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News Article | August 11, 2016
Site: www.huffingtonpost.com

If all goes as planned, in 18 days the hatch will open and our one-year mission to simulated space will end. Thanks in part to this mission, if all goes as planned, a generation from now we'll be waist-deep in our first attempt to land humans on Mars. Between now and then, plans will accumulate: a plan for building a launch vehicle; a plan for getting our stuff there (hopefully, most of it in advance); a plan for how to select and train and feed and water a crew of four or more for three years. Sometimes, twenty years feels like enough time to make all this happen. Then, I remember how long it took to plan, design, build, test, launch, and land the Mars Curiosity Rover: ~2004-2012. When a robot's one-way trip was eight years in the making, twenty years to get people safely to Mars and back suddenly seems like a mighty tall order. To be fair, it took ~8 years to build not 1 but 2.5 Curiosity Rovers: the one that went to Mars, the one that lived in the test bed on Earth, and the one that existed in pieces in a software and hardware testing lab. Credit: By NASA via Wikimedia Commons. Simulations like ours are a critical part of any serious endeavor. The reason is simple: humans need to practice in order to get things right. Whatever we attempt - be it a geometry problem, a round-house kick, or an asteroid rendezvous - the odds of our success are inextricably linked to how many times we've tried that particular maneuver before. Entropy will always introduce unforeseen twists and turns. The more times we've simulated the scenario, the less likely we are to fall flat when our standing plans fail. This was due to a mechanical failure on their end. On our end, there is an emergency water tank for just such scenarios. However, it hadn't been touched in years. Like a stubborn Schrodinger's box, the quality of the water in our tank was totally unknown, even after we opened it. Also unknown: when we would get more water delivered. Fortunately, though our initial plan failed, we've been practicing water extraction and water restriction for nearly the entire mission. A a result, we had the power to SCIENCE our way out of disaster by distilling the emergency water: by boiling it and channeling the evaporated contents into a container. Within hours of us realizing that we weren't going to get our scheduled water delivery, we had just such a system set up and running . Thanks to water restriction days, which were an invention of this crew, we knew how much water we needed to produce to survive and by what margin. Experience also told us how much power we could spare to run the electric heaters that were boiling the water one pot at a time into steam that collected onto plastic sheeting, which then ran down until it gathered underneath the weight of a metal spoon and dripped into the bottom of the black storage bin in which the entire contraption was contained. In this way, clean water collected slowly and steadily. Every so often, one of us would come along with a baster, suck the distilled water out of the bottom of the bins and add more water to the pots. This evaporation system produced liters of purified water: enough to keep us going, at least for a while. This crew dealt with that level of potential disaster without so much as breaking a sweat. We didn't even have to change the rhythm of our day much to do it. I'm not sure how a crew who had only been up here for only a month, or four, would have handled it, which brings us to a question we are asked fairly frequently: What would happen in a real emergency? Let's say that we hadn't been up here for very long, or that the crew was inexperienced with water reclamation; let say there wasn't enough plastic sheeting to make such a system work, or there weren't enough clamps to hold the sheeting in place (we would default to duct tape, but let's just assume for now that we're running low on that, too). What would have been our fate? In a real emergency, there are people on this land mass who could make their way up the mountain with bottled water. On Mars, not so much. Going forward, to be sure that crews can handle it both physically and psychologically, we should probably simulate water shortages, as well as food shortages, power shortages, and all the depravation-situations with which the six of us are now intimately familiar. It goes without saying: for most of us, becoming an expert in water purification was never the plan - nor was mastering composting toilet maintainence, repairing hiking boots with duct tape, or any of several dozen things we've taught ourselves over these last 11.5 months. The wonderful thing about our experiment is that we have the opportunity to learn and the freedom to fail - even, one could argue, the imperative. Now is the time to test out these scenarios; to try our hands at pushing limits and pulling ourselves back from the brink. Sometimes, we won't quite make it, and that's ok. We won't fall too hard or fall too far - for now. Our relative successes and failures from the last 348 days - at growing radishes, conserving water and power, staying in shape, and getting along with each other - will become part of data that goes into planning the first human missions to Mars. Owing to successes and failures from this and other simulations, humankind will master the art and science of planning long-duration space missions. It's the only way we can acquire this skill in advance. In a generation or more, whether the actual plan succeeds as intended (they rarely do), mastery of interplanetary mission planning will sooner or later see us safely through to the next world. Of that much, at least, I am certain.


