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Mar 24, 2016

Modified NWChem Code Utilizes Supercomputer Parallelization

Posted by in categories: chemistry, climatology, evolution, materials, quantum physics, supercomputing

Quicker time to discovery. That’s what scientists focused on quantum chemistry are looking for. According to Bert de Jong, Computational Chemistry, Materials and Climate Group Lead, Computational Research Division, Lawrence Berkeley National Lab (LBNL), “I’m a computational chemist working extensively with experimentalists doing interdisciplinary research. To shorten time to scientific discovery, I need to be able to run simulations at near-real-time, or at least overnight, to drive or guide the next experiments.” Changes must be made in the HPC software used in quantum chemistry research to take advantage of advanced HPC systems to meet the research needs of scientists both today and in the future.

NWChem is a widely used open source software computational chemistry package that includes both quantum chemical and molecular dynamics functionality. The NWChem project started around the mid-1990s, and the code was designed from the beginning to take advantage of parallel computer systems. NWChem is actively developed by a consortium of developers and maintained by the Environmental Molecular Sciences Laboratory (EMSL) located at the Pacific Northwest National Laboratory (PNNL) in Washington State. NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

“Rapid evolution of the computational hardware also requires significant effort geared toward the modernization of the code to meet current research needs,” states Karol Kowalski, Capability Lead for NWChem Development at PNNL.

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Mar 24, 2016

Synthetic microbe lives with less than 500 genes

Posted by in category: biological

But function of many of these remains a mystery.

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Mar 24, 2016

DNA Devices Perform Bio-Analytical Chemistry Inside Live Cells

Posted by in categories: biotech/medical, chemistry, electronics, nanotechnology

Last summer, the team reported another achievement: the development of a DNA nanosensor that can measure the physiological concentration of chloride with a high degree of accuracy.

“Yamuna Krishnan is one of the leading practitioners of biologically oriented DNA nanotechnology,” said Nadrian Seeman, the father of the field and the Margaret and Herman Sokol Professor of Chemistry at New York University. “These types of intracellular sensors are unique to my knowledge, and represent a major advance for the field of DNA nanotechnology.”

Chloride sensor

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Mar 24, 2016

What Basket Weaving Teaches Us About Spin Liquids

Posted by in category: particle physics

Atoms in spin liquids take the form of a kagome lattice structure, named after a Japanese basket weaving technique.

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Mar 24, 2016

Quantum computing breakthrough paves way for ultra-powerful machines

Posted by in categories: computing, information science, quantum physics

A crucial hurdle in the development of ultra-powerful quantum computers has been overcome through the development of the world’s first programmable system that can be scaled.

Researchers at the University of Maryland College Park built a quantum computer module that can be linked to other modules to perform simultaneous quantum algorithms.

“Quantum computers can solve certain problems more efficiently than any possible conventional computer,” states a paper published this week that details the researchers’ findings. “Small quantum algorithms have been demonstrated in multiple quantum computing platforms, many specifically tailored to hardware to implement a particular algorithm or execute a limited number of computational paths.

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Mar 24, 2016

Good News Bad News

Posted by in categories: biological, biotech/medical, health, homo sapiens

One of the things I love most about being a Surgical Oncologist is that I see my patients for years after I have treated them. However, my clinic days are inevitably like the opening scenes from the old Wide World of Sports television program that aired on Saturday afternoons on ABC. I remember watching this show on weekends as a child and teenager. The “thrill of victory”, with images of athletes crossing the finish line in first place, equates to those patients who receive good news during their clinic visit. I tell them I am confident I can perform an operation to remove their cancer; or I confirm that their blood tests and scans show that tumors have not recurred after surgery, chemotherapy, and other treatments; or we pass some major chronologic milestone without evidence of cancer rearing its ugly head again (many patients still believe the 5 year anniversary of being cancer-free equates with being “cured”, if only that were always true). In contrast, the “agony of defeat”, forever seared in my memory in the opening scenes of Wide World of Sports with the ski jumper falling off the end of the jump and bouncing hard off the slope, represents the distress and depression felt by patients and their family members when I deliver bad news.

