Impressing

In this section you can find links that have impressed me. The links are grouped by sections: Biology , Bioinformatics , Mathematics , Physics , Robotics .

Biology

Lamarck's signature. How retrogenes are changing Darwin's natural selection paradigm

The main topic of this book by by Edward J. Steele, Robyn A. Lindley and Robert V. Blanden is inheritance of acquired features which contradicts modern Darwinian paradigm. However what impressed me in this book was the description of the immune answer mechanism. It turns out that genome is supplied with a mechanism of directional engineering and synthesis of antibodies that selectively bind to specific antigens. In terms of Informatics it means that genomes are supplied with highly-effective procedures of global optimization which solve problems of tremendous computational complexity (at least NP-hard problems). You can find Russian translation here.

A Genetic Switch. Gene Control and Phage Lambda

Another exciting book by Mark Ptashne. In this book author describes the life-cycle of a virus (phage Lambda) that parasitizes on bacteria (E. coli). The virus has a dozen of genes so it's relatively easy to trace the role of each of them in the virus life-cycle. You get impressed by the efficiency, robustness and elegance of the gene control mechanism. Each time I think about this book I realize how far from excellence nowadays machinery is.

Bacteriophage T4 Assembly

The virus is being assembled inside the host cell.

BioVisions

They do fantastic movies about intracellular processes basing on experimental data. The movies are available on their site. Must see.

DNA replication

During this process genetic information is being copied.

DNA translation and transcription

During this process proteins being produced by the instructions encoded in mRNA.

Ribosome

Molecule that assembles protein by the instruction encoded in mRNA.

ATP synthesis

This process supplies cell metabolism with energy.

Kinesin

Transport protein.

Myosin

Muscule protein.

Apoptosis

Programmed cell death.

Belousov-Zhabotinsky reaction

Oscillating chemical reaction that was discovered as inorganic analog of Krebs cycle reactions.

Visualizations of Molecular Biology Central Dogma

From DNA to RNA to protein.

Bioinformatics

NCBI

One of the biggest bioinformatics resources. Here you can download sequenced genomes, protein structures, use different tools for bioinformatics data analysis, and much more. Try it...

Bioinformatics. The machine learning approach

Researcher's hand-book by P. Baldi and S. Brunak. It's about applications of machine learning techniques in Bioinformatics. Get it...

JMol

An open-source Java viewer for chemical structures in 3D. Because of its simplicity and open-source nature it already has became standard de-facto. This library is used as molecule visualization technique in many scientific journals; it is also used in Wikipedia. Get it...

BioJava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. See more...

Mathematics

Mathematics. The Loss of Certainty

A book by Morris Kline about foundations of Mathematics. Author gives some historical notes and argues that Mathematics lacks rigid basement. Must read.

Whither Mathematics?

An article by Brian Davies in Notices of the American Mathematical Society, December 2005, vol. 52, #11. The topic of the article is current "state of the art" in Mathematics. If you liked "Mathematics. The Loss of Certainty" by Morris Kline you definitely going to like this one (and vice versa). See original in English or Russian translation

Artificial Intelligence

Ironical lectures on AI. Though the lectures are funny and easy-to-read, you can find many deep thoughts in them. Make sure to read other authors ironical writings. See original in Russian...

Gregory Chaitin

It was him who generalized famous Godel's incompleteness theorem. Make sure to see some his talks online, it is worth of it. See Chaitin's homepage...

The Game of Life by John Conway

The evolution of cellular automata on the square lattice. Each element becomes dead or alive depending on its current neighboring elements. The only way to predict the state of the system in future is following the rules of the game.Try game of life java applet

TSPLIB

Library of sample instances for Traveling Salesman Problem (the most common NP-complete problem) from various sources and of various types. You can find also best known solutions. See more...

Ising Model

Ising model simulation using the demon algorithm Markov Chain Monte Carlo simulation is widely used for modeling statistical physics phenomena. In this case Demon Algorithm is used for Ising model simulation. Make sure you have java applets enabled in your browser. See more...

List of NP-Complete Problems

There are more than 3000 known NP-complete problems. See also the book Computers and Intractability: A Guide to the Theory of NP-Completeness by M. Garey and D. Johnson.

Physics

Is it Hard Being Maxwell Demon?

Sorting particles game. You are to separate red and blue particles. It resembles Maxwell Demon separating fast (hot) and slow (cold) molecules. Try it...

Shadows of the Mind

A book by famous scientist Roger Penrose where he tries to find out the basic mechanisms of the process of thinking. Much attention is payed to to Godel's incompleteness result

The Emperor's New Mind

In the preface author describes 100%-constructive Godel-type proposition. He represents a procedure which convergence can not be proven nor disproven in Peano axiomatics. However the convergence can be proven in broader ZFC axiomatics using transfinite induction.

What is Life? The Physical Aspect of the Living Cell

A book by Erwin Schrodinger. It was written before structure of DNA had been discovered. However it contains lot of brave ideas.

Classical Ideal Gas Simulation with Demon Algorithm

Markov Chain Monte Carlo simulation is widely used for modeling statistical physics phenomena. In this case demon algorithm is used for modeling the molecule velocity distribution of the ideal gas. Try it...

The Trouble with Physics

A book by Lee Smolin where he describes problems in Standard Model. This book resembles me Mathematics. The Loss of Certainty by Morris Kline. See more...