Stochastic simulation of reaction-diffusion processes in molecular biology
Ice sheets and ice shelves

Stochastic simulation of reaction-diffusion processes in molecular biology

Recent papers
P Lötstedt, Derivation of continuum models from discrete models of mechanical forces in cell populations, J Math Biol, 83 (2021), 75.

P Lötstedt, The Linear Noise Approximation for spatially dependent biochemical networks, Bull Math Biol, 81 (2019), 2873-2901.

S Engblom, P Lötstedt, L Meinecke, Mesoscopic modeling of random walk and reactions in crowded media, Phys Rev E, 98 (2018), 033304.

Z Bashardanesh, P Lötstedt, Efficient Green's Function Reaction Dynamics (GFRD) simulations for diffusion limited reversible reactions, J Comput Phys, 357 (2018), 78-99.

S Engblom, A Hellander, P Lötstedt, Multiscale simulation of stochastic reaction-diffusion networks, in Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, ed. D Holcman, pp 55-79, Springer, Cham, 2017.

A Hellander, J Klosa, P Lötstedt, S MacNamara, Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuations, SIAM J Appl Math, 77 (2017), 1157-1183.

B Drawert, A Hellander, B Bales, D Banerjee, G Bellesia, B Daigle, G Douglas, M Gu, A Gupta, S Hellander, C Horuk, G Narayanasamy, D Nath, S Wu, P Lötstedt, C Krintz, L Petzold, Stochastic Simulation Service: Bridging the gap between the computational expert and the biologist, PLoS Comput. Biol., 12 (2016), e1005220.

E Blanc, S Engblom, A Hellander, P Lötstedt, Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime, revision in Multiscale Model. Simul., 14 (2016), 668-707.

L Meinecke, S Engblom, A Hellander, P Lötstedt, Analysis and design of jump coefficients in discrete stochastic diffusion models, revision in SIAM J. Sci. Comput., 38 (2016), A55-A83.

L Meinecke, P Lötstedt, Stochastic Diffusion Processes on Cartesian Meshes, J. Comput. Appl. Math., 294 (2016), 1-11.

P Lötstedt, L Meinecke, Simulation of Stochastic Diffusion via First Exit Times, revised version in J. Comput. Phys., 300 (2015), 862-886.

Ice sheet and ice shelf modeling

This is a collaboration with Nina Kirchner at the Bert Bolin Centre for Climate Research at Stockholm University with support from FORMAS. See also the homepage.

Recent papers
G Cheng, N Kirchner, P Lötstedt, Sensitivity of ice sheet surface velocity and elevation to variations in basal friction and topography in the Full Stokes and Shallow Shelf Approximation frameworks using adjoint equations, Cryosphere, 15 (2021), 715-742.

G Cheng, P Lötstedt, L von Sydow, A full Stokes subgrid scheme in two dimensions for simulation of grounding line migration in ice sheets using Elmer/ICE (v8.3), Geosci. Model Dev., 13 (2020), 2245-2258.

G Cheng, P Lötstedt, Parameter sensitivity analysis of dynamic ice sheet models-numerical computations, Cryosphere, 14 (2020), 673-691.

S Marchenko, G Cheng, P Lötstedt, V Pohjola, R Pettersson, W van Pelt, C Reijmer, Thermal conductivity of firn at Lomonosovfonna, Svalbard, derived from subsurface temperature measurements, Cryosphere, 13 (2019), 1843-1859.

E van Dongen, N Kirchner, M van Gijzen, R van de Wal, T Zwinger, G Cheng, P Lötstedt, L von Sydow, Dynamically coupling full Stokes and shallow shelf approximation for marine ice sheet flow using Elmer/Ice (v8.3), Geosci. Model Dev., 11 (2018), 4563-4576.

G Cheng, P Lötstedt, L von Sydow, Accurate and stable time stepping in ice sheet modeling, J. Comput. Phys., 329 (2017), 29-47.

N Kirchner, J Ahlkrona, E J Gowan, P Lötstedt, J M Lea, R Noormets, L von Sydow, J A Dowdeswell, T Benham, Shallow Ice Approximation, Second Order Shallow Ice Approximation and Full Stokes models: a discussion of their roles in palaeo-ice sheet modelling and development, Quat. Sci. Rev., 135 (2016), 103-114.

J Ahlkrona, P Lötstedt, N Kirchner, T Zwinger, Dynamically coupling the non-linear Stokes equations with the Shallow Ice Approximation in glaciology: Description and first applications of the ISCAL method, revised version in J. Comput. Phys., 308 (2016), 1-19.

J Ahlkrona, N Kirchner, P Lötstedt, A numerical study of scaling relations for non-Newtonian thin film flows with applications in ice sheet modeling, Quart. J. Mech. Appl. Math., 66 (2013), 417-435.

J Ahlkrona, N Kirchner, P Lötstedt, Accuracy of the zeroth and second order shallow ice approximation - Numerical and theoretical results, Geosci. Model Dev., 6 (2013), 2135-2152.

Top