For the fragments that contain stable hydrophobic contacts (which cause the protein to fold), the protein/computer enforces these contacts and adds more residues to enlarge these points. If new hydrophobic contacts are formed again, the process continues until no more contacts are found.“The protein doesn’t ‘know’ it has the right starting points at the early stages,” Dill explained. “It explores many possible avenues. But, we find that when the chain pieces have reached roughly the 16-to-24-mer stage, then the differences in free energy begin to become compelling, and structures begin to emerge fairly clearly.”In some cases, this zipping procedure alone is enough for a protein to reach its native form. For other cases, the ZA algorithm switches to the assembly procedure, combining two or more fragments to form additional structures until the native form is achieved. The ZA method was tested on nine small proteins, eight of which closely matched the experimental results of samples in the Protein Data Bank. The greatest sign that the ZA method is on the right track is its speed. For example, using ZA, protein G could fold in about 1 CPU year on a 2.8-Ghz Xeon Intel machine.“We don’t know exactly what the speed gain is,” Dill said. “Our largest protein studied is a 112-mer (subsequent to the PNAS paper). Currently the most extensive all-atom physical simulations on Folding@Home, with 100,000 processors, or IBM’s Blue Gene, built for this problem, are on smaller proteins, typically in the range of 20-40 amino acids long. However, those simulations are also more directed at physical questions of folding, rather than at protein structure prediction, so it’s hard to make a direct comparison.”Citation: Ozkan, S. Banu, Wu, G. Albert, Chodera, John D., and Dill, Ken A. “Protein folding by zipping and assembly.” Proceedings of the National Academy of Sciences, July 17, 2007, vol. 104, no. 29, 11987-11992.Copyright 2007 PhysOrg.com. All rights reserved. This material may not be published, broadcast, rewritten or redistributed in whole or part without the express written permission of PhysOrg.com. Citation: Divide-and-conquer strategy key to fast protein folding (2007, August 6) retrieved 18 August 2019 from https://phys.org/news/2007-08-divide-and-conquer-strategy-key-fast-protein.html Researchers have found that proteins may use a divide-and-conquer strategy to fold into their native states in mere microseconds. The physical strategy, called “zipping and assembly” (ZA), can increase the speed at which supercomputers predict protein folding structures, greatly increasing scientists’ understanding of these building blocks of life. Explore further Ribbon diagrams of nine protein structures: Protein Data Bank structures are in orange, while Zipping & Assembly structures are in blue. Credit: Ozkan, et al. ©2007 PNAS. The scientists, Banu Ozkan, Albert Wu, John Chodera, and Ken Dill from the University of California at San Francisco, have published their research in a recent issue of the Proceedings of the National Academy of Sciences. Their results show that the ZA search strategy provides a physics-based model of protein folding that could lead to advances such as computer-based drug discovery and genetic engineering.“Our research has two significant points, I believe,” Dill told PhysOrg.com. “First, it shows that all-atom physical force fields are pretty good (but not perfect), and may be useful for protein structure prediction. And second, it proves that zipping and assembly is a highly efficient conformational search method, and supports the view that ZA may be the physical mechanism of protein folding.”Proteins, which consist of an unstructured linear chain of amino acids, can fold into complex 3D structures within microseconds. On the other hand, high-speed supercomputers might take tens of years to compute the correct structure due to the vast assortment of possible forms the protein could take. When folded incorrectly, proteins can cause neurodegenerative diseases such as Alzheimer’s and mad cow disease. How proteins fold so quickly is a mystery that researchers are approaching from many different angles, including, for example, physics-based force fields. By assigning force fields to different parts of the protein, computers can track the movement of each individual part.Using the ZA strategy, Ozkan, Wu, Chodera and Dill have sped up the rate at which computers using force fields can predict protein structures. In the ZA model, the first step that proteins (or computers) take is breaking the amino acid chain into 8-12 fragments to search for a very small fraction of favorable folding points (traditional methods usually search the entire chain).“The speed gain in our method comes from not exploring all possible folding routes, but instead from following only those routes that entail small conformational search steps,” Dill explained. “This reduces the search problem, in principle, from one that grows exponentially with the chain length to one that, instead, grows only as the first or second power of the chain length. While we haven’t actually proven that quantitatively, it is clear that the method is much faster than brute force Monte Carlo or molecular dynamics.” Parsley and dill help fight cancer, research shows This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.
