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Posts Tagged ‘structure’

The mechanisms behind plant interactions

Sunday, December 20th, 2009

Plants cannot move.  This limitation causes plants to develop various mechanisms for adapting to their surroundings, attracting and repelling other organisms, absorbing and releasing nutrients and chemicals, and using these organisms and chemicals for their benefit and sustenance.

A plant’s interaction with the environment happens at the surface.  Substances enter and exit through diffusion or active transport by transport proteins embedded in the surface membrane of the plant.  The border control operation is mediated by the selective binding affinity of transport proteins and also by a membrane potential that exists across the membrane.  This membrane potential drives directional flow, providing a pulling force.

At the surface are other sensory receptors that activate a protein kinase chain reaction to produce a particular response in this part of the plant.  These chain reactions often multiply a signal to initiate a systematic response in other parts of the plant as well.

The mechanism for carrying substances or chemical signals to other parts of the plant is the vascular network of xylems and phloems.  Water and minerals enter into the root system and travel upwards through the xylem into other parts of the plant.  Sugars are produced in the leaves through photosynthesis and move from the point of sugar production to sugar storage via the phloem.

vascular network of a plant

vascular network of a plant

The xylem sap, which contains water and minerals, is pulled upward through the xylem by water escaping through the stomata located at the surface of the plant.  The water escapes when sunlight strikes the surface of the plant, causing the water to evaporate through the stomata.  As the water evaporates, the water curves around the mesophyll cells, increasing surface tension, which causes increased water loss from the mesophyll cells.  This water loss causes mesophyll cells to bring in more water from the xylem, which leads to the negative pressure pull of water into the roots.  When the water comes in through transport proteins embedded in the epidermis of the root system, it also brings in the nutrients and substances necessary for the plant to survive.

When sunlight strikes the surface of a leaf, it also activates an electron donated by a water molecule, which flows down an electron transport chain in the thylakoid membrane of chloroplasts found in mesophyll cells.  The electron transport chain ends with the the conversion of NADP into NADPH and the release of O2.  The Calvin Cycle then combines NADPH with CO2 and converts it to glyceraldehyde 3-phosphate, a 3-carbon sugar, that is recombined to form sucrose and starch.  Starch is stored as reserve energy for the plant, and sucrose is immediately transported to other parts of the plant for use and storage.

Sucrose is transported throughout the plant via phloem.  The phloem consists of sieve tubes and companion cells.  The sieve tubes are made up of sieve cells that have plasmodesmata at each end to allow substances through.  The companion cells regulate the substances that enter and exit the sieve tubes.  Substances move through the sieve tube by positive pressure flow, a push factor caused by density.  A high concentration of organic substances at the source creates a diffusion gradient that draws water into the cells.  This sugar-water sap moves by bulk flow through the sieve tube from the sugar source to the sugar sink.

In a living system, the architecture is found in the thickness of the wall, through the interactions between the elements that make up the thickness, and through the communication that happens in the void between the opposite walls.  Communication happens by channeling forces that already exist, and making these forces do all the work.  The intelligence is found not only in the complexity of the system, but in how little effort is required for the system to sustain itself over time.

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Cor-Ten

Tuesday, September 22nd, 2009

A singular substance creates a visible dialogue between the past and the present.  It changes every day.  It flows onto the pavement like a river delta leaving behind striations cut in the color of orange.  Massive yet graceful, Cor-Ten speaks in echoes and pattering of rain drops.

