## PUBLICATIONS

A description of the different research subjects and publications can be found under the Research heading, and slides from some presentations I have given are 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:

- "Dynamic Density Functional Theory with hydrodynamic interactions and fluctuations", A. Donev and E. Vanden-Eijnden, to appear in J. Chem. Phys., 2014 [ArXiv:1403.3959].
- "Metropolis Integration
Schemes for Self-Adjoint Diffusions", N.
Bou-Rabee and A. Donev and E. Vanden-Eijnden, to appear in
SIAM MMS, 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, to appear in CiCP, 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, 2013 [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].
- "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 Explicit 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., 225:509â€“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.

- "
**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 UniversitÃ 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.

- 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).