Category Archives: Science

New Paper: Direct Transformation of Vacancy Voids to Stacking Fault Tetrahedra

Direct Transformation of Vacancy Voids to Stacking Fault Tetrahedra

B. P. Uberuaga, R. G. Hoagland, A. F. Voter, and S. M. Valone
Phys. Rev. Lett. 99, 135501 (2007)

Defect accumulation is the principal factor leading to the swelling and embrittlement of materials during irradiation. It is commonly assumed that, once defect clusters nucleate, their structure remains essentially constant while they grow in size. Here, we describe a new mechanism, discovered during accelerated molecular dynamics simulations of vacancy clusters in fcc metals, that involves the direct transformation of a vacancy void to a stacking fault tetrahedron (SFT) through a series of 3D structures. This mechanism is in contrast with the collapse to a 2D Frank loop which then transforms to an SFT. The kinetics of this mechanism are characterized by an extremely large rate prefactor, tens of orders of magnitude larger than is typical of atomic processes in fcc metals.

Science? We don’t need no stinking science!

Not a surprise, really, but the previous Surgeon General of the US, Richard H. Carmona, testified before Congress that the Bush administration put politics before science, delibrately watering down or delay scientific reports that went against their policies and actively asking the Surgeon General to play politics.

In relation to my previous rant, this shows the danger of having leaders who have no real knowledge nor care about science and use their personal beliefs and convications to set policy that is in direct conflict with scientific evidence.

New Paper: Stick-slip behavior of grain boundaries

Stick-slip behavior of grain boundaries studied by accelerated molecular dynamics

Y. Mishin, A. Suzuki, B. P. Uberuaga, A. F. Voter
Phys. Rev. B 75, 224101 (2007)

We apply parallel-replica molecular-dynamics (MD) simulations to study the peak stress versus velocity relation during stress-driven grain-boundary (GB) migration coupled to shear deformation. Because of the limited time scale of regular MD, all previous atomistic simulations of GB migration were implemented at velocities orders of magnitude higher than experiment. By accelerating MD simulations, the parallel-replica method has allowed us to greatly expand the velocity range and finally approach the experimental velocities. The GB motion observed in this work follows the general stress-velocity relation characteristic of stick-slip dynamics over a wide velocity interval. At the high-velocity end of this interval, the finite damping rate causes a reversal of the stress-velocity curve. At low velocities, we begin to see reverses of GB displacements, indicating the approaching crossover between the stick-slip and driven Brownian regimes. This study points to a close analogy between couple GB motion in crystals and other known cases of stick-slip dynamics, including the tip movements in atomic friction microscopy.

Belief and Politics

There has been a lot of talk recently, thanks to the candidacy of Mitt Romney, about the role of personal belief in politics. Jacob Weisberg, writing for Slate, asks if it is religious bigotry to not vote for Romney just because he is Mormon. He argues that this is a valid question because if Romney believes in a religion that is based upon a con-man’s lies, we, as the voters, should know about it and judge him on his gullibility. From a different perspective, Jerry Coyne, in his Edge article, discusses the various candidates’ view of evolution. He discusses Brownback’s claim that we should reject scientific findings if they conflict with our faith, but accept them if they’re compatible (Coyne’s paraphrase of Brownback). Coyne’s point is that if candidates reject science that they are uncomfortable with but that the scientific community strongly supports, we should seriously question if that candidate is worth our vote.

(Incidentally, one minor quibble with Coyne’s otherwise excellent article: He draws the analogy of not believing in evolution to be the same as not believing in atoms and states: …there is just as much evidence for the fact of evolution as there is for the existence of atoms. While I think that the scientific evidence in support of the theory of evolution is strong, atoms are directly observable by several techniques while evolution, to the best of my knowledge, is not directly observed.)

Both articles bring up the role of belief in politics and whether we, as the voting public, should take into account the belief of a candidate before voting for him or her. I would venture to say that both Weisberg and Coyne conclude that not only should we, but we absolutely must take belief into consideration. After all, personal belief plays a major role in people’s lives, informing their decisions and how they act. Just look at the role that religion and belief have played in Bush’s presidency.

Weisberg focuses specifically on Mormonism, feeling that Mormonism was essentially started by a con-man and that anyone who believes what Joseph Smith said is too gullible to deserve his vote. I think this is a little unfair, as the one major disadvantage of Mormonism compared to other religions is its age: it is young enough that a lot more is known about the people who started it than most main stream religions. For all we know, most religions were started by con-men (check out this description by Harlan Ellison on the origins of Scientology).

This, however, raises a bigger point: is anyone who has deep religious conviction then unfit for office? All religions have aspects to them that contradict modern scientific findings. Things that are either untestable or unverifiable. Things that they later have to recant as science uncovers new facts about the universe we live in, facts such as the age of the planet, the age of the universe, the origin of species, the Earth’s place in the universe, the origin of the universe, the nature of free will, the origin of a person’s orientation, and the list goes on. Weisberg points out that, just as he wouldn’t vote for a Mormon, he wouldn’t vote for a fundamentalist that truely believed the Earth was only 7000 years old. But what of a candidate that believed in a literal Garden of Eden? At what point do you draw the line between beliefs that are ok for a public servant to have and ones that are too out there?

