The Dependence of All-Atom Statistical Potentials on Structural Training Database
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新编研究生英语系列教程博士研究生英语综合教程(第二版/教师用书)北京市研究生英语教学研究会主编陈大明徐汝舟副主编刘宁王焱华许建平编者赵宏凌邹映辉杨凤珍来鲁宁张剑柳君丽曹莉郑辉中国人民大学出版社KEY TO THE EXERCISESUnit One ScienceText 1 Can We Really Understand Matter?I. Vocabulary1. A2. B3. A4. C5. D6. B7. B8. CII. Definition1. A priority2. Momentum3. An implication4. Polarization5. the distance that light travels in a year, about 5.88 trillion miles or 9.46 trillion km.6. a contradictory or absurd statement that expresses a possible truth7. a device that speeds up charged elementary particles or ions to high energiesIII. Mosaic1. The stress: (Omitted)Pronunciation rule: An English word ended with–tion or –sion has its stress on the last syllable but one.2. molecule3. A4. B5. C6. B7. A8. AIV. TranslationA.(Refer to the relevant part of the Chinese translation)B.In September 1995, anti-hydrogen atom—an anti-matter atom—was successfullydeveloped in European Particle Physics Laboratory in Switzerland. After the startling news spread out, scientists in the West who were indulged in the research of anti-matter were greatly excited. While they were attempting to produce and store anti-matter as the energy for spacecraft, they raised a new question: Many of the mysterious nuclear explosions in the recent one hundred years are connected with anti-matter. That is to say, these hard-to-explain explosions are tricks played by anti-mat ter. They are the “destruction”phenomenon caused by the impact between matter and anti-matter.V. GroupingA.Uncertainty:what if, illusory, indescribable, puzzle, speculation, seemingly, in some mysterious wayB.Contrast:more daunting, the hardest of hard sciences, do little to discourage, from afar, close scrutiny, work amazingly wellC. Applications of Quantum mechanics:the momentum of a charging elephant, building improved gyroscopes1. probabilities2. illusory3. discourage4. scrutinyVI. Topics for Discussion and Writing(Omitted)WRITING•STRATEGY•DEFINITIONI. Complete the following definitions with the help of dictionaries.1. To bribe means to influence the behavior or judgment of others (usually in positions ofpower) unfairly or illegally by offering them favors or gifts.2. Gravity is defined as the natural force by which objects are attracted to each other,especially that by which a large mass pulls a smaller one to it.3. The millennium bug refers to the computer glitch that arises from an inability of thesoftware to deal correctly with dates of January 2000 or later.4. Globalization is understood as the development so as to make possible internationalinfluence or operation.II. Write a one-paragraph definition of the following words.1. hypothesisA hypothesis is an idea which is suggested as a possible way of explaining facts,proving an argument, etc. Through experiments, the hypothesis is either accepted as true (possibly with improvements) or cast off.2. scienceScience is defined as the intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and natural world through observation and experiment.3. superstitionSuperstition refers to a belief which is not based on reason or fact but on old ideas about luck, magic, etc. For example, it is a common superstition that black cats are unlucky.4. pessimismPessimism is a tendency to give more attention to the bad side of a situation or to expect the worst possible result. A person with pessimism is a pessimist who thinks that whatever happens is bad.5. individualismIndividualism is the idea that the rights and freedom of the individual are the most important rights in a society. It has a bad sense in that little attention is paid to the rights of the collective or a good one in that independence is emphasized rather than dependence on others.Text 2 Physics Awaits New Options as Standard Model IdlesI. Vocabulary1. C2. A3. B4. A5. C6. D7. D8. BII. Definition1. A refrain2. A spark3. A jingle4. Symmetry5. develops or studies theories or ideas about a particular subject.6. studies the origin and nature of the universe.7. studies the stars and planets using scientific equipment including telescopes.III. Mosaic1. gravity2. anti-/opposite3. D4. B5. A6. A7. B8.AIV. TranslationA.(Refer to the relevant part of the Chinese translation)B.The Standard Model of particle physics is an unfinished poem. Most of the pieces are there,and even unfinished, it is arguably the most brilliant opus in the literature of physics. With great precision, it describes all known matter – all the subatomic particles such as quarks and leptons –as well as the forces by which those particles interact with one another.These forces are electromagnetism, which describes how charged objects feel each other’s influence: the weak force, which explains how particles can change their identities, and the strong force, which describes how quarks stick together to form protons and other composite particles. But as lovely as the Standard Model’s description is, it is in pieces, and some of those pieces – those that describe gravity – are missing. It is a few shards of beauty that hint at something greater, like a few lines of Sappho on a fragment of papyrus. V. GroupingA.Particle physics:supersymmetry, equation, superpartners, stringB.Strangeness:bizarre, beyond the ken ofC.Antonyms:gravity–antigravity1. novelty2. revelatory3. Symmetry4. gravityVII. Topics for Discussion and Writing(Omitted)WRITING • STRATEGY• EXEMPLIFICATION AN D ILLUSTRATION(Omitted)Text 3 Supporting ScienceI. Vocabulary1. D2. C3. A4. C5. C6. A7. B8. A9. C 10. D 11. B 12. AII. Definition1. A portfolio2. A vista3. Cryptography4. Paleontology5. a business or an undertaking that has recently begun operation6. a group of people having common interests7. a person with senior managerial responsibility in a business organizationIII. Rhetoric1. pouring money into2. column3. unbridled4. twilight5. blossomed intoIV. Mosaic1. phenomenon criterion datum medium(because these words originated from Latin and retain their Latin plural form)2. A3. A4. B5. B6. B7. C8. BV. TranslationA.(Refer to the relevant part of the Chinese translation)B. The five scientists who won the 1996 Nobel Prize point out that the present prosperityand development are based on the fruits of basic scientific research and the negligence of basic scientific research will threaten human development of the 21st century.EU countries noticed that one of their weaknesses is “insufficient investment in research and development.” Korea and Singapore do not hesitate to pour money into research and development. The developed countries in the West have used most of the scientific and technological development resources for the research and development of new and high technology. This has become an obvious trend at present. It is evident from the experiences of various countries that new and high technology can create and form new industries, open up and set up new markets. The innovation of traditional industries with new and high technology is a key method to strengthen the competitive competency of an enterprise.VI. Grouping:A.Negligence of basic research:corporate breakups, cut back on research, ignore it, subject to a protracted dissection and review, second-guessing, dropped dramatically, subjected to a scrutiny, skirling our supportB.Significant examples of basic research:computing, biotechnology, the Internet, number theory, complex analysis, coding theory, cryptography, dinosaur paleontology, genetics research)C.Ways to intensify arguments:moved support for science from a “want to have” squarely into the “need to have”column1. resounding2. second-guessing3. downsized4. subjectedVII. Topics for Discussion and Writing(Omitted)WRITING • STRATEGY • COMPARISON, CONTRAST, AND ANALOGY (Omitted)Text 4 Why Must Scientists Become More Ethically Sensitive Than They Used to Be?I. Vocabulary1. B2. B3. A4. C5. B6. D7. D8. A9. D 10. B 11. B 12. DII. Definition1. A constraint2. Algorithm3. A prerequisite4. Ethics5. an important topic or problem for debate or discussion6. a person’s principles or standards of behaviour; one’s judgement of what is important inlife.7. a formal plan put forward for consideration to carry out a projectIII. Rhetoric1. brushed under the carpet2. smell3. hands and brains4. battle front5. module . . . moduleIV. Mosaic1. /z/ /s/ /s/ /z/ /s//s/ /iz/ /z/ /s/ /z//iz/ /z/ /s/ /z/ /z//z/ /s/ /s/ /z/ /z//s/ after voiceless consonants/z/ after voiced consonants/iz/ after a word ended with –es2. B3. D4. A5. D6. A7. CV. TranslationA.