Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics. - Aleksandar Donev; Frank H. Stillinger; Salvatore Torquato (J. Comput. Phys., 2007)

Stochastic Event-Driven Molecular Dynamics. - Aleksandar Donev; Alejandro L. Garcia; Berni J. Alder (J. Comput. Phys., 2008)

Asynchronous Event-Driven Particle Algorithms. - Aleksandar Donev (Simul., 2009)

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion-reaction systems. - Aleksandar Donev; Vasily V. Bulatov; Tomas Oppelstrup; George H. Gilmer; Babak Sadigh; Malvin H. Kalos (J. Comput. Phys., 2010)

A Hybrid Particle-Continuum Method for Hydrodynamics of Complex Fluids. - Aleksandar Donev; John B. Bell; Alejandro L. Garcia; Berni J. Alder (Multiscale Model. Simul., 2010)

Staggered Schemes for Fluctuating Hydrodynamics. - Florencio Balboa Usabiaga; John B. Bell; Rafael Delgado-Buscalioni; Aleksandar Donev; Thomas G. Fai; Boyce E. Griffith; Charles S. Peskin (Multiscale Model. Simul., 2012)

Metropolis Integration Schemes for Self-Adjoint Diffusions. - Nawaf Bou-Rabee; Aleksandar Donev; Eric Vanden-Eijnden (Multiscale Model. Simul., 2014)

An Immersed Boundary method with divergence-free velocity interpolation and force spreading. - Yuanxun Bao; Aleksandar Donev; Boyce E. Griffith; David McQueen; Charles S. Peskin (J. Comput. Phys., 2017)

A fluctuating boundary integral method for Brownian suspensions. - Yuanxun Bao; Manas Rachh; Eric E. Keaveny; Leslie Greengard; Aleksandar Donev (J. Comput. Phys., 2018)

An integral-based spectral method for inextensible slender fibers in Stokes flow. - Ondrej Maxian; Alex Mogilner; Aleksandar Donev (CoRR, 2020)

A fast spectral method for electrostatics in doubly-periodic slit channels. - Ondrej Maxian; Raúl P. Peláez; Leslie Greengard; Aleksandar Donev (CoRR, 2021)

Simulations of dynamically cross-linked actin networks: Morphology, rheology, and hydrodynamic interactions. - Ondrej Maxian; Raúl P. Peláez; Alex Mogilner; Aleksandar Donev (PLoS Comput. Biol., 2021)

The hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow. - Ondrej Maxian; Brennan Sprinkle; Charles S. Peskin; Aleksandar Donev (CoRR, 2022)

Bending fluctuations in semiflexible, inextensible, slender filaments in Stokes flow: towards a spectral discretization. - Ondrej Maxian; Brennan Sprinkle; Aleksandar Donev (CoRR, 2023)

A simulation platform for slender, semiflexible, and inextensible fibers with Brownian hydrodynamics and steric repulsion. - Ondrej Maxian; Aleksandar Donev (CoRR, 2024)

Universally Adaptable Multiscale Molecular Dynamics (UAMMD). A native-GPU software ecosystem for complex fluids, soft matter, and beyond. - Raúl P. Peláez; Pablo Ibáñez-Freire; Pablo Palacios-Alonso; Aleksandar Donev; Rafael Delgado-Buscalioni (Comput. Phys. Commun., 2025)