News Article | November 8, 2016
Site: www.eurekalert.org

A little frustration can make life interesting. This is certainly the case in physics, where the presence of competing forces that cannot be satisfied at the same time - known as frustration - can lead to rare material properties. Just as water molecules become more ordered when they cool and freeze into ice crystals, the atoms of magnets become more ordered with decreasing temperature as the tiny magnetic fields or 'spins' of individual atoms start to point in the same direction. So-called 'spin liquids' are the exception to this rule, with spins continuing to fluctuate and point in different directions even at very low temperatures. They offer exciting possibilities for new discoveries in physics. Scientists from the Okinawa Institute of Science and Technology Graduate University (OIST) have modelled a particular spin liquid, showing that disorder can co-exist with order. Three major publications mark the milestones in this field of research. First, Dr. Ludovic Jaubert from OIST's Theory of Quantum Matter Unit worked alongside scientists at University College London and the Ecole Normale Supérieure of Lyon to propose a model for the co-existence of both magnetic order and disorder back in 2014. By simulating what would happen when neutrons are fired at frustrated magnets - so-named because of the strong competition of forces between the spins of individual atoms - Jaubert and colleagues were able to produce brightly-colored neutron-scattering maps. If the spins in the atoms of the material were lining up in an ordered fashion in the magnet you would expect to see spots on the maps known as 'Bragg peaks', whereas with spin liquids you would expect to see bow-tie shapes, called 'pinch points'. To their surprise, the scientists noticed both Bragg peaks and pinch points on their neutron-scattering maps, suggesting that the disordered properties of a spin liquid can simultaneously exist with ordered magnetism. "Spin liquids are paragons of magnetic disorder. It was very exciting to see the characteristic features of a spin liquid in a partially ordered magnet. It is really motivating to think of the fundamental opportunities this offers for our understanding of condensed matter," says Jaubert. The second milestone in this field of research occurred earlier this year, when a publication in Nature Physics showed that the theory of Dr. Jaubert and coworkers held up in experimental observation, using the magnetic material neodymium zirconate (Nd2Zr2O7). "The results of this experiment confirm the theory that Dr. Jaubert presented on the co-existence of magnetic order and disorder in 2014," says Dr. Owen Benton, a former Postdoctoral Scholar in the Theory of Quantum Matter Unit, led by Professor Nic Shannon. However, more work was necessary to link this new experiment to Jaubert's original idea. To uncover how neodymium zirconate could be both ordered and disordered at the same time, Benton set to work on the latest milestone of this research, theorizing an appropriate microscopic model for this magnetic material. Using his model, Benton showed that neodymium zirconate exists in both an ordered and fluctuating state, making it a very unusual kind of magnet. The work also shows that neodymium zirconate is on the edge of becoming a quantum spin liquid - a rare state of matter opening a back door into the quantum world. In a true quantum spin liquid, the spins of a material would not just fluctuate through many different directions as a function of time but would point in many different directions at the same time. "If you could show that there was such a thing as a quantum spin liquid it would be like an example of Schrodinger's cat on a large object," says Benton. Schrodinger's cat is a famous thought experiment in physics in which a cat in a sealed box with a radioactive source is both alive and dead at the same time. Just as the cat exists in multiple states, i.e. alive and dead, simultaneously, this research paves the way for finding real magnets that are in many states at once. "This study also demonstrates that we can get a very complete picture of the physics of neodymium zirconate using a model," says Benton. Further theoretical and experimental research of this and related materials could reveal even more unexpected and exciting phenomena.


