phys. Rev. F, 1(7):074103, 2016 [ArXiv:1607.05361]. - "
**Hydrodynamics of Suspensions of Passive and Active Rigid Particles: A Rigid Multiblob Approach**", F. Balboa Usabiaga, B. Kallemov, B. Delmotte, A. Pal Singh Bhalla, B. E. Griffith and A. Donev,*Communications in Applied Mathematics and Computational Science*, 11(2): 217--296, 2016 [ArXiv:1602.02170]. See our RigidMultiblobsWall github for PyCUDA codes (Section II), and RigidBodyIB github for immersed-boundary codes (Section III). - "
**Coupling a nano-particle with isothermal fluctuating hydrodynamics: Coarse-graining from microscopic to mesoscopic dynamics**", P. Español and A. Donev,*J. Chem. Phys.*, 143, 234104, 2015 [ArXiv:1509.01540]. - "
**Brownian Dynamics of Confined Rigid Bodies**", S. Delong, F. Balboa Usabiaga and A. Donev,*J. Chem. Phys*., 143, 144107, 2015 [Arxiv:1506.08868], see our RotationalDiffusion github for codes. - "
**An immersed boundary method for rigid bodies**", B. Kallemov and A. Pal Singh Bhalla and B. E. Griffith and A. Donev,*Communications in Applied Mathematics and Computational Science*, 11(1): 79-141, 2016 [ArXiv:1505.07865].**MobilityFunctions.c**is a stand-alone C code that contains the empirical fits of the pairwise marker mobility (documentation is in comments); more codes/documentation can be found on our RigidBodyIB github. The new 6pt immersed boundary kernel used in our work (and also a more recent 5pt version) is described in a recent note "**A Gaussian-Like Immersed Boundary Kernel with Improved Translational Invariance and Smoothness**" by Bao, Keiser, Kaye and Peskin [ArXiv:1505.07529], see our IBMethod github repo for codes. - "
**Fluctuating hydrodynamics of multispecies reactive mixtures**", A. K. Bhattacharjee, K. Balakrishnan, A. L. Garcia, J. B. Bell and A. Donev,*J. Chem. Phys.*, 142, 224107, 2015 [ArXiv:1503.07478]. - "
**Dynamic scaling for the growth of non-equilibrium fluctuations during thermophoretic diffusion in microgravity**", R. Cerbino, Y. Sun, A. Donev and A. Vailati,*Scientific Reports*, 5:14486, 2015 [ArXiv:1502.03693]. For the code used see our MixingIBAMR github repo. - "
**Low Mach Number Fluctuating Hydrodynamics of Multispecies Liquid Mixtures**", A. Donev and A. J. Nonaka and A. K. Bhattacharjee and A. L. Garcia and J. B. Bell,*Physics of Fluids*, 27(3):037103, 2015 [ArXiv:1412.6503]. Computer code available from our BoxLib github. Here is an animated Fig. 6 (QuickTime). - "
**Slowing-down of non-equilibrium concentration fluctuations in confinement**", C. Giraudet and H. Bataller and Y. Sun and A. Donev and J. M. O. de Zárate and F. Croccolo,*Europhysics Letters*(EPL), 111(6):60013, 2015 [ArXiv:1410.6524]. A longer and more detailed paper "**Confinement effect on the dynamics of non-equilibrium concentration fluctuations far from the onset of convection**" by the same authors has appeared as*Eur. Phys. J. E*, 39:120, 2016 . For the code used see our MixingIBAMR github repo. - "
**Finite element discretization of non-linear diffusion equations with thermal fluctuations**", J.A. de la Torre and P. Español and A. Donev,*J. Chem. Phys.*142, 094115, 2015 [ArXiv:1410:6340]

- "
**Low Mach Number Fluctuating Hydrodynamics of Binary Liquid Mixtures**", A. J. Nonaka and Y. Sun and J. B. Bell and A. Donev,*Communications in Applied Mathematics and Computational Science*(CAMCoS) 10-2, 163-204, 2015 [ArXiv:1410.2300]. - "
**Multiscale temporal integrators for fluctuating hydrodynamics**", S. Delong, Y. Sun, B.E. Griffith, E. Vanden-Eijnden and A. Donev,*Phys. Rev. E*, 90, 063312, 2014 [ArXiv:1410.0240]. For codes regarding diffusive mixing in binary fluid mixtures see our MixingIBAMR github repo. - "
**Modeling Multi-phase Flow using Fluctuating Hydrodynamics**", A. Chaudhri, J. B. Bell, A. L. Garcia and A. Donev,*Phys. Rev. E*, 90, 033014, 2014 [ArXiv:1407.6749].

