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I will discuss mathematical and computational methods for spatiotemporal modelling in molecular and cell biology, including allatom and coarsegrained molecular dynamics (MD), Brownian dynamics (BD), stochastic reactiondiffusion models and macroscopic meanfield equations. Microscopic (BD, MD) models are based on the simulation of trajectories of individual molecules and their localized interactions (for example, reactions). Mesoscopic (latticebased) stochastic reactiondiffusion approaches divide the computational domain into a finite number of compartments and simulate the time evolution of the numbers of molecules in each compartment, while macroscopic models are often written in terms of meanfield reactiondiffusion partial differential equations for spatially varying concentrations.
In the first part of my talk, I will discuss connections between these different modelling frameworks. I will consider chemical reactions both at a surface and in the bulk, summarizing our results reported in [1, 2, 3, 4]. In the second part of my talk, I will discuss the development, analysis and applications of multiscale methods for spatiotemporal modelling of intracellular processes, which use (detailed) BD or MD simulations in localized regions of particular interest (in which accuracy and microscopic details are important) and a (lessdetailed) coarser model in other regions in which accuracy may be traded for simulation efficiency [5, 6, 7]. I will discuss error analysis and convergence properties of the developed multiscale methods [8, 9], their software implementation [10] and applications of these multiscale ethodologies to modelling of intracellular calcium dynamics [11], actin dynamics [12, 13] and DNA dynamics [14]. I will also discuss the development of multiscale methods which couple MD and coarser stochastic models in the same dynamic simulation [15, 16].
\n\nSPEAKER:
Radek Erban, Mathematical Institute, Univesity of Oxford
144 Loomis Lab
falseBiological Physics Seminar (PoLS): "Multiscale Methods for Modelling Intracellular Processes"
Speaker 
(signup)
Radek Erban, Mathematical Institute, Univesity of Oxford 

Date:  9/1/2017 
Time:  2 p.m. 
Location:  144 Loomis Lab 
Event Contact:  Sandra K. Patterson 2173333393 skpttrsn@illinois.edu 
Cost:  N/A 
Sponsor:  Zaida LutheySchulten 
Event Type:  Seminar/Symposium 
I will discuss mathematical and computational methods for spatiotemporal modelling in molecular and cell biology, including allatom and coarsegrained molecular dynamics (MD), Brownian dynamics (BD), stochastic reactiondiffusion models and macroscopic meanfield equations. Microscopic (BD, MD) models are based on the simulation of trajectories of individual molecules and their localized interactions (for example, reactions). Mesoscopic (latticebased) stochastic reactiondiffusion approaches divide the computational domain into a finite number of compartments and simulate the time evolution of the numbers of molecules in each compartment, while macroscopic models are often written in terms of meanfield reactiondiffusion partial differential equations for spatially varying concentrations. In the first part of my talk, I will discuss connections between these different modelling frameworks. I will consider chemical reactions both at a surface and in the bulk, summarizing our results reported in [1, 2, 3, 4]. In the second part of my talk, I will discuss the development, analysis and applications of multiscale methods for spatiotemporal modelling of intracellular processes, which use (detailed) BD or MD simulations in localized regions of particular interest (in which accuracy and microscopic details are important) and a (lessdetailed) coarser model in other regions in which accuracy may be traded for simulation efficiency [5, 6, 7]. I will discuss error analysis and convergence properties of the developed multiscale methods [8, 9], their software implementation [10] and applications of these multiscale ethodologies to modelling of intracellular calcium dynamics [11], actin dynamics [12, 13] and DNA dynamics [14]. I will also discuss the development of multiscale methods which couple MD and coarser stochastic models in the same dynamic simulation [15, 16].

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