(Refer to the relevant part of the Chinese translation)B. Scientists and medical ethicists advocate the prohibition of human cloning as a way toproduce life. They all agree that human cloning exerts severe threats on human dignity.Social critics point out that cloned children will lack personality and noumenon. G. Annas, professor of health laws in Boston university, points out that “human cloning should be banned because it may fundamentally alter the definition of ourselves.”VI. Grouping:A.The change of attitudes towards ethical consideration:occupy media slots and Sunday supplements, latest battle front, can no longer be swept aside, more sensitiveB.Academic science:a worldwide institutional web, peer review, respect for priority of discovery,comprehensive citation of the literature, meritocratic preferment, smuggle ethical considerations from private life, from politics, from religion, from sheer humanitariansympathyC.Industrial science:intimately involved in the business of daily lifeD.Post-academic science:a succession of “projects”, compound moral risks with financial risks, largely the work ofteams of scientists1. individualistic2. energized3. comprehensive4. heterogeneousVII. Topics for Discussion and Writing(Omitted)WRITING • STRATEGY • CAUSE AND EFFECT(Omitted)Text 5 Beauty, Charm, and Strangeness: Science as MetaphorI. Vocabulary1. B2. A3. C4. B5. C6. B7. A8. B9. A 10. CII. Rhetoric1. pitch2. landscape3. unblinking4. yawn5. wringsIII. Mosaic1.physical poetic political scientific optical atomic2. (Omitted)3. B4. B5. A6. C7. DIV. TranslationA.(Refer to the relevant part of the Chinese translation)B. There are only two forms of human spiritual creation: science and poetry. The formergives us convenience; and the latter gives us comfort. In more common words, the former enables us to have food to eat when we are hungry; and the latter makes us aware that eating is something more than eating, and it is very interesting as well. To have science without poetry, atomic bomb will be detonated; to have poetry without science, poets will starve to death.Scientists should not despise poets; and poets should not remain isolated from scientists.If the two fields conflict each other, human beings would be on the way to doom. In fact, the greatest scientists like Newton, Einstein and Mrs. Currie were all endowed with poetic spirit.I assert that in observing the apple falling to the ground, Newton not only discovered thegravity of the earth, he also wrote a beautiful poem.V. GroupingA.Human reason:guilty of hubris, cramped imagination, commonsense logic, an ignorant manB.Differences between art and science:different in their methods and in their ends, a scientific hypothesis can be proven, new combinations of old materials, transform the ordinary into extraordinary, a practical extension into technology, the sense of an endingC.Similarities between art and science:in their origin, quest to reveal the world1. indistinguishable2. transform3. poetic4. extension5. subdueVI. Topics for Discussion and Writing(Omitted)WRITING • STRATEGY • DIVISION AND CLASSIFICATIONI. Organize the following words into groups.People: physician; driver; boxer; mother; teacherSchools: school; college; institute; kindergarten; universityColors: brown; purple; violet; black; yellowPrepositions: along; toward; upon; without; intoVerbs:listen; read; write; hear; lookII. Complete the following lists.1. College students can be classified according to:A.academic achievementB.attitude toward politics, friendship, etc.C.sexD.heightE.place of originF.value of lifeG.major2. Transportation means can be classified according to:A.speedB.sizeeD.fuelfortF.historyG.water, land, or airIII. Write a paragraph of classification on the books which you like to read.(Omitted)Text 6 Is Science Evil?I. Vocabulary1. C2. A3. D4. B5. B6.A7. C8. C9. D 10. AII. Definition1. Canon2. Validity3. A premise4. Disillusionment5. the process of establishing the truth, accuracy, or correctness of something6. a mode of thinking based on guessing rather than on knowledgeIII. Mosaic1. 1) / / illusion dis-=not -ment=noun ending2) / / science pseudo-=false3) / / conscious -ness=noun ending4) / / question -able=adjective ending5) / / extenuate -ation=noun ending6) / / indict -ment=noun ending7) / / rebut -al=noun ending8) / / perpetrate -ion=noun ending9) / / problem -ic=adjective ending10) / / dissolute -ion=noun ending2. Para. 13: Only when scientific criticism is crippled by making particulars absolute can aclosed view of the world pretend to scientific validity –and then it is a falsevalidity.Para.14: Out of dissatisfaction with all the separate bits of knowledge is born the desire to unite all knowledge.Para. 15: Only superficially do the modern and the ancient atomic theories seem to fit into the same theoretical mold.1) Para. 13: Only + adverbial clause of time + inverted orderPara. 14: Prepositional phrase + inverted orderPara. 15: Only + adverb + inverted order2) Inverted order is used to emphasize.3. C4. B5. A6. CIV. TranslationA.(Refer to the relevant part of the Chinese translation)B. At present there exist two conflicting tendencies towards the development of science andtechnology. The opponents of science hold that the development of modern science has not brought blessings to human beings, instead it has brought human beings to the very edge of disaster and peril. On the other hand, the proponents of scientific and technological progress maintains that the crises facing human beings today—such as environmental pollution, ecological unbalance, natural resource exhaustion—are the natural consequences of the development of science, and the solution to which lies in the further development of science. Both of the above tendencies are reasonable in a sense with their respective one-sided view. If we view the development of modern science and technology from the point of view of our times and with dialectic viewpoints, we can find out that the problem facing modern science and technology is not how to understand the progress of modern science and technology, but how to find out the theoretical basis for the further development of science and technology in order to meet the needs of the times.V. GroupingA.Attitudes toward science:expect to be helped by science and only by science, the superstition of science, the hatred of science, the one great landmark on the road to truthB.Characteristics of science:powerful authority, solve all problems, thoroughly universalC.Scientific knowledge:a concrete totality, cannot supply us with the aims of life, cannot lead usD.Contrast between ancient and modern science:progress into the infinite, making particulars absolute, not as an end in itself but as a tool of inquiry1. corruption2. totality3. inquiry4. superstition5. landmarkVI. Topics for Discussion and Writing(Omitted)WRITING • STRATEGY • GENERALIZATION AND SPECIFICATIONWRITING • STRATEGY • COMBINATION OF WRITING STRATEGIES (Omitted)Unit Two EngineeringText 7 Engineers’ Dream of Practical Star FlightI. Vocabulary1. D2. C3. B4. D5. A6. C7.CII. Definition1. Annihilation2. A skeptic3. A cosmic ray4. Anti-matter5. A workshop6. the curved path in space that is followed by an object going around another larger object7. any one of the systems of millions or billions of stars, together with gas and dust, heldtogether by gravitational attractionIII. Mosaic1. 闭音节, 字母u 发/ / 的音,如A, C and D.2. (Omitted)3. (Omitted)4. C5. C6. B7. A8. BIV. TranslationA.(Refer to the relevant part of the Chinese translation)B. Human beings have long been attempting sending unmanned devices, called interstellarprobes, into the outer space to understand the changes of climates, geological structures and the living beings on the stars and planets out there. A probe is usually sent into the orbit of the earth by “riding” a spacecraft or carrier rockets. After its orbital adjustments are made, the rocket engine is ignited and the probe continues its journey to the orbit of the other star or planet. With the rocket engine broken off, the probe immediately spreads its solar-cell sails and antenna, controlling its posture with sensors. When convinced that it is in the orbit of the targeted star, the probe starts its propeller and flies to the preset destination.V. GroupingA.Astronomical phenomena:interstellar medium, a wind of particles, galaxy, reserves of comets, the Kuiper Belt,orbit, Pluto, the Oort Cloud, the bombardment photonB.Space equipment:interstellar probe, gravitational lens, chemical rocket, thruster, reflective sailC.To explore the universe:scoop, bend, sampleD.Challenges and solutions in interstellar flights:carry its own supply of propellant, matter-antimatter, nuclear power1. gravitational2. propulsion3. probed4. interstellarVI. Topics for Discussion and Writing(Omitted)WRITING • RHETORIC • SIMILE AND METAPHORI. Complete the following similes with the words given, using one word once only.1. as drunk as a ___ bear 11. as cool as ___ cucumber______2. as faithful as a ___ dog_____ 12. as white as ____ snow ________3. as greedy as ____Jew_____ 13. as cunning as a ____ fox__________4. as rich as _____ king_____ 14. to fight like a ____ _lion_________5. as naked as a ___ frog_____ 15. to act like a stupid __ ass_________6. as red as a _ _lobster_ 16. to spend money like __ water_______7. as beautiful as a _ butterfly__ 17. to eat like a _ wolf________8. as busy as a ____ bee______ 18. to sleep like a _____ log ______9. as firm as a ____ rock _____ 19. to swim like a ____ fish________10. as rigid as a ___stone____ 20. to tremble like a _____ _ leaf_________II. Explain the following metaphors.1. Creaking doors hang the longest.creaking door: anything or anybody in a bad condition2. I could hardly put up with his acid comment.acid comment: bitter remark.3. Her eyes were blazing as she stormed at me.blazing: filled with angerstormed: shouted; screamed4. She burnt with love, as straw with fire flames.burnt with love: extremely excited with love5. The talk about raising taxes was a red flag to many voters.a red flag: a danger signal (that might stop the support of many voters)6. The charcoal fire glowed and dimmed rhythmically to the strokes of bellows.glowed and dimmed: became bright and gloomy7. The city is a jungle where nobody is safe after the dark.a jungle: a disorderly place8. To me he is power—he is the primitive, the wild wolf, the striking rattlesnake, thestinging centipede.the primitive, the wild wolf, the striking rattlesnake, and the stinging centipede: the most terrifying creatureText 8 Blinded By The LightI. Vocabulary1. A2. C3. A4. C5. D6. A7. BII. Rhetoric1. riveted2. pack3. pours4. creepsIII. Mosaic1. 