- "Dynamic
Density Functional Theory with hydrodynamic interactions and
fluctuations", A. Donev and E. Vanden-Eijnden,
*J. Chem. Phys.*, 140, 234115, 2014 [ArXiv:1403.3959]. - "Metropolis Integration Schemes for Self-Adjoint Diffusions", N. Bou-Rabee and A. Donev and E. Vanden-Eijnden, SIAM J. Multiscale Modeling and Simulation, 12(2):781-831, 2014 [ArXiv:1309.5037]
- "Efficient
Variable-Coefficient Finite-Volume Stokes Solvers",
M. Cai and A. J. Nonaka and J. B. Bell and B. E. Griffith and A.
Donev,
*Commun. Comput. Phys.*(CiCP), 16(5):1263-1297, 2014 [ArXiv:1308.4605]. - "A
reversible mesoscopic model of diffusion in liquids: from giant
fluctuations to Fick's law", A. Donev, T. G. Fai, and E.
Vanden-Eijnden,
*J. Stat. Mech.*, P04004, 2014 [ArXiv:1312.1894]. A short summary is available as "Reversible Diffusion by Thermal Fluctuations", A. Donev, T. G. Fai, and E. Vanden-Eijnden, chapter 5 in the Proceedings from the Symposium in Honor of Dr Berni Alder's 90th birthday, 2017 [ArXiv:1306.3158]. - "Brownian
Dynamics without Green's Functions", S. Delong, F.
Balboa Usabiaga, R. Delgado-Buscalioni, B. E. Griffith and A.
Donev,
*J. Chem. Phys.*, 140, 134110, 2014 [ArXiv:1401.4198], see our FIB github repo for codes. - "Low
Mach Number Fluctuating Hydrodynamics of Diffusively Mixing
Fluids", A. Donev and A. J. Nonaka and Y. Sun and
T. G. Fai and A. L. Garcia and J. B. Bell,
*Communications in Applied Mathematics and Computational Science*(CAMCOS), 9-1:47-105, 2014 [ArXiv:1212.2644]. - "Fluctuating hydrodynamics of multispecies nonreactive mixtures" by K. Balakrishnan and A. L. Garcia and A. Donev and J. B. Bell, Phys. Rev. E 89:013017, 2014 [ArXiv:1310.0494].
- "A Minimally-Resolved Immersed Boundary Model for Reaction-Diffusion Problems", A. Pal Singh Bhalla, B. E. Griffith, N. A. Patankar and A. Donev, J. Chem. Phys., 139:214112, 2013 [ArXiv:1306.3159].
- "The Stokes-Einstein Relation at Moderate Schmidt Number", F. Balboa Usabiaga and X. Xie and R. Delgado-Buscalioni and A. Donev, J. Chem. Phys., 139:214113, 2013 [ArXiv:1309.7361]
- "Inertial
Coupling Method for particles in an incompressible fluctuating
fluid", F. Balboa Usabiaga and R.
Delgado-Buscalioni and B. E. Griffith and A. Donev,
*Computer Methods in Applied Mechanics and Engineering*, 269:139-172, 2014 [ArXiv:1212.6427], code available at https://code.google.com/p/fluam. - "Temporal Integrators for Fluctuating Hydrodynamics", S. Delong and B. E. Griffith and E. Vanden-Eijnden and A. Donev, Phys. Rev. E, 87(3):033302, 2013 [arXiv:1212.1033].