Cor-Ten (or weathering steel) is a steel product that oxidizes very rapidly, then maintains a stable, dark-brown, rusted surface.  Alloyed with copper (Cu) and chromium (Cr), Cor-Ten resists atmospheric corrosion by developing and continuously regenerating a protective layer of rust on its surface that inhibits deeper penetration by atmospheric agents when subjected to the weather.  Made primarily of steel, or iron oxide (Fe2O3) with a little bit of carbon (C), Cor-Ten has high tensile strength and compressive strength, allowing it to be used as a structural component for buildings, sculptures, and bridges.  The addition of chromium increases hardness and melting temperature and prevents corrosion by forming a hard oxide layer on the surface.  Consequently, Cor-Ten exhibits much greater resistance to atmospheric corrosion than unalloyed steels.1

Richard Serra, Torqued Ellipse, UCLA

Richard Serra, Torqued Ellipse, UCLA

The surface texture of Cor-Ten depends largely on the nature of its surrounding atmosphere.  The macroclimate (industrial, urban, or maritime) drastically changes the effectiveness of the material against corrosion.  Although Cor-Ten resists weathering by rain, snow, fog, and ice, it cannot stand up to a constantly submerged environment or the presence of salt.  The readiness of salt to take up moisture maintains a constantly damp environment on the metal surface, causing it to rust beyond its ability to regenerate a protective layer.  As a result, Cor-Ten should not be used within 2km of the coast line.  In a marine environment, applying conventional coating and performing maintenance works on the Cor-Ten by removing salt buildup quickly gives it the chance to regenerate its protective rust layer.

Cor Ten

Cor Ten

The orientation of the Cor-Ten (exposed to or shaded from weathering, vertical or horizontal position) also affects how the material stands up to the climate. Cor-Ten surfaces facing south and west and those exposed to frequent wet and dry cycles develop a smoother fine-grained texture.   North and east facing surfaces and those that are shaded develop a coarser texture.2

Lastly, the connection points between panels of Cor-Ten must be detailed such that weld-points and bolts weather at the same rate as the Cor-Ten.  Using welded consumables matching the base material ensures that the welded joint also resists corrosion.  Threading bolts made of weathering steel into the Cor-Ten material prevents the formation of localized electrochemical cells.  (When a metal loses electrons, it becomes positively charged and quickly reacts with oxygen to create iron oxide, or rust.  If this process happens too rapidly, the Cor-Ten cannot regenerate its protective layer in time.)3  In addition, applying sealants around the joints stops capillary action from inflicting permanent moisture damage by corrosion.

Although a finicky material to deal with, Cor-Ten expresses every architect’s desire to design the building to express the passing of time, poetically, beautifully.

1. Thyssen Krupp.  COR-TEN.

2. Finishing.com.  “Marine environment effects on corten steel in relation to public art”

3. NASA. Corrosion Technology Laboratory.

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Membrane Structure and Function

Wednesday, September 2nd, 2009

The best architectural curtain walls are built to resist air and water infiltration, wind forces acting on a building and their own dead weight, while allowing daylight to penetrate into the space.  They are also very expensive, create an enormous amount of heat build-up, and function in binary.

A film of roughly 8nm in thickness (that is, 1/8000 the thickness of a sheet of computer paper), cell membranes have an amazing ability to regulate the substances that enter and exit a cell.

Fluid mosaic model for membranes, with phospholipid bilayer penetrated with proteins

Fluid mosaic model for membranes, with phospholipid bilayer penetrated with proteins and supported by cytoskeleton.

Cell membranes are made up of two layers of phospholipids.  Phospholipids have hydrophilic (water-loving) heads and hydrophobic (water-repelling) tails.  Water exists on both the exterior and interior sides of the membrane.  The hydrophobic tails hide behind the hydrophilic heads on both sides of the membrane, forming a non-rigid boundary around the inside of the cell.  This non-rigid membrane is held in its shape by microfilaments of cytoskeleton.

However, not all membranes are the same; some are thicker than others, some have higher percentage of proteins, and others have different kinds of phospholipids.  After each protein is synthesized in the ribosome with the information coded in RNA translated from the DNA, the proteins are individually inserted into the phospholipid bilayer with their hydrophilic ends sticking out.

Proteins determine most of the membrane’s functions.  One protein can have several functions.  Integral proteins – those that penetrate through the phospholipid bilayer – regulate what comes in and out of a cell.  Peripheral proteins are like appendages bound to the surface of the membrane.  Integral proteins include:

1. Transport proteins (acting as a diffusion channel or as a pump to bring substances into and out of cells),

2. Enzymes (working individually or in teams to carry out sequential steps of a metabolic pathway through induced chemical reactions),

3. Signal transducers (reading the message from a chemical messenger to relay a message to the inside of the cell),

4. Cell-to-cell recognition (serving as ID tags recognized by membrane proteins of other cells, especially useful in producing cells for a specific tissue or organ),

5. Intercellular joints (allowing cells to hook up in various kinds of junctions), and

6. Attachments to extracellular matrix (maintaining cell shape).

Peripheral proteins can also act as enzymes and transporters, but they only interact with different parts within the same cell.  They help transport small hydrophobic molecules, toxins, and antimicrobial peptides.

A cell membrane is a fine example of a supramolecular structure, where many molecules are ordered into a higher level of organization with emergent properties beyond those of the individual molecules.  It is architecture.

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The Origins of Life

Monday, August 31st, 2009

I must begin a blog about life with an examination of how life began.  Instead of beginning with a theory, whether Big Bang or creation, I would like to introduce the beginning of life at a point in which humans have the capacity to fully understand.  This beginning is molecular architecture.

Molecular architecture is based on carbon (C) bonding with the elements hydrogen (H), oxygen (O), sulphur (S), nitrogen (N), and phosphorus (P) in different organizational configurations to produce complexity.  These elements bonded together under heat, pressure and lightning in the early atmosphere to produce the fundamental molecules of methane (CH4), hydrogen gas (H2), ammonia (NH3), and water vapor (H2O) that were essential for generating the amino acids and hydrocarbons essential for life to begin.  Varying in length, single/double bonding, branching, rings, and positioning, molecules of many types could emerge out of these simple elements.

These molecules could not have emerged without carbon.  Its tetravalence allows carbon to bond covalently with four other molecules to form 3-dimensional polymers.  With the versatility of a spider joint used in curtain wall construction, carbon can even bond covalently with other carbons to form increasingly larger chains.

Seven functional groups have the ability to form every type of carbohydrate, lipid, protein, and nucleic acid.  They are hydroxyl (OH), carbonyl (CO), carboxyl (COOH), amino (NH2), sulfhydrl (SH), phosphate (PO4) and methyl (CH3).

When a carbon atom (C) bonds covalently with an amino (NH2), a carboxyl (COOH), and a sidechain (R, of which there are 20 types), an amino acid emerges which has properties that have not existed before in its base polymers.  Multiple amino acids bonded together form polypeptides, and polypeptides form proteins.

The sequence of the polypeptide is dictated by the DNA (deoxyribonucleic acid) within a cell’s nucleus.   DNA is formed by a nitrogenous base bonded to a sugar which is bonded to a phosphate.  The sugar and phosphate form the backbone for the nitrogenous bases.  The sequence of these nitrogenous bases transcribes directly into the amino acid sequence of the polypeptide.

Proteins have four degrees of structure, each of which is determined by the amino acids that make up its polypeptides, and each one occurring at a greater scale than the one before.  The first degree is the organization of their amino acid sequence.  The second degree, an increase in scale of one degree, is the formation of an alpha helix or a beta sheet via folding or coiling.  The third degree structure is the overall shape of the polypeptide, composed of many alpha helixes and beta sheets.  The fourth degree structure is the overall protein shape.  The protein shape determines its functionality.  Proteins are instrumental in almost everything that organisms do.  Some proteins known as enzymes speed up chemical reactions, others form structures in cells, and yet others aid in storage, transport, cellular communication, movement, and defense against foreign substances.

Thus from six basic elements found in the early natural system, we have the beginnings of life, the emergence of complex organisms, and the fundamental organization and structures from which we can become inspired.

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