## Category Archives: Math

### The Reimann curvature tensor

I have harpooned the great white whale of mathematics (for me at least) the Reimann curvature tensor.  Even better, I understand what curvature is, and how the Reimann curvature tensor expresses it.  Below you’ll see the nightmare of notation by which it is expressed.

Start with curvature.  We all know that a sphere (e.g. the earth) is curved.  But that’s when you look at it from space.  Gauss showed that you could prove a surface was curved just be performing measurements entirely within the surface itself, not looking at it from the outside (theorem egregium).

Start with the earth, assuming that it is a perfect sphere (it isn’t because its rotation fattens its middle).  We’ve got longitude running from pole to pole and the equator around the middle.  Perfect sphere means that all points are the same distance from the center — e.g. the radius.  Call the radius 1.

Now think of a line from the north pole to the plane formed by the equator (radius 1).  Take the midpoint of that line and inscribe a circle on the sphere, parallel to the plane of the equator.  Its radius is the half the square root of 3 (or 1.73). This comes from the right angle triangle just built with hypotenuse is 1 and  one side 1/2.   The circumference of the equator is 2*pi (remember the sphere’s radius is 1).  The circumference of the newly inscribed circle is 1.73 * pi.

Now pick a point on the smaller circle and follow a longitude down to the equator.  Call this point down1.  Move in one direction by 1/4 of the circumference of the sphere (pi/2).  Call that point on the equator down then across

Now go back to the smaller circle at the first point you picked and move in the same direction as you did on the equator by absolute distance pi/2 (not by pi/2 radians).  Then follow the longitude down to the equator.  Call that point across then down.  The two will not be the same.  Across then down is farther from down 1 than down then across.

The difference occurs because the surface of the sphere is curved, and the difference in endpoints of the two paths is exactly what the Reimann curvature tensor measures.

Here is the way the Riemann curvature tensor is notated.  Hideous isn’t it? If you’re going to have any hope of understanding general relativity (not special relativity) you need to understand curvature.

I used paths in the example, Riemann uses the slope of the paths (e.g derivatives) which makes things much more complicated.  Which is where triangles (dels), and the capital gammas (Γ) come in.

To really understand the actual notation, you need to understand what a covariant derivative actually is, which is much more complicated, but knowing what you know now, you’ll see where you are going when enmeshed in thickets of notation.

What the Riemann curvature tensor is actually saying is that the order of taking covariant derivatives (which is the same thing as the order of taking paths)  is NOT commutative.

The simplest functions we grow up with are commutative.  2 + 3 is the same as 3 + 2, and 5*3 = 3*5.  The order of the terms doesn’t matter.

Although we weren’t taught to think of it that way, subtraction is not.  5 – 3 is not the same as 3 – 5.  There is all sorts of nonCommutativity in math.  The Lie bracket is one such, the Poisson bracket  another, and most groups are nonCommutative.  But that’s enough.  I wish I’d known this when I started studying general relativity.

### Is the microtubule alive ??

When does inanimate matter become animate?  How about cilia — they beat and move around.  No one would call  the alpha/beta tubulin dimer from which they are formed alive.  The tubulin proteins contain 450 amino acids or so and form a globule 40 Angstroms (4 nanoMeters) in diameter.  The dimer is then 40 x 80 Angstroms and looks like an oil drum.  Then they form protofilaments stacked end to end — e.g. alpha beta alpha beta.  Then 13 protofilaments then align side by side to form the microtubule (which is 250 Angstroms in diameter, with a central hole about half that size.  Do you think you could design a protein to do this?

Lets make it a bit more complicated, and add another 10 protofilaments forming a second incomplete ring.  This is the microtubule doublet, and each cilium has 9 of them all arranged in a circle.

Hopefully you have access to the 31 October cell where the repeating unit of the microtubule doublet is shown in exquisite detail — https://www.cell.com/action/showPdf?pii=S0092-8674%2819%2931081-5. — Cell 179, 909–922 ’19

The structure is from the primitive eukaryote Chlamydomonas, the structure repeats every 960 Angstroms (e.g every 12 alpha/beta tubulin dimers).  So just for one repeating unit which is just under 1/10 of a micron (10,000 Angstroms) there are (13 + 10) * 12 = 276 dimers.  The cilium is 12 microns long so that’s 12 * 276 * 100 = 298,080 alpha tubulin dimers/microtubule doublet. The cilium has 9 of these + another doublet in the center, so thats 2,980,800 alpha tubulin dimers/cilium.

