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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…)

Mathematician Sees Artistic Side To Father of Computer

By Guest PostFebruary 23, 2012Science, Technologyalan turing, barry cooper, bletchley park, british cryptographic service, british mathematical colloquium, british prime minister, canterbury, classical art, classical recursion theory, computability theory, david, electronic computer, father, gerald sacks, gordon brown, homosexual, italian high renaissance, jan van leeuwen, john von neumann, mathematical logic, mathematical problems, mathematician, michelangelo, modern computer, potassium cyanide, princeton university, robert soare, sistine ceiling, statue, turing renaissance, united kingdom, united states, university of cambridge, university of chicago, university of kent, winston churchill, world war

This year a series of events around the world will celebrate the work of Alan Turing, the father of the modern computer, as the 100th anniversary of his birthday approaches on June 23. In a book chapter that will be published later this year, mathematician Robert Soare, the founding chairman of the University of Chicago’s computer science department, will propose that Turing’s achievement was artistic as well as scientific.

Soare, the Paul Snowden Russell Distinguished Service Professor in Mathematics and Computer Sciences, has played a leading role in computability theory — the field that Turing founded and which is devoted to determining how effectively complex mathematical problems can be solved. In Mathematical Logic in the 20th Century, Gerald Sacks ranked a paper Soare published in the Annals of Mathematics as one of the century’s 31 most important papers in mathematical logic, including computability theory. (more…)

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How Computers Push on the Molecules They Simulate

Mathematician Sees Artistic Side To Father of Computer