开音节发字母读音, 如A, B and C.2. (Omitted)3. (Omitted)4. C5. D6. D7. C8. AIV. TranslationA.(Refer to the relevant part of the Chinese translation)B. The energy released from nuclear fusion is much more than that from nuclear fission, andthe radioactivity given out from fusion is only one hundredth of that from fission. The major fuel used for nuclear fusion is hydrogen and its isotopes, deuterium and tritium, among which deuterium could be directly extracted from sea water. The energy of deuterium contained in one liter of sea water is equal to 300 liters of petroleum. In the ocean there are about 35,000 billion tons of deuterium, which could be used for more than one billion years. Compared to the fission energy, the fusion energy on the earth is nearly limitless.V. GroupingA. Nuclear-fusion:the doughnut-shaped hollow, reactor, the Tokamak Fusion reactor, fusion, generate, consumeB. Verbs related to nuclear-fusion reaction:ignite, release, stickC. Excitement and cool-down:not a few tears, The experiment is an important milestone, but fusion power is still along way . . . , But no one knows for sure whether…, Even then it will take decades of engineering before…1. nuclear fusion2. repel3. blastVI. Topics for Discussion and Writing(Omitted)W RITING • R HETORIC • METONYMY AND SYNECDOCHEI. Study the uses of metonymy in the following sentences and then put them into Chinese.1.The election benched him in the district court.他在这次竞选中当上了地区法官。
附件2:论文中英文摘要格式作者姓名:陈骏论文题目:钛酸铅基化合物晶体结构及其负热膨胀性作者简介:陈骏,男,1979年8月出生;2001年9月在北京科技大学攻读冶金物理化学硕士学位,2003年9月提前攻读博士学位,一直师从北京科技大学邢献然教授,2007年3月获博士学位;2007年4月留在北京科技大学物理化学系,加入邢献然教授长江学者学术梯队从事教学科研工作;2008年得到德国洪堡博士后研究基金资助,在TU-Darmstadt继续开展钛酸铅基化合物相结构等方面的研究。
读博士及其后的一年期间内,在国际著名期刊上发表第一作者论文12篇、第二作者论文5篇,作为主要研究人员获教育部科技奖励(自然科学奖)一等奖1项、授权专利2项;2008年获得北京市首届优秀博士论文称号。
中文摘要钛酸铅(PbTiO3)是一种重要的钙钛矿结构的铁电体,在介电、压电、铁电、热释电等方面具有重要的研究与应用价值;同时,它在室温至居里温度范围内还表现出奇特的热缩冷胀行为,即负热膨胀性(NTE),这种负热膨胀行为是其它钙钛矿结构化合物所不具有的,如CaTiO3、BaTiO3、KNbO3、BiFeO3等。
研究PbTiO3的负热膨胀性将有利于开发出负热膨胀性可控以及零膨胀材料,拓展负热膨胀材料在实际中的应用,PbTiO3负热膨胀机理的研究可指导新型负热膨胀材料的开发。
本论文主要以钙钛矿结构的铁电化合物Pb1-x A x Ti1-y B y O3(A=La、Sr、Cd、Bi、(La1/2K1/2)等;B=Fe、Zn等不同价态金属原子)为中心,研究A位与B位替代对其负热膨胀性、晶体结构、点阵动力学的影响,实现负热膨胀性能可控,开发零膨胀材料,并研究PbTiO3负热膨胀机理。
本文研究了Pb1-x A x TiO3(A=La、Sr、(La1/2K1/2)、Cd)体系的固溶体特性、晶体结构以及负热膨胀性能受掺杂的影响。
La、Sr、(La1/2K1/2)的掺杂都使PbTiO3的轴比(c/a)及居里温度(T C)不同程度地线性下降,La的掺杂大幅度地降低了PbTiO3的负热膨胀性能,在0.15≤x La ≤0.20范围内,Pb1-x La x TiO3表现出零膨胀性能。
U11. disaster2. compelled3. historical4. disciplined5. destruction6. output7. retreat8. abandoned9. trace 10. eternal 11. investment 12. transfer 13. justify 14. nonetheless 15. contributions 16. accelerate 17. threaten1. show signs of2. called upon3. off limits4. in fear of5. slow down6. cut down7. from head to foot8. come by9. lost out 10. As yet 11. reside inIN CREASING YOUR WORD POWERsmoke + fog; web + log; breakfast + lunch ;medical + care ;motor + hotel; net + citizen ;science + fiction; work + alcoholicAnthropology: the scientific study of the human race, especially of its origins, development, customs and beliefsArchaeology: the study of the buried remains of the ancient times, such as houses, pots, tools, and weapons Ecology: the study of the relations of plants, animals, and people to each other and to their surroundingsGeology: the study of rocks, soils, etc. which make up the Earth, and of their changes during the history of the world Ideology: a set of ideas that an economic or political system is based onMusicology: the study of the history and theory of music Psychology: the scientific study of the mind and how it influences behaviourSociology: the scientific study of the nature and development of society and social behaviourZoology: the scientific study of animals and their behaviour1. collective individual2. consistent contradictory3. constructive destructive4. irrational rational5. modern primitive6. natural synthetic7. nearby distant8. optimistic pessimistic9. replaceable irreplaceable10. small enormousGRAMMAR REVIEW1. She wished us health and success in the new year.2. He asked how we were getting along with our work.3. Jack said to me that I would be happy to know that his condition had improved.4. Rose asked Jack whether he was sure his mother would like the idea.5. He asked John how long he had been waiting for them.6. She said I needn't have done all that myself.</(2)1. The strikers protested to the police that they had no right to arrest them.2. He promised that he would give us whatever assistance we needed.3. He agreed (that) that was the best solution to the problem.4. My sister admitted that it was she who had broken the glass.5. He declared that he meant what he said and would never go back on his word.6. The man insisted that we give an explanation of what hadhappened.7. Mrs. Don't complained that no one showed concern for the elderly in that country.8. The sales manager explained that he couldn't give us a definite answer because he had not received instructions from his company.CLOZE(1) realm (2) elemental (3) obtain (4) stubbornly (5) transferred (6) transformed (7) subdued (8) expansion (9) irreplaceable (10) extinct (11) dynamic (12) verge (13) moderate (14) ecological (15) rationalTRANSLATION1.The village is so close to the border that thevillagers live in constant fear of attacks from the enemy.2. In only twenty years the country was transformed intoan advanced industrial power.3. This company has evolved into one of the major chemicalmanufacturing bases in this region.4. Given the current financial situation, it is inevitablethat the US dollar will be further devalued.5. The government's call for suggestions about the controlof water pollution produced very little response from the citizens.6. The weather showed no signs of getting better so thegovernment called upon us to get prepared for floods.7. At one time scientists thought that there was nothingsmaller than an atom but now most people know that an atom consists of even smaller particles.8. The students were all very much concerned about theWorld Cup, spending at least two hours every day watching the live matches on TV.9. The department store lost out because loans were veryhard to come by and it could not start business on time.10. We can't go there for a walk because there is a navybase there, which is off limits to tourists.Human brings live in the realm of nature. They are not only dwellers in nature, but also transformers of it. With the development of society and its economy, people tend to become less dependent on nature directly, but indirectly their dependence grows. Human beings are connected with nature by "blood" ties. No one can live outside nature.However, the previous dynamic balance between man and nature has shown signs of breaking down. Problems such as the population explosion, ecological imbalance and the shortage of natural resources have become major factors keeping human society from being further developed. Professor Spirkin holds that the only choice for human beings is the wise organization of production and care for Mother Nature.My Understanding of Environmental Protection Man and the environment are closely related. Man relies on the environment for water, food and shelter. A harmonious relationship between man and However, man and the environment have never been on such bad terms as they are now. As society develops, man’s transformation of nature has severely polluted his living environment. Deforestation leads to changes in rainfall patterns, causing devastating floods, droughts and sandstorms. The discharge of chemical pollutants endangers our health and the lives of other beings. And mass production has resulted in the shortage of irreplaceable natural resources such as coal and oil. If we take no immediate and effective stepsto protect our environment, human beings may be the next species to become extinct. ••••••We should do our best to protect our environment by planting more trees, taking care of wildlife, reducing industrial wastes, using renewable energy, and imposing heavy fines on environmentally-unfriendly activities, so as to preserve the environment for future generations.U21. 1) monitor2) phenomenon3) isolation4) gradual5) opponent6) advent7) genetic8) consciously9) extreme10) nasty11) boom12) formal13) soar14) survey15) Similarly16) modify17) rough2. 