The Brookhaven team, has been refin­ing tech­niques to use strands of arti­fi­cial DNA as a highly spe­cific kind of Vel­cro or glue to link up nanopar­ti­cles. Such DNA-based self-assembly holds promise for the ratio­nal design of a range of new mate­ri­als for appli­ca­tions in mol­e­c­u­lar sep­a­ra­tion, elec­tron­ics, energy con­ver­sion, and other fields. But none of these struc­tures has had the abil­ity to change in a pro­gram­ma­ble man­ner in response to mol­e­c­u­lar stim­uli — until now. “Now we’re using a spe­cial type of DNA-linking device — a kind of ‘smart glue’ — that affects how the par­ti­cles con­nect to make struc­tures that are switch­able between dif­fer­ent con­fig­u­ra­tions,” says Oleg Gang a team lead. This reli­able, reversible switch­ing could be used to reg­u­late func­tional prop­er­ties — for exam­ple, a material’s flu­o­res­cence and energy trans­fer prop­er­ties — to make new mate­ri­als that are respon­sive to chang­ing con­di­tions, or to alter their func­tions on demand.

a) Ide­al­ized schematic illus­trat­ing the struc­ture of the device (l_d) link­age, with A’, D’ and B’ recog­ni­tion sequences. b) A bcc unit cell rep­re­sen­ta­tion of a bulk three-dimensional super­lat­tice con­sist­ing of nanopar­ti­cles A – p and B – p inter­con­nected by l_d. © Nature Pub­lish­ing Group.

Con­tinue reading →

22nd December, 2009 Comments Off

IBM’s Almaden Research Cen­ter announced in Novem­ber that it had pro­duced a “cor­ti­cal sim­u­la­tion” of the scale and com­plex­ity of a cat brain. This sim­u­la­tion ran on one of IBM’s Blue Gene super­com­put­ers, in this case at the Lawrence Liv­er­more National Lab­o­ra­tory (LLNL):

Sci­en­tists, at IBM Research — Almaden, in col­lab­o­ra­tion with col­leagues from Lawrence Berke­ley National Lab, have per­formed the first near real-time cor­ti­cal sim­u­la­tion of the brain that exceeds the scale of a cat cor­tex and con­tains 1 bil­lion spik­ing neu­rons and 10 tril­lion indi­vid­ual learn­ing synapses.

The fig­ure presents the results of our weak scal­ing study, where the prob­lem size is increased with increas­ing amount of mem­ory. The plot demon­strates nearly per­fect weak scal­ing in terms of mem­ory, since twice the model size could be sim­u­lated when the amount of mem­ory is dou­bled. The largest sim­u­lated model cor­re­sponds to a scale larger than the cat cere­bral cor­tex, reach­ing 4.5% of the human cere­bral cor­tex.

Scal­ing of Cor­ti­cal Sim­u­la­tions. Copy­right © 2009, ACM, Inc.

2nd December, 2009 2451 Commenthttp://www.isayev.info/simulation-a-cat-like-brain/Simulation+a+Cat-Like+Brain2009-12-02+19%3A28%3A41Olexandr+Isayev

I couldn’t resist to share this graph. Absolutely fan­tas­tic results!

28th May, 2009 Comments Off

For decades DNA has been regarded as a poten­tial build­ing block for mol­e­c­u­lar elec­tron­ics, but ran­dom sequences of DNA vary in their con­duc­tiv­ity — charge trans­fer through G – C (gua­nine – cyto­sine) pairs is much faster than through A – T (ade­nine – thymine) pairs. Charge can migrate along an A – T rich sequence by ‘hop­ping’ between G – C pairs, but this decreases its elec­tri­cal con­duc­tiv­ity. Japan­ese researchers have improved the elec­tri­cal con­duc­tiv­ity of DNA through sim­ple chem­i­cal mod­i­fi­ca­tions. Their work could pave the way for build­ing DNA cir­cuits and self-assembling, DNA-based electronics.

Recently Tet­suro Majima and col­leagues at Osaka Uni­ver­sity in Japan have found a way to tune the elec­tronic char­ac­ter­is­tics of the A-T pairs, mean­ing charge trans­port is no longer sequence depen­dent. They replaced one nitro­gen atom in ade­nine to C – H. This new deaza­ade­nine base is the same from the genetic point of view. On the other hand, its elec­tronic char­ac­ter­is­tics are quite sim­i­lar to gua­nine, so then elec­tri­cal con­duc­tiv­ity of DNA would increase dra­mat­i­cally.

Chem­i­cal struc­tures of ade­nine (A), 7-deazaadenine (Z), the pho­to­sen­si­tizer naph­thal­im­ide (NI) and the hole trap phe­noth­iazine (PTZ). © 2009, Nature Pub­lish­ing Group.

To prove that, the researchers made short sequences of A-T rich DNA mod­i­fied at one end with a pho­to­sen­si­tiser and at the other with a pos­i­tive charge ‘trap’ – phenothiazine (PTZ). Con­tinue reading →

15th April, 2009 Comments Off

Much of the last week I spent at Sani­bel Sym­po­sium. The Sani­bel Sym­po­sium is an inter­na­tional sci­en­tific con­fer­ence in quan­tum chem­istry, solid-state physics, and quan­tum biol­ogy. It has been orga­nized by the Quan­tum The­ory Project at the Uni­ver­sity of Florida in Gainesville, Florida, every win­ter since 1960. It was founded by Per-Olov Löwdin who was involved in its orga­ni­za­tion every year from 1960 to his death in 2000. The Sym­po­sium is noted for its long his­tory and for the breadth of both the par­tic­i­pants and the pre­sen­ta­tions and con­sid­ered as “highly respected reg­u­lar con­fer­ence” in a field.

This year was my first Sani­bel meet­ing. I am really excited, that my work on clas­si­cal mol­e­c­u­lar dynam­ics sim­u­la­tion of bac­te­r­ial nitrore­duc­tase enzyme has been awarded by IBM – Löwdin memo­r­ial fel­low­ship.

The pic­ture above rep­re­sents front view of nitrore­duc­tase with vec­tor pro­jec­tions of PCA com­po­nent #1. Back­bone col­or­ing cor­re­sponds to empir­i­cal defor­ma­tion energy per residue. Over­all, our sim­u­la­tion of the inhib­ited enzyme shows increased flex­i­bil­ity of H6 helix (sym­met­ric wings with largest vec­tor pro­jec­tions on pic­ture). These motions may rep­re­sent a mech­a­nism for accom­mo­dat­ing var­ied substrates.

4th March, 2009 Comments Off