- "Staggered Schemes for Fluctuating Hydrodynamics", F. Balboa and J. Bell and R. Delgado-Buscalioni and A. Donev and T. G. Fai and B. Griffith and C. Peskin, SIAM J. Multiscale Modeling and Simulation, 10(4):1369-1408, 2012 [arXiv:1108.5188].
- "Diffusive Transport Enhanced by Thermal Velocity Fluctuations", A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, Phys. Rev. Lett., 106:204501, 2011 [ArXiv:1103.5532]. See longer paper below for further details.
- "Enhancement
of Diffusive Transport by Nonequilibrium Thermal Fluctuations",
A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, J.
Stat. Mech., P06014, 2011, [arXiv:1103.5244].

- "On the Accuracy of Finite-Volume Schemes for Fluctuating Hydrodynamics", by A. Donev, E. Vanden-Eijnden, A. L. Garcia, and J. B. Bell, Communications in Applied Mathematics and Computational Science, 5(2):149-197, 2010 [arXiv:0906.2425].
- "A hybrid particle-continuum method for hydrodynamics of complex fluids", by A. Donev and J. B. Bell and A. L. Garcia and B. J. Alder, SIAM J. Multiscale Modeling and Simulation 8(3):871-911, 2010 [arXiv:0910.3968].
- "A First-Passage Kinetic Monte Carlo Algorithm for Complex Diffusion-Reaction Systems", by A. Donev, V. V. Bulatov, T. Oppelstrup, G. H. Gilmer, B. Sadigh and M. H. Kalos, J. Comp. Phys., 229(9):3214-3236, 2010 [arXiv:0905.3576].
- "First-passage Kinetic Monte Carlo method", by T. Oppelstrup, V. V. Bulatov, A. Donev, M. H. Kalos, G. H. Gilmer and B. Sadigh, Phys. Rev. E, 80(6):066701, 2009 [arXiv:0905.3575].
- "Tethered DNA Dynamics in Shear Flow", by Y. Zhang, A. Donev, T. Weisgraber, B. J. Alder, M. D. Graham and J. J. de Pablo, J. Chem. Phys., 130:234902, 2009.
- "A Thermodynamically-Consistent Non-Ideal Stochastic Hard Sphere Fluid", by A. Donev and A. L. Garcia and B. J. Alder, J. Stat. Mech., P11008, 2009 [arXiv:0908.0510].
- "Stochastic
Hard-Sphere Dynamics for Hydrodynamics of Non-Ideal Fluids",
by A. Donev, A. L. Garcia and B. J. Alder, Phys.
Rev. Lett., 101:075902, 2008 [arXiv:0803.0359].

- "Stochastic Event-Driven Molecular Dynamics", by A. Donev, A. L. Garcia and B. J. Alder, J. Comp. Phys., 227(4):2644-2665, 2008, [arXiv:0708.0251].
- "Asynchronous Event-Driven Particle Algorithms", by A. Donev, SIMULATION: Transactions of the Society for Modeling and Simulation International, 85(4):229-242, 2009.
- "Configurational Entropy of Binary Hard-Disk Glasses: Nonexistence of an Ideal Glass Transition", by A. Donev, F. H. Stillinger and S. Torquato, J. Chem. Phys., 127:124509, 2007.
- "Underconstrained Jammed Packings of Hard Ellipsoids", by A. Donev, R. Connelly, F. H. Stillinger and S. Torquato, Phys. Rev. E, 75:051304, 2007 [cond-mat/0608334].
- "Calculating the Free Energy of Nearly Jammed Hard-Particle Packings Using Molecular Dynamics", by A. Donev, F. H. Stillinger, and S. Torquato, J. Comp. Phys., 225:509–527, 2007.
- "Do Binary Hard Disks Exhibit an Ideal Glass Transition?", by A. Donev, F. H. Stillinger, and S. Torquato, Phys. Rev. Lett., 96:225502, 2006, [cond-mat/0603183].
- "Packing Hyperspheres in High-Dimensional Euclidean Spaces", by M. Skoge, A. Donev, F. H. Stillinger and S. Torquato, Phys. Rev. E, 74:041127, 2006 [ibid 75:029901, 2007], [cond-mat/0608362].