Image: Kyoto University The device is supposed to be especially handy for use in tight spaces; the intention is to help users of electric wheelchairs maneuver their movements with greater freedom than they have in the past. What is not such good news is that the vehicle on display cost $36,300 to produce, The research lead, Masaharu Komori, an associate professor of mechanical engineering at Kyoto University, is well aware of the price shortcoming and plans to continue work on the chair to bring costs down, and make the chair lighter and more compact. The eventual target price is $12,000. Komori and team hope to commercialize the Permoveh in three to five years.This Permoveh “rollout” comes at a time when Japan is showing much interest in bringing on improved assistive technology, from robots to motorized chairs, that can help the elderly. Among the innovations reported have been a bed that changes into an electric wheelchair and a robot that can wash hair.Whether or not this omnidirectional vehicle can eventually be a popular wheelchair of choice (the top speed is 3.7 mph) for the elderly remains to be seen, but it is being suggested that the Permoveh wheel technology could be adapted for use in conveyor equipment in factories and warehouses. One site notes the wheel technology is like that seen in Honda’s “U3-X” which also enables the rider to move backwards, forwards, and side to side using an omnidirectional wheel. Honda’s description about how the wheel structure enables movement in all directions is that “multiple small-diameter motor-controlled wheels are connected in-line to form one large-diameter wheel. Rotating the large-diameter wheel moves the U3-X forward and backward, while rotating the small-diameter wheels moves it side-to-side. Combining these movements causes the U3-X to move diagonally.” This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only. The driver uses a hand control that can turn the chair in the desired direction. The driver just needs to tip the lever in the direction he or she wants to move. The wheels alone move if the driver wants to go backwards or forwards. The rollers move if the driver wants to go sideways. Both wheels and rollers move if the driver wants to go diagonally. Japan’s Honda unveils futuristic unicyle (w/ Video) Explore further (PhysOrg.com) — A mechanical engineering professor has taken the wraps off his vehicle that is designed to become a next-generation wheelchair. As its formal name suggests, this is the Personal Mobile Vehicle, or Permoveh for short. Rolling it around at his lab in Kyoto, Japan, earlier this month, the professor carried out the demo before an audience of observers and photographers. They watched him ride the device, with its clever wheel-within-wheel system, which allowed the vehicle to move in any direction. The Permoveh has four same-sized wheels with 32 rollers each. They rotate in a perpendicular direction to the rim. The rollers sit inside the main wheels, allowing the vehicle to move in more directions than just back and forth. More information: www.kyoto-u.ac.jp/ja/news_data … s6/2011/120322_1.htm (in Japanese) Citation: Kyoto prof rolls out omnidirectional wheelchair (2012, March 27) retrieved 18 August 2019 from https://phys.org/news/2012-03-kyoto-prof-omnidirectional-wheelchair.html © 2012 PhysOrg.com
This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only. New dating of Neanderthal remains from Vindija Cave finds them older than thought Artifacts from the Anzick site. Credit: Texas A&M University © 2018 Phys.org Journal information: Proceedings of the National Academy of Sciences The Anzick site in Montana. The white post signals where the burial was found. Credit: PNAS Lorena Becerra-Valdivia at the Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, working on the equipment (HPLC) that was used to extract hydroxyproline from the Anzick site bone samples. Credit: Eileen Jacob (University of Oxford, Oxford). Explore further More information: Lorena Becerra-Valdivia et al. Reassessing the chronology of the archaeological site of Anzick, Proceedings of the National Academy of Sciences (2018). DOI: 10.1073/pnas.1803624115AbstractFound in 1968, the archaeological site of Anzick, Montana, contains the only known Clovis burial. Here, the partial remains of a male infant, Anzick-1, were found in association with a Clovis assemblage of over 100 lithic and osseous artifacts—all red-stained with ochre. The incomplete, unstained cranium of an unassociated, geologically younger individual, Anzick-2, was also recovered. Previous chronometric work has shown an age difference between Anzick-1 and the Clovis assemblage (represented by dates from two antler rod samples). This discrepancy has led to much speculation, with some discounting Anzick-1 as Clovis. To resolve this issue, we present the results of a comprehensive radiocarbon dating program that utilized different pretreatment methods on osseous material from the site. Through this comparative approach, we obtained a robust chronometric dataset that suggests that Anzick-1 is temporally coeval with the dated antler rods. This implies that the individual is indeed temporally associated with the Clovis assemblage. Artifacts from the Anzick site. Credit: Texas A&M University In 1968, construction workers came upon the remains of an infant skeleton. Those remains became known as Anzick-1 and were believed to represent a member of the Clovis people. The Clovis