1) at the same time2) are stuck with3) for certain4) make no difference5) on average6) when it comes to7) depends on8) built into9) come to mind10) at workIncreasing Your Word Power 1.AdjectivesNounsAdjectivesNouns1) technologicaltechnology6) luxurious luxury2) eternaleternity7) leisurely leisure3) miraculous miracle8) subjective subject4) relevantrelevance9) prosperous prosperity5) analytical Analysis10) innovative innovation2. 2) multi-faith 3) multiform4) multifunction 5) multi-ethnic6) multilateral7) multi-lingual 8) multimedia9) multimillionaire 10) multinational1) a multi-faith society2) a multi-lingual secretary3) a multimillionaire4) a multinational motor-manufacturing corporation5) a multifunction video camera6) a multi-ethnic community7) a multimedia dictionary8) multi-cultural education9) a multilateral trade negotiation10) multiform technological cooperation3. 1) j 2) c 3) b 4) i5) a 6) g 7) d 8) e9) f 10) h4.Adjectives NounsAdjectives Nouns1) creative creativity 6) minorminority2) cruelcruelty7) original originality3) equalequality8) purepurity4) locallocality9) regularregularity5) majormajority10) superiorsuperiority1) superiority 2) equality 3) originality 4) minority5) Creativity6) purity 7) crueltyGrammar Review1. 1) My mother would not be worried about me if she knew what my life was like.2) They would probably allow you to do the job if youwere in better health.3) They wouldn’t work with such enthusiasm if they didn’t know what they were working for.4) I would have to look it up in the dictionary if I didn’t know the meaning of the word.5) She would understand what we say if she knew Chinese.6) I would be quite satisfied if you spoke with greater accuracy.2. 1) If we knew where he was, we would try to get in touch with him.2) If it were not for the expense involved, we would go there by plane.3) If we were to miss the train, we would have to wait another four hours.4) If we pooled all our resources, we would have enoughmoney to buy the equipment.5) If he didn’t have a strong love for the handicappedchildren, he wouldn’t be working so tirelessly forthem.Cloze1) emphasize 2) opposite3) improved 4) luxuries 5) benefited6) obviously 7) consciously8) fractures 9) eternal10) groundbreaking11) entitled 12) correlation 13) depends 14) exclusivelyTranslation1. 1) He really knows a lot about theory, but when itcomes to actual work, he seems to be quite ignorant.2) The latest survey shows / showed that the majority of the citizens support / supported the government’s plan to build a new library.3) The two countries could reach agreement successfully on scientific and technological cooperation because several factors favorable to their cooperation had been at work.4) I saw the film when I was in the primary school, but the title just won’t come to mind for the moment.5) He has been stuck with heavy debt though he works about twelve hours every day on average.6) Is it necessary to know his height? To me, it is not relevant to whether he can be a good lawyer or not.7) The cupboard is built into the wall so that it both saves space and is convenient to use.8) These workers earn more than we do, but the other side of the coin is their job is more dangerous.9) Helen majors in economics at the university and at the same time she studies philosophy as her second major.10) What is most important is that you must find out and solve the problems by yourselves. It makes no difference whether I go there or not.2.Nowadays, many people are enjoying the benefits brought about by material and technological advances unimaginable in previous eras. With the development of scienc e and technology, people’s standard of living is getting higher and higher. People’s life expectancy has soared, too.However, oddly enough, many people do not feel happier than they used to be. It can be seen that there is noclose correlation between pe ople’s income and their happiness. Happiness cannot, after all, be bought with money.Although the majority of people are not very satisfied with their lives, they are happy to be alive, and the more time they get on earth, the better off they feel they’l l be. What is important is that material wealth is far from enough. People need spiritual happiness, too.Theme-related WritingSample Essay:The Impact of the Mobile Phone on People’s livesAmong the many technological inventions, the mobile phone impresses me most.The mobile phone brings considerable convenience to our lives. It not only enables us to keep in touch with each other almost anytime and anywhere but also helps ussolve problems or do business efficiently. In emergencies, a mobile phone can even be a life-saver. Besides, its multi-functions add ease and color to our lives. With a mobile phone, we can receive mail, read news, listen to music, play games, and take pictures.Yet, the mobile phone has its disadvantages, too. Most of us have experienced the nuisance of unwanted or wrong calls. We are inconvenienced by calls on occasions when we least expect one. Besides, the technology infrastructure to support mobile communication has consumed valuable natural resources and caused significant environmental problems. It is reported that electromagnetic radiation waves from the phone may result in health problems.Despite its negative side, the advantages of the mobile phone outweigh its disadvantages. I believe that with advances in science and technology, improved and safer models of mobile phones will surely serve us still better.U31.quest2.remained3.consume4.likewise5.vessel6.qualify7.stiff8.collapsed9.predict10.nevitably 11.absorbed12.sheer13.refining14.paralyzed15.exchange1.In a way2.act on3.to such an extent that4.opens up5.close off6.look into1.pic2.eates3.ally4.asp5.re6.posite7.ntradictory 8.ality9.ysical10.idity11.vidual12.ility13.nbow14.sehood1. Most people strongly believe that the court will nodoubt punish the bank robbers severely.2. The medical workers overcame one difficulty afteranother in their long-term quest for a cure for the disease.3. Acting on the information they received, the policeclosed off the streets and caught the bank robbers.4. We were amazed at learning that the newly-built TVfactory can produce 500,000 TV sets in the first year.5. The government is looking into the causes of so manylayoffs and is trying to help the laid-off workers to be re-employed.6. To expand the sales of its product, the company hastaken up various measures to open up new markets and to improve its services.7. He has neglected his studies to such an extent thatI am afraid it is impossible for him to catch up withthe other students in a month.8. The fireworks factory was closed last month for failingto comply with the government safety regulations. 9. It remains to be seen whether our football team can beatits opponent.10. Mr. Smith predicted that the recent oil discoveries,together with the use / employment of new technologies, would lead to a decline in the price of crude oil.U 4填单词1.mass2.gambled3.voluntary4.hunted5.classified6.abolished7.division8.senseless9.fashions10.coordination11.declarations12.spanned13.recommends/recommended14.moderately15.slightest填词组1.stands a chance/stood a chance2.ruled out3.worthy of4.gone through5.in the strict sense6.At a guess7.earns a living8.coincide with9.gone in for10.got their teeth into完型填空1.enjoy2.physicalpelled4.necessity5.support6.mental7.idealize8.status9.values10.classified11.essential12.mind13.attitude14.fortunate句子翻译1. As more and more details of her private life were disclosed by the media, shewas compelled to resign her post as general manager (or: resign asgeneral manager / resign from the post of general manager) of thecompany.2. She is very satisfied with her new job as it coincides with her interests.3. I bought this shirt because the price was reduced from 300 yuan to 80 yuan.4. To bring her children up, the mother really went through all kinds ofhardships.5. The police have ruled out murder in the case of the old lady's death.6. The municipality (municipal government) promised to take effective steps assoon as possible to solve the problems of air pollution.7. I did not go in for the Campus Tennis Championships held last monthbecause of my injured leg.8. If you can get the support of the majority of the girls, you stand a goodchance of winning the election and becoming Chairman of the Students Union.9. Not all the books he wrote were as successful as this one so I recommendthat you borrow it from the library and read it.10. At the 2004 Athens Olympic Games Liu Xiang won the championship of themen's 110-meter hurdle and broke the world record, which had beenpreviously held by an American athlete.短文翻译Some people think that they've fulfilled their tasks as long as they go on duty and come off duty on time. They never think about what is meant by"work" and why they should work at all. In fact, "work" involves suchqualities as wisdom, enthusiasm, imagination and creativity. To do his work well, a worker must have a spirit of dedication, and be capable of bearing hardships and standing hard work. In addition, he should have initiative and creativity. Having initiative means the worker should beready to grasp every opportunity to display his outstanding ability. Inaddition, a worker should make clear the nature and significance of the work he does, be responsible for whatever he is doing and plunge himself into the work with vigorous enthusiasm. If he can do so, he will find a job no longer a burden but an indispensable part of his life. Whatever he does, he can always find values and pleasure in the work and achieveextraordinary results in otherwise ordinary work.