- "Some Observations on the Random Packing of Hard Ellipsoids", by P. M. Chaikin, A. Donev, W. Man, F. H. Stillinger, and S. Torquato, Ind. Eng. Chem. Res., 45(21):6960-6965, 2006.
- "Tetratic Order in the Phase Behavior of a Hard-Rectangle System", by A. Donev, J. Burton, F. H. Stillinger, and S. Torquato, Phys. Rev. B, Vol. 73:054109, 2006, [cond-mat/0508550].
- "Unexpected Density Fluctuations in Jammed Disordered Sphere Packings", by A. Donev, F. H. Stillinger, and S. Torquato, Phys. Rev. Lett., 95:090604, 2005, [cond-mat/0506406].
- "Manufacturable extremal low-dielectric, high-stiffness porous materials", S. Torquato, A. Donev, A. G. Evans, and C. J. Brinker, J. Appl. Phys., 97:124103, 2005.
- "Experiments on Random Packings of Ellipsoids", W. Man, A. Donev , F. H. Stillinger, M. T. Sullivan, W. B. Russel, D. Heeger , S. Inati, S. Torquato and P. M. Chaikin, Phys. Rev. Lett., 94:198001, 2005.
- "Pair Correlation Function Characteristics of Nearly Jammed Disordered and Ordered Hard-Sphere Packings", by A. Donev, F. H. Stillinger, and S. Torquato, Phys. Rev. E, 71:011105, 2005, [cond-mat/0408550].
- "Neighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids", by A. Donev, F. H. Stillinger, and S. Torquato, J. Comp. Phys, 202(2):737-764 (part I) and 202(2):765-793 (part II), 2005, [physics/0110034].
- "
**Comment on "Jamming at zero temperature and zero applied stress: The epitome of disorder"**, by A. Donev, S. Torquato, F. H. Stillinger, and R. Connelly, Phys. Rev. E, 70:043301, 2004. - "
**Unusually Dense Crystal Packings of Ellipsoids**", by A. Donev, F. H. Stillinger, P. M. Chaikin and S. Torquato, Phys. Rev. Lett., 92:255506, 2004, [cond-mat/0110034]. - "
**Improving the Density of Jammed Disordered Packings using Ellipsoids**" by A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato and P. M. Chaikin, Science, 303:990-993, 2004. - "
**Breakdown of Elasticity Theory for Jammed Hard-Particle Packings: Conical Nonlinear Constitutive Theory**", by S.Torquato, A. Donev, and F. H. Stillinger, Int. J. Solids Structures, 40(25):7143-7153, 2003. - "
**Energy-Efficient Actuation in Infinite Lattice Structures**", by A. Donev and S. Torquato, J. Mech. Phys. Solids, 51(8):1459-1475, 2003. Related animations can be found in the page devoted to**Design of Adaptive Periodic Trusses** - "
**Jamming in Hard Sphere and Disk Packings"**, by A. Donev, S. Torquato, F. H. Stillinger, and R. Connelly, J. Appl. Phys., 95(3):989, 2004. - "
**A Linear Programming Algorithm to Test for Jamming in Hard-Sphere Packings**", by A. Donev, S. Torquato, F. H. Stillinger, and R. Connelly, J. Comp. Phys., 197(1):139-166, 2004. - "
**Minimal Surfaces and Multifunctionality**", by S.Torquato and A. Donev, Proceedings of the Royal Society of London: Mathematical, Physical and Engineering Sciences, 460(2047):1849 - 1856, 2004. - "
**Optimal design of manufacturable three-dimensional composites with multifunctional characteristics**", by S.Torquato, S. Hyun and A. Donev, J. Appl. Phys., 94(9):5748-5755, 2003. - "
**Multifunctional Optimal Composite Microstructures: Simultaneous Transport of Heat and Electricity**", by S.Torquato, S. Hyun and A. Donev, Phys. Rev. Lett., 89(26):266601, 2002. - "
**Random manifolds in non-linear resistor networks: applications to varistors and superconductors**", by A. Donev, C. E. Musolff and P. M. Duxbury, J. Phys. A: Math. Gen., 35:L327-L333, 2002 [cond-mat/0110034]. - "
**Generalized von Smoluchowski model of reaction rates, with reacting particles and a mobile trap**", by A. Donev, J. Rockwell and D. ben-Avraham, J. Stat. Phys., 95(1-2):97-112, 1999 [cond-mat/9810305].

