Astounding protein folding paper

Posted in Chemistry, General physics by Mike Stay on 2011 February 22

By assuming that to get from point A to point B you don’t have to hit a sequence of points in between—i.e. the way quantum particles work—these guys accurately predict protein folding rates in 15 different real proteins. This is huge.

The Word of God

Posted in Astronomy, Chemistry, Evolution, General physics, History, Poetry, Theocosmology by Mike Stay on 2010 November 3

From desert cliff and mountaintop we trace the wide design,
Strike-slip fault and overthrust and syn and anticline…
We gaze upon creation where erosion makes it known,
And count the countless aeons in the banding of the stone.
Odd, long-vanished creatures and their tracks & shells are found;
Where truth has left its sketches on the slate below the ground.
The patient stone can speak, if we but listen when it talks.
Humans wrote the Bible; God wrote the rocks.

There are those who name the stars, who watch the sky by night,
Seeking out the darkest place, to better see the light.
Long ago, when torture broke the remnant of his will,
Galileo recanted, but the Earth is moving still.
High above the mountaintops, where only distance bars,
The truth has left its footprints in the dust between the stars.
We may watch and study or may shudder and deny,
Humans wrote the Bible; God wrote the sky.

By stem and root and branch we trace, by feather, fang and fur,
How the living things that are descend from things that were.
The moss, the kelp, the zebrafish, the very mice and flies,
These tiny, humble, wordless things–how shall they tell us lies?
We are kin to beasts; no other answer can we bring.
The truth has left its fingerprints on every living thing.
Remember, should you have to choose between them in the strife,
Humans wrote the Bible; God wrote life.

And we who listen to the stars, or walk the dusty grade,
Or break the very atoms down to see how they are made,
Or study cells, or living things, seek truth with open hand.
The profoundest act of worship is to try to understand.
Deep in flower and in flesh, in star and soil and seed,
The truth has left its living word for anyone to read.
So turn and look where best you think the story is unfurled.
Humans wrote the Bible; God wrote the world.

-Catherine Faber, The Word of God

Imaginary Time 2

Posted in Chemistry, General physics, Math by Mike Stay on 2010 July 26

Another part of the analogy I started here, but this time using inverse temperature instead of imaginary time. It describes a thermometer where a mass changes position with temperature. I’m guessing this stuff only applies when the temperature is changing adiabatically.

Thermometer (unitless temperature):
\displaystyle \beta [1] inverse temperature (unitless)
\displaystyle y(\beta) [m] y coordinate
\displaystyle r [kg/s^2 K] spring constant * temp unit conversion
\displaystyle v(\beta) = \frac{dy(\beta)}{d\beta} [m] how position changes with (inverse) temperature
\displaystyle F(\beta) = r \; v(\beta) [kg m/s^2 K] force per Kelvin
\displaystyle T(\beta) = \frac{r}{2}v(\beta)^2 [kg m^2/s^2 K] stretching energy per Kelvin
\displaystyle V(\beta) [kg m^2/s^2 K] potential energy per Kelvin
\displaystyle S = \int (T + V)(\beta) \; d\beta

[kg m^2/s^2 K] entropy
\displaystyle \beta [1/K] inverse temperature
\displaystyle y(\beta) [m] y coordinate
\displaystyle r [kg/s^2 K^2 = bits/m^2 K] how information density changes with temp
\displaystyle v(\beta) = \frac{dy(\beta)}{d\beta} [m K] how position changes with (inverse) temperature
\displaystyle F(\beta) = r \; v(\beta) [kg m/s^2 K = bits/m] force per Kelvin
\displaystyle T(\beta) = \frac{r}{2}v(\beta)^2 [kg m^2/s^2 = bits K] stretching energy = change in stretching information with invtemp
\displaystyle V(\beta) [kg m^2/s^2 = bits K] potential energy = change in potential information with invtemp
\displaystyle S = \int (T + V)(\beta) \; d\beta

[bits] entropy

I assume that the dynamics of such a system would follow a path where \displaystyle \delta S=0; is that a minimum-entropy path or a maximum?

"I looked out the window and what did I see…"

Posted in Chemistry, Fun links by Mike Stay on 2006 December 2

Salting your popcorn with liquid sodium and chlorine gas!