News Article | October 31, 2016
Site: www.24-7pressrelease.com

ST. PAUL, AB, October 31, 2016-- Unsettling questions about the roles organized crime, governments, and law enforcement covertly play in controlling the internet are raised in Eileen Schuh's new thriller, OPERATION MAXTRACKER.This fourth book in her ongoing BackTracker series is a fast-flowing follow-up to FIREWALLS, and continues the saga of young Katrina Buckhold's fight against The Traz biker gang.With uncanny references to actual news headlines, Schuh creates in readers a quiver of anticipation and dread, leaving them to wonder who controls the Web (in both the story and reality) and for what purposes? Also unsettling, is the incredible power wielded in secret by those trying to keep cyberspace and the nation safe.Well known for her past portrayals of psychological drama, Schuh takes OPERATION MAXTRACKER to a new level as danger, cunning and espionage spill out of the virtual world into real life.Schuh is also known for her surprising and satisfying endings and OPERATION MAXTRACKER definitely delivers on that count.Sergeant Kindle is counting on his top secret Operation MaxTracker team to thwart a surging attempt by criminal gangs to hijack cyberspace and take control of the world.The tremendous power of the defensive system the team is creating and the potential for its abuse, has computer guru, Katrina Buckhold, on edge. Shrug, Head of Project Security, is supposedly keeping everyone and everything safe, but based on her past experiences with him, she's not confident he's up to that task.Katrina's toughest battles, though, are not against those threatening cyberspace but against those who are concerned about her ability to raise her children, and Shrug's not helping with that, either.Then unspeakable tragedy strikes, stripping all friendships to the core and laying bare the stunning truths behind the secrets, fears and mistrust."I was inexorably drawn into this dark and claustrophobic world of coercion, mysterious antagonisms and deep mistrust." ~Gilli Allan, award-winning author ofthat explore the social, legal, and ethical issues touched on in the novel.For those who can't get enough of the BackTracker characters, Schuh advises that Sergeant Kindle's law enforcement team plays a major role in her other recent thriller, SHADOW RIDERS In addition to the four novels in her ongoing BackTracker series, The Traz, Fatal Error, Firewalls and Operation MaxTracker (The Traz also comes in a school edition), Eileen Schuh is the author of the adult thriller, Shadow Riders and two adult SciFi novellas (Schrodinger's Cat and Dispassionate Lies).Born Eileen Fairbrother in Tofield, Alberta, Schuh now lives with her husband in the boreal forest near St. Paul in north eastern Alberta, Canada.She invites you to visit her online:To request an interview email: eileenschuh@yahoo.com


Dyall K.G.,Schrodinger
Theoretical Chemistry Accounts | Year: 2011

Relativistic basis sets of double-zeta, triple-zeta, and quadruple-zeta quality have been optimized for the 6d elements Rf-Cn. The basis sets include SCF exponents for the occupied spinors and for the 7p shell; exponents of correlating functions for the valence shell, the 6s and 6p shells, and the 5f shell; and exponents of functions for dipole polarization of the 6d shell. A finite nuclear size was used in all optimizations. Prescriptions are given for constructing contracted basis sets. The use of the basis sets is demonstrated for some atomic and molecular systems. The basis sets are available as an Internet archive and from the Dirac program Web site, http://dirac.chem.sdu.dk. © 2011 Springer-Verlag.


Bell J.A.,Schrodinger | Ho K.L.,Schrodinger | Farid R.,Schrodinger
Acta Crystallographica Section D: Biological Crystallography | Year: 2012

All-atom models are essential for many applications in molecular modeling and computational chemistry. Non-bonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R free values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15 - fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions. © 2012 International Union of Crystallography.


Beuming T.,Schrodinger | Sherman W.,Schrodinger
Journal of Chemical Information and Modeling | Year: 2012

The growing availability of novel structures for several G protein-coupled receptors (GPCRs) has provided new opportunities for structure-based drug design of ligands against this important class of targets. Here, we report a systematic analysis of the accuracy of docking small molecules into GPCR structures and homology models using both rigid receptor (Glide SP and Glide XP) and flexible receptor (Induced Fit Docking; IFD) methods. The ability to dock ligands into different structures of the same target (cross-docking) is evaluated for both agonist and inverse agonist structures of the A2A receptor and the β1- and β2-adrenergic receptors. In addition, we have produced homology models for the β1-adrenergic, β2-adrenergic, D3 dopamine, H1 histamine, M2 muscarine, M3 muscarine, A2A adenosine, S1P1, κ-opioid, and C-X-C chemokine 4 receptors using multiple templates and investigated the ability of docking to predict the binding mode of ligands in these models. Clear correlations are observed between the docking accuracy and the similarity of the sequence of interest to the template, suggesting regimes in which docking can correctly identify ligand binding modes. © 2012 American Chemical Society.