people are believed to have been the first widespread group of people living in North America. Prior research has suggested they lived approximately 13,000 to 12,600 years ago. Their name comes from the distinctive Clovis-style projectiles they created.In the years after Anzick-1 was found, teams of researchers studying the remains found mixed results when testing for age. Some showed the remains as very nearly the same age as nearby Clovis artifacts, while others found the remains to be thousands of years more recent. In this new effort, the researchers sought to settle the matter once and for all using new and improved dating techniques.The new techniques involved using pretreatments of collagen found in the remains to factor out decontamination and for extracting a single amino acid for radiocarbon dating. The researchers report that all of their tests showed that antlers found near the burial site and the skull of a second specimen (Anzick-2) were roughly the same age—which was approximately the same as prior testing had shown. But some of the testing showed the remains of Anzick-1 to be approximately 1000 years younger. Another test the team performed, though, called HYP extraction, showed the infant remains to be approximately the same age as the antlers and Anzick-2. The differing results from the other tests, the researchers suggest, were likely due to contamination issues. They contend that because HYP is the more precise measurement technique, their results show that Anzick-1 is approximately the same age as the other artifacts. And this, they claim, suggests that the debate about the age of the remains should be considered resolved. A team of researchers from the University of Oxford, Texas A&M University and Stafford Research LLC has found evidence bolstering the theory that the skeletal remains of an infant unearthed in Montana are those of the only known Clovis burial. In their paper published in Proceedings of the National Academy of Sciences, the group describes their testing methods and what they found. Citation: New testing method suggests baby Anzick-1 was same age as surrounding Clovis artifacts (2018, June 19) retrieved 18 August 2019 from https://phys.org/news/2018-06-method-baby-anzick-age-clovis.html Lorena Becerra-Valdivia at the Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, working on the equipment (HPLC) that was used to extract hydroxyproline from the Anzick site bone samples. Credit: Eileen Jacob (University of Oxford, Oxford).
In an ironic twist, physicists have shown that the very property that can be used to show that quantum computing devices can solve some problems that classical computers cannot also makes it impossible to efficiently certify that this “quantum supremacy” has indeed been achieved, for a wide variety of schemes. In quantum computing, the issue of certification is crucial for formally verifying the superior computing power of quantum devices. More information: Dominik Hangleiter, Martin Kliesch, Jens Eisert, and Christian Gogolin. “Sample Complexity of Device-Independently Certified ‘Quantum Supremacy.'” Physical Review Letters. DOI: 10.1103/PhysRevLett.122.210502Also at arXiv:1812.01023 [quant-ph] This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only. Citation: Quantum supremacy and its efficient certification difficult to achieve simultaneously (2019, June 5) retrieved 18 August 2019 from https://phys.org/news/2019-06-quantum-supremacy-efficient-certification-difficult.html Boson sampling with photons found to produce useful output in spite of photon leaks for quantum supremacy Explore further © 2019 Science X Network The team from Germany, Dominik Hangleiter, Martin Kliesch, Jens Eisert, and Christian Gogolin, has published a paper on their work on quantum supremacy certification in a recent issue of Physical Review Letters.”We rigorously prove an intuition that many in the field shared, namely, that certifying random sampling schemes proposed for a quantum supremacy demonstration requires exponentially many samples,” Hangleiter, at the Free University of Berlin, told Phys.org. “One of the most intriguing findings of our work is that this is due to the very property that allows to prove approximate sampling hardness in the first place, namely, the flatness of the sampled distributions. Our work also points towards a potential way out of this dilemma: interactive or quantum certification protocols.”The term “quantum supremacy” refers to the possibility that quantum computing devices can solve some problems that are practically infeasible for classical computers to solve. One problem that is considered intractable for classical computers is random sampling from certain very flat distributions (in which all outcomes are nearly equally likely) over exponentially large datasets. Currently, no universal, fault-tolerant quantum computer is available to experiment with, but even the limited quantum devices that are available today are thought to be capable of performing the random sampling task. Intuitively, this is because quantum devices can prepare a state in the correct superposition of all elements of a set, while classical devices need to access the exponentially many probabilities one by one. One of the limitations of all physical devices (quantum or classical) is that they are only capable of approximate sampling. So in order to demonstrate quantum supremacy, researchers must show that a quantum device’s approximate sampling