The cell article is far better than this, because it shows how the motor proteins which climb along the outside of the doublet (such as dynein) attach.The article also describes the molecular ruler (basically a 960 Angstrom coil coil which spans the repeat. They found some 38 different proteins associated with the microtubule repeat.  They repeat as well at 80, 160, 240, 480 and 960 Angstrom periodicity.  The proteins in the hole in the center of the microtubule (e.g. the lumen) are rich in a protein module called the EF hand which binds calcium, and which likely causes movement of the microtubule, at which point the damn thing (whose structure we now know) appears alive.

Because of the attachment of the partial ring (B ring) to the complete ring of protofilaments, each of the 23 protofilaments has a unique position in the doublet, and each of the proteins in the lumen is bound to a specific mitotubule profilament. There are 6 different coiled coil proteins inside the A ring, occupying  specific furrows between the protofilaments.

Staggering complexity built from a simple subunit, but then Monticello is only made of bricks.

### Want to understand Quantum Computing — buy this book

As quantum mechanics enters its second century, quantum computing has been hot stuff for the last third of it, beginning with Feynman’s lectures on computation in 84 – 86.  Articles on quantum computing  appear all the time in Nature, Science and even the mainstream press.

Perhaps you tried to understand it 20 years ago by reading Nielsen and Chuang’s massive tome Quantum Computation and Quantum information.  I did, and gave up.  At 648 pages and nearly half a million words, it’s something only for people entering the field.  Yet quantum computers are impossible to ignore.

That’s where a new book “Quantum Computing for Everyone” by Chris Bernhardt comes in.  You need little more than high school trigonometry and determination to get through it.  It is blazingly clear.  No term is used before it is defined and there are plenty of diagrams.   Of course Bernhardt simplifies things a bit.  Amazingly, he’s able to avoid the complex number system. At 189 pages and under 100,000 words it is not impossible to get through.

Not being an expert, I can’t speak for its completeness, but all the stuff I’ve read about in Nature, Science is there — no cloning, entanglement, Ed Frenkin (and his gate), Grover’s algorithm,  Shor’s algorithm, the RSA algorithm.  As a bonus there is a clear explanation of Bell’s theorem.

You don’t need a course in quantum mechanics to get through it, but it would make things easier.  Most chemists (for whom this blog is basically written) have had one.  This plus a background in linear algebra would certainly make the first 70 or so pages a breeze.

Just as a book on language doesn’t get into the fonts it can be written in, the book doesn’t get into how such a computer can be physically instantiated.  What it does do is tell you how the basic guts of the quantum computer work. Amazingly, they are just matrices (explained in the book) which change one basis for representing qubits (explained) into another.  These are the quantum gates —  ‘just operations that can be described by orthogonal matrices” p. 117.  The computation comes in by sending qubits through the gates (operating on vectors by matrices).

Be prepared to work.  The concepts (although clearly explained) come thick and fast.

Linear algebra is basic to quantum mechanics.  Superposition of quantum states is nothing more than a linear combination of vectors.  When I audited a course on QM 10 years ago to see what had changed in 50 years, I was amazed at how little linear algebra was emphasized.  You could do worse that read a series of posts on my blog titled “Linear Algebra Survival Guide for Quantum Mechanics” — There are 9 — start here and follow the links — you may find it helpful — https://luysii.wordpress.com/2010/01/04/linear-algebra-survival-guide-for-quantum-mechanics-i/

From a mathematical point of view entanglement (discussed extensively in the book) is fairly simple -philosophically it’s anything but – and the following was described by a math prof as concise and clear– https://luysii.wordpress.com/2014/12/28/how-formal-tensor-mathematics-and-the-postulates-of-quantum-mechanics-give-rise-to-entanglement/

The book is a masterpiece — kudos to Bernhardt

### Why it is sometimes good to read the preface7

“the (gravitational) field equations are derived  . . .  from an analysis of tidal forces.”  Thus sayeth p. xii of the preface to “The Geometry of Spacetime” by James J. Callahan.  This kept me from passing over pp. 174 –> on tides, despite a deep dive back into differentiating complicated functions, Taylor series etc. etc. Hard thinking about tidal forces finally gave me a glimpse of what general relativity is all about.