A method and system for calculating the free energy difference between a target state and a reference state. The method includes determining one or more intermediate states using a coupling parameter, performing molecular simulations to obtain ensembles of micro-states for each of the system states, and calculating the free energy difference by an analysis of the ensembles of micro-states of the system states. The method can be particularly suited for calculating physical or non-physical transformation of molecular systems such as ring-opening, ring-closing, and other transformations involving bond breaking and/or formation. A soft bond potential dependent on a bond stretching component of the coupling parameter and different from the conventional harmonic potential is used in the molecular simulations of the system states for the bond being broken or formed during the transformation.


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 1.06M | Year: 2010

DESCRIPTION (provided by applicant): Dysfunction of G protein-coupled receptors (GPCRs) results in diseases as diverse as Alzheimer's, Parkinson's, diabetes, dwarfism, color blindness, retina pigmentosa and asthma. GPCRs are also involved in depression, schizophrenia, sleeplessness, hypertension, impotence, anxiety, stress, renal failure, several cardiovascular disorders and inflammations. Unfortunately, only a handful of GPCR crystal structures are available in the public domain. Therefore, in order to employ structure-based approaches to the design of drugs that target GPCRs, there is a critical need to develop technology that can lead to the production of accurate models of GPCRs. An essential part of constructing accurate GPCR models is the proper treatment of the lipid bilayer membrane. We propose to develop a novel commercial software package capable of performing long length-scale and time-scale molecular dynamics simulations of all-atom GPCR models in coarse grain lipid bilayer/water environments. A recently introduced multi-scale methodology using simplified and computationally efficient coarse-grain representations of lipid bilayers and water in combination with atomistic models for proteins has been validated in exploratory studies. This mixed AA-CG methodology will be incorporated into a powerful, user-friendly commercial software package directed at pharmaceutical and biotechnology researchers focusing on development of drugs that target class A GPCRs. PUBLIC HEALTH RELEVANCE: G protein-coupled receptors (GPCRs) are one of the most important families of target proteins for the development of new medicines; approximately 50-60% of all approved drugs on the market today target GPCRs and nearly all pharmaceutical companies are actively investigating GPCRs. GPCRs are involved in Alzheimer's, Parkinson's, diabetes, dwarfism, color blindness, retina pigmentosa, asthma, depression, schizophrenia, sleeplessness, hypertension, impotence, anxiety, stress, renal failure, cardiovascular disorders, and inflammations. We propose to develop easy-to-use commercial software aimed at producing accurate models for GPCRs that can be used in the design of new medicines that target this important superfamily of proteins.


Patent
Schrodinger | Date: 2015-04-29

Methods and systems for drug discovery collaboration provide collaborative drug discovery electronic workplaces simultaneously accessible by multiple user computing devices. In certain embodiments, a server computer running a server side application communicates with multiple user computing devices. The server side application communicates with electronic databases that define the parameters of each electronic workplace. Each workplace includes an indication of one or more items, such as compounds, and data pertaining to such items, such as computational and experimental data. Updates to a workplace made by one user may be saved to the workplace definition and propagated and displayed to other users. New items of interest may be added to a workplace. A new item added to a workplace may also be saved to the database and registered with the system for use by other users and in connection with other workplaces.


Methods for assessing the consistency and reliability of the calculations using cycle closures in relative binding free energy calculation paths. The methods are used for determining relative strength of binding between a receptor and individual members of a set ligands to form complexes between individual ligand set members and the receptor, in which the binding free energy difference with the lowest error is determined by probabilistic determination of the free energy differences and error distributions about those differences along each of the legs of the closed thermodynamic cycle that probabilistically lead to the hysteresis(es) value(s) observed for each closed of the closed thermodynamic cycle.

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