Tag Archives: photosynthesis

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…)

Blades and Clades: Why Some Grasses Got Better Photosynthesis

By Guest PostDecember 25, 2012Scienceagriculture, anatomical difference, anatomical traits, ancestral state reconstruction, atmospheric co2, bep clade, blades, bundle sheath cells, c3, c4, c4 evolution, cellular anatomy, clades, david chatelet, dry condition, erika edwards, evolutionary time scale, evolutionary tree, genetic data, grasses, laura garrison, lineage, mesophyll cells, pacmad clade, pascal antoine christin, photosynthesis, physiology

Two groups — clades — of grasses that once had a common ancestry diverged. The PACMAD clade was predisposed to evolve a more efficient “C4” means of photosynthesis than grasses in the BEP clade. In a new study in the Proceedings of the National Academy of Sciences, a Brown-led team pinpoints the anatomical differences between the clades that led to the PACMAD’s tendency toward C4.

PROVIDENCE, R.I. [Brown University] — Even on the evolutionary time scale of tens of millions of years there is such a thing as being in the right shape at the right time. An anatomical difference in the ability to seize the moment, according to a study led by Brown University biologists, explains why more species in one broad group, or clade, of grasses evolved a more efficient means of photosynthesis than species in another clade. (more…)

Crowdsourcing Site Compiles New Sign Language for Math and Science

By Guest PostDecember 11, 2012Education, Scienceamerican sign language, asl, asl stem forum, byte, caroline solomon, crowdsourcing, dictionary, eukaryote, Europe, google corp, harry lang, kyle rector, lexicon of science, light year, multimedia feature, national science foundation, new york times, organism, photosynthesis, raja kushalnagar, richard ladner, science signs lexicon, sign language, united states, university, urban dictionary, Washington, Wikipedia

A multimedia feature published this week in the New York Times, “Pushing Science’s Limits in Sign Language Lexicon,” outlines efforts in the United States and Europe to develop sign language versions of specialized terms used in science, technology, engineering and mathematics.

The article shares newly defined signs for terms like “light-year,” “organism” and “photosynthesis.” It also describes a successful crowdsourcing effort started at the University of Washington in 2008 that lets members of the deaf and hard-of-hearing community build their own guide to the evolving lexicon of science.

“It’s not a dictionary,” explained Richard Ladner, a UW professor of computer science and engineering. “The goal of the forum is to be constantly changing, a reflection of the current use.” (more…)

Small Organisms Could Dramatically Impact World’s Climate

By Guest PostOctober 26, 2012Environment21st century, atmospheric, carbon, carbon dioxide, christopher klausmeier, climate change, colin kremer, cycle, david garrison, diversity, element, elena litchman, equatorial water, evolutionary adaptation, food chain, global climate, impact, level, marine microorganism, michigan, mridul thomas, nitrogen, ocean, ocean floor, organism, phosphorous, photosynthesis, phytoplankton, population, science express, state university, temperature, tropical water, warmer

EAST LANSING, Mich. — Warmer oceans in the future could significantly alter populations of phytoplankton, tiny organisms that could have a major impact on climate change.

In the current issue of Science Express, Michigan State University researchers show that by the end of the 21st century, warmer oceans will cause populations of these marine microorganisms to thrive near the poles and may shrink in equatorial waters. Since phytoplankton play a key role in the food chain and the world’s cycles of carbon, nitrogen, phosphorous and other elements, a drastic drop could have measurable consequences. (more…)

Researchers Share Surprising Discovery about Coral Reef Ecology

By Guest PostSeptember 4, 2012Environment, Natureacidification, algae, algal symbionts, american samoa, climate change, coastal development, coral reef, coral species, coral tissue, david garrison, DNA, ecology, endosymbionts, environment disturbance, environmental change, environmental stress, french polynesia, functional ecosystem, future, generalists, global stressors, hawaii, himb, hollie putnam, host, manoa, moorea, nsf, ocean acidification, photosynthesis, pollution, prediction, reef corals, ruth gates, skeletal growth, skeletons, soest, stresss, symbiodinium, taiwan, temperatures, theory, threat, tissue sample

Researchers at the UH Manoa School of Ocean and Earth Science and Technology (SOEST) made a discovery that challenges a major theory in the field of coral reef ecology.

The general assumption has been that the more flexible corals are, regarding which species of single-celled algae (Symbiodinium) they host in coral tissues, the greater ability corals will have to survive environmental stress. In their paper published August 29, 2012, however, scientists at the Hawaii Institute of Marine Biology (HIMB) at SOEST and colleagues documented that the more flexible corals are, the more sensitive to environment disturbances they are. (more…)

UCLA Research Makes Possible Rapid Assessment of Plant Drought Tolerance

By Guest PostAugust 2, 2012Environmentassessment, carbon dioxide, China, christine scoffoni, drought tolerance, evaporation, lawren sack, megan bartlett, method, osmometer, osmometry, osmotic potential, p v curve, photosynthesis, plant drought tolerance, pressure volume curve, stomata, temperature, turgor loss point, ucla, xtbg, yunnan

UCLA life scientists, working with colleagues in China, have discovered a new method to quickly assess plants’ drought tolerance. The method works for many diverse species growing around the world. The research, published in the journal Methods in Ecology and Evolution, may revolutionize the ability to survey plant species for their ability to withstand drought, said senior author Lawren Sack, a UCLA professor of ecology and evolutionary biology.

“This method can be applied rapidly and reliably for diverse species across ecosystems worldwide,” he said of the federally funded research by the National Science Foundation. (more…)

Scientists Discover New Trigger for Immense North Atlantic Ocean Spring Plankton Bloom

By Guest PostJuly 7, 2012Environmentadam huxtable, amala mahadevan, atlantic ocean, biological pump, bjarni saemundsson, carbon dioxide, climate, climate on earth, CO2, craig lee, diatoms, don rice, eddies, emily kallin, eric d asaro, fossil fuel, global carbon cycle, holiday fireworks, mary jane perry, michael ohmart, microscopic plants, modulate, north atlantic bloom, not sunlight, nsf, ocean physics, oceanic cycling, oxygen, photosynthesis, physical biological model, phytoplankton, research vessel, silica, sun, surface warming, university of maine, university of washington, us beachgoers, whirlpools, whoi, zooplankton

Ocean eddies help jump-start plankton blooms that spread across hundreds of square miles

On this July 4^th week, U.S. beachgoers are thronging their way to seaside resorts and parks to celebrate with holiday fireworks. But across the horizon and miles out to sea toward the north, the Atlantic Ocean’s own spring and summer ritual unfolds. It entails the blooming of countless microscopic plants, or phytoplankton.

In what’s known as the North Atlantic Bloom, an immense number of phytoplankton burst into existence, first “greening,” then “whitening” the sea as one or more species take the place of others.

What turns on this huge bloom, what starts these ocean fireworks? Is it the Sun’s warmth? (more…)

A New Way of Looking at Photosystem II

By Guest PostJune 14, 2012Sciencealgae, angstroms, bacteria, berkeley lab, carbon dioxide, catalytic cycle, critical formation, cryogenic freezing, electrochemical energy, electrons, femtosecond timescale, femtosecond x ray pulses, green, green plants, hydrogen atom, hydrogen ions, jan kern, junko yano, knowledge, lcls, microcrystals, nicholas sauter, oxidation states, oxygen molecules, paul adams, photooxidation, photosynthesis, photosystem ii, protein crystallography, proteins, protons, renewable energy, resolution, slac, solar energy, synchrotron radiation, terabytes of data, uwe bergmann, vittal yachandra, water, xray diffraction, xrays

Berkeley Lab and SLAC Researchers Study Key Protein Complex Crucial to Photosynthesis

Future prospects for clean, green, renewable energy may hinge upon our ability to mimic and improve upon photosynthesis – the process by which green plants, algae and some bacteria convert solar energy into electrochemical energy. An artificial version of photosynthesis, for example, could use sunlight to produce liquid fuels from nothing more than carbon dioxide and water. First, however, scientists need a better understanding of how a large complex of proteins, called photosystem II, is able to split water molecules into oxygen, electrons and hydrogen ions (protons). A new road to reaching this understanding has now been opened by an international team of researchers, led by scientists at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and SLAC National Accelerator Laboratory.

Using ultrafast, intensely bright pulses of X-rays from SLAC’s Linac Coherent Light Source (LCLS), the research team produced the first ever images at room temperature of microcrystals of the photosystem II complex. Previous imaging studies, using X-rays generated via synchrotron radiation sources, required cryogenic freezing, which alters the samples. Also, to catalyze its reactions, photosystem II relies upon an enzyme that contains a manganese-calcium cluster that is highly sensitive to radiation. With the high-intensity femtosecond X-ray pulses of the LCLS, the research team was able to record intact images of these clusters before the radiation destroyed them. (more…)