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How Computers Push on the Molecules They Simulate

By Guest PostJanuary 9, 2013Scienceacceleration, albert einstein, algorithm, analytical results, artifacts, atoms and molecules, behavior, Berkeley, berkeley lab, calculation, california, california institute, chemical fuel, collide, computer method, conserve energy, david sivak, digital representation, digitize time, dna repair, driving force, effective friction, energy dense, equation, error, finite time steps, fluid, french physicist, gavin crooks, john chodera, langevin dynamics, model brownian motion, modeling molecular system, modern computer, molecular machines, molecular scale motion, molecule, momentum, natural system, nonequilibrium driving force, nonequilibrium statistical mechanics, particle, passage of time, paul langevin, photosynthesis, pollen grain, qb3, quantitative biosciences, quantum mechanics, real world, simulation, source, tenacious errors, theoretical method, thermal energy, toy models, university, velocity, water, water molecules

Berkeley Lab bioscientists and their colleagues decipher a far-reaching problem in computer simulations

Because modern computers have to depict the real world with digital representations of numbers instead of physical analogues, to simulate the continuous passage of time they have to digitize time into small slices. This kind of simulation is essential in disciplines from medical and biological research, to new materials, to fundamental considerations of quantum mechanics, and the fact that it inevitably introduces errors is an ongoing problem for scientists.

Scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have now identified and characterized the source of tenacious errors and come up with a way to separate the realistic aspects of a simulation from the artifacts of the computer method. The research was done by David Sivak and his advisor Gavin Crooks in Berkeley Lab’s Physical Biosciences Division and John Chodera, a colleague at the California Institute of Quantitative Biosciences (QB3) at the University of California at Berkeley. The three report their results in Physical Review X. (more…)

Latest JBEI Startup to Speed Up Biotech Industry

By Guest PostOctober 3, 2012Scienceautocad, berkeley lab, biofuels, biology, chemicals, cutting edge, design, DNA, dna manipulation, eduardo abeliuk, electrical engineering, expressing, inertia, iso27001, j5 software, jbei, majed abolfazli, medicine, metabolic pathway, mike fero, modern cloning, molecular biology, nathan hillson, organism, pharmchem, protocol, qb3, san francisco, Science, sequencing, splicing, stanford university, teselagen

TeselaGen’s DNA construction technology makes genetic engineering cheaper and faster.

Sequencing, splicing and expressing DNA may seem to be the quintessence of cutting-edge science—indeed DNA manipulation has revolutionized fields such as biofuels, chemicals and medicine. But in fact, the actual process can still be tedious and labor-intensive, something Lawrence Berkeley National Laboratory (Berkeley Lab) scientist Nathan Hillson learned the hard way.

After struggling for two days to design a protocol to put together a genetic circuit with 10 pieces of DNA—using a spreadsheet as his primary tool—he was dismayed to discover that an outside company could have done the whole thing, including parts and labor, for lower cost than him ordering the oligonucleotides himself. “I learned two things: one, I never wanted to go through that process again, and two, it’s extremely important to do the cost-effectiveness calculation,” said Hillson, a biochemist who also directs the synthetic biology program at the Berkeley Lab-led Joint BioEnergy Institute (JBEI). “So that was the genesis of the j5 software. This is the perfect thing to teach a computer to do.” (more…)

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How Computers Push on the Molecules They Simulate

Latest JBEI Startup to Speed Up Biotech Industry