Category Archives: research

An introduction to the water structure problem

Although the macroscopic properties of water have been heavily studied, there are things we don’t understand about this ubiquitous substance. In this post, I will provide an introduction to the problem of describing water’s structure. At first glance, the idea of a liquid having structure seems preposterous. Indeed, liquids cannot maintain a structural arrangement of atoms like solids can. Instead, the atoms/molecules tumble past each other in constant state of motion. This allows for the defining property of the liquid state – the ability to fill a container.   Continue reading

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Our Nature Communciations paper – ice-like phonons in liquid water

Our paper, “The hydrogen-bond network of water supports propagating optical phonon-like modes” was published on January 4th in Nature Communications (full open access pdf). A press release about our work has been issued by the Stony Brook Newsroom and picked up by news aggregator Phys.org.

Our work shows that propagating vibrations or phonons can exist in water, just as in ice. The work analyzes both experimental data and the results of extensive molecular dynamics simulations performed with a rigid model (TIP4P/eps), a flexible model (TIP4P/2005f), and an ab-initio based polarizable model (TTM3F). Many of these simulations were performed on the new supercomputing cluster at Stony Brook’s Institute for Advanced Computational Science.

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Exclusion zone water

Note: this is rather technical. 

This spring I had the pleasure of speaking briefly with a distinguished engineer, inventor, businessperson, and benefactor of science. He explained how he has recently become interested in the work of Prof. Gerald Pollack, who discovered what he calls the “4th phase of water”. The very term “4th phase of water” immediately raised an alarm bell in my head, since there are actually 19 or so known phases of water. I decided to check out what this “4th phase” was. It turns out this ‘phase’ has so far only been observed at the boundary with an odd material called Nafion, so really, it’s interfacial water with special properties, not a new phase of the liquid itself. My research focus the past three years has been understanding the microscopic details underlying the dielectric properties of water.  I am very interested in the structure and behavior of water around proteins and dissolved ions (and have read numerous papers on the subject) so naturally I am interested in Dr Pollack’s claims. Additionally, Pollack has shown that he can use the exclusion done phenomena to build a device that filters out nanospheres, and he claims his discovery can be used for desalination technology. He has not yet actually presented a functioning desalination apparatus, but he has filed a patent for the technology.
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A physicist’s visualization of Bayes’ theorem

Have you noticed that everyone is talking about Bayes’ theorem nowadays?

Bayes’ theorem itself is not very complicated. The human mind, however, is extremely bad at trying to gain an intuitive understanding of Bayes’ theorem based (Bayesian) reasoning. The counter-intuitive nature of Bayesian reasoning, combined with the jargon and intellectual baggage that usually accompanies descriptions of Bayes’ theorem, can make it difficult to wrap one’s mind around. I am a very visual thinker, therefore, I quickly came up with a visualization of the theorem. A little Googling shows that there are many different ways of visualizing Bayes’ theorem. A few months ago I came across a visualization of Bayes’ theorem which I found somewhat perplexing.  Even though mathematical truths are universal, they are internalized differently by every individual. I would love to hear whether others find my visualization approach useful. It is a very physicist-oriented visualization.
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Crackpot Nobelists

I have mixed feelings about the Nobel Prize. To some degree, I sympathize with Feynman:

I agree with Feynman that the discoveries that people made about the nature of reality are more important than titles and distinctions. The true test of scientific work is what it tells us about reality.  Of course “importance” is subjective, but importance can be defined operationally in terms of how much implication a discovery has for the workings of the universe, as made manifest through the breadth of experimental results that it can help explain. The importance of a discovery can also be defined through the impact a discovery has on technology and society.  The later definition is actually closer to Nobel’s intent, although the former version of “importance” usually implies the later as well. The invention of the transistor, a singular event by a few people, surely passes the test. Scrolling through the Nobel prizes in physics, they all appear to pass these operational tests at the highest level. Still, more generally prizes and awards are often corrupted by human cognitive biases and by the insularity of certain social networks – ie winning the prize becomes more about ‘who you know’ rather than ‘what you discovered’. Continue reading