## Presentations

As an academic I frequently give presentations at various scientific meetings, conferences, symposia, etc. Here are PDFs of selected presentations produced with the

`handout`

option of the
Beamer latex class. Some of the latest presentations can be found
under What's New?.Note: The movies are typically not included in the PDF files, but some are available below.

- "
**Fast Electrostatics and (Brownian) Hydrodynamics in Doubly-Periodic Geometries**," presentation at SIAM CSE19 virtual conference, March 2021. - "
**Numerical methods for inextensible slender fibers in Stokes flow**," seminar given at U Colorado Boulder and MIT, October 2020. - "
**Active dynamics in dense suspensions of microrollers**", online 13th Northeast Complex Fluids & Soft Matter, June 19th 2020. See this MP4 movie (QuickTime) illustrating the two-layer structure of driven uniform suspension of microrollers, and this movie predicting the formation of critters (QuickTime). - "
**Fluctuating Hydrodynamics and Debye-Huckel-Onsager Theory for Electrolytes**", talk given at Celebrating 50 years of CECAM, Lausanne, Switzerland September 2019. - "
**Fluctuating hydrodynamics and coarse-graining**" --- mini course given at the First Berlin - Leipzig Workshop on Fluctuating Hydrodynamics, Berlin, August 2019. - "
**Brownian HydroDynamics of Colloidal Suspensions**", lecture given at the Summer School on Particulate Suspensions in MPI Magdeburg, August 27th 2019. - "
**Large Scale Brownian Dynamics of Confined Suspensions of Rigid Particles**", talk at the Minisymposium on Complex Fluids at Small Scales, ICIAM, Valencia, Spain, July 17th 2019. Here are the movies for this presentation. - "
**Dynamics of Colloids Above a Bottom Wall Driven by Active Torques and Forces**" talk at SIAM CSE19 and math colloquium at Drexel University, April 2019. - "
**Fluctuating hydrodynamics of reactive electrolyte mixtures**", talk given at the 8th International Workshop on Nonequilibrium Thermodynamics, Netherlands, July 2018. - "
**Brownian Dynamics of Confined Colloidal Suspensions**", widely applied math seminar, Harvard University, October 2017. - "
**Brownian dynamics of colloids in quasi two-dimensional confinement**", seminar given at Univ. of Arizona October 2018 (and a preliminary version earlier at ETH Polymer Physics July 2017). - "
**A fluctuating boundary integral method for Brownian suspensions**", Simons Foundation Biophysical Modeling seminar, May 16th 2017. - "
**Hydrodynamics of Suspensions of Passive and Active Rigid Particles**", Chemical & Biological Engineering Seminar, Colorado School of Mines, September 16th 2016. - "
**Coupling a nano-particle with fluctuating hydrodynamics**", talk at workshop on Advances in theory and simulation of non-equilibrium systems, NESC16, Sheffield, England, July 2016. - "
**Fast Reactive Brownian Dynamics**", invited talk at workshop on Spatially Distributed Stochastic Dynamical Systems in Biology, Newton Institute, Cambridge, June 2016. - "
**Computer Simulations of Giant Fluctuations**", talk at IMT12, Madrid, May 2016. - "
**Rigid Multiblob Models of Suspensions of Rigid Particles of Complex Shapes in Confinement**", talk in minisymposium on Numerical Methods for Low Reynolds Number Suspensions of Passive and Active Particles, SIAM MS16, Philadelphia, PA, May 2016. - "
**Rigid Multiblob Methods for Stokesian Suspensions of Rigid Particles**" invited talk at CECAM workshop on Hydrodynamic Fluctuations in Soft-Matter Simulations, Monash University Prato Centre, February 11th 2016 - "
**Rigid Multiblob Methods for Confined Brownian Rigid Particles**", Soft Matter Seminar, Tufts University, Nov 4th 2015 - "The Truth about diffusion (in liquids)", seminar given at UMD College Park, October 28th 2015.
