The experiments developed from the work of Christoph Bräuchle and a team at Ludwig-Maximilians University in Munich, who developed a technique for tracking individual dye molecules dissolved in alcohol that then pass through a nanoporous material. Such diffusion is of more than just academic interest because it plays an important role in a number of technologies, including molecular sieves, catalysis and drug delivery.

This composite image illustrates both methods used to track dye molecules through the channels in the nanoporous material (grey background). Individual molecules (ball and stick figures) can be tracked using the light (orange glow) that they give off. Meanwhile, the collective motion of all the dye molecules is measured using NMR, which focuses on the magnetic moments (blue arrows) of the molecules.

The theory basically states that repeated measurements of a given variable — such as the distance covered by a particle in a given time interval — should yield the same average value as a single measurement of the same variable on a collection of particles — provided the system considered is in a state of equilibrium. However, diffusive processes have been investigated for the past 150 years, the principle of ergodicity has not yet been experimentally verified.

To proof the ergodic theorem experimentally the diffusivities of guest molecules inside a nanostructured porous glass were measured using two conceptually different approaches under identical conditions. The data obtained through the direct observation of dye molecule diffusion by single-molecule tracking experiments (red circles) was in perfect agreement with the ensemble value obtained in pulsed-field gradient NMR experiments (black squares).

Jobs founded Apple in 1976 along with Steve Wozniak and Ronald Wayne. In his time at Apple, he redefined personal computing, Human-computer interaction (HCI) multiple times in ways that the industry is still coming to grasps with. His vision will impact the direction of electronics for decades to come.

Think different! I join in paying tribute to the late Steve Jobs, who inspires countless numbers of designers, scientists and thinkers to challenge the boundaries of our own creativity.

We will miss you, Steve…

They figured out the protein structure of a monomeric protease enzyme, which is “a cutting agent in the complex molecular tailoring of retroviruses, a family that includes HIV”. The understanding of this structure is an important step towards discovering the causes of many diseases related to this enzyme and coming up with treatments for them.

This is where Foldit comes in. Developed in 2008 by the University of Washington, it is a fun-for-purpose video game in which gamers, divided into competing groups, compete to unfold chains of amino acids – the building blocks of proteins – using a set of online tools. To the astonishment of the scientists, the gamers produced an accurate model of the enzyme in just three weeks. It is believed to be the first time that gamers have resolved a long-standing scientific problem.

One of Foldit’s creators, Seth Cooper, explained why gamers had succeeded where computers had failed.

People have spatial reasoning skills, something computers are not yet good at. Games provide a framework for bringing together the strengths of computers and humans. The results in this week’s paper show that gaming, science and computation can be combined to make advances that were not possible before.

Khatib, F., DiMaio, F., Cooper, S., Kazmierczyk, M., Gilski, M., Krzywda, S., Zabranska, H., Pichova, I., Thompson, J., Popović, Z., Jaskolski, M., & Baker, D. (2011). Crystal structure of a monomeric retroviral protease solved by protein folding game players Nature Structural & Molecular Biology DOI: 10.1038/nsmb.2119 [Free PDF]

[via SMH and TNW]

QDOS, otherwise known as 86-DOS, was designed by SCP to run on the Intel 8086 processor, and was originally thrown together in just two months for a 0.1 release in 1980. Meanwhile, IBM had planned on powering its upcoming Personal Computer with CP/M-86, which had been the standard OS for Intel 8086 and 8080 architectures at the time, but a deal could not be struck with CP/M’s developer, Digital Research. IBM then approached Microsoft, which already had a few years of experience under its belt with M-DOS, BASIC, and other important tools — and as you can probably tell from the landscape of the computer world today, the IBM/Microsoft partnership worked out rather well indeed:-)

The following month IBM announces the original IBM Personal Computer (IBM PC), featuring a 4.77-MHz Intel 8088 CPU, 16, 48 or 64 KB of RAM (expandable to 256 KB), 40 KB ROM, up to two 160 KB single-sided, double density (SS/DD) 5¼-inch soft sectored floppy disk drives, 4 KB RAM Monochrome Display Adapter or 16 KB RAM Color Graphics Adapter and the IBM Personal Computer DOS 1.0, which the trade press soon shortened to PC-DOS.

