Reality tunnels

Go Replicants!

jmbr — Tue, 21 Jun 2011 20:31:03 +0000

Last November I wrote a molecular simulator called Go Replicants! that uses Go potentials to simulate protein folding processes and study some of their thermodynamic properties. Its source code and some instructions can be found here.

My goals while writing the program were manifold (pun intended):

First and foremost, I wanted to understand the simulation techniques used by a research group that I collaborate with. Among these are parallel tempering (a.k.a. replica exchange) Monte Carlo, WHAM, etc.
I was also looking forward to learning OpenMP and the GNU Scientific Library for quite some time, so this gave me the perfect opportunity to do so.
Many projects have been migrating from GNU autotools to CMake. I was curious about it and wanted to become acquainted with CMake too.

The code can still be improved upon, of course. But besides cleanups or feature additions, and considering that my new toycomputer at work has two NVIDIA Tesla M2050s, I think the next step is to develop GPU capabilities.

Oh, I almost forgot that its Git repository is cloned at Github.

Applications of the absolute quadratic complex and the quadric of segments in 3D reconstruction.

jmbr — Wed, 16 Dec 2009 09:56:25 +0000

The final project in my post-graduate degree in Mathematics explains two approaches for computing a Euclidean upgrading of a projective 3D reconstruction, which has applications in Computer Vision. The slides for a talk I gave a couple of weeks ago explaining the subject matter are also available online.

Camera calibration talk

Halberd screencast

jmbr — Tue, 13 Oct 2009 22:19:49 +0000

Vivek Ramachandran has created a screencast demonstrating the use of my program Halberd. Do watch it if you want to see Halberd in action!

Introductory talk on Geometric Algebra

jmbr — Sat, 15 Aug 2009 07:16:37 +0000

A few weeks ago I gave at work an introductory talk on Geometric Algebra. In my slides, I mostly followed the exposition in David Hestenes’ New Foundations for Classical Mechanics. And since we’re mostly a MATLAB shop I also used Gable to show how to perform some practical computations.

Introduction to Geometric Algebra

Functional programming in Maple

jmbr — Mon, 09 Feb 2009 20:45:59 +0000

I have written some notes on functional programming in Maple mainly to help me find my way around it. For the moment these notes are very terse but I find them useful as a cheat sheet and I might expand them in the future.

Emacs bankruptcy

jmbr — Fri, 10 Oct 2008 00:25:44 +0000

I decided to follow the zeitgeist and declare .emacs bankruptcy. This is the outcome.

Abalastow Compendium

jmbr — Thu, 25 Sep 2008 12:00:44 +0000

My friend François asked me to flex my PageRank muscles to help him in a competition. Good luck!

LibraryThingy

jmbr — Tue, 10 Jun 2008 08:32:41 +0000

I uploaded the list of books I own to LibraryThing. Feel free to take a look at my shelves.

Changes

jmbr — Mon, 05 May 2008 12:04:40 +0000

I’ll be writing future concert reviews and whatnot at http://jmbr.superadditive.com

The Gutter Twins, Madrid 2008.04.27

jmbr — Tue, 29 Apr 2008 16:08:56 +0000

Whenever you buy a ticket for a show in which Mark Lanegan is involved, you can rest assured that he and his band will play top notch rock and roll, as it was the case. The act left me in a pleasant mood that was unfortunately cut short by sad news.