Probably most dangerous is, as Coyne points out, those candidates that just plain deny science because it conflicts with their beliefs. This is the same attitude that caused the Church to lock up Galileo when he said the Earth wasn’t the center of the universe. When this attitude prevails, it causes politicians to ignore scientific evidence and use their faith as a guide in times of difficulty. And this can have potentially disasterous results, as our delay in addressing Global Warming may soon show us.

Personal belief has a role in personal life, where the decisions are smaller scale. And faith is probably part of human nature, stemming from a need to place some kind of order on the world around us. But, when faith is the dominant mechanism for making decisions that affect millions and perhaps billions of people, it becomes dangerous. We don’t all agree on what faith is the correct one, which one better informs us about the world around us. Your faith doesn’t necessarily jive with mine. While science isn’t perfect, it has three advantages, in my mind, over faith. First, it is self-correcting. If I publish results that are suspect, other people will check and double-check them to verify if I have done a good job. Theories and hypotheses are updated and replaced as new evidence is found that does or does not support them. Second, science is relatively objective. All science has a bit of the researcher’s bias in it, but that is again the role of peer review, to uncover those biases and make the results as objective as possible. Finally, science is predictive. That is the ultimate test of scientific theories: once we have a theory, can we predict something new that can then be verified. Science can be tested, faith cannot.

A final point about the role of science in society: science, as a way of looking at the world, has spread throughout the world without any coersion on the part of missionaries or conquerors. It has done so on its own merits. It is thus, in some sense, the one view of the world that the world has come to some level of consensus on. People in all parts of the world have adopted, to varying degrees, a scientific outlook. And they have done this on their own initiative.

The symbols are those approved for use on graves at Arlington Cemetery (minus a few that have copyrights).

Some Cool Science Sites

Whether you like it or not, science holds a central and critical role in modern society. Even those of us who are science-adverse still have the cell phone, the car, and the TV that are the direct result of scientific innovation. But, beyond that, science has transformed how we view the universe, as well as how we view our place within it. It behooves all of us to know at least a little bit about science so that we can better understand the world in which we live. Here are a few science related sites I stumbled upon that are worth the visit.

The American Institute of Physics, publisher of Physics Today, also runs the Center for History of Physics. Their mission (from their website):

AIP’s Center for History of Physics works to to preserve and make known the historical record of modern physics and allied sciences. Through documentation, archival collections and educational initiatives, the Center ensures that the heritage of modern physics is safeguarded and its story accurately told.

One of the exhibits in the Center is Cosmic Journey: A History of Scientific Cosmology. This exhibit traces the development of human understanding and views of the universe in which we live, from the beginnings of a scientific approach to looking at the universe of the Greeks to the most recent tools scientists are using today to examine the mysteries of the universe. They also have exhibits on Marie Curie, Albert Einstein, the transistor, Heisenberg and uncertainty and more.

Game theory is an up and coming field that tries to bring the rigor of mathematics to human endeavors such as economics, political science and business. Perhaps the most famous game in game theory is the prisoner’s dilemma, as described on the site

A game frequently displayed in television police dramas. Two partners in crime are separated into separate rooms at the police station and given a similar deal. If one implicates the other, he may go free while the other receives a life in prison. If neither implicates the other, both are given moderate sentences, and if both implicate the other, the sentences for both are severe.

The role of game theory is to understand what choices people would make in situations like this, if those choices can be predicted, and if those choices are “rational,” or make sense. gives a nice introduction to this field, including interactive games to demonstrate some of the basic principles of game theory.

Mathematics is a broad field with differing levels of applicability to other, more “mundane” disciplines. One example of a branch of mathematics that started off as mathematicians doing math just for the hell of it, but has begun having ramifications for science, is the area of knot theory. For example, knot theory is playing a role in string theory, the supposed successor to quantum field theory and the current best candidate for a Grand Unified Theory of everything. offers an amazing software package, for Mac, Windows and even Linux, for manipulating knots on your computer. In addition to generating pretty pictures (like the one above), you can use the software to examine the topology of knots, such as reducing complex knots to their simplest form (unfolding them). The software is very fun to play with and generates some stunning graphics that would make for an excellent screen saver.

The final site I wanted to mention today is Ben Goldacre’s Bad Science blog. Dr. Goldacre is a doctor and journalist in Britain and he writes a bad science column for The Guardian. His work has appeared in other media as well. In his blog, he discusses the scientific “merits” (or non-merits, more often than not) of reports in the media that claim some scientific legitimacy. He has taken it upon himself to expose bad scientific claims in order to both educate the public about misleading reports as well as to help people learn when scientific claims are not so scientific after all.