is close enough to ideal sampling so that it is still intractable for classical computers. All current proofs of this concept, which is called approximate sampling hardness, use small second moments. In the random sampling task, a distribution is randomly chosen. Essentially, small second moments mean that the randomly chosen distribution concentrates around the uniform distribution and is therefore very flat. In the new paper, the researchers show that small second moments also forbid efficient certification from the samples alone. That is, sampling distributions with small second moments cannot be certified with polynomially many samples, but instead require exponentially many samples. This makes certification inefficient and unrealistic to perform in a reasonable amount of time. The results hold for a variety of widely used sampling schemes, including boson sampling and universal random circuit sampling, among others. However, the results do not mean that efficient certification is necessarily impossible by any method. The researchers hope that, instead, the findings will motivate the development of alternative certification schemes, as well as proofs of approximate sampling hardness that apply to distributions with larger second moments. “Our work guides the way for where to look for feasible certification schemes,” Hangleiter said. “In particular, it often makes sense to use device-specific knowledge to leverage certification. One direction of research is to develop device-specific certification schemes both for quantum sampling schemes, but thinking further, also for more elaborate tasks that can be performed on quantum computers. “Quantum sampling schemes are very ‘clean’ quantum supremacy proposals in the sense that they allow for a complexity-theoretic hardness argument. At the same time, they do not have real applications (yet). A second direction of research is to develop schemes that are feasible on near-term devices and yet hard, which also solve a useful task, as well as to find applications for the known sampling schemes.” A test to certify quantum supremacy will accept a probability distribution if it is classically hard, and otherwise will reject it. Credit: Hangleiter et al. Journal information: Physical Review Letters
The Hungarian Information and Cultural Centre brings an array of events to the month. You can encounter the rich array of wildlife and nature photography from the Bakony Mountains and Lake Balaton regions of Hungary, by a passionate photo artiste and forester József Mesterházi at the exhibition Glimpses of Hungarian Widlife. He captures the rare moments of animal and forest life in its own habitat, as well as the changes and the eternal secrets of nature. The exhibition features evocative animal portraits and spectacular wildlife images that are sure to engage visitors of all ages. The exhibition was inaugurated and highly appreciated by Raghu Rai, India’s ace photographer. Also Read – ‘Playing Jojo was emotionally exhausting’Next is a musical treat Music Without Boundaries by Capital City Minstrels on May 6. The evening’s repertoire will showcase a diverse range of music, bringing out the contrast and subtle shades and themes that run through different genres from sacred and gospel to Western and Indian classical compositions and a few popular pieces as well.The next highlight of the month is screening of the film Children of Glory on May 7. The movie commemorates Hungary’s Revolution of 1956 and the ‘Blood in the Water’ match. Taking place in Budapest and at the Melbourne Olympic Games in October and November of that year, the film takes viewers into the passion and sadness of one of the most dramatic popular revolts of the twentieth century. In the same year, Soviet tanks were violently suppressing the Revolution in Hungary, when the Hungarian water polo team was winning over Russia in the Olympic pool in Melbourne. This event is sometimes described as the bloodiest water polo match in history. While telling the story of 1956 in part through fictional lead characters, the film-makers simultaneously recreated many of the key public events of the Revolution, including the huge demonstrations and the street fights in the of Budapest. Also Read – Leslie doing new comedy special with NetflixNext is a sculpture exhibition titled Being a Child from May 10 -15. In this exhibition, Christine Margotin brings us back to childhood, a crucial period of life that ‘one should never completely leave’ as she likes to state. What can be learned from observing children? What can we -adults- gain in reconnecting somewhat with our childhood? The artist explores the dialectics between childhood and adulthood through 3 series of artworks sculptures of life-size children playing simple games, sculptures of children showing joyful or moving attitudes and 3D-canvases displaying messages about childhood. May 17 will screen the film Questioning Life and Beyond Through Films of Seema Kohli. Habiart presents selected eight experiential video performances, including Swayamsiddha – Myth, Mind and Movement; Parikrima and Unending Dance of Light- Raks E Shams. The artist would be resent for an interactive session with the audience.Starting from May 26 is the exhibition that features the best of the award winning paintings of the on-the-spot children’s painting competition hosted by HICC in February 2015. The theme of this year’s event is Hungarian folktales. It’ll be on till August 28.