作文范文My Career ChoiceWhen it comes to the choice of career, different people consider the matter from different perspectives. Personally I prefer to be a teacher. I have three reasons for my decision. The first reason is that the profession of teaching is in agreement with my personality. Being an outgoing, patient and understanding person, I think I am able to communicate with my students and understand their feelings easily, which constitutes an important factor in ensuring success in teaching. The second reason is that I am interested in the job. It would always give me great joy and satisfaction to see the happy faces of my students, to share my knowledge and life experience with them and to participate in their process of growing up. The third reason is related to my occupational attitude. I always believe that school teachers all over the world are respected for their profound knowledge and higher social status. I have always held my teachers in respect and I hope I would be respected as a teacher, too, in the future. I think teaching is an ideal career for me. Being a university student now, I will work hard to realize my dream.U51)fortune 2)dull 3)chased 4)launched 5)finance 6)reputation 7)liberty8)publicity 9)sufficiently 10)sympathy 11)target 12)educate 13)commerce14)alike 15)bored 16)audiences 17)regard 18)assure1)thrown out 2)and so on 3)for dear life 4)dedicate himself to 5)was tired of6)turn away 7)hang on 8)for the sake of(1)chase (2)reputation (3)dedicate (4)reward (5)sufficiently (6)measured(7)assure (8)Momentary (9)celebrity (10)target (11)frank (12)liberty(13)illusory (14)regard1、他试图拯救这家濒临倒闭的企业,但失败了。
当大漠的苍茫点缀了蘑菇云的硝烟,当五星红旗升起在联合国的上空。
是他,长空铸剑,吼出雄师的愤怒;是他,以身许国,写下山河的颂歌。
殷红热血,精忠报国,他就是共和国忠诚的奠基人,他是中华民族不倒的脊梁,他就是中国核武器研制与发展的主要领导者,被称为“两弹元勋”的邓稼先,他是中国知识分子的优秀代表,是我最崇拜的人。
首先,我崇拜他的爱国情怀和艰苦奋斗,他那伟大的抱负和精忠报国的感人精神深深震撼着我的心灵!1950年,从Purdue University获得博士学位的邓稼先,放弃了在美国优越的生活和工作条件,毅然回到了一穷二白的祖国,从事原子核理论研究工作。
中国研制原子弹正值三年困难时期,经常饥肠响如鼓。
就是在这样艰苦的条件下,他们日夜加班。
还经常到飞沙走石的戈壁试验场。
他冒着酷暑严寒,奋斗在第一线,从而掌握了大量的第一手材料。
1964年10月,中国成功爆炸的第一颗原子弹,并于原子弹爆炸后的两年零八个月试验成功。
这同法国用8年、美国用7年、苏联用7年的时间相比,创造了世界上最快的速度。
邓稼先同志在弥留之际,叮咛:“在尖端武器方面,不要让其他把我们落得太远”他用生命的智慧和最后一丝力气,与于敏合著了一份关于中国核武器发展的建议书,向祖国献上了一片真诚,该建议书的内容至今仍然保密。
其次,我崇拜他的不计名利、甘当无名英雄,20多年来,他甘当无名英雄,默默无闻地奋斗着,他把自己的姓名埋在祖国最荒凉最偏僻的地方。
连妻子也不知道他去了哪儿,在做什么,他在中国核武器的研制方面做出了卓越的贡献,却鲜为人知,直到他死后,人们才知道了他的事迹。
1971年,当杨振宁质疑中国的原子弹是一个美国人帮助研制的时候,邓稼先写信告诉他:“无论是原子弹,还是氢弹,都是中国人自己研制的。
”杨振宁看后激动得流出了泪水。
中国正是由于有了像他这样不计名利、无私奉献的大批知识分子,才挺起了坚强的民族脊梁。
最后,我崇拜他的舍生忘死的革命精神,他常常在关键时刻,不顾个人安危,出现在最危险的岗位上,在一次爆炸失败后,为了找到真正的原因,邓稼先深知危险,却一个人抢上前去把摔破的原子弹碎片拿到手里仔细检验。
外文原文SemiconductorA semiconductor is a solid material that has electrical conductivity between those of a conductor and an insulator; it can vary over that wide range either permanently or dynamically.[1]Semiconductors are important in electronic technology. Semiconductor devices, electronic components made of semiconductor materials, are essential in modern consumer electronics, including computers, mobile phones, and digital audio players. Silicon is used to create most semiconductors commercially, but dozens of other materials are used.Bragg reflection in a diffuse latticeA second way starts with free electrons waves. When fading in an electrostatic potential due to the cores, due to Bragg reflection some waves are reflected and cannot penetrate the bulk, that is a band gap opens. In this description it is not clear, while the number of electrons fills up exactly all states below the gap.Energy level splitting due to spin state Pauli exclusionA third description starts with two atoms. The split states form a covalent bond where two electrons with spin up and spin down are mostly in between the two atoms. Adding more atoms now is supposed not to lead to splitting, but to more bonds. This is the way silicon is typically drawn. The band gap is now formed by lifting one electron from the lower electron level into the upper level. This level is known to be anti-bonding, but bulk silicon has not been seen to lose atoms as easy as electrons are wandering through it. Also this model is most unsuitable to explain how in graded hetero-junction the band gap can vary smoothly.Energy bands and electrical conductionLike in other solids, the electrons in semiconductors can have energies only within certain bands (ie. ranges of levels of energy) between the energy of the ground state, corresponding to electrons tightly bound to the atomic nuclei of the material, and the free electron energy, which is the energy required for an electron to escape entirely from the material. The energy bands each correspond to a large number of discrete quantum states of the electrons, and most of the states with low energy (closer to the nucleus) are full, up to a particular band called the valence band. Semiconductors and insulators are distinguished from metals because the valence band in the semiconductor materials is very nearly full under usual operating conditions, thus causing more electrons to be available in the conduction band.The ease with which electrons in a semiconductor can be excited from the valence band to the conduction band depends on the band gap between the bands, and it is the size of this energy bandgap that serves as an arbitrary dividing line (roughly 4 eV) between semiconductors and insulators.In the picture of covalent bonds, an electron moves by hopping to a neighboring bond. Because of the Pauli exclusion principle it has to be lifted into the higher anti-bonding state of that bond. In the picture of delocalized states, for example in one dimension that is in a wire, for every energy there is a state with electrons flowing in one direction and one state for the electrons flowing in the other. For a net current to flow some more states for one direction than for the other direction have to be occupied and for this energy is needed. For a metal this can be a very small energy in the semiconductor the next higher states lie above the band gap. Often this is stated as: full bands do not contribute to the electrical conductivity. However, as the temperature of a semiconductor rises above absolute zero, there is more energy in the semiconductor to spend on lattice vibration and — more importantly for us — on lifting some electrons into an energy states of the conduction band, which is the band immediately above the valence band. The current-carrying electrons in the conduction band are known as "free electrons", although they are often simply called "electrons" if context allows this usage to be clear.Electrons excited to the conduction band also leave behind electron holes, or unoccupied states in the valence band. Both the conduction band electrons and the valence band holes contribute to electrical conductivity. The holes themselves don't actually move, but a neighboring electron can move to fill the hole, leaving a hole at the place it has just come from, and in this way the holes appear to move, and the holes behave as if they were actual positively charged particles.One covalent bond between neighboring atoms in the solid is ten times stronger than the binding of the single electron to the atom, so freeing the electron does not imply destruction of the crystal structure.Holes: electron absence as a charge carrierThe notion of holes, which was introduced for semiconductors, can also be applied to metals, where the Fermi level lies within the conduction band. With most metals the Hall effect reveals electrons to be the charge carriers, but some metals have a mostly filled conduction band, and the Hall effect reveals positive charge carriers, which are not the ion-cores, but holes. Contrast this to some conductors like solutions of salts, or plasma. In the case of a metal, only a small amount of energy is needed for the electrons to find other unoccupied states to move into, and hence for current to flow. Sometimes even in this case it may be said that a hole was left behind, to explain why the electron does not fall back to lower energies: It cannot find a hole. In the end in both materials electron-phonon scattering and defects are the dominant causes for resistance.Fermi-Dirac distribution. States with energy εbelow the Fermi energy, here μ, have higher probability n to be occupied, and those above are less likely to be occupied. Smearing of the distribution increases with temperature.The energy distribution of the electrons determines which of the states are filled and which are empty. This distribution is described by Fermi-Dirac statistics. The distribution is characterized by the temperature of the electrons, and the Fermi energy or Fermi level. Under absolute zero conditions the Fermi energy can be thought of as the energy up to which available electron statesare occupied. At higher temperatures, the Fermi energy is the energy at which the probability of a state being occupied has fallen to 0.5.The dependence of the electron energy distribution on temperature also explains why the conductivity of a