Start with a lemma.  Given a large object (say the sun) and a single small object (say a satellite, or a spacecraft), the path traced out by the spacecraft will lie in a plane.  Why?

All gravitational force is directed toward the sun (which can be considered as a point mass – it is my recollection that it took Newton 20 years to prove this delaying the publication of the Principia , but I can’t find the source).  This makes the gravitational force radially symmetric.

Now consider an object orbiting the sun (falling toward the sun as it orbits, but not hitting the sun because its angular momentum carries away). Look at two close by points in the orbit and the sun, forming a triangle.  The long arms of the triangle point toward the sun.  Now imagine in the next instant that the object goes to a fourth point out of the plane formed by the first 3.  Such a shift in direction requires a force to produce it, but in the model there is only gravity, so this is impossible meaning that all points of the orbit lie in a plane containing the sun considered as a point mass.

You are weightless when falling, even though you are responding to the gravitational force (paradoxic but true).   An astronaut in a space capsule is weightless because he or she is falling but the conservation of angular momentum keeps them going around the sun.

Well if the sun can be considered a point mass, so can the space capsule.  Call the local coordinate of the point representing the capsule point mass x.  The orbit of x around the sun is in the x — sun plane.

Next put two objects 1 foot above and below the x — sun plane.

object1

x  ——————————sun point mass

object2

Objects 1 and 2 orbit in a plane containing the sun point mass as well.  They do not orbit parallel to x (but very close to parallel).

What happens with the passage of time?   The objects approach each other.  To an astronaut inside the capsule it looks like a force (similar to gravity) is pushing them together.  These are the tidal forces Callahan is talking about.

Essentially the tidal are produced by gravitational force of the sun even though everything in the capsule floats around feeling no gravity at all.

Consider a great circle on a sphere — a longitudinal circle on the earth will do.  Two different longitudinal great circles will eventually meet each other.  No force is producing this, but the curvature of the surface in which they are embedded.

I think that  what appear to be tidal forces in general relativity are really due to the intrinsic curvature of spacetime.  So gravity disappears into the curvature of spacetime produced by mass.   I’ll have to go through the rest of the book to find out.  But I think this is pretty close, and likely why Callahan put the above quote into the preface.

If you are studying on your own, a wonderful explanation of just what is going on under the algebraic sheets of the Taylor series is to be found pp. 255 –> of Fundamentals of Physics by R. Shankar.  In addition to being clear, he’s funny.  Example: Nowadays we worry about publish and perish, but in the old days it was publish and perish.

### Book recommendation

Tired of reading books about physics?  Want the real McCoy”?  Well written and informal?  Contains stuff whose names you know but don’t understand — Jones Polynomial, Loop Quantum Gravity, Quantum field theory, Gauge groups and transformations —  etc. etc.

Up to date?  Well no, it’s 25 years old but still very much worth a read, so very unlike molecular biology, chemistry, computer science etc. etc.

Probably you should know as much physics and math as a beginning chemistry grad student. If you studied electromagnetism through Maxwell’s equations it would be a plus.  I stopped at Coulomb’s Law, and picked up enough to understand NMR.

This will give you a sample of the way it is written

“Much odder is that we are saying the vector field v is the linear combination of . .  partial derivatives.  What we are doing might be regarded as rather sloppy, since we are identifying two different although related things: the vector  field and the operator v^i * d-/dx^i which takes a directional derivative in the direction of v.”

“Now let us define vector fields on a manifold M. .. . these will be entities whose sole ambition in life is to differentiate functions”

The book is “Gauge FIelds, Knots and Gravity” by John Baez and Javier P. Muniain.

The writing, although clear has a certain humility.  “Unfortunately understanding these new ideas depends on a through mastery of quantum field theory, general relativity, geometry, topology and algebra.  Indeed, it is almost certain that nobody is sufficiently prepared to understand these ideas fully.”