- "
**Fluctuating Hydrodynamics of Reactive Fluid Mixtures**", invited talk at the workshop on Molecular and Chemical Kinetics (MOLKIN'15), Berlin, Germany, Sept 2015. - "
**Diffusion in liquids: DDFT with hydrodynamic interactions and (giant) fluctuations**", presentation given at the 7th International Workshop on Nonequilibrium Thermodynamics, Hilvarenbeek, The Netherlands, July 2015. - "
**Fluctuating hydrodynamics of complex fluid flows**", review given at the CECAM Workshop on Molecular Dynamics meets Fluctuating Hydrodynamics, Miraflores, Spain, May 11th 2015. - "
**Brownian Suspensions of Rigid Particles**", minisymposium on Hydrodynamics at Small Scales, SIAM CSE15, Salt Lake City, Utah, March 18th 2015. Also see the presentation on "**Temporal integrators for Langevin equations arising in Fluctuating Hydrodynamics**" given by my student Steven Delong. - "
**An Immersed Boundary Method for Suspensions of Rigid Bodies**", NA Courant Seminar, Dec 5th 2014. - "
**A Fluctuating Immersed Boundary Method for Brownian Suspensions of Rigid Particles**", presentation given at the APS DFD meeting, San Francisco, Nov 23rd 2014. - "
**Fluctuating Hydrodynamics of Suspensions of Rigid Particles**", invited talk at the workshop on Multiscale simulation methods for soft matter systems, Oct 6th 2014, Schloss Waldthausen, Mainz, Germany. - "
**Brownian Dynamics without Green's Functions**", minisymposium on Particle Methods for Micro- and Nano-flows at ECFD VI, July 21st 2014, Barcelona, Spain. - "
**Computational Modeling of Reaction-Diffusion Systems: From particle to hydrodynamic simulations**", CEA Saclay seminar, July 18th, 2014. - "
**Multiscale models of diffusive mixing: from giant fluctuations to Fick's law**", invited talk at the Multiscale Computational Methods in Materials Modelling Meeting (MCM3), June 18th 2014, ICMS, Edinburgh, UK. - "
**Computational modeling of diffusive mixing: from giant fluctuations to Fick's law**", plenary talk at the 11th International Meeting on Thermodiffusion (IMT11), June 3rd 2014. - "
**A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law**", polymer physics seminar at ETH Zurich, May 22nd 2014. - "The Truth about diffusion (in liquids)", Applied Math Seminar at UC Berkeley February 2014.
- "The Truth about diffusion (in liquids)", invited contribution to minisymposium on Multiscale modeling at SciCADE 2013, Valladolid, Spain, September 2013, and Applied Math Seminar at Courant October 2013.
- "Minimally-Resolved Simulations of Suspensions of Active Brownian Particles", presentation given at the AFOSR Computational Math Program Review BRICC, Arlington VA, July 2013.
- "Coupling an Incompressible Fluctuating Fluid with Suspended Structures", presentation given at the SIAM Conference on Mathematical Aspects of Materials Science, session on Multiscale Computation of Fluctuating Hydrodynamics and Microscale Mechanics, Philadelphia June 2013.
- "Coupling an Incompressible Fluctuating Fluid with Suspended Structures", presentation given at the Mechanical Engineering Department at Northwestern University, May 2013.
- "Coupling an Incompressible Fluctuating Fluid with Suspended Structures", presentation given at the Scientific Computing Seminar at Brown University, March 2013.
- "Low Mach Number Fluctuating Hydrodynamics of Diffusively Mixing Fluids", talk given at the minisymposium on Hydrodynamics of Complex Fluids at the Micro and Nano-Scales, SIAM CSE13 Conference, Boston, February 2013.
