AC2MB Seminar: Spring 2017
Applied and Computational Mathematics
and
Mathematical Biology seminar
Time: Wednesdays at 2:15pm
Location: CM.T01
- 25.01., 2:15pm in CM.T01
Efficient stochastic algorithms for molecular and coarse-grained simulation in and out of equilibrium
Benedict Leimkuhler (UoE)
Abstract: Stochastic numerical methods are increasingly popular in molecular, soft-matter and materials simulation. I will first review our work on efficient stochastic numerical methods for Langevin dynamics, including new constrained molecular integrators that allow a doubling of the timestep for molecular dynamics. Much of our current work is focussed on adapting our schemes to generalized forms of Langevin dynamics including dissipative particle dynamics and the generalized Langevin equation. In the case of DPD, which is widely used for nonequilibrium modelling (e.g. shear flows), I will discuss the use of a pairwise adaptive Langevin scheme which is suited for simulation in both transient and steady-state regimes.
Joint work with Charlie Matthews (Chicago), Matthias Sachs (UoE), Xiaocheng Shang (Brown) and Martin Kroeger (ETH)
- 01.02, 2:15pm in CM.T01
Free boundaries on cell boundaries: asymptotic limits of a model for receptor-ligand dynamics
Chandrasekhar Venkataraman (St. Andrews)
Abstract: Receptor-ligand interactions, constitute a fundamental part of a number of phenomena in cell biology. Hence their mathematical modelling and computational simulation is an important task. We consider a coupled bulk-surface system of partial differential equations with nonlinear coupling, that arises as a simplification of a mathematical model for the reaction between cell surface resident receptors and ligands present in the bulk region surrounding the cell. Nondimensionalisation of the model using biologically relevant values for the various characteristic scales leads one to consider a number of biologically relevant asymptotic limits of the model. In this talk we develop a mathematical theory for the treatment of the original model together with a rigorous proof of convergence to a number of limiting bulk-surface free boundary problems in the aforementioned limits. The theoretical results are supported by computations of the original and reduced problems on realistic geometries.
Joint work with Charles Elliott (Warwick) and Tom Ranner (Leeds)
- 08.02., 2:15pm in CM.T01
Diffusion of finite-size particles and application to heterogeneous domains
Maria Bruna (Oxford)
Abstract: We discuss nonlinear Fokker-Planck models describing diffusion processes with particle interactions. These models are motivated by the study of many particle systems in biology, and arise as the population-level description of a stochastic particle-based model. In particular, we consider a system of impenetrable diffusing spheres and use the method of matched asymptotic expansions to obtain a systematic model reduction. The same method can be applied to soft spheres (particles interacting via a soft short-range repulsive potential. In the second part of the talk, we discuss how this method can be used to derive an effective transport equation in heterogeneous domains, such as porous media or crowded environments. A nice feature of this approach is that it can easily account for macroscopic gradients in porosity or crowding.
- 01.03., 2:15pm in CM.T01
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Name (US Geological Survey)
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- 08.03., 2:15pm in CM.T01
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Chris Eilbeck (HWU)
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- 15.03., 2:15pm in CM.T01
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Euan Spence (Bath)
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- 22.03., 2:15pm in CM.T01
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SPEAKER (UNI)
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JOINT WORK?
- 05.07., 2:15pm in CM.T01
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Matteo Icardi (Warwick)
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- DATE, TIME, Maxwell Institute Applied Maths Seminar at ICMS
(jointly with ACM seminar, UoE)
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SPEAKER (UNI)
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3:50pm Coffee break
4:10pm 2nd talk at ICMS
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SPEAKER (UNI)
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5:00pm Reception
- DATE, 2:15pm in CM.T01 (HWU)
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SPEAKER (UNI)
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