The MS-DOS 1.0 includes three major modules: the BIOS initialization module SYSINIT, the kernel (IBMDOS.COM), including the MS-DOS API, and the shell (COMMAND.COM) supporting internal commands COPY, DIR, ERASE, RENAME and TYPE, plus Paterson’s EDLIN line editor and DEBUG debugger, linker LINK.EXE and a few external commands: FORMAT, CHKDSK, SYS, BASIC, BASICA, TIME and DATE. MS-DOS 1.0 was not shipped to any other OEMs. It consisted of 4000 lines of x86 assembly language source code and ran in 8 KB of memory.

The 160 KB DOS diskette also included 23 sample BASIC programs demonstrating the capabilities of the PC, including the game DONKEY.BAS. The two standard formats for program files are COM and EXE. The third kind of command processing file is the batch file. AUTOEXEC.BAT is checked for, and executed by COMMAND.COM at start-up. I/O is made device independent by treating peripherals as if they were files. Whenever the reserved filenames CON (console), PRN (printer), or AUX (auxiliary serial port) appear in the file control block of a file named in a command, all operations are directed to the device. Serial and parallel ports are added via ISA expansion cards.

Today, MS-DOS is rarely used for desktop computing. Since the release of Windows 95, it was integrated as a full product used for bootstrapping and troubleshooting, and no longer released as a standalone product. Unfortunately, most of interned kiddies from Generation Y have no idea about DOS, but for myself it is so nice to recall warm memories about good old days of early computers and long forgotten abbreviations like ISA or COMMAND.COM name…

Seattle Computer Products advertisement

The original MS-DOS advertisement in 1981.

 

 

 
← DOS command line promt.

 

 

 
See also full history of x86 DOS operating systems on Wikipedia.

To create a scalable DNA circuit architecture, authors proposed a simple DNA gate motif—a “seesaw” gate—that makes use of a reversible strand displacement reaction that exchanges the activity of DNA signals. A pair of seesawing steps completes a catalytic cycle, allowing signal amplification and signal isolation. A pair of seesaw gates can perform AND or OR operation, sufficient for universal Boolean function evaluation using dual-rail logic.[3]

In the seesaw abstraction, each DNA gate is represented by a two-sided node (A). Each DNA signal is represented by a wire. Each side of the node can be connected to any number of wires. Each wire connects two different sides of two nodes. Each red number indicates one DNA species with its initial relative concentration: Each number on a wire corresponds to a free signal strand; each number within a node at the end of a wire corresponds to a bound signal strand (positive number) or a threshold that absorbs a signal when it arrives at the gate (negative number). A reporter that transforms a DNA signal into a fluorescence signal is represented by half a node with a zigzag arrow (B), with its initial relative concentration written similar to a threshold.

To build their circuits, the researchers used pieces of DNA to make logic gates. Instead of depending on electrons flowing in and out of transistors, DNA-based logic gates receive and produce molecules as signals. The molecular signals travel from one specific gate to another, connecting the circuit as if they were wires.

The new logic gates are made from pieces of either short, single-stranded DNA or partially double-stranded DNA, in which single strands stick out like tails from the DNA’s double helix. The single-stranded DNA molecules act as input and output signals that interact with the partially double-stranded ones.

All the logic gates have identical structures with different sequences. As a result, they can be standardized, so that the same types of components can be wired together to make any circuit you want. What’s more, Qian says, you don’t have to know anything about the molecular machinery behind the circuit to make one. If you want a circuit that, say, automatically diagnoses a disease, you just submit an abstract representation of the logic functions in your design to a compiler that the researchers provide online, which will then translate the design into the DNA components needed to build the circuit. In the future, an outside manufacturer can then make those parts and give you the circuit, ready to go.

The circuit components are also tunable. By adjusting the concentrations of the types of DNA, the researchers can change the functions of the logic gates. The circuits are versatile, featuring plug-and-play components that can be easily reconfigured to rewire the circuit. The simplicity of the logic gates also allows for more efficient techniques that synthesize them in parallel.