I would never make it as a professional poker player because I can’t bluff when I’m holding a bad hand or keep from grinning when I have a good one. My patients can tell from my face when I walk into the clinic room what the news is going to be. When all of the blood tests and scans reveal no evidence of cancer recurrence, I walk in smiling and immediately tell all gathered in the room that everything looks great and I see no evidence of any cancer. The remainder of the visit becomes a combination of medical checkup and social enterprise. I inquire about the well-being of their children, grandchildren, parents, other friends and relatives I have met, their pets, their gardening, their recent travels, and sundry snippets of their ongoing lives. Patients frequently bring pictures of children and grandchildren, or travel photos of places they have been since their last visit with me. Often I’m asked for medical advice on conditions totally unrelated to their cancers as they get farther and farther away from that diagnosis. My patients also know about tidbits from my life. They ask about the status of soccer teams that I coached, how my son or daughter were doing in college (both graduated and onto successful careers, thank you), and whether I have progressed from owning a Ferrari lanyard to hold and display my medical badge (I’m a fan of Ferrari F1 racing) to actually owning a Ferrari automobile (I do not).

I am told by patients, family members, and members of my patient care team that I am quite solemn when I walk in a clinic room to deliver bad news. No “light-hearted” chatter or discussion of recent family events or outings occurs. The nervous, hopeful smiles on the faces of the patient and the family members in the room quickly fade as I describe what I am seeing on their blood tests and the scans I have reviewed. Friedrich Nietzsche, the pejorative poster boy of pessimism, is credited with the aphorism, “Hope is the worst of evils, for it prolongs the torments of man.” Thankfully, he was not involved in the care of patients with cancer or other chronic illnesses. A particular patient comes to mind when I remember the importance of dealing with both the highs and the lows of talking with cancer patients.

The patient in question was the wife of an Emeritus Professor of Engineering at a prestigious American university. The Professor knew a thing or two about scientific investigation, statistics, and assessments of probability. Mrs. Professor had a large, grapefruit-sized malignant vascular tumor in the center of her liver called an epithelioid hemangioendothelioma. Quite a mouthful of a name for a rare malignant tumor of the liver. Her tumor was in an unfortunate location in the center of the liver and was wrapped around two of the three veins that drain all of the blood out of the liver into a large blood vessel called the inferior vena cava. The tumor was abutting a portion of the third vein. As a hepatobiliary surgical oncologist, I know I must preserve at least one of these veins to allow blood that flows into the liver to flow back out properly. She had seen surgeons at several other hospitals in the United States and was told that the tumor was inoperable and untreatable. If she was lucky, she might live a year, these doctors told my patient and her husband. The Professor contacted me, and I examined Mrs. Professor and evaluated her prior scans, and then obtained some additional high resolution scans to better understand the appearance of her tumor. I realized that her particular tumor had a very thick fibrous capsule surrounding it. I explained to the patient and her husband that it may be possible to remove the tumor, but that it would be challenging. This lady who had been sullen, withdrawn, and tearful every time I had met with them previously suddenly looked up and said, “If there’s any chance, I’m willing to take it!” I preceded the next week to perform an operation that removed the entire left lobe and a portion of the right lobe of her liver and I was able to gently dissect the tumor capsule free from the third hepatic vein. The operation was successful and the patient recovered well over the next several weeks.

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Mar 24, 2016

Are parallel universes real?

Posted by in categories: cosmology, physics

Are parallel universes real?
Right now there might be a whole other universe where instead of brown hair you have red hair, or a universe where you’re a classical pianist, not an engineer. In fact, an infinite number of versions of you may exist in an infinite number of other universes.

The idea sounds like science fiction, but multiverse theories — especially those that are actually testable — are gaining traction among physicists. Here are three of the most compelling theories:

If the universe is infinite, multiple universes probably exist.

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Mar 24, 2016

Rocket Lab plans to begin launches mid-year

Posted by in category: space travel

Rocket Lab now plans to begin launches of its Electron vehicle in the middle of this year after completing qualification tests of its main engine.

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Mar 24, 2016

Genome Discovery Holds Key to Designer Organisms

Posted by in category: biotech/medical

Genomic pioneer Craig Venter has created a cell with the smallest possible number of genes needed to survive.

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Mar 24, 2016

Transhumanism: Zoltan Istvan vs. Professor R. Jones

Posted by in category: transhumanism

In this technology edition’s impact essay, Zoltan Istvan and Professor Richard Jones debate the merits and faults of transhumanism.

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