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Filed under Musings, non-technical, pseudoscience

Why physicists still use Fortran

“I don’t know what the programming language of the year 2000 will look like, but I know it will be called FORTRAN.” –  Charles Anthony Richard Hoare, circa 1982

Fortran is rarely used today in industry — one ranking ranks it behind 29 other languages. However, Fortran is still a dominant language for the large scale simulation of physical systems, ie. for things like the astrophysical modeling of stars and galaxies, hydrodynamics codes (cf. Flash), large scale molecular dynamics, electronic structure calculation codes (cf. SIESTA), large scale climate models, etc.  In the field of high performance computing (HPC), of which large scale numerical simulation is a subset, there are only two languages in use today — C/C++ and “modern Fortran” (Fortran 90/95/03/08). The popular Open MPI libraries for parallelizing code were developed for these two languages. So basically, if you want fast code that an run on many processors, you are limited to these two options. Modern Fortran also has a feature called ‘coarrays‘ which puts parallelization features directly into the language. Coarrays started as an extension of Fortran 95 and were incorporated into Fortran 2008 standard.

The heavy use of Fortran by physicists often confounds computer scientists and other outsiders who tend to view Fortran as a historical anachronism.

What I would like to do in this article is explain why Fortran is still a useful language. I am not advocating that physics majors learn Fortran — since most physics majors will end up in research, their time may be better invested in learning C/C++ (or just sticking with Matlab/Octave/Python). What I would like to explain is why Fortran is still used, and show that it is not merely because physicists are ‘behind the time’ (although this is sometimes true – about a year ago I saw a physics student working on a Fortran 77 code, and both the student and adviser were unaware of Fortran 90). Computer scientists should (and do) consider the continued dominance of Fortran in numerical computing as a challenge. Continue reading

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Neuromorphic hardware – a path towards human-level artificial intelligence

Recently we have seen a slew of popular films that deal with artificial intelligence – most notably The Imitation Game, Chappie, Ex Machina, and Her. However, despite over five decades of research into artificial intelligence, there remain many tasks that humans find simple which computers cannot do. Given the slow progress of AI, for many the prospect of computers with human-level intelligence seems further away today than it did when Isaac Asimov’s classic I, Robot was published in 1950.  The fact is, however, that today neuromorphic chips offer a plausible path to realizing human-level artificial intelligence within the next few decades. Continue reading

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The chance that a child will have a severe reaction to the MMR vaccine is less than the chance they will die in 200 mile car ride

Backstory: Several weeks ago Newsday refused to publish a comment I posted on the article “Vaccine court protects ‘big pharma‘”. Having experienced this before (they have a very limited window to submit comments), I decided to rewrite the comment and submit it as an editorial. Recently I discovered it had been published. Unfortunately, the editor removed one of the key points from my piece, and also botched the grammar on the third line, so I am republishing the full piece here, with minor copyediting.

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“Halting State” by Charles Stross

Halting_State(1stEd)Halting State
by Charles Stross
2007, 336 pgs

I originally learned about Charles Stross at the Rensselaer Polytechnic Institute transhumanism club, where his books Singularity Sky and Accelerando where highly lauded. Shamefully, I have not yet read either of these yet. As it turned out I picked up some different books by Stross when the Borders Books in Smithtown closed down. Continue reading

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“The Moon is a Harsh Mistress” by Robert A. Heinlein

The Moon is  Harsh Mistress
by Robert A. Heinlein
1966, 382 pages
A few months ago I finished reading The Moon is a Harsh Mistress by Robert A. Heinlein.  I was shamefully unaware that this was one of the greatest works of science fiction ever written. Previously the only other work by Heinlein I had read was A Stranger in a Strange Land. What drew my attention to The Moon is a Harsh Mistress was the fact that it was recommended by Elon Musk as one of his favourite books.

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