A multidisciplinary approach including computer science and biochemistry was key to the project’s success. In addition to biochemistry laboratory techniques, computer science techniques were essential. Dual rail logic converted arbitrary Boolean logic (NOT, AND, and OR) into seesaw gates executing only AND and OR operations. Computer simulations of seesaw gate circuitry optimized the design and correlated experimental data. Design compilers for DNA sequences of seesaw gates were developed.

Two limitations of the work by Qian and Winfree present further challenges. The speed of execution of seesaw gates is a major obstacle to scalability and usability of seesaw circuits for biological applications. Each seesaw gate takes 30 to 60 min. Their computation of four-bit square roots has a circuit depth (the maximum number of Boolean operations that need to be sequentially executed) of 7 and takes 6 to 10 hours. By contrast, biological regulatory circuits can respond much faster, often in less than a second. Another limitation is the number of molecules used in computations. Qian and Winfree executed a seesaw circuit computation simultaneously on a vast number (trillions) of DNA molecules within a test tube, whereas biological regulatory circuits make use of relatively small numbers of molecules for a given task.[4]

Reference:
1. a) L. M. Adleman, Science 266, 1021 (1994). DOI: 10.1126/science.7973651
    b) J. Elbaz et al., DNA computing circuits using libraries of DNAzyme subunits. Nat. Nanotechnol. 5, 417 (2010). DOI: 10.1038/nnano.2010.88
2. Lulu Qian, Erik Winfree (2011). Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades Science, 332 (6034), 1196-1201 DOI: 10.1126/science.1200520
3. L. Qian, E. Winfree, A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface (2011). DOI: 10.1098/rsif.2010.0729
4. John H. Reif Science, 332 (6034), 1156-1157 DOI: 10.1126/science.1208068

On a photo a torii (鳥居・鳥栖・鶏栖, lit. bird perch) is a traditional Japanese gate most commonly found at the entrance of or within a Shinto shrine, where it symbolically marks the transition from the profane to the sacred. Amazingly, how this gate stands above the ruins untouched by the blast.

And today I came across another photo. Above you may see the extend of destruction in one of the northern prefectures of Japan, the most affected by the recent tsunami. Stunning similarity… Both of these gates stand as a symbols and give us hope that there is something out there, that can not be destroyed. Please consider donating to Red Cross to support disaster relief efforts to help those affected by the earthquake in Japan and tsunami throughout the Pacific.

In US you can also text REDCROSS to 90999 to give $10 for Japan earthquake and Pacific Tsunami.

Academician Andrei Kokoshin of the Russian Academy of Sciences, Member of the State Duma lower house of parliament and ex-Secretary of the RF Security Council, told ITAR-TASS in comment on the information:

The recent introduction of a supercomputer of petaflop class at the Russian Federal nuclear center ‘Russian Experimental Physics Research Institute’ in Sarov is a great event in Russia’s science and technology. It is important that this supercomputer is also based on the original products of the development efforts of the experimental physics institute and that this computing system is provided with software, the main components of which have also been devised and adapted by the Institute’s specialists.

Unfortunately, no further details about the system configuration and architecture were released. I would really love to see its specs. I am really anxious to see those “original products” developed in Russia. To my knowledge the best chip technology available in Ruissa is only 65nm.

Kokoshin also said, “This supercomputer will serve as a tangible contribution to the strengthening of national security and national competitiveness of Russia”.

The career structure for scientific research in universities is broken… we should professionalize the postdoc role and turn it into a career rather than a scientific stepping stone.

The scientific enterprise is run on what economists call the ‘tournament’ model, with practitioners pitted against one another in bitter pursuit of a very rare prize. Given that cheap and disposable trainees — PhD students and postdocs — fuel the entire scientific research enterprise, it is not surprising that few inside the system seem interested in change. A system complicit in this sort of exploitation is at best indifferent and at worst cruel.

Permanent research staff positions could be generated and filled with talented and experienced postdocs who do not want to, or cannot, lead a research team — a job that, after all, requires a different skill set.

This is so true…

 

Jennifer Rohn (2011). Give postdocs a career, not empty promises Nature [doi:10.1038/471007a]