semiconductor has a strong temperature dependency, as a semiconductor operating at lower temperatures will have fewer available free electrons and holes able to do the work.Energy–momentum dispersionIn the preceding description an important fact is ignored for the sake of simplicity: the dispersion of the energy. The reason that the energies of the states are broadened into a band is that the energy depends on the value of the wave vector, or k-vector, of the electron. The k-vector, in quantum mechanics, is the representation of the momentum of a particle.The dispersion relationship determines the effective mass, m*, of electrons or holes in the semiconductor, according to the formula:The effective mass is important as it affects many of the electrical properties of the semiconductor, such as the electron or hole mobility, which in turn influences the diffusivity of the charge carriers and the electrical conductivity of the semiconductor.Typically the effective mass of electrons and holes are different. This affects the relative performance of p-channel and n-channel IGFETs, for example (Muller & Kamins 1986:427).The top of the valence band and the bottom of the conduction band might not occur at that same value of k. Materials with this situation, such as silicon and germanium, are known as indirect bandgap materials. Materials in which the band extrema are aligned in k, for example gallium arsenide, are called direct bandgap semiconductors. Direct gap semiconductors are particularly important in optoelectronics because they are much more efficient as light emitters than indirect gap materials.Carrier generation and recombinationWhen ionizing radiation strikes a semiconductor, it may excite an electron out of its energy level and consequently leave a hole. This process is known as electron–hole pair generation. Electron-hole pairs are constantly generated from thermal energy as well, in the absence of any external energy source.Electron-hole pairs are also apt to recombine. Conservation of energy demands that these recombination events, in which an electron loses an amount of energy larger than the band gap, be accompanied by the emission of thermal energy (in the form of phonons) or radiation (in the form of photons).In some states, the generation and recombination of electron–hole pairs are in equipoise. The number of electron-hole pairs in the steady state at a given temperature is determined by quantum statistical mechanics. The precise quantum mechanical mechanisms of generation and recombination are governed by conservation of energy and conservation of momentum.As the probability that electrons and holes meet together is proportional to the product of their amounts, the product is in steady state nearly constant at a given temperature, providing that there is no significant electric field (which might "flush" carriers of both types, or move them from neighbour regions containing more of them to meet together) or externally driven pair generation. The product is a function of the temperature, as the probability of getting enough thermal energy to produce a pair increases with temperature, being approximately 1×exp(−E G / kT), where k is Boltzmann's constant, T is absolute temperature and E G is band gap.The probability of meeting is increased by carrier traps – impurities or dislocations which can trap an electron or hole and hold it until a pair is completed. Such carrier traps are sometimes purposely added to reduce the time needed to reach the steady state.DopingThe property of semiconductors that makes them most useful for constructing electronic devices is that their conductivity may easily be modified by introducing impurities into their crystal lattice. The process of adding controlled impurities to a semiconductor is known as doping. The amount of impurity, or dopant, added to an intrinsic(pure) semiconductor varies its level of conductivity. Doped semiconductors are often referred to as extrinsic.DopantsThe materials chosen as suitable dopants depend on the atomic properties of both the dopant and the material to be doped. In general, dopants that produce the desired controlled changes are classified as either electron acceptors or donors. A donor atom that activates (that is, becomes incorporated into the crystal lattice) donates weakly-bound valence electrons to the material, creating excess negative charge carriers. These weakly-bound electrons can move about in the crystal lattice relatively freely and can facilitate conduction in the presence of an electric field. (The donor atoms introduce some states under, but very close to the conduction band edge. Electrons at these states can be easily excited to conduction band, becoming free electrons, at room temperature.) Conversely, an activated acceptor produces a hole. Semiconductors doped with donor impurities are called n-type, while those doped with acceptor impurities are known as p-type. The n and p type designations indicate which charge carrier acts as the material's majority carrier. The opposite carrier is called the minority carrier, which exists due to thermal excitation at a much lower concentration compared to the majority carrier.For example, the pure semiconductor silicon has four valence electrons. In silicon, the most common dopants are IUPAC group 13(commonly known as group III) and group 15(commonly known as group V) elements. Group 13 elements all contain three valence electrons, causing them to function as acceptors when used to dope silicon. Group 15 elements have five valence electrons, which allows them to act as a donor. Therefore, a siliconcrystal doped with boron creates a p-type semiconductor whereas one doped with phosphorus results in an n-type material.Carrier concentrationThe concentration of dopant introduced to an intrinsic semiconductor determines its concentration and indirectly affects many of its electrical properties. The most important factor that doping directly affects is the material's carrier concentration. In an intrinsic semiconductor under thermal equilibrium, the concentration of electrons and holes is equivalent. That is,n = p = n iIf we have a non-intrinsic semiconductor in thermal equilibrium the relation becomes:n0 * p0 = (n i)2Where n is the concentration of conducting electrons, p is the electron hole concentration, and n i is the material's intrinsic carrier concentration. Intrinsic carrier concentration varies between materials and is dependent on temperature. Silicon's n i, for example, is roughly 1.6×1010 cm-3 at 300 kelvin (room temperature).In general, an increase in doping concentration affords an increase in conductivity due to the higher concentration of carriers available for conduction. Degenerately (very highly) doped semiconductors have conductivity levels comparable to metals and are often used in modern integrated circuits as a replacement for metal. Often superscript plus and minus symbols are used to denote relative doping concentration in semiconductors. For example, n+ denotes an n-type semiconductor with a high, often degenerate, doping concentration. Similarly, p−would indicate a very lightly doped p-type material. It is useful to note that even degenerate levels of doping imply low concentrations of impurities with respect to the base semiconductor. In crystalline intrinsic silicon, there are approximately 5×1022 atoms/cm³. Doping concentration for silicon semiconductors may range anywhere from 1013 cm-3to 1018cm-3. Doping concentration above about 1018cm-3is considered degenerate at room temperature. Degenerately doped silicon contains a proportion of impurity to silicon in the order of parts per thousand. This proportion may be reduced to parts per billion in very lightly doped silicon. Typical concentration values fall somewhere in this range and are tailored to produce the desired properties in the device that the semiconductor is intended for.Effect on band structureDoping a semiconductor crystal introduces allowed energy states within the band gap but very close to the energy band that corresponds with the dopant type. In other words, donor impurities create states near the conduction band while acceptors create states near the valence band. The gap between these energy states and the nearest energy band is usually referred to as dopant-site bonding energy or E B and is relatively small. For example, the E B for boron in silicon bulk is 0.045 eV, compared with silicon's band gap of about 1.12 eV. Because E B is so small, it takes little energy to ionize the dopant atoms and create free carriers in the conduction or valence bands.Usually the thermal energy available at room temperature is sufficient to ionize most of the dopant.Dopants also have the important effect of shifting the material's Fermi level towards the energy band that corresponds with the dopant with the greatest concentration. Since the Fermi level must remain constant in a system in thermodynamic equilibrium, stacking layers of materials with different properties leads to many useful electrical properties. For example, the p-n junction's properties are due to the energy band bending that happens as a result of lining up the Fermi levels in contacting regions of p-type and n-type material.This effect is shown in a band diagram. The band diagram typically indicates the variation in the valence band and conduction band edges versus some spatial dimension, often denoted x. The Fermi energy is also usually indicated in the diagram. Sometimes the intrinsic Fermi energy, E i, which is the Fermi level in the absence of doping, is shown. These diagrams are useful in explaining the operation of many kinds of semiconductor devices.Preparation of semiconductor materialsSemiconductors with predictable, reliable electronic properties are necessary for mass production. The level of chemical purity needed is extremely high because the presence of impurities even in very small proportions can have large effects on the properties of the material. A high degree of crystalline perfection is also required, since faults in crystal structure (such as dislocations, twins, and stacking faults) interfere with the semiconducting properties of the material. Crystalline faults are a major cause of defective semiconductor devices. The larger the crystal, the more difficult it is to achieve the necessary perfection. Current mass production processes use crystal ingots between four and twelve inches (300 mm) in diameter which are grown as cylinders and sliced into wafers.Because of the required level of chemical purity and the perfection of the crystal structure which are needed to make semiconductor devices, special methods have been developed to produce the initial semiconductor material. A technique for achieving high purity includes growing the crystal using the Czochralski process. An additional step that can be used to further increase purity is known as zone refining. In zone refining, part of a solid crystal is melted. The impurities tend to concentrate in the melted region, while the desired material recrystalizes leaving the solid material more pure and with fewer crystalline faults.In manufacturing semiconductor devices involving heterojunctions between different semiconductor materials, the lattice constant, which is the length of the repeating element of the crystal structure, is important for determining the compatibility of materials.中文译文半导体半导体是一种导电性能介于导体与绝缘体之间的固体材料。
Chapter 11.Every law has no atom of stregth,as far as no public opinion supports it.若是没有公众舆论的支持,法律是丝毫没有力量的。
---(Wendell phillips,American leader against slavery 美国废奴运动领袖菲力普斯)2.Good order is the foundation of all things.良好的秩序是一切的基础。
---(E.Burke,Btritish statesman 英国政治家伯克)3.Guilt always hurries towards its complement ,punishment;only there does its satisfaction lie.犯罪总是以惩罚相补偿;只有处罚才能使犯罪得到偿还。
---(Lawence Durrell,British writer 英国作家达雷尔L)4.I disapprove of what you say,but I will defend to the death your right to say it.我不同意你说的话,但是我愿意誓死捍卫你说话的权利。
---(Voltaire,Frech writer 法国作家伏尔泰)5.If there were no bad people,there would be no good lawyers.倘若世上没有坏人,也就不会有好的律师。
---(Charles Dickens,British novelist 英国小说家狄更斯)6.If we only had some God in the country's laws,instead of beng in such a sweat to get him into the Constitution,it would be better all around.如果我们国家的法律中只有某种神灵,而不是殚精竭虑将神灵揉进宪法,总体上来说,法律就会更好。
The Dependence of All-Atom Statistical Potentials on StructuralTraining DatabaseChi Zhang,Song Liu,Hongyi Zhou,and Yaoqi ZhouHoward Hughes Medical Institute Center for Single Molecule Biophysics,Department of Physiology and Biophysics,State University of New York at Buffalo,Buffalo,New YorkABSTRACT An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction.Here,two high-resolution,low-sequence-identity structural databases of333a-proteins and271b-proteins were built for examining the database dependence of three all-atom statistical energy functions.They are RAPDF(residue-specific all-atom conditional probability discriminatory function),atomic KBP(atomic knowledge-based potential),and DFIRE(statistical potential based on distance-scaledfinite ideal-gas reference state).These energy functions differ in the reference states used for energy derivation.The energy functions extracted from the different structural databases are used to select native structures from multiple decoys of64a-proteins and28b-proteins.The performance in native structure selections indicates that the DFIRE-based energy function is mostly independent of the structural database whereas RAPDF and KBP have a significant dependence.The construction of two additional structural databases of a/b and a1b-proteins further confirmed the weak dependence of DFIRE on the structural databases of various structural classes.The possible source for the difference between the three all-atom statistical energy functions is that the physical reference state of ideal gas used in the DFIRE-based energy function is least dependent on the structural database.INTRODUCTIONOne simple method for estimating the interaction between the proteins and within a single protein is the knowledge-based approach in which known protein structures are used to generate the statistical potentials(or energy functions; Tanaka and Scheraga,1976).Knowledge-based statistical potentials have been applied to fold recognition and assessment(Bryant and Lawrence,1993;Casari and Sippl, 1992;Hendlich et al.,1990;Jones et al.,1992;Lu and Skolnick,2001;Melo et al.,2002;Miyazawa and Jernigan, 1999;Samudrala and Moult,1998;Sippl,1990;Zhou and Zhou,2004),structure predictions(Lee et al.,1999;Pillardy et al.,2001;Simons et al.,1997;Skolnick et al.,1997;Sun, 1993;Tobi and Elber,2000;Vendruscolo et al.,2000),and validations(Luthy et al.,1992;MacArthur et al.,1994;Melo and Feytmans,1998;Rojnuckarin and Subramaniam,1999; Sippl,1993),docking and binding(Altuvia et al.,1995;Liu et al.,2004;Pellegrini and Doniach,1993;Wallqvist et al., 1995;Zhang et al.,1997),and mutation-induced changes in stability(Gilis and Rooman,1996,1997;Zhang et al.,1997; Zhou and Zhou,2002).One natural consequence of this commonly used statistical approach is that the outcome(the energy function)is strongly dependent on input(the structural database).For example, the structural database of single-chain proteins and the in-terface database of dimeric proteins produce quantitatively different pair potentials for folding and binding studies(Lu et al.,2003;Moont et al.,1999).This is caused by sig-nificantly different compositions of amino acid residues at the surface,core,and interface of proteins(Glaser et al., 2001;Lu et al.,2003;Ofran and Rost,2003).In another example,the residue-level,distance-dependent,Sippl poten-tial extracted from all-a protein structures is quantitatively different from that extracted from all-b protein structures (Furuichi and Koehl,1998).This suggests that different structural patterns(topology)also change the outcome of the statistical energy function.The distance-independent statis-tical energy parameters,however,appear to be less sensitive to different subsets of protein structure database except that there is large difference between the parameters from the crystallographic structures and that from the NMR structures (Godzik et al.,1995).The database dependence of statistical energy functions, however,is unphysical.This is because the same physical interaction(water-mediated interaction between amino-acid residues)is responsible for protein folding and binding and for the formation of b-strands and a-helices.The unphysical, database dependence of a statistical potential is difficult to avoid because it is equivalent to requiring the output to be independent of(or insensitive to)different input information. Recently,a residue-specific all-atom,distance-dependent potential of mean-force was extracted from the structures of single-chain proteins by using a physical state of uniformly distributed points infinite spheres(distance-scaled,finite, ideal-gas reference,i.e.,DFIRE,state)as the zero-interaction reference state(Zhou and Zhou,2002).Remarkably,the phy-sical reference state yields a potential of mean-force that no longer possesses some unphysical characteristics associatedSubmitted October14,2003,and accepted for publication January20,2004.Address reprint requests to Dr.Yaoqi Zhou,Howard Hughes MedicalInstitute Center for Single Molecule Biophysics and Dept.of Physiologyand Biophysics,State University of New York at Buffalo,124ShermanHall,Buffalo,NY14214.Tel.:716-829-2985;Fax:716-829-2344;E-mail:yqzhou@.Ó2004by the Biophysical Society0006-3495/04/06/3349/10$2.00doi:10.1529/biophysj.103.035998 Biophysical Journal Volume86June20043349–33583349with other statistical potentials.It was shown that the accu-racy of DFIRE-based potential is insensitive to the parti-tioning of hydrophobic and hydrophilic residues within a protein(Zhou and Zhou,2002).More importantly,the new structure-derived potential can quantitatively reproduce the likelihood of a residue to be buried(i.e.,the composition difference of amino-acid residues between core and surface; Zhou and Zhou,2003).The potential also yields a stability scale of amino acid residues in quantitative agreement with that independently extracted from mutation experimental data(Zhou and Zhou,2003).Moreover,the monomer po-tential(derived from single-chain proteins)is found to be equally successful in discriminating against docking decoys, distinguishing true dimeric interface from crystal interfaces, and predicting binding free energy of protein-protein and protein-peptide complexes(Liu et al.,2004).The indepen-dence of the performance for the systems with various amino-acid compositions suggests that the DFIRE-based potential possesses some physical characteristics not ob-served in some other knowledge-based potentials.The above results raise an interesting question:does the DFIRE-based potential depend on the structural database used for statistics?Although the performance of the DFIRE potential on structure selections has been shown to be insensitive to the size of the database(number of protein structures;Zhou and Zhou,2002)and the database of either single-chain or dimeric proteins(Liu et al.,2004),it is not clear whether or not the structural database of all-a proteins will yield a DFIRE potential that is different from that generated from the database of all-b proteins.Answering this question is important for the application of the DFIRE-based statistical energy function to structure prediction of proteins with different structural topology.In this article,we built structural databases of all-a,all-b, a1b,and a/b proteins based on SCOP classification.The database dependence of three all-atom knowledge-based potentials(i.e.,RAPDF,Samudrala and Moult,1998;atomic KBP,Lu and Skolnick,2001;and DFIRE,Zhou and Zhou, 2002)are compared.Results show that unlike RAPDF and KBP,the DFIRE energy function is mostly independent of the database used for training.The origin for the difference in database dependence between DFIRE and RAPDF/KBP is discussed.METHODSComposition-averaged observed state as the reference stateThe derivation of a distance-dependent,pairwise,statistical potential uði;j;rÞstarts from a common inverse-Boltzmann equation given byuði;j;rÞ¼ÿRT lnN obsði;j;rÞN expði;j;rÞ;(1)where R is the gas constant,T is the temperature,N obs(i,j,r)is the observed number of atomic pairs(i,j)within a distance shell r–D r/2to r1D r/2in a database of folded structures,and N exp(i,j,r)is the expected number of atomic pairs(i,j)in the same distance shell if there were no interactions between atoms(the reference state).Clearly,the method used to calculate N exp(i,j,r)is what makes one potential differ from another because the method to calculate N obs(i,j,r)is the same(except the difference in database and bin procedures).Samudrala and Moult(1998)used a conditional probability functionN expði;j;rÞ¼N obsði;jÞN totalN obsðrÞ;(2)where N obsðrÞ[+i;jN obsði;j;rÞ;N obsði;jÞ[+rN obsði;j;rÞ;andN total[+i;j;rN obsði;j;rÞ:Lu and Skolnick(2001)employed a quasichemical approximation ofN expði;j;rÞ¼x i x j N obsðrÞ;(3)where x k is the mole fraction of atom type k.The common approximationmade by the above two potentials is that+i;jN expði;j;rÞ¼N obsðrÞ:This approximation has its origin in the uniform density reference state used by Sippl(1990)to derive the residue-based,distance-dependent potential.In this approximation,the total number of pairs in any given distance shell for a reference state is the same as that for folded proteins.That is, a composition-averaged observed state is used as the reference state.ThisTABLE1The standard92multiple decoy setsSource Decoynumber Target(PDB ID)4state*630–6871r69,2cro,3icblattice_ssfit y20001beo,1nkl,4icblmds z343–5001b0n-B,1fc2,1shf-A,zz2crofisa§500–12001hdd-C,2cro,4icbfisa_casp3{500–12001bg8-A,1bl0,1jweCASP4k42–112t0096(1e2x),t0098(1fc3),t0100(1qjv),zz t0106(1ijx),t0107(1i8u),zz t0108(1j83),zzt0123(1exs),zz t0125(1gak)Rosetta{10001aa2,1ail,1bdo,zz1cc5,1eca,1csp,zz1gvp,zz1tit,zz1hlb,1lfb,1lis,1wiu,zz1mbd,1ark,zz1mzm,1pal,1r69,1tul,zz1utg,1vls,1who,zz2erl,2ncm,zz2gdm,4fgf,zz5icb,1ksr,zz1sro,zz5ptihg_structural**301ash,1bab-b,1col-A,1cpc-A,1ecd,1flp,2lhb,4sdh-A,1gdm,1hbg,1hlb,1hlm,1ith-A,1mba,1mytLKF yy2001a7v,1ab0,zz1abo,zz1ae3,zz1ag6,zz1an2,1anu,zz1avs,1bbh,1b2p,zz1b7v,1b8r,1bai,zz1baj,1bbb,1beo,1bfs,zz1bg8,1bhd,1bja,1bk2,zz1bm9,1bre,zz1bzd zz*Park and Levitt(1996).y Xia et al.(2000).z Keasar and Levitt(2003).§Simons et al.(1997).{Simons et al.(1999).k Feig and Brooks(2002).**R.Samudrala,E.S.Huang,and M.Levitt,unpublished results.yy Loose et al.(2004).zz These PDB codes are b-type proteins;all the others are a-type proteins.3350Zhang et al. Biophysical Journal86(6)3349–3358composition-averaged state is the most commonly used reference state for a distance-dependent pair potential.Other reference states for distance-dependent potentials were also proposed (Jernigan and Bahar,1996;Mitchell et al.,1999;Moult,1997;Vijayakumar and Zhou,2000).Distance-scale finite ideal-gas reference (DFIRE)stateThe DFIRE state (Zhou and Zhou,2002)was derived directly from a formally exact equation for potential of mean force in statistical mechanics which is given by Friedman (1985)asu ði ;j ;r Þ¼ÿRT ln g ij ðr Þ¼ÿRT lnN obs ði ;j ;r ÞVN i N j ð4p r 2D r Þ;(4)where g ij (r )is the pair distribution function,V is the volume of the system,and N i and N j are the number of atoms i and j ,respectively.The final equation for the DFIRE-based energy function is then obtained after two approximations are made.In the first approximation,we assume that the number of pairs for an ideal gas system increases in r a for an finite system,rather than r 2for an infinite system.In the second approximation,we assumethat all interactions become zero after a cutoff distance r cut ,i.e.,u ði ;j ;r Þ¼0for r .r cut .The final equation for the DFIRE potential of mean force u ði ;j ;r Þbetween atom types i and j that are distance r apart is given by Zhou and Zhou (2002)asu ði ;j ;r Þ¼ÿh RT ln N obs ði ;j ;r Þr cut a D r cutN obs ði ;j ;r cut Þ;r ,r cut ;0r ,r cut ;8>><>>:(5)where h (¼0.0157)is a scaling constant,R is the gas constant,T ¼300K,a ¼1.61,r cut ¼14.5A˚,and D r (D r cut )is the bin width at r (r cut ).(D r ¼2A ˚,for r ,2A˚;D r ¼0.5A ˚for 2A ˚,r ,8A ˚;D r ¼1A ˚for 8A ˚,r ,15A ˚.)The prefactor h was determined so that the regression slope between the predicted and experimentally measured changes of stability due to muta-tion (895data points)is equal to 1.0.The exponent a for the distance depen-dence was determined by optimizing the fit between r a and the distance dependence of the pair distribution function for uniformly distributed points in finite spheres (finite ideal-gas reference state;Zhou and Zhou,2002).Residue-specific atomic types were used (167atomic types;Lu and Skolnick,2001;Samudrala and Moult,1998).FIGURE 1Success rates in rank-ing native states within a given num-ber of top-ranked structures given by a -protein-trained energy functions versus those by b -protein-trained energy functions for a -protein decoys (left )and b -protein decoys (right ).The results for RAPDF,KBP,and DFIRE are shown at top,middle,and bottom panels,re-spectively.Database Dependence of Potentials 3351Biophysical Journal 86(6)3349–3358Structural training databasesTo test the dependence of three statistical potentials (RAPDF,atomic KBP,and DFIRE)on training databases,we built training databases of all-a and all-b proteins based on the SCOP classification (1.63release;Conte et al.,2002;Murzin et al.,1995).Specifically,we began with the ,40%identity set built by the authors of SCOP (/),then removed the structures obtained by the NMR methods,the structures whoseresolution .2.5A˚,the structures from composite domains (Furuichi and Koehl,1998;Zhang and Kim,2000),and the structures not from all-a or all-b structure classes (defined by authors of SCOP).Then,we extracted the experimentally determined secondary structural states (a ,b ,and others)of residues in these structures from DSSP database (Kabsch and Sander,1983)using a simple mapping scheme similar to Zhang and Kim (2000).We removed the structures in a (b )class that have .10%content of b (a ).Finally,we removed the structures with .30%identity to decoys (calculated with FASTA package;Pearson,1990;Pearson and Lipman,1988).The final a -protein and b -protein databases have 333and 271single-domain proteins,respectively.In addition,we built training databases of a /b and a 1b proteins.The procedure used to build them is exactly the same as described above except that the a /b and a 1b classes (according to SCOP definition)of ,40%identity SCOP set are used instead.We required that both a /b and a 1b proteins have .10%content of a and b .There are 515a /b and 399a 1b single-domain proteins that are ,30%identity to decoys.(A list of proteins is given in .)The DFIRE energy functions based on 333a -proteins,271b -proteins,515a /b ,and 399a 1b proteins are labeled as DFIRE-a ,DFIRE-b ,DFIRE-a /b ,and DFIRE-a 1b ,respectively.The original structural database (Zhou and Zhou,2002)for calculating N obs (i ,j ,r )was a structural database of 1011non-homologous (,30%homology)proteins with resolution ,2A˚,which was collected by Hobohm et al.(1992)(/research/labs/dunbrack/culledpdb.html).The DFIRE energy function extracted from this database will be labeled as DFIRE-all .In addition to generating several DFIRE energy functions by using the new structural databases,RAPDF and atomic KBP potentials are also regenerated for comparison.The bin procedures for RAPDF and KBP are as follows.For RAPDF (Samudrala and Moult