2016

L. Meinecke and P. Lötstedt.Stochastic diffusion processes on cartesian meshes.J. Comput. Appl. Math.294:1–11, 2016.
B. Drawert, M. Trogdon, S. Toor, L. Petzold, and A. Hellander.MOLNs: A cloud appliance for interactive, reproducible and scalable spatial stochastic computational experiments.SIAM J. Sci. Comput. (to appear), 2016.
B. Drawert, A. Hellander, B. Bales, D. Banerjee, G. Bellesia, B.J. Daigle, Jr., G. Douglas, M. Gu, A. 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):e1005220, 2016.

2015

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.

2014

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.

2013

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.

2012

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.