Silly project of the week: molecule dynamics

This week’s project is a molecular dynamics simulation. Don’t get too excited, it’s not using any of the state-of-art algorithms nor is assembling 3-dimensional structures of complex proteins. I began with a simple carbon chain using only coulomb’s law in a spring-mass system.

The molecule I’m using is this:

Molecular Dynamics

The drawing program is quite simple and wont work for most molecules, but for the 2-dimensional simple molecules (max. of 3 connections per atom) it kinda works.

Later on, putting the program to run, each atom “pushes” all others electrically and the spring “pulls” them back. A good way to solve that is to say that q1 . q2 / x² = – k . x = m . d²x/dx² (where x is a vector) and integrate numerically using Runge-Kutta.

But that’s my first openGL program, so I decided to go easy on the model and actually see it pseudo-working with an iterative-based simulation following the same equations above. This picture is a frame after a few iterations.

Quoting its page: “As this simulation is not using any differential solution, the forces grow and grow until the atom becomes unstable and break apart. Some Runge-Kutta is required to push the realism further.


The webpage of the fully-functional prototype is HERE.

Book: Flat and Curved Space Times

The first time I read this book was during my special relativity course at university. I couldn’t understand a thing the teacher was saying (probably because his explanations were always: “you won’t be able to understand that”) and I needed to replace a 35% grade I got in the first exam to complete the course.

Well, hopeless as I was, headed to the library in search of a magical book (other classmates were helpless as well) and found this one. The magic in it is that, instead of trying to force the Lorentz transformations down the throat first and then explain the basic principles of relativity, it does it by simply showing the topology of the space and assuming that the speed of light is constant (pretty much the same path Einstein took in the first place).

So, the first chapter has no equations whatsoever, only graphics with light waves going back and forth and he derives the light-cones automagically from it, what happens to the “world” at high speeds and how does it affect our senses of reality. It goes on for all kinematic principles only using Newton equations and gamma. Lorentz transformations only appear in the fourth chapter.

After that, not only I could understand relativity as a whole, but I also got 90% grade on the final exam! It’s an old (88) book but time has no meaning for a very good book, especially for a subject that hasn’t changed that much in the last decades.

I recommend it to physics-wannabe as well as lay people with little background in math, and if your teacher is as hopeless as mine was, ignore him and read this book.

Click here for the US version.

How close is nano-computing?

In September, Sunny Bains wrote Why Nano still macro? and since then I’m thinking about it once in a while.

Recently, a study in the University of California showed how to create a demodulator using nanotubes. So far there were advances in memory containers such as this and that and also batteries but all of them, as Sunny remembers, trying to build small structures following the design of big things.

Quantum computation nowadays have exactly the same problem, quantum effects in a classic assembly, big, clumsy and very expensive. If it was required a quantum effect (the transistor) to make classical computational cheap and available what will be required to make quantum computers cheap? A SuperString effect? Something messing around with the Calabi–Yau shape of the 6 additional dimensions?

Anyway, back to nanotech, building a nano-battery is cool but using ATPs as the primary source for energy would be much cooler! Using the available nano-gears and nanotubes to make a machine is also cool but creating a single 2,3 Turing machine (recently proven to be universal) would be way better!

Once you have the extremely simple processor like that, a nano-modem, some storage and ATP as food you can do whatever you want for how long you like inside any living being on Earth. Add a few gears to make a propeller and you’re mobile! 😉

Of course it’s not that simple, but most of the time to state that something is viable means exactly the same as to say that it’s classic as in boring and clumsy and expensive and brute force… well, you got the idea…