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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…)

Renewable News

By Guest PostDecember 10, 2012Environmentrenewable energy, renewable news, solar power, source, technology costs, wind power

Wind, solar power paired with storage could be cost-effective way to power grid

Renewable energy could fully power a large electric grid 99.9 percent of the time by 2030 at costs comparable to today’s electricity expenses, according to new research by the University of Delaware and Delaware Technical Community College. (more…)

What’s that Noise?

By Guest PostSeptember 26, 2012Scienceabhyudai singh, brandon razooky, cell, delaware, expression, gene, hiv, hiv virus, human, immunodeficiency virus, leor weinberger, mrnas, new method, noise, protein level, roy dar, san francisco, source, university, variability

Paper describes new method to understand sources of noise in gene-expression

Abhyudai Singh, assistant professor of electrical and computer engineering at the University of Delaware, describes a new method to understand sources of “noise” in gene-expression that create variability in protein levels in a paper published in Molecular Systems Biology, a publication of Nature, on Aug. 28.

This noise is expressed as variability in the levels of proteins/mRNAs in a cell. (more…)

Space Weather Forecast: Sunspotty, With an Increasing Chance of Solar Storms

By Guest PostApril 15, 2012Environmentatmosphere, coronal mass ejections, dark sky, earth, flagpole, fm broadcasts, forecast, frank lind, gps, john sahr, k p index, kuow, laura vertatschitsch, magnetic field, magnetosphere, mars, mary levin, mechanical energy, molecular plasma, northern light, satellites, seattle, sieg hall, solar flares, solar storms, source, space weather, sunspot cycle, sunspotty, transmitter, xray

The past few months have seen a spate of solar flares – bringing spectacular views of the northern lights as far south as Seattle – along with media speculation that the electrical activity could disrupt power grids, satellites or ground airplanes.

John Sahr, a UW professor of electrical engineering who studies the upper atmosphere, is the regional go-to guy for such questions. We found some time in Sahr’s busy schedule (he’s also the UW’s associate dean of undergraduate academic affairs and a part-time zombie hunter) to get his read on the space weather forecast. (more…)

Thawing Permafrost 50 Million Years Ago Led To Warm Global Events, Says New Study

By Guest PostApril 7, 2012EnvironmentAntarctica, arctic permafrost, carbon, climate, climatic threshold, CO2, earth, eccentric orbits, ecosystem, Environment, floor sediment, fossil fuel, frozen-soil, greenhouse gas levels, italy, kevin schaefer, methane gas, ocean, orbit, organic matter, paleocene eocene, permafrost, permafrost thaw, petm, rob deconto, soil, source, thermal maximum, university of urbino

A new study led by the University of Massachusetts Amherst and involving the University of Colorado Boulder proposes a simple new mechanism to explain the source of carbon that fed a series of extreme warming events on Earth about 50 million years ago called the Paleocene-Eocene Thermal Maximum, or PETM, as well as a sequence of similar, smaller warming events afterward.

“The standard hypothesis has been that the source of carbon was in the ocean in the form of frozen methane gas in ocean-floor sediments,” said lead study author Rob DeConto of the University of Massachusetts Amherst. “We are instead ascribing the carbon source to the continents in polar latitudes where permafrost can store massive amounts of carbon that can be released as CO2 when the permafrost thaws.” (more…)

Tag Archives: source

How Computers Push on the Molecules They Simulate

Renewable News

What’s that Noise?

Space Weather Forecast: Sunspotty, With an Increasing Chance of Solar Storms

Thawing Permafrost 50 Million Years Ago Led To Warm Global Events, Says New Study