R. Jiang, B. Jacob, M. Geiger, S. Matthew, B. Rumsey, P. Singh, F. Wrede, T-M. Yi, B. Drawert, A. Hellander, L. Petzold (2021) Epidemiological modeling in StochSS Live!, Bioinformatics, 2021;, btab061.
doi: 10.1093/bioinformatics/btab061 | PMID: 33512399


S. Hellander and A. Hellander (2020) Hierarchical Reaction-Diffusion Master Equation, J. Chem. Phys, 152, 034104.
doi: 10.1063/1.5095075 | PMCID: PMC6964990


Drawert, B., Jacob, B., Li, Z., Yi, T-M, & Petzold, L. (2019). A Hybrid Smoothed Dissipative Particle Dynamics (SDPD) Spatial Stochastic Simulation Algorithm (sSSA) for Advection-Diffusion-Reaction Problems. J. Comp. Phys. 378, pp. 1-17.
doi: 10.1016/ | PMCID: PMC6481948

Jang, J., Han, D., Golkaram, M., Audouard, M., Liu, G., Bridges, D., Hellander, S., Chialastri, A., Dey, S. S., Petzold, L. R., & Kosik, K. S. (2019). Control over single-cell distribution of G1 lengths by WNT governs pluripotency. PLoS Biol 17(9): e3000453.
doi: 10.1371/journal.pbio.3000453 | PMCID: PMC6782112

Alber, M., Tepole, A. B., Cannon, W. R., De, S., Dura-Bernal, S., Garikipati, K., Karniadakis, G., Lytton, W. W., Perdikaris, P., Petzold, L., & Kuhl, E. (2019). Integrating machine learning and multiscale modeling–perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences. npj Digital Medicine, 2:115
doi: 10.1038/s41746-019-0193-y | PMCID: PMC6877584

Drawert, B., Jacob, B., Li, Z., Yi, T-M, & Petzold, L. (2019). Validation Data for a Hybrid Smoothed Dissipative Particle Dynamics (SDPD) Spatial Stochastic Simulation Algorithm (sSSA) Method. Data in Brief, 22, pp. 11-15.
doi: 10.1016/j.dib.2018.11.103 | PMCID: PMC6293021


Trogdon, M., Drawert, B., Gomez, C., Banavar, S. P., Yi, T-M., Campas, O., & Petzold, L. R. (2018). The Effect of Cell Geometry on Polarization in Budding Yeast. PLoS Comput. Biol. 14(6):e1006241
doi: 10.1371/journal.pcbi.1006241 | PMCID: PMC6013239


Hellander, S., Hellander, A., & Petzold, L. (2017). Mesoscopic-microscopic Spatial Stochastic Simulation with Automatic System Partitioning. J. Chem. Phys. 147, 234101.
doi: 10.1063/1.5002773 | PMCID: PMC5732015

Drawert, B., Thakore, N., Mitchell, B., Pioro, E., Ravits, J., & Petzold, L. R. (2017). Modeling the Neuroanatomic Propagation of ALS in the Spinal Cord. AIP Conference Proceedings 1863, 500002
doi: 10.1063/1.4992656

Hellander, S. & Petzold, L. (2017). Reaction Rates for Reaction-Diffusion Kinetics on Unstructured Meshes. J. Chem. Phys. 146, 064101
doi: 10.1063/1.4975167 | PMCID: PMC5303170

Golkaram, M., Jang, J., Hellander, S., Kosik, K. S., & Petzold, L. R. (2017). The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation. Scientific Reports, 7(1), 13307
doi:10.1038/s41598-017-13731-3 | PMCID: PMC5645312

Drawert, B., Griesemer, M., Petzold, L. R., Briggs, C. J. (2017). Using Stochastic Epidemiological Models to Evaluate Conservation Strategies for Endangered Amphibians. J. R. Soc. Interface 14: 20170480
Journal Version | doi: 10.1098/rsif.2017.0480 | PMCID: PMC5582134


Drawert, B., Hellander, S., Trogdon, M., Yi, T-M, & Petzold, L. (2016). A Framework for Discrete Stochastic Simulation on 3D Moving Boundary Domains. J. Chem. Phys., 145, 184113.
doi:10.1063/1.4967338 | PMCID: PMC5116030

Golkaram, M., Hellander, S., Drawert, B., & Petzold, L. R. (2016). Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. PLoS Comput. Biol. 12(11):e1005122
doi:10.1371/journal.pcbi.1005122 | PMCID: PMC5125560

Drawert, B., Trogdon, M., Toor, S., Petzold, L., & Hellander, A. (2016). MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. SIAM J. Sci. Comput., 38(3), C179-C202
doi:10.1137/15M1014784 | PMCID: PMC5302863

Hellander, S., & Petzold, L. (2016). Reaction Rates for a Generalized Reaction-Diffusion Master Equation. Phys. Rev. E 93, 013307.
doi: 10.1103/PhysRevE.93.013307 | PMCID: PMC4854577

Drawert, B., Hellander, A., Bales, B., Banerjee, D., Bellesia, G., Daigle, Jr., B. J., Douglas, G., Gu, M., Gupta, A., Hellander, S., Horuk, C., Nath, D., Takkar, A., Wu, S., Lötstedt, P., Krintz, C., & Petzold, L. R. (2016). Stochastic Simulation Service: Bridging the Gap Between the Compuational Expert and the Biologist. PLoS Comput. Biol. 12(12): e1005220
doi:10.1371/journal.pcbi.1005220 | PMCID: PMC5145134


E. Blanc, S. Engblom, A. Hellander, and P. Lötstedt.Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime.arXiv:1503.07009 (to appear in Multiscale Model. Simul.), 2015.