- "Coupling an Incompressible Fluctuating Fluid with Suspended Structures", invited presentation given at the workshop on Fluid-Structure Interactions in Soft-Matter Systems, Monash University Prato Center, Italy, November 2012.
- "Computational Fluctuating Hydrodynamics Modeling of Giant Fluctuations", presentation given at the Department of Physics at Università degli Studi di Milano, Italy, November 2012.
- "Coupling a Fluctuating Fluid with Suspended Particles", presentation at UPenn and NJIT applied mathematics seminar, October 2012.
- "Multiscale Problems in Fluctuating Hydrodynamics", talk at the Workshop on Modelling the Dynamics of Complex Molecular Systems, Lorentz Center, Leiden, Netherlands, August 2012. Some movies can be found here.
- "Stochastic Simulation of Complex Fluid Flows", talk at the Workshop on Multiscale Modeling in Soft Condensed Matter held at the KITP institute, UCSB, April 2012. Some movies can be found below.
- "Numerical Methods for Fluctuating Hydrodynamics", talk at Center for Computational and Integrative Biology, Rutgers-Camden, November 2011.
- "Coupling a Fluctuating Fluid with Suspended Particles", presentation at the CECAM workshop "Multiscale Modeling of Simple and Complex Liquid Flow Using Particle-Continuum Hybrids", Zaragoza, Spain, October 2011.
- "Diffusive Transport Enhanced by Thermal Velocity Fluctuations", seminar at U.N.E.D., Madrid, Spain, October 2011.
- "Numerical Methods for Fluctuating Hydrodynamics", talk at DSFD 2011, Fargo, ND, August 2011.
- "Diffusive Transport Enhanced by Thermal Velocity Fluctuations", minisymposium on Fluctuating Hydrodynamics, ICIAM 2011, Vancouver, Canada, July 2011.
- "Coupling a Fluctuating Fluid with Suspended Structures", minisymposium talk at ICIAM 2011, Vancouver, Canada, July 2011.
- "A Hybrid Particle-Continuum Method Coupling a Fluctuating Fluid with Suspended Structures", plenary talk at the AMS von Neumann Symposium, Snowbird, Utah, July 6th 2011.
- "Diffusive Transport by Thermal Velocity Fluctuations", Rochester University mathematical physics colloquium, April 15th 2011.
- "Finite-Volume Schemes for Fluctuating Hydrodynamics", Courant Numerical Analysis Seminar, March 2011
- "A Hybrid Particle-Continuum Approach to Hydrodynamics at Small Scales", XXVI Inter University Seminar on Mathematical Sciences Research (SIDIM), February 25, 2011, University of Puerto Rico at Humacao.
- "Enhancement of Diffusive Mass Transfer by Thermal Fluctuations", Courant Materials Working Group, February 14th 2011.
- "Coarse-grained particle, continuum and hybrid models for complex fluids", at the Workshop for Multiscale Simulation of Heterogeneous Materials and Coupling of Thermodynamic Models, Leuven, Belgium, January 13th 2011.
- "Coupling a Fluctuating Fluid with Suspended Structures", Part I. "Particle-Continuum Hybrid" (with movies), and "Part II: Inertial Stochastic Immersed Boundary Method", Courant BioMathematics Seminar, December 2010.
- "An Event-Driven Kinetic Monte Carlo Algorithm for Reaction-Diffusion Systems", Courant Graduate Student Seminar, December 2010.
- "Numerical Methods for Fluctuating Hydrodynamics", Courant Applied Math Seminar, September 2010. This has the movies embedded in it as flash animations so it is larger (~20MB)
- "Finite-Volume Schemes for Fluctuating Hydrodynamics", SIAM MS10 Conference, May 2010
- "A hybrid particle-continuum method for hydrodynamics of complex fluids", UCSB Applied Math Seminar, January 2010
- "Fluctuating Hydrodynamics of Non-Ideal Fluids Via Stochastic Hard-Sphere Molecular Dynamics (SHSD)", DSMC09 Conference, September 2009
- "Asynchronous Event-Driven Particle Algorithms in Computational Materials Science", AMS Meeting, January 2009
- "Jammed Packings of Hard Particles", thesis defense presentation, June 2006

### MOVIES

Here are some selected animations from my presentations. I often use two dimensions to make it easier to visualize. Newer animations are in the QuickTime format (extension mov). To play MNG animations (file extension mng), I use mngplay under Linux and IrfanView for Windows.

