How can living organisms be so highly ordered?

This may seem to violate the second law of thermodynamics.

In the Intermediate Biophysics class meeting today we agreed to start reading through Philip Nelson's excellent book, Biological Physics: Energy, Information, and Life.

Each chapter begins with a biological question, and a terse slogan encapsulating a physical idea relevant to the question. Chapter 1 begins with:

Biological question: How can living organisms be so highly ordered?
Physical idea: The flow of energy can leave behind increased order.

He introduces the idea of free energy as the useful energy or quality of energy. The distinction between high and low quality energy is a matter of order or organisation.

Living beings consume order not energy.
Free energy transduction is what the biosphere does to create order.

The figure below is a nice way to illustrate transduction of free energy.
A machine uses osmotic flow to convert disorder (random molecular motion) into work in the upper part of the figure.

In the lower part of the figure doing work pulling on the weight increases the order in the system, i.e., the sugar solution becomes more concentrated (reverse osmosis).

More fundamentalism

Which is more fundamental? Elementary particles or elastic solids?

In his book A Different Universe, Bob Laughlin considers the implications of the observation that quantities such as the Josephson constant and the von Klitzing resistance are known will incredible accuracy, the latter to one part in ten billion (pp.15-16):

``Paradoxically, the existence of these highly reproducible experiments leads us to think in two mutually incompatible ways about what is fundamental. One is that exactness reveals something about the primitive building blocks out of which our complicated, uncertain world is made…. The other is that exactness is a collective effect that comes into existence because of a principle of organization…. There is no way to reconcile these two ideas; they are exact opposites. Yet we use the fundamental to describe both.”

Laughlin points out:

“The fractional quantum Hall effect reveals that ostensibly indivisible quanta—in this case the electron charge e—can be broken into pieces through self-organization of phases. The fundamental things, in other words, are not necessarily fundamental.”

He further claims that in quantum field theory the vacuum state is not fundamental but is “an emergent phenomena characteristic of a phase of matter” (p.110-115).

Laughlin claims that if Einstein were alive today then he would,

“conclude that his beloved principle of relativitiy was not fundamental at all but emergent – a collective property of the matter constituting space-time that becomes increasingly exact at long length scales but fails at short ones.’’ (p. 126)

Key concepts in molecular electronics

This morning at MM2009 Abe Nitzan gave a beautiful talk which gave a unified physical picture of many of the important processes (electron transfer, solvation, transition state theory, vibrational relaxation, ....) that are key to understanding molecular conduction. On his website I found an earlier and more detailed version of the talk, given a few years ago in Cape Town.

This makes a nice companion to reading his book.

Observing the collapse of the wave function

Here is the talk I just gave at the MM2009 meeting.

One point I tried to bring out was how the "peak shift" that one observes in photon echo spectroscopy (see figure below which is taken from this paper by Cho, Carlsson, and Jimenez) is actually the time scale involved in the collapse of the wavefunction due to the environment making a continuous "measurement" of the quantum state of the chromophore.
The first photon pulse creates a coherent superposition of the electronic ground and first excited states.This is discussed in more detail in this review I wrote with Joel Gilmore.

Can we truly predict crystal structures?

This post was stimulated by a nice talk that Richard Catlow gave at MM2009 last night.
He began with the fact that twenty-one years ago, the Editor of Nature, John Maddox made the provocative claim,

"One of the continuing scandals in the physical sciences is that it remains impossible to predict the structure of even the simplest crystalline solids from a knowledge of their composition."

Woodley and Catlow recently wrote a nice review in Nature Materials, entitled, Crystal structure from first principles, which highlights recent progress and future challenges. I acknowledge the impressive progress, particularly with the developing of ingenious new algorithms for searching configuration space that has been made, but most of this seems to be using semi-empirical force fields and/or empirically based cost functions based on bond valence sums.

I think I would rewrite Maddox claim as,

One of the greatest scientific and philosophical challenges in the physical sciences is that it remains impossible to consistently predict from Schrodinger's equation the structure of crystalline solids solely from a knowledge of their composition and without knowledge of the structure of related materials.

I include "philosophical" challenge because this strikes at the heart of issues relating to emergence and reductionism.

Teaching biological physics

Preparing to teach PHYS3170 Intermediate Biophysics I have been looking at some material on Phillip Nelson's website. He is author of one of the nicest texts, Biological Physics: Energy, Information, and Life.

Several things particularly worth looking at are:

Teaching biological physics, an article in Physics Today.

A course on physical models for biological systems, a talk to the Biophysical Society.
(the syllabus of the actual course is here).

Modelling complex molecular materials

Tomorrow I head down to the Gold Coast to attend MM2009, a conference on Molecular Modelling, mostly attended by computational chemists. There are several great international speakers. Some I look forward to hearing and talking to are:

Richard Catlow (UCL)
He has worked on many things, including cerium oxides. I want to talk to him about some recent results that Elvis Shoko recently obtained concerning charge distribution near oxygen vacancies in cerium oxides.

Weitau Yang (Duke)
Besides being the Y in B2LYP, he has recently written some really nice papers elucidating the limitations of density functional theory (DFT). This short paper in Science gives a nice introduction to the issues.

Abraham Nitzan (Tel Aviv)
Most of his research interests in and approach to chemical physics are similar to my own. He is also author of the only modern text I am aware of on the important topic , Chemical dynamics in condensed phases. I wish I had this when I started working in the area.