L. Meinecke, S. Engblom, A. Hellander, and P. Lötstedt.Analysis and design of jump coefficients in discrete stochastic diffusion models.arXiv:1503.01653v1 (to appear in J. Sci. Comp.), 2015.

P. Lötstedt and L. Meinecke.Simulation of stochastic diffusion via first exit times.J. Comput. Phys.300:862–886, 2015.

M. Lawson, L. Petzold, and A. Hellander.Accuracy of the Michaelis- Menten approximation when analyzing effects of molecular noise.J. Roy. Soc. Interface12(106):20150054, 2015.

S. Hellander, A. Hellander, and L. Petzold.Reaction rates for mesoscopic reaction-diffusion kinetics.Phys. Rev. E91(2):9930, 2015.

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.

J. H. Abel, B. Drawert, A. Hellander, and L. R. Petzold.GillesPy: A Python package for stochastic model building and simulation.FOSBE 2015 Conference Proceedings, 2015.

S. Wu, J. Fu, and L. R. Petzold.Adaptive deployment of model reductions for tau-leaping simulation.J. Chem. Phys.142(20):204108, 2015.

H. Jayathilaka, R. Wolski, and C. Krintz.Service-level agreement durability for web service response time.IEEE Conference on Cloud Computing Technology and Science (CloudCom’15), 2015.

C. Krintz, R. Wolski, J. E. Pinsker, S. Dimopoulos, J. Brevik, and E. Dassau.On the use of consumer-grade activity monitoring devices to improve predictions of glycemic variability.EAI International Conference on Smart Wearable Devices and IoT for Health and Wellbeing Applications, 2015.

H. Jayathilaka, R. Wolski, and C. Krint.Response time service level agreements for cloud-hosted web applications.ACM Symposium on Cloud Computing (SoCC’15), 2015.

A. Pucher, R. Wolski, and C. Krintz.Providing lifetime service-level agreements for cloud spot instances.International Conference on Grid and Cloud Computing and Applications (GCA’15), 2015.

S. Dimopoulos, C. Krintz, and R. Wolski.Supercontra: Cross-language, cross-runtime contracts as a service.IC2E Workshop on the Future of PaaS, 2015.

A. Pucher, C. Krintz, and R. Wolski.Using trustworthy simulation to engineer cloud schedulers.IEEE International Conference on Cloud Engineering (IC2E), 2015.


A. Hellander, M. Lawson, B. Drawert, and L. Petzold.Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting.J. Comput. Phys.266:89–100, 2014.

S. Wang, S. Hellander, J. Elf, and P. Lötstedt.Stochastic reaction-diffusion processes with embedded lower dimensional structures.Bull. Math. Biol.76(4):819–853, 2014.

M. Sturrock, A. Hellander, S. Aldakheel, L. R. Petzold, and M. A. J. Chaplain.The role of dimerisation and nuclear transport in the HES1 gene regulatory network.Bull. Math. Biol.76(4):766–798, 2014.

J. Fu, S. Wu, H. Li, and L. R. Petzold.The time dependent propensity function for acceleration of spatial stochastic simulation of reaction-diffusion systems.J. Comput. Phys.274:520–549, 2014.

D. Gillespie, L. R. Petzold, and E. Seitaridou.Validity conditions for stochastic chemical kinetics in diffusion-limited systems.J. Chem. Phys.140(5):22601, 2014.

G. Douglas, B. Drawert, C. Krintz, and R. Wolski.Cloudtracker: Using execution provenance to optimize the cost of cloud use.International Conference on Economics of Grids, Clouds, Systems, and Services, 2014.

C. Horuk, G. Douglas, A. Gupta, C. Krintz, B. Bales, G. Bellesia, B. Drawert, R. Wolski, L. Petzold, and A. Hellander.Automatic and portable cloud deployment for scientific simulations.IEEE/ACM International Conference on High Performance Computing and Simulation, 2014.

H. Jayathilaka, C. Krintz, and R. Wolski.Towards automatically estimating porting effort between web service APIs.IEEE International Conference on Services Computing, 2014.

C. Krintz, H. Jayathilaka, S. Dimopoulos, A. Pucher, R. Wolski, and T. Bultan.Cloud platform support for api governance.IC2E Workshop on the Future of PaaS, 2014.


M. J. Lawson, B. Drawert, M. Khammash, L. R. Petzold, and T. Yi.Spatial stochastic dynamics enable robust cell polarization.PLoS Comput. Biol.9(7):0, 2013.

D. T. Gillespie, A. Hellander, and L. R. Petzold.Perspective: Stochastic algorithms for chemical kinetics.J. Chem. Phys.138(1):6211, 2013.

S. Hellander.Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures.J. Chem. Phys.130(1):6211, 2013.

C. Krintz.The Appscale cloud platform: Enabling portable, scalable web application deployment.IEEE Internet Computing17(2):72–75, 2013.


C. Bunch, V. Arora, N. Chohan, C. Krintz, S. Hegde, and A. Srivastava.A Pluggable Autoscaling Service for Open Cloud PaaS Systems.IEEE/ACM International Conference on Utility and Cloud Computing, 2012.

N. Chohan.Data and Application Management in an Open Cloud Platform.UCSB Technical Report #2013-01 (PhD thesis), 2012.

C. Bunch.Automated Configuration and Deployment of Applications in Heterogeneous Cloud Environments.UCSB Technical Report #2013-02 (PhD thesis), 2012.

B. Drawert, S. Engblom, and A. Hellander.URDME: A modular framework for stochastic simulation of reaction-transport processes in complex geometries.BMC Syst. Biol.6:27, 2012.

S. Hellander, A. Hellander, and L. R. Petzold.Reaction-Diffusion Master Equation in the Microscopic Limit.Phys. Rev. E85(4), 2012.