- An MP4 movie (QuickTime) illustrating the two-layer structure of driven uniform suspension of microrollers.
- An animation produced by Northwestern graduate student Brennan Sprinkle of an active uniform suspension of microrollers, either 256 spheres with 42 blobs each (gif), or 1024 spheres with 12 blobs each (gif), see Fig. 6 in the paper "Large Scale Brownian Dynamics of Confined Suspensions of Rigid Particles". And here is an animation of an equilibrium suspension of boomerangs sedimented above a bottom wall, see Fig. 2 in the paper.
- Supplementary Material Movies for the paper "Brownian Dynamics of Confined Suspensions of Active Microrollers", showing the formation of a nonlocal shock front and a fingering instability in a suspension of microrollers above a bottom wall.
- Animation produced by collaborator Changho Kim showing the propagation of a spherical chemical wave (gif) leaving behind a Turing-like pattern, without thermal fluctuations (left) and with fluctuations (right), see Fig. 8 in the paper "Stochastic Simulation of Reaction-Diffusion Systems: A Fluctuating-Hydrodynamics Approach", Here is animation of the formation of a Turing pattern in the BPM model with FHD or RDME, as studied in section V.B in the paper
- Animation produced by collaborator Andy
Nonaka showing the development
of an instability during diffusive mixing of a solution of salt
on top of a solution of sugar (QuickTime),
comparing the cases when thermal fluctuations are included (and
trigger the instability) versus when they are only included
initially until the instability is triggered.

- Development of giant fluctuations (GIF) during diffusive mixing in two dimensions without bare diffusion (reversible, top) and with bare diffusion (irreversible, bottom).
- "Diffusive" evolution of a line of tracers simulated using fluctuating hydrodynamics (animated GIF) without bare-diffusion, and hard-disk molecular dynamics (GIF).
- Giant fluctuations observed using the Inertial Incompressible Coupling method (left) and a stochastic advection-diffusion approach (right). A fluctuation-aware version of the immersed boundary code IBAMR was used to produce these animations.
- Giant fluctuations during diffusive mixing of two hard-disk fluids, simulated with event-driven molecular dynamics (left) and also with low Mach number fluctuating hydrodynamics. In three dimensions fluctuating hydrodynamics predicts much smaller but still giant fluctuations, as illustrated by the mixing of two hard-sphere fluids.
- Giant fluctuations during diffusive mixing of two miscible fluids in two dimensions, with no gravity (top), weak gravity (middle), and strong gravity (bottom). A similar "fractal" interface is seen for a wide range of Schmidt numbers, but there are also visible differences and the rescaling is not perfect.
- Rayleigh-Taylor
instability (unstable mixing of two ideal gases under
gravity) driven entirely by thermal fluctuations, that is,
starting with no initial
interface perturbation, as calculated using a fluctuating
hydrodynamic compressible solver (also as QuickTime,
Flash).

- Calculation of plug flow past a disk using our particle-continuum hybrid method, which combines a stochastic particle fluid with a fluctuating hydrodynamics continuum (also as QuickTime).
- Simulation of the Brownian motion of disk through a fluid using the particle-continuum hybrid code (also as QuickTime, Flash).
- Equilibration of an adiabatic piston toward thermal equilibrium, as simulated using the particle-continuum hybrid code (also as QuickTime, Flash).
- Brownian motion of a hard-disk polymer chain through a stationary deterministic (hard-sphere) molecular dynamics fluid (also as QuickTime, Flash).
- Brownian motion of a hard-disk polymer chain through a sheared stochastic (DSMC) fluid (also as QuickTime, Flash).