Kolkata: A youth was stabbed to death in broad daylight by some unidentified miscreants. The incident took place on platform number 1 at Baidyabati station in Hooghly on Tuesday.The Railway police have arrested two persons in this connection so far. According to the police, the victim, Joyprakash Das, a resident of Champdani area in Hooghly, was standing at the station on Tuesday afternoon when he got engaged in an altercation with some other youth. A scuffle soon broke out between the youth and other accused. One of the group members suddenly took out a knife and stabbed him. Also Read – Heavy rain hits traffic, flightsThe miscreants fled the spot immediately after the incident. Locals rushed the victim to Srerampur Welsh Hospital where he was declared brought dead.The body has been sent for post-mortem. After starting an investigation, the railway police have arrested two youth in this connection so far.They have been identified as Raju Das and Pradhan Das. According to the preliminary investigation, police suspect that the victim had a relationship with the wife of Pradhan Das. The accused are also residents of Champdani area. Also Read – Speeding Jaguar crashes into Merc, 2 B’deshi bystanders killedAn eyewitnesses told the police that he heard people shouting and when came out of his stall found that the victim was lying in a pool of blood on the platform. He was immediately rushed to the hospital. Three youth were seen fleeing the spot.Police are interrogating the duo and trying to know if other persons were involved in the incident. Police are yet to confirm the exact reason behind the incident. A senior official of the railway station said a murder has taken place on the platform. Police have started a detailed probe into the incident.
In a jolt to the CPI(M) ahead of next year’s Assembly polls, CPI(M) MLA from Khandaghosh on Thursday joined the TMC accusing its leadership of failing to reach out to the masses.Nabin Chandra Bag along with other CPI(M) leaders from Bardhaman district joined the TMC in the presence of senior ruling party leaders Partha Chatterjee and Arup Biswas.“He has decided to join the TMC to become part of the developmental work ushered in by our party leader Mamata Banerjee,” Chatterjee said.Bag said he was unhappy with the CPI(M)leadership as the party had completely lost touch with the masses.The CPI(M) leadership is yet to officially react to the development.
