introduction to bio-architecture - unesco · 2018. 4. 19. · murray’s theory murray suggests...

ESC-484

Melik Demirel, PhD

*Pictures and tables in this lecture notes are copied

from Internet sources for educational use only.

Complex Patterns

Leiseggang Patterns

Brain imagingBZ reaction

Stripes in animal kingdom

Can order increase without breaking 2nd law of Thermodynamics?

1. Reaching equilibrium

2. Oscillatory reactions out of equilibrium

Max-Planck-Institut für Metallforschung, Stuttgart Abteilung Neue Materialien und Biosysteme

Diblock Copolymer Self-Assembly

Frank Bates et al.

http://www.cems.umn.edu/about/ people/faculty.php?id=20164

Tom Russell et al. http://www.pse.umass.edu/trussell/

Diblock Copolymer Assembly

1. REACHING EQUILIBRIUMSystem dissipate energy as heat, and system gained entropy, equilibrium structure

obtained (surrounding entropy increased!)

Examples of Symmetry Breaking

• Belousov-Zhabotinsky Reaction (BZR)

• AngleFish Stripe formation

2. Oscillatory reactions out of equilibrium

Does it violate 2nd law of thermodynamics: (Ofcourse!) No

belousov-zhabotinsky (BZ) reaction

Belousov, a Russian Biochemist, were unable to publish his results initially!!!

Later Zhabotinsky (as a graduate student) rediscovered Belousov’sfindings

2. Oscillatory reactions out of equilibrium

• Alfred J. Lotka

(1880-1949)

– American mathematical biologist

– primary example: plant population/herbivorous animal dependent on that plant for food

• Vito Volterra

(1860-1940)

– famous Italian mathematician

– Retired from pure mathematics in 1920

– Son-in-law: D’Ancona

A system reaching steady supply of energy (oscillatory reactions) can reach steady state

Lotka-Volterra Model

xyyy

yxx

Introduction to Ordinary Differential EquationsStephen Sapesrtone

x: Prey or Activator

y: Predator or Inhibitor

Reaction-Diffusion Model

Pattern Formation

• Patterns can be …– Time dependent (periodic in time or space)– Transient or persistent– Free energy away from equilibrium to maintain

pattern (thermo – dissipative structure)

• Turing Theory and Pattern Formation– Steady state stable to homogeneous perturbations– Unstable to inhomogeneous perturbations– Final structure stationary in time, periodic in space– Intrinsic wavelength– Inhibition diffuses faster than activation

Alan Turing (1952 Phil. Trans. Roy. Soc. )“The Chemical Basis of Morphogenesis”

Diffusion

• u(t,x) : density function of a chemical

• The chemical will move from high density places to lower density places, this is called diffusion

• Diffusion is the mechanism of many molecular or cellular motions

• Diffusion can be described by a heat equation

Reaction-diffusion equations

• Let U(x,t) and V(x,t) be the density functions of two chemicals or species which interact or react

Morphogenesis (from the Greek morphê shape and genesis creation) is one of three fundamental aspects of developmental biology along with the control of cell growth and cellular differentiation. Morphogenesis is concerned with the shapes of tissues, organs and entire organisms and the positions of the various specialized cell types.

• The kinetics are always chosen such that, in the absence of diffusion, the homogeneous steady state is stable (and thus the instability is diffusion driven)

Why do animals’ coats have patterns like spots, or stripes?

Murray’s theory

Murray suggests that a single mechanism could be responsible for generating all of the common patterns observed. This mechanism is based on a reaction-diffusion system of the morphogen prepatterns, and the subsequent differentiation of the cells to produce melanin simply reflects the spatial patterns of morphogen concentration.

Melanin: pigment that affects skin, eye, and hair color in humans and other mammals.

Morphogen: Any of various chemicals in embryonic tissue that influence the movement and organization of cells during morphogenesis by forming a concentration gradient.

“Theorem 1”: Snakes always have striped (ring) patterns, but not spotted patterns.

Turing-Murray Theory: snake is the example of b/a is large.

Snake pictures (stripe patterns)“Theorem 1”: Snakes always have striped (ring) patterns, but not spotted patterns. Turing-Murray Theory: snake is the example of b/a is large.

“Theorem 2”: There is no animal with striped body and spotted tail, but there is animal with spotted body andstriped tail.

Turing-Murray theory: The body is always wider than the tail. The same reaction-diffusion mechanism should be responsible for the patterns on both body and tail. Then if the body is striped, and the parameters are similar for tail and body, then the tail must also be striped since the narrower geometry is easier to produce strips.

Examples: zebra, tiger (striped body and tail), leopard (spotted body and tail), genet, cheetah (spotted body and striped tail)

Spotted body and striped tail or legs

Cheetah (upper), Okapi (lower) Tiger (upper), Leopard (lower)

Spotted body and striped tail

Genet (left), Giraffe (right)

Natural Patterns of cos(kx)

cos(x): Valais goat

(single color: f(x)=1, a lot of examples)

Cos(2x): Galloway belted Cow

cos(2x): Giant Panda