I’m going to take it with me to the amateur chamber music festival.  As usual, at least 2 math full professors will be there to help me out.  Buy it and enjoy

### Book Review — The Universe Speaks in Numbers

Let’s say that back in the day, as a budding grad student in chemistry you had to take quantum mechanics to see where those atomic orbitals came from.   Say further, that as the years passed you knew enough to read News and Views in Nature and Perspectives in Science concerning physics as they appeared. So you’ve heard various terms like J/Psi, Virasoro algebra, Yang Mills gauge symmetry, Twisters, gluons, the Standard Model, instantons, string theory, the Atiyah Singer theorem etc. etc.  But you have no coherent framework in which to place them.

Then “The Universe Speaks in Numbers” by Graham Farmelo is the book for you.  It will provide a clear and chronological narrative of fundamental physics up to the present.  That isn’t the main point of the book, which is an argument about the role of beauty and mathematics in physics, something quite contentious presently.  Farmelo writes well and has a PhD in particle physics (1977) giving him a ringside seat for the twists and turns of  the physics he describes.  People disagree with his thesis (http://www.math.columbia.edu/~woit/wordpress/?p=11012) , but nowhere have I seen anyone infer that any of Farmelo’s treatment of the physics described in the book is incorrect.

40 years ago, something called the Standard Model of Particle physics was developed.  Physicists don’t like it because it seems like a kludge with 19 arbitrary fixed parameters.  But it works, and no experiment and no accelerator of any size has found anything inconsistent with it.  Even the recent discovery of the Higgs, was just part of the model.

You won’t find much of the debate about what physics should go from here in the book.  Farmelo says just study more math.  Others strongly disagree — Google Peter Woit, Sabine Hossenfelder.

The phenomena String theory predicts would require an accelerator the size of the Milky Way or larger to produce particles energetic enough to probe it.  So it’s theory divorced from any experiment possible today, and some claim that String Theory has become another form of theology.

It’s sad to see this.  The smartest people I know are physicists.  Contrast the life sciences, where experiments are easily done, and new data to explain arrives weekly.

### A mathematical kludge and its repair

If you are in a train going x miles an hour and throw a paper airplane forward at x feet per second (or x * 3600/5280 miles per hour, relative to someone outside the train sees the plane move a bit faster than x miles an hour.  Well that’s the whole idea of the Galilean transformation.  Except that they don’t really see velocities adding that way for really fast velocities (close to the speed of light).

Relativity says that there are no privileged sites of observation and that no matter how fast two observer frames are moving relative to each other light will zing past both at the same speed (3 x 10^8 meters/second, 186,000 miles/second).

All of Newton’s mechanics and force laws obeys the Galilean transformation (e.g. velocities add).  Maxwell conceived a series of 4 laws linking electricity and magnetism together, which predicted new phenomena (such as radio waves, and the fact that light was basically a form of wave traveling through space).

Even though incredibly successful, Maxwell’s laws led to an equation (the wave equation) which didn’t obey the Galilean transformation.  This led Lorentz to modify it so the wave equation did obey Galileo.  If you’ve got some mathematical background an excellent exposition of all this is to be found in “The Geometry of Spacetime” by James J. Callahan pp. 22 – 27.

The Lorentz transformation is basically a kludge which makes things work out.  But he had no understanding of why it worked (or what it meant).  The equations produced by the Lorentz transformation are ugly.

Here are the variables involved.

t’ is time in the new frame, t in the old, x’ is position in the new frame x in the old. v is the constant velocity at which the two observation frames are moving relative to each other. c is the common symbol for the velocity of light.

Here are the two equations

t’ =  ( t – vz/c^2 )/ sqrt (1 – v^2/c^2)

x’ = ( z – vt ) /  sqrt (1 – v^2/c^2)

Enter Einstein — he derived them purely by thought.  I recommend Appendix 1 in Einstein’s book “Relativity”.  Amazingly you do not need tensors or even calculus to understand his derivation — just high school algebra (and not much of that — no trigonometry etc. etc.)  You will have the pleasure of watching the power of a great mind at work.

One caveat.  The first few equations won’t make much sense if you hit the appendix without having read the rest of the book (as I did).

Light travels at c miles/hour, so multiplying c by time gives you where it is after t seconds.  In equations x = ct.  This is also true for another reference frame x’ = ct’.

This implies that both x – ct =  0 and x’ – ct’ = 0

Then Einstein claims that these two equations imply that

(x – ct) = lambda * (x’ – ct’) ; lambda is some nonzero number.

Say what?  Is he really saying  0 = lambda * 0.