In an attempt to honour the works of different authors in 24 recognised Indian languages, Sahitya Akademi presented Sahitya Akademi Awards to writers at a ceremony in FICCI Golden Jubilee Auditorium in the national capital on Tuesday. Twenty one male authors and three female authors won the Awards. Seven poetry collections, six collections of short stories, four novels, five collections of essays / criticism and two plays won the Award.Dr Gopi Chand Narang, eminent Urdu scholar and Fellow of Sahitya Akademi was the chief guest at the function while Vishwanath Prasad Tiwari, president, Sahitya Akademi, presented the Awards to the writers. Also Read – ‘Playing Jojo was emotionally exhausting’K Sreenivasarao, secretary, Sahitya Akademi and Dr Chandrashekhar Kambar, vice president of Sahitya Akademi were also present at the ceremony.In his speech, the chief guest Dr Gopi Chand Narang applauded Sahitya Akademi for carrying out literary service in all the 24 recognised languages and he highlighted various details and Akademi’s achievements to point out how Akademi has been rendering literary service to the nation with writers at the core. He reiterated that the Akademi will always stand by the writers of all kinds. Also Read – Leslie doing new comedy special with NetflixIn his welcome speech, Dr K Sreenivasarao, secretary, Sahitya Akademi, stated that the Akademi is a home of writers and for the writers. Vishwanath Prasad Tiwari said: “It is through literature that unity can be achieved and communal dividing elements can be defeated.” He added that he is proud to be associated with the Akademi which is preserving and propagating all the Indian literary traditions. List of award winners include Assamese – Kula Saikia; Bengali – Alok Sarkar; Bodo – Birendra Kumar Bodo; Dogri – Dhian Singh; English – Cyrus Mistry; Gujarati – Rasik Shah; Hindi – Ramdarash Mishra; Kannada – KV Thirumalesh; Kashmiri – Basir Bhadarwahi; Konkani – Uday Bhembre; Maithili – Man Mohan Jha; Malayalam – K R Meera; Manipuri – Kshetrimayum Rajen Singh; Marathi – Arun Khopkar; Nepali – Gupta Pradhan; Odia – Bibhuti Pattanaik; Punjabi – Jaswinder Singh; Rajasthani – Madhu Acharya ‘Ashawadi’; Sanskrit – Ram Shanker Awasthi; Santali – Rabi Lal Tudu; Sindhi – Maya Rahi; Tamil – A Madhavan; Telugu – Volga and Urdu – Shamim Tariq.
Kolkata: Senior officials of the Customs along with the police seized gold biscuits worth nearly Rs 53 lakh from Bongaon in North 24-Parganas on Friday night. One person has been arrested in this connection so far. The accused, Suman Mondal, a resident of Boyalda village in Bongaon, had been carrying a bag containing the gold biscuits. Acting on a tip-off, the Customs officials conducted raids and arrested him from Choruigachi area for his alleged involvement in a gold smuggling racket. The accused was later handed over to the police by Customs officials for further investigation. Also Read – Rain batters Kolkata, cripples normal lifeAccording to the preliminary investigation, the police and Customs officials suspect that the accused might be a part of an international gold smuggling racket. There are others involved in the racket as well, police suspect. According to the cops, as many as 14 gold biscuits were found in his possession weighing around 600 grams. It may be mentioned that the police and Customs have intercepted a number of youths in the district in the past few months and seized gold from them. Also Read – Speeding Jaguar crashes into Mercedes car in Kolkata, 2 pedestrians killedA probe is being conducted to ascertain if there are any connections between all the incidents. The district police have also intensified the surveillance in the bordering areas of Bongaon. The preliminary investigation suggests that the accused changed route following some recent incidents in which smugglers bringing gold bars and biscuits from abroad were intercepted at Kolkata airport. The accused then began smuggling gold along the India-Bangladesh border in certain districts. As there was stringent surveillance in all the airports these days, it has become difficult for the smugglers to bring in gold from abroad.
Kolkata: The state government has not given any order to suspend screening of the film The Accidental Prime Minister, Indranil Sen, minister of state for Information and Cultural Affairs, said on Friday.The matter came to front after the authorities of Hind Inox suspended the first show of the film, following a protest by Youth Congress supporters in front of the cinema hall. However, the second show was screened on time. Youth Congress supporters led by Suman Pal staged a demonstration outside the movie theatre on Friday afternoon. They raised slogans against Prime Minister Narendra Modi and burnt his effigy. The screening of the first show was in progress when the incident took place. The authorities of Hind Inox suspended the show for the safety and security of the employees. Also Read – 3 injured, flight, train services hit as rains lash BengalThe protest by Youth Congress supporters has revealed infighting in the camps of Somen Mitra, PCCI chief and Adhir Chowdhury, the former PCCI head. Pal, who led the protest, is believed to be a close aide of Adhir Chowdhury. Rohan Mitra, vice-president of Youth Congress, said no step was taken by Congress to suspend screening of the film. Congress has always believed in freedom of speech and so there is no question of suspension of screening of the film.