EMPAQUETAMIENTO DE ESFERAS

Introduction: Many biological processes involve the aggregation of cells into a cluster.
For example, in animals, small cells called platelets cluster at the site of an injury to the
skin or blood vessels. Also, during the development of an embryo, space between
aggregated cells decreases and cell-to-cell contact increases. The amount of space between
aggregated cells can affect the permeability of solutes into the cells from the surrounding
solution. The number of cell-to-cell contacts, places where the cell membranes of different
cells touch, can affect flow of solutes and communication between cells.

Importance: The ability to objectively examine aggregations of cells requires a

quantitative measure of the closeness of cells. We can use the geometrical principles of
sphere packing to quantify the density of aggregated cells.

Questions: How does the arrangement of cells within a cluster affect the space between
cells and the number of cell-to-cell contacts? How do biological examples of sphere
packing compare to mathematical theory?

Variables:

P packing density

Vsphere volume of spheres within a cube

Vcube volume of a cube

r radius of a sphere

l, w, h length, width, height of a cube

R ratio of aggregate volume to individual cell volume

Vagg volume of cell aggregate

Vcell volume of individual cell

Methods: Sphere packing is a problem by which mathematicians try to determine how

tightly spheres can be packed in a box. Imagine a grocer trying to pack oranges into a box
or stack oranges in his store: his goal is to pack the oranges as tightly as possible.
Randomly arranging the oranges may result in an inefficient use of the space.
We will examine three different models from sphere packing theory: simple cubic packing,
face-centered cubic packing, and hexagonal close packing. In simple cubic packing, spheres
are stacked directly next to and on top of each other. In face-centered cubic packing, each
layer has spheres placed diagonally next to each other. The next layer of spheres is placed
in the crevices between spheres on the bottom layer. Every third layer directly overlies each
other. In hexagonal packing, the bottom layer has spheres directly next to each other.
Spheres in the next layer are placed in the crevices of the underlying layer. In hexagonal
packing, every other layer directly overlies each other.

We can determine which of these formations is the most efficient use of space when
packing spheres in a cube by calculating the packing density, or fraction of the cube's
volume that is occupied by spheres. The packing density (P) is

P = Vsphere / Vcube

where Vsphere is the total volume of the spheres in a cube and Vcube is the total volume of the
cube.
In simple cubic packing, each sphere is stacked directly on another sphere. We can
visualize each sphere being contained within an individual cube.

We can then calculate the packing density as the volume of a single sphere divided by the
volume of a single cube. The volume of a sphere is given as

Vsphere = 4/3 π r3,

where r is the radius of the sphere. The volume of the cube is given as

Vcube = l w h,

or length times width times height. The width, height, and length of the cube are exactly
equal to the diameter, or twice the radius of the sphere. So Vcube=(2r)(2r)(2r). We can
therefore calculate the packing density as

P = Vsphere / Vcube = (4/3 π r3) / (2r)3

which is approximately P=0.524. In other words, 52.4% of the space in the cube is
occupied by the sphere and 47.6% is empty space. For any number of spheres we stack in
this formation, the density remains the same.

We can use a similar approach to determine the packing density for face-centered cubic
packing. First, following the above procedure, we must determine how many spheres fill an
individual cube. Visualize a group of 6 spheres placed in an equilateral triangle, with an
additional sphere placed on top. Take another group of 7 spheres in the same formation, but
oriented in the opposite direction. Now place each group of 7 back to back. A symmetrical
cube emerges containing eight 1/8 spheres in each corner, and six 1/2 spheres at each face.
Stacking additional cubes next to each other gives us the same packing arrangement of
spheres. It is easiest, however, to calculate the packing density for a single cube.
With face-centered cubic packing, the cube contains eight 1/8 spheres and six 1/2 spheres.
Therefore, knowing the volume of a whole sphere is 4/3 π r3, we can calculate the volume
of spheres within the cube as the volume of 1/8 of a sphere, times 8, plus the volume of 1/2
sphere, times 6:

Vsphere = 8 (1/8)(4/3 π r3 ) + 6 (1/2)(4/3 π r3 ) = (1+3)(4/3 π r3 ) = 16/3 π r3

where r is the radius of a single sphere.

We can also calculate the volume of the cube since we know the diagonal distance along
the face of the cube is 4r, where r is the radius of a single sphere. In order to calculate the
volume of a cube, however, we need to know the length of one side of the square (length =
width = height). Since the diagonal and two sides of a square form a right triangle, we can
use the Pythagorean Theorem to find the length of one side. In this case, l=w=h=2√ 2r , and
the volume of the cube is

We can therefore calculate the packing density as

In other words, with face-centered cubic packing, 74.05% of the space is occupied by
spheres and 25.95% is unoccupied space.

Hexagonal close packing is very similar to face-centered cubic packing, except spheres are
shifted to a slightly different angle. Consequently, the packing density for hexagonal
packing is also P=0.7405, but is more difficult to verify using simple geometry.
Demonstrations with ball bearings in a box and computer simulations have shown that
when spheres are packed randomly, the packing density is around P=0.64.

Interpretation: By relating sphere packing to the aggregation of individual cells, scientists

can gain a better understanding of the packing density of cells. Mathematicians have found
that the most efficient packing of spheres is that of face-centered cubic packing or
hexagonal close packing, P=0.7405. The outside surface of many viruses is formed of
proteins that are packed in this way. Mature yeast cells, however, have a packing density of
about 78%. Yeast cell shape is a slight departure from spherical, allowing a slightly tighter
packing. Since randomly packed spheres have a packing density of approximately 64%, this
suggests there is some order in yeast cell aggregation to reduce the amount of space
between cells or increase cell-to-cell contact.

The volume of a single cell can affect the density of aggregated cells and the amount of
intercellular space. For an aggregate of cells in an extra-cellular solution with a high
osmality (see Water Movement and the Vant Hoff Equation), water tends to flow out of the
cells. As the volume of individual cells decreases, the packing density decreases and the
space between cells increases. For aggregates of yeast cells submerged in solution, Arnold
and Lacy (1977) showed that the space between cells increases, or the packing density
decreases, with increasing osmality.

In embryo development, cells are packed tightly together. As cells differentiate and the
embryo develops, the amount of space between cells decreases and the number of cell-to-
cell contacts increases. In order to test hypotheses about embryo development, scientists
must be able to count the number of cells in each aggregate for different treatments. Martin
et al. (1997) use sphere packing theory to estimate the number of cells in an aggregate.

If the volume of an aggregate is completely filled with cells and contains no intercellular
space, then the number of cells in an aggregate would be given by the ratio (R) of the total
volume of the aggregate of cells (Vagg) to the volume of a single cell (Vcell):

R = Vagg/Vcell

To account for intercellular space, however, we multiply this ratio (R) by the fraction of the
total volume occupied by cells, or the packing density (P). Therefore the number of cells in
an aggregate (N) is given by N=RP.

Mathematicians know that face-centered cubic packing or hexagonal packing obtains one
of the greatests possible densities of spheres, P = 0.7405. One of the looser packings of
spheres is simple cubic packing, P=0.5235. Consequently, Martin et al. (1997) estimate the
number of spherical cells in an aggregate by assuming their packing density lies between
0.5235 and 0.7405. By simply calculating R, the ratio of the total aggregate volume to the
volume of a single cell, they can estimate the number of cells in an aggregate as

0.5235R < cell number < 0.7405R

This is a much quicker, more efficient, and reliable way to estimate cell number than by
counting.

Sphere packing theory is also useful in testing the effects of different medications on
platelet aggregation. When animals suffer damage to their skin and blood vessels, small
cells called platelets cluster at the site of injury. In order to test the effects of anti-
aggregating drugs, scientist must be able quantify how densely packed platelets are into
aggregates.

Conclusions: Biologists often need measurements of cell aggregation in order to

understand aspects of biology such as embryo development, platelet aggregation, and
permeability. Sphere packing density allows scientists to take a quantitative approach to
examine cell aggregation. Mathematicians can calculate packing densities for different
sphere packing formations. By comparing their experiments to mathematical models,
biologists can determine characteristics of individual cells and cell aggregates, test
hypotheses about the effects of drugs or other external factors, and understand the nature of
cell aggregation.

Additional Questions:

1. For simple cubic packing, why is the packing density for an individual sphere within a
cube the same as the packing number for any number of spheres packed within a larger
cube? For example, calculate the packing density (P) for a simple cubic packing of 27
spheres, and verify it is P=0.524.

2. Use the Pythagorean Theorem (the sum of the squares of each side, a and b, is equal to
the square of the hypotenuse, c; a2 + b2 = c2) to verify the length of one side of the cube in
face-centered cubic packing. Remember in a cube, length = width = height.

3. Using Martin et al.'s method, estimate an upper and lower bound for the number of
spherical cells in an aggregate of cells with volume Vagg=50µ m3. The volume of an
individual cell is approximately Vcell=0.05 µ m3.

Sources:

Arnold, W. N. 2000. From cannon balls to yeast cells. Science 288:55

Arnold, W. N. and J. S. Lacy. 1977. Permeability of the cell envelope and osmotic behavior
in Saccharomyces cerevisiae. Journal of Bacteriology 131:564-571.
Martin, I., B. Dozin, R. Quarto, R. Cancedda, and F. Beltrame. 1997. Computer-based
technique for cell aggregation analysis and cell aggregation in in vitro chondrogenesis.
Cytometry 28:141-146.

Weisstein, E. W. 2000. http://mathworld.wolfram.com/SpherePacking.html and references

therein

Crystallography

The branch of science that deals with the geometric forms of crystals. How to describe,
classify, and measure such forms are the first questions of crystallography. Revealing the
forces that made them and the activities within them are the modern directions of the field.
Crystallography is essential to progress in the applied sciences and technology and
developments in all materials areas, including metals and alloys, ceramics, glasses, and
polymers, as well as drug design. It is equally vital to progress in fundamental physics and
chemistry, mineralogy and geology, and computer science, and to understanding of the
dynamics and processes of living systems. See also Crystal structure; Polymorphism
(crystallography).

The external morphology of crystals reflects their growth rates in different directions.
These directions remain constant during the course of the growth process, and are
represented mathematically as the normals to sets of parallel planes that are imagined as
being added on as growth proceeds. The faces that meet and define an edge belong to a
zone, a zone being a set of planes that share one common direction, the zone axis. The
invariance of interfacial angles, measured by rotation about an axis that is defined by the
zone direction, was discovered in the seventeenth century. See also Crystal growth.

Interfacial angles are calculated from spherical geometry. Figure 1 illustrates the procedure
for a crystal having well-developed faces of which three are mutually perpendicular. The
normals to these faces are the natural directions for constructing an orthogonal frame of
reference for measurement. The crystal is imagined to be shrunk and placed at the center of
a sphere with coordinates (0,0,0). The face normals, labeled [100], [010], and [001], define
the directions of an orthogonal reference system. Normals to the same set of planes, but
oppositely directed, are labeled [100], [010], [001]. The reversal of sign indicates that the
crystal must be rotated 180° to obtain the same view. Rotation about the [001] direction
interchanges the positions of [100] and [100] faces and their bounding edges. Rotation
about [010] turns these faces upside down. Correct designations for group movements and
symmetry operations are clearly essential for establishing and maintaining orientation in
crystal space. The directions of face normals determine points at which the imagined sphere
is pierced. The solid angles between an array of such points, all lying on the same great
circle of the sphere, belong to a zone.
 Spherical projection of normals to crystal faces.

Optical measurements and stereographic projections established the constancy of interfacial

angles, independent of how well developed the faces are. Such properties as the cleavage of
large rhombohedral crystals of calcite (CaCO3) into little rhombs suggested that the large
crystal could be represented by geometrically identical smaller units stacked together, by
translation, to fill space. The 14 lattices of Bravais (Fig. 2) enlarged the seven crystal
systems of optical mineralogy by adding centering points to them: body (I), face (F), and
base (C) centers. The 14 lattices define three-dimensional distributions of mathematical
points such that the environments of all points of the lattice are identical. They also define
the symmetries of frameworks for constructing mathematical models to represent the
observed and measured realities—models made from cells of the smallest volume, but also
highest symmetry, that stack together by translation to fill space.

The 14 Bravais lattices, derived by centering of the seven crystal classes (P and R) defined
by symmetry operators.
Stacking of model cells does not imply that a crystal grows by stacking identical bricks; a
lattice of identically surrounded mathematical points does not imply that any real objects,
atoms or molecules, are located at the points; and filling space by translation of identical
cells does not imply that the space defined by the cells is filled. Rather, the Bravais lattices
are a formalism for representing observed geometries and symmetries of real crystals by
three-dimensional lattices of identically surrounded points.

The lattices also provide the means to identify imaginary planes within the cell; these are
called Miller indices (h,k,l). They consist of small whole numbers. For example, each of the
six faces of a simple cube, with the origin of a coordinate frame of reference at the cube
body center, is normal to one of the reference axes and parallel to the plane defined by the
two others. The six faces are indexed as their normals in Fig. 1—(100), (100), (010), (010),
(001), and (001)—to represent a face that intercept the x, x axis but not the y and z; the y, y
axis but not the x and z; and so forth. Hypothetical parallel planes with 1/2 the interplanar
spacing are represented as (200), (200), (020), and so forth.

A complete mathematical formalism exists for modeling an external morphological form

and the symmetry relations between imagined units of structure within it. The symmetry
operators include rotation axes, glide and mirror planes, and left- and right-handed screw
axes which will simultaneously rotate and translate a three-dimensional object to create its
clone in a different spatial position and orientation. The operators minimize the detail
required to specify the spatial arrangements of patterns and objects that fill two-
dimensional and three-dimensional space. The so-called color space groups of
crystallography greatly increase the number of distinguishably different symmetries beyond
the classical 230 by adding a fourth coordinate to the three space coordinates. This is done
to encode a real difference that will be manifested in some property. The different
directions of the magnetic moments of chemically identical atoms of an element such as
iron provide an example of the need for representing a difference on the atomic level
between cells that are otherwise identical.

The sharp x-ray line spectra characteristic of the bombarded element are the primary probes
for determining interior structural detail of crystals. Cameras with cylindrical film and
enclosed powdered samples record all diffraction lines as arcs of concentric circles. This
fundamental powder method has endured since 1917 and is now employed with improved
beam purity and optics, improved diffractometers which couple sample and detector
rotation, electronic detection, rapid sequential recording, and computer indexing programs
that provide patterns of compounds, mixtures of phases, and dynamic changes that occur
when crystals are subjected and respond to external stress. The method is applied to single
crystals, polycrystalline aggregates, and multiple-phase mixtures, randomly disposed either
in space or in geometrically designed composite materials. See also X-ray crystallography;
X-ray powder methods.

The dynamics of living systems, the difficulties in distinguishing light elements, and the
inherent ambiguities of measuring, decoding, and mapping crystal structures are continuing
challenges. Major achievements of crystallography include the determination of the
structures of deoxyribonucleic acid (DNA), proteins, other biological compounds, and
boranes; the development of direct methods of phase determination; and the determination
of the structure and mechanism of a photosynthetic center. See also Borane;
Deoxyribonucleic acid (DNA); Photosynthesis; Protein.