a brief summary of my scientific contribution
DESCRIPTION
computational science, multidisciplinary research projects; modelling and simulations; morphogenesis;TRANSCRIPT
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My Computational Science Research
18 July 2014Nol Chindapol, PhD Candidate
Section Computational ScienceUniversity of AmsterdamScience Park 904, C31561098 XH Amsterdam
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About MeMathematics
& Computer Engineering backgrounds
Passion in Computational science
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Research Projects
Flow & Morphological Plasticity of Coral Growth
Re-Modelling of Purkinje Cells Forest
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Research questions Is morphological plasticity the emergent property of
the external stressors induced by flow constraint to the sessile organisms?
What is the interaction between those constraints and intrinsic property of the organism that leads to self-generation property of the growth forms?
How to quantify plastic response relevant to such constraints?
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Accretive growth model is coupled with FEM modelling software (COMSOL) in order to investigate the plasticity of the resulting growth forms under uni-directional & bi-directional flow
(Tali et al. 2011)
Data Acquisition
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Unidirectional Flow & Accretive Growth Model
Inflo
w
OutFlow
Nutrient Injection C = 1 mol/m3
Object and Ground = Sink; C = 0
Schematic diagram of the simulation (A) A spherical objected represents a simulated object in a first growth step. (B) A simulation phase involves solving the Navier-Stokes equations and the Advection-Diffusion equation. (C) Simulated growth form: the accretive growth process generates new growth layers on top of the previous one.
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Bidirectional Flow & Symmetry perseverance Hypotheses
Schematic diagram of the bi-directional flow simulation coupled with the accretive growth model: (a) initialization phase, (b) the simulation phase consists of two subsequence flow simulation steps. . (c) The solutions of the nutrient transport are acquired and translocated on the surface of the simulated corals. The next growth layer is built on top of the previous one by the local growth function
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Advance Morphometric
Morphometric traits used in our quantitative analysis; (a) local morphometric traits (LMT) are defined as local traits that are not associated with directional bias e.g. branch spacing (br_spacing), branch angle (br_angle), ground angle (g_angle), and diameter of branches (da, db and dc) whereas (b) symmetric-oriented traits (SOT) are those associated with directional bias (h_angle, v_angle, and spd_angle) i.e. requiring the reference axis.
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Bifurcations in nature are locally flat – using data from Neurons & Corals
We do not touch upon this.
Yihawa et al. 2012
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Morphospace of the flow-induced forms
An overview of the morphospace showing the transition from compact colony to thin branching form by means of intrinsic model parameter n, while exposed to the flow condition with increasing Pe number (i.e. decreasing diffusivity D). Red arrows indicate directional variation of flow. . (a) In silico corals group 1 (b) In silico corals group 2(c) In silico corals group 3
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Unpublished Work in Turbulent Flow Simulation
Solved high Reynolds number flow by using the one equation Spalart-Allmaras turbulent model, and coupled with growth model.
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Flow & Morphological Plasticity of Coral Growth
Re-Modelling of Purkinje Cells Forest
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Research Questions
How neuron’s complex morphology is created during nervous development, and eventually leads to the development of neuron forest.
How the interaction of genes mediates dendrite self-avoidance by means of repulsive signal – discriminates self/non self.
The role of traveling waves in Purkinje cells during early developmental stage and their significance in cortical microcircuit wiring.
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Dendritic infrastructureWe simulate the
growing micro tubes i.e. the mechanic property (e.g. contact-mediated) is reduced to a non-volumetric abstraction.
With VTKLines and Tube Filter
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Start
Fint
Contact-mediated
Spatial Gradient
Branch
Re-mode
l
Global Maturation check
For each neuron
Fext
L
stochastic
End
Update Geometry
Li = A set of growth event
Li = Gi (N)
Gi = FIntrinsic + Fextrinsic
Growth Mechanisms at each time step
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Branching and remodeling definition
Let dendritic tree composes of a n number of cell (n=0,…k), in which each cell constitutes of a finite set Li (i=0,..m)of non-bifurcated line; branching mechanism is the addition of cellk+1 to a non-terminated cell k.
Branch?
Re-model
?
; re-modeling, on the other hand denotes an action of trimming terminal cell, by which the line Lm is eliminated, or redefined.
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N=0
N=7
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Simulation of Neuronal Forest Initialization (spherical
objects N=100 at rand(position)
Neurite elongation
Neurite branching (1,2,3 chem) and dendritic shape formation prob(gradients)
Stopping criteria (rule based)
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Thank You!
Please Check coral growth movie 1
Movie 2