This is mathematical fantasy.  Lambda could be anything and the statement lacks mathematical content.

Yes, but . . .

It does not lack physical content, which is where the rest of the book comes in.

This is because the two frames (x, t) and (x’ , t’) are said to be in ‘standard configuration which is a complicated state of affairs. We’ll see why y, y’, z, z’ are left out shortly

The assumptions of the standard configuration are as follows:

• An observer in frame of reference K defines events with coordinates t, x
• Another frame K’ moves with velocity v relative to K, with an observer in this moving frame K’ defining events using coordinates t’, x’
• The coordinate axes in each frame of reference are parallel
• The relative motion is along the coincident xx’ axes (y = y’ and z = z’ for all time, only x’ changes, explaining why they are left out)
• At time t = t’ =0, the origins of both coordinate systems are the same.

Another assumption is that at time t = t’ = 0 a light pulse is emitted by K at the origin (x = x’ = 0)

The only possible events in K and K’ are observations of the light pulse. Since the velocity of light (c) is independent of the coordinate system, K’ will see the pulse at time t’ and x’ axis location ct’, NOT x’-axis location ct’ – vt’ (which is what Galileo would say). So whenever K sees the pulse at time t and on worldline (ct, t), K’ will see the pulse SOMEWHERE on worldline (ct’, t’).

The way to express this mathematically is by (3) (x – ct) = lambda * (x’ – ct’)

This may seem trivial, but I spent a lot of time puzzling over equation (3)

Now get Einstein’s book and watch him derive the complicated looking Lorentz transformations using simple math and complex reasoning.

### Bye bye stoichiometry

Until recently, developments in physics basically followed earlier work by mathematicians Think relativity following Riemannian geometry by 40 years.  However in the past few decades, physicists have developed mathematical concepts before the mathematicians — think mirror symmetry which came out of string theory — https://en.wikipedia.org/wiki/Mirror_symmetry_(string_theory). You may skip the following paragraph, but here is what it meant to mathematics — from a description of a 400+ page book by Amherst College’s own David A. Cox

Mirror symmetry began when theoretical physicists made some astonishing predictions about rational curves on quintic hypersurfaces in four-dimensional projective space. Understanding the mathematics behind these predictions has been a substantial challenge. This book is the first completely comprehensive monograph on mirror symmetry, covering the original observations by the physicists through the most recent progress made to date. Subjects discussed include toric varieties, Hodge theory, Kahler geometry, moduli of stable maps, Calabi-Yau manifolds, quantum cohomology, Gromov-Witten invariants, and the mirror theorem. This title features: numerous examples worked out in detail; an appendix on mathematical physics; an exposition of the algebraic theory of Gromov-Witten invariants and quantum cohomology; and, a proof of the mirror theorem for the quintic threefold.

Similarly, advances in cellular biology have come from chemistry.  Think DNA and protein structure, enzyme analysis.  However, cell biology is now beginning to return the favor and instruct chemistry by giving it new objects to study. Think phase transitions in the cell, liquid liquid phase separation, liquid droplets, and many other names (the field is in flux) as chemists begin to explore them.  Unlike most chemical objects, they are big, or they wouldn’t have been visible microscopically, so they contain many, many more molecules than chemists are used to dealing with.

These objects do not have any sort of definite stiochiometry and are made of RNA and the proteins which bind them (and sometimes DNA).  They go by any number of names (processing bodies, stress granules, nuclear speckles, Cajal bodies, Promyelocytic leukemia bodies, germline P granules.  Recent work has shown that DNA may be compacted similarly using the linker histone [ PNAS vol.  115 pp.11964 – 11969 ’18 ]

The objects are defined essentially by looking at them.  By golly they look like liquid drops, and they fuse and separate just like drops of water.  Once this is done they are analyzed chemically to see what’s in them.  I don’t think theory can predict them now, and they were never predicted a priori as far as I know.

No chemist in their right mind would have made them to study.  For one thing they contain tens to hundreds of molecules.  Imagine trying to get a grant to see what would happen if you threw that many different RNAs and proteins together in varying concentrations.  Physicists have worked for years on phase transitions (but usually with a single molecule — think water).  So have chemists — think crystallization.

Proteins move in and out of these bodies in seconds.  Proteins found in them do have low complexity of amino acids (mostly made of only a few of the 20), and unlike enzymes, their sequences are intrinsically disordered, so forget the key and lock and induced fit concepts for enzymes.

Are they a new form of matter?  Is there any limit to how big they can be?  Are the pathologic precipitates of neurologic disease (neurofibrillary tangles, senile plaques, Lewy bodies) similar.  There certainly are plenty of distinct proteins in the senile plaque, but they don’t look like liquid droplets.

It’s a fascinating field to study.  Although made of organic molecules, there seems to be little for the organic chemist to say, since the interactions aren’t covalent.  Time for physical chemists and polymer chemists to step up to the plate.

### Book recommendation

“Losing the Nobel Prize”  by Brian Keating is a book you should read if you have any interest in l. physics. 2. astronomy 3. cosmology 4. the sociology of the scientific enterprise (physics division) 5. The Nobel prize 6. The BICEPs and BICEP2 experiments.

It contains extremely clear explanations of the following

l. The spiderweb bolometer detector used to measure the curvature of the universe

2. How Galileo’s telescope works and what he saw

3. How refracting and reflecting telescopes work

4. The Hubble expansion of the universe and the problems it caused

5. The history of the big bang, its inherent problems, how Guth solved some of them but created more

6. How bouncing off water (or dust) polarizes light

7. The smoothness problem, the flatness problem and the horizon problem.

8. The difference between B modes and E modes and why one would be evidence of gravitational waves which would be evidence for inflation.

The list could be much longer.  The writing style is clear and very informal.   Example: he calls the dust found all over the universe — cosmic schmutz.   Then there are the stories about explorers trying to reach the south pole, and what it’s like getting there (and existing there).

As you probably know BICEP2 found galactic dust and not the polarization pattern produced by gravitational waves.  The initial results were announced 17 March 2014 to much excitement.  It was the subject of a talk given the following month at Harvard Graduate Alumni Day, an always interesting set of talks.  I didn’t go to the talk but there were plenty of physicists around to ask about the results (which were nowhere nearly as clearly explained as this book).  All of them responded to my questions the same way — “It’s complicated.”

The author Brian Keating has a lot to say about Nobels and their pursuit and how distorting it is, but that’s the subject of another post, as purely through chance I’ve known 9 Nobelists before they received their prize.

It will also lead to another post about the general unhappiness of a group of physicists.

### How to study math by yourself far away from an academic center

“Differential geometry is the study of things that are invariant under a change of notation.”   Sad but true, and not original as it appears in the introduction to two different differential geometry books I own.

Which brings me to symbol tables and indexes in math books. If you have a perfect mathematical mind and can read math books straight through understanding everything and never need to look back in the book for a symbol or concept you’re not clear on, then you don’t need them.  I suspect most people aren’t like that.  I’m not.

Even worse is failing to understand something (say the connection matrix) and trying to find another discussion in another book.  If you go to an older book (most of which do not have symbol tables) the notation will likely be completely different and you have to start back at ground zero.  This happened when I tried to find what a connection form was, finding the discussion in one book rather skimpy.  I found it in O’Neill’s book on elementary differential geometry, but the notation was completely different and I had to read page after page to pick up the lingo until I could understand his discussion (which was quite clear).

Connections are important, and they underlie gauge theory and a lot of modern physics.

Good math books aren’t just theorem proof theorem proof, but have discussions about why you’d want to know something etc. etc.  Even better are discussions about why things are the way they are.  Tu’s book on Differential geometry is particularly good on this, showing (after a careful discussion of why the directional derivative is the way it is) how the rather abstract definition of a connection on a manifold arises by formalizing the properties of the directional derivative and using them to define the connection.

Unfortunately, he presents curvature in a very ad hoc fashion, and I’m back to starting at ground zero in another book (older and without a symbol table).

Nonetheless I find it very helpful when taking notes to always start by listing what is given.  Then a statement of the theorem, particularly putting statements like for all i in { 1, …. ,n} in front.  In particular if a concept is defined, put how the concept is written in the definition

e.g.

Given X, Y smooth vector fields

def:  Lie Bracket (written [ X, Y ] ) ::= DxY – DyX

with maybe a link to a page in your notes where Dx is defined

So before buying a math book, look to see how fulsome the index is, and whether it has a symbol table.