Stefan Hellander
Researcher
Department of Information Technology
Division of Scientific Computing
Uppsala University
ITC Room 2348
Publications

S. Hellander and L. Petzold.  Reaction rates for reaction-diffusion kinetics on unstructured meshes.  J. Chem. Phys., 146(6):064101, 2017.

M. Golkaram, J. Jang, S. Hellander, L. Petzold, and K. Kosik.  The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation.  Accepted for publication in Nature Scientific Reports, 2017.

Stefan Hellander and Linda Petzold.  Reaction rates for a generalized reaction-diffusion master equation.  Phys. Rev. E, 93(1):013307, 2016.

M. Golkaram, S. Hellander, B. Drawert, and L. Petzold.  Macromolecular crowding regulates the gene expression profile by limiting diffusion.  PLOS Comp. Biol., 12(11), 2016.

B. Drawert, A. Hellander, B. Bales, D. Banerjee, G. Bellesia, B. J. Daigle, Jr., G. Douglas, M. Gu, A.d Gupta, S. Hellander, C. Horuk, D. Nath, A. Takkar, S. Wu, P. Lötstedt, C. Krintz, and L. R. Petzold.  Stochastic Simulation Service: Bridging the gap between the computational expert and the biologist.  PLOS Comp. Biol., 12(12), 2016.

B. Drawert, S. Hellander, and M. Trogdon.  A Framework for Discrete Stochastic Simulation on 3D Moving Boundary Domains.  J. Chem. Phys., 145(18):184113, 2016.

M. B. Flegg, S. Hellander, and R. Erban.  Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations.  J. Comput. Phys., 289:1-17, 2015.

S. Hellander, A. Hellander, and L. Petzold.  Reaction rates for mesoscopic reaction-diffusion kinetics.  Phys. Rev. E, 91(2):023312, 2015.

S. Wang, J. Elf, S. Hellander, and P. Lötstedt.  Stochastic reaction-diffusion processes with embedded lower dimensional structures .  Bull. Math. Biol., 2013.

H. Bani-Hashemian, S. Hellander, and P. Lötstedt.  Efficient Sampling in Event-Driven Algorithms for Reaction-Diffusion Processes.  Commun. Comput. Phys., 13(4):958-984, 2013.

S. Hellander.  Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures.  J. Chem. Phys., 130(1):014103, 2013.

S. Hellander.  Stochastic simulation of reaction-diffusion processes.  PhD Thesis, Acta Universitatis Upsaliensis, 2013.

A. Hellander, S. Hellander, and P. Lötstedt.  Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions.  Multiscale Model. Simul., 10(2):585-611, 2012.

S. Hellander, A. Hellander, and L. Petzold.  Reaction-Diffusion Master Equation in the Microscopic Limit.  Phys. Rev. E., 85(4):042901, 2012.

S. Hellander and P. Lötstedt.  Flexible Single Molecule Simulation of Reaction-Diffusion Processes.  J. Comput. Phys., 230(10):3948-3965, 2011.