Tag Archives: molecule

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…)

Do We Live in a Computer Simulation? UW Researchers Say Idea Can be Tested

By Guest PostDecember 12, 2012Scienceatom, belief, binds subatomic particles, british philosopher, computer model, computer simulation, concept, cosmic rays, evolutionary history, four dimensional grid, fundamental forces, gluons, human species, lattice quantum chromodynamics, martin savage, model, molecule, Nature, neutrons, nick bostrom, notion, nucleus, parallel universe, physical laws, posthuman civilization, posthuman stage, potential test, primitive simulations, protons, quarks, scale, silas beane, small scale simulations, space time continuum, supercomputers, technique, universe, university of oxford, university of washington, zohreh davoudi

A decade ago, a British philosopher put forth the notion that the universe we live in might in fact be a computer simulation run by our descendants. While that seems far-fetched, perhaps even incomprehensible, a team of physicists at the University of Washington has come up with a potential test to see if the idea holds water.

The concept that current humanity could possibly be living in a computer simulation comes from a 2003 paper published in Philosophical Quarterly by Nick Bostrom, a philosophy professor at the University of Oxford. In the paper, he argued that at least one of three possibilities is true:

The human species is likely to go extinct before reaching a “posthuman” stage.
Any posthuman civilization is very unlikely to run a significant number of simulations of its evolutionary history.
We are almost certainly living in a computer simulation. (more…)

The Best of Both Catalytic Worlds

By Guest PostOctober 13, 2012ScienceBerkeley, berkeley lab, biochemistry, biomolecule, california, cancer, catalysis program, catalyst, catalytic reactivity, chemical reaction, cholesterol medicine, complex reaction, cyclopropanation reaction, cyclopropane, dean toste, dendrimers, elad gross, enzyme, gabor somorjai, gold nanocluster, heterogeneous, homogeneous, industrial catalyst, metal catalysts, metal nanocluster, molecule, palladium, pamam, platinum, product selectivity, property, protein, recyclability, rhodium, substance, university

Berkeley Lab Researchers Develop New Technique for Heterogenizing Homogenous Nano Catalysts

Catalysts are substances that speed up the rates of chemical reactions without themselves being chemically changed. Industrial catalysts come in two main types – heterogeneous, in which the catalyst is in a different phase from the reactants; and homogeneous, in which catalyst and the reactants are in the same phase. Heterogeneous catalysts are valued for their sustainability because they can be recycled. Homogeneous catalysts are valued for their product selectivity as their properties can be easily tuned through relatively simple chemistry.

Researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have combined the best properties of both types of industrial catalysts by encapsulating nanoclusters of a metallic heterogeneous catalyst within the branched arms of the molecules known as dendrimers. (more…)

Forcing the Molecular Bond Issue

By Guest PostSeptember 6, 2012Scienceadsorb, aerosol droplets, aleksandr noy, antibody, berkeley lab, binding free energy, biosensing assay, data, dfs, dynamic force spectroscopy, energy barrier, force spectra, formation, interaction, intermolecular bond, jim deyoreo, material, molecular bond, molecular foundry, molecular system, molecule, nanoscience center, nonlinear force, property, raymond friddle, rupture, single bond model, standard model, synthetic analogue, synthetic polymer, torsional force

New and Improved Model of Molecular Bonding from Researchers at Berkeley Lab’s Molecular Foundry

Material properties and interactions are largely determined by the binding and unbinding of their constituent molecules, but the standard model used to interpret data on the formation and rupturing of molecular bonds suffers from inconsistencies. A collaboration of researchers led by a scientist at the U.S Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) has developed a first-of-its-kind model for providing a comprehensive description of the way in which molecular bonds form and rupture. This model enables researchers to predict the “binding free energy” of a given molecular system, which is key to predicting how that molecule will interact with other molecules.

“Molecular binding and unbinding events are much simpler than we have been led to believe from the standard model over the past decade,” says Jim DeYoreo, a scientist with the Molecular Foundry, a DOE nanoscience center at Berkeley Lab who was one of the leaders of this research. “With our new model, we now have a clear means for measuring one of the most important parameters governing how materials and molecules bind together.” (more…)

To Cap or Not to Cap: Scientists Find New RNA Phenomenon That Challenges Dogma

By Guest PostSeptember 2, 2012Sciencebaskar bakthavachalu, brian kennedy, cancer, cell, cell life, chandrama mukherjee, cytoplasm, daniel schoenberg, deepak patil, embryonic development, gene, hibernation, messenger rna, mitotic cell cycle, molecule, mrna, neurological activity, ohio state university, protein, rna

COLUMBUS, Ohio – Some RNA molecules spend time in a restful state akin to hibernation rather than automatically carrying out their established job of delivering protein-building instructions in cells, new research suggests.

And instead of being a fluke or a mistake, the research suggests that this restful period appears to be a programmed step for RNA produced by certain types of genes, including some that control cell division and decide where proteins will work in a cell to sustain the cell’s life.

This could mean that protein production in cells is not as clear-cut as biology textbooks suggest, scientists say. (more…)

A Revealing Hand

By Guest PostJune 3, 2012Health, Scienceaustralia, biomarker, blood, blue laser light, brenda cartmel, chronic disease epidemiology, diabetes, electron, fiberoptic probe, fruit, heart disease, lycopene, macular degeneration, molecule, new technology, north dakota, nutrition research, prototype device, resonance raman spectroscopy, retina, rrs, serum, skin, skin biopsy, skin carotenoids, stephanie scarmo, susan t mayne, telltale substances, university of utah, vegetable, vegetable intake, yale school

What did you have for lunch yesterday? How many times a month do you eat nuts? How about your kids — how many servings of vegetables did they consume today?

It’s no secret that it is hard to recall the details of our meals, and that frustrating fact lies at the heart of nutrition research, complicating the task of linking foods to health outcomes like diabetes and heart disease. Some researchers look instead for telltale substances, or biomarkers, in the body that give information about how much of a certain type of food a person has eaten recently. But that solution isn’t ideal, as measuring biomarkers often requires blood, urine or even skin samples. The process can be costly, painful and cumbersome. (more…)

Energy in Action

By Guest PostMay 16, 2012Scienceaction, ambre alexander, attraction, biomolecule, blind date, bulletproof body armor, crystallographic structure, dispersion method, dispersionless density functional, dldf, dutch physicist, energy, Europe, force, krzysztof szalewicz, molecule, motions of electrons, new method, nobel prize, physics, poland, polymorphs, rafal podeszwa, repulsion, thomson reuters, tracey bryant, tylenol, university of delaware, university of silesia, van der waals

For two molecules on blind date, new method predicts potential for attraction or repulsion

Krzysztof Szalewicz, professor of physics and astronomy at the University of Delaware, and Rafal Podeszwa of the University of Silesia Institute of Chemistry in Poland have developed and validated a more accurate method for predicting the interaction energy of large molecules, such as biomolecules used to develop new drugs.

The research is reported as a communication in the April 27 issue of the Journal of Chemical Physics, which is the most highly cited journal in atomic, molecular and chemical physics according to Thomson Reuters. The journal is published by the American Institute of Physics. Despite appearing at the end of April, the paper was on the list of the 20 most-read articles in JCP for that month. (more…)

Brighter, Smaller Probes to Uncover the Secret Lives of Proteins

By Guest PostMay 10, 20121 commentSciencealexis ostrowski, andrew mueller, berkeley lab, bruce cohen, cellular mechanism, daniel gargas, delia milliron, disease, elan katz, emory chan, erbium, function, gang han, imagine tracking, james schuck, lanthanide, live cell, los angeles, molecule, nanocrystal, nanoparticle, nayf4, photobleach, protein, radio transmitter, sodium yttrium fluoride, vistamar school, wanda robot, ytterbium

Berkeley Lab scientists create nanoparticle probes that may lead to a better understanding of diseases

Imagine tracking a deer through a forest by clipping a radio transmitter to its ear and monitoring the deer’s location remotely. Now imagine that transmitter is the size of a house, and you understand the problem researchers may encounter when they try to use nanoparticles to track proteins in live cells.

Understanding how a protein moves around a cell helps researchers understand the protein’s function and the cellular mechanisms for making and processing proteins. This information also helps researchers study disease, which at a cellular level may mean that a protein is malfunctioning, stops being made, or is sent to the wrong part of the cell. But nanoparticle probes that are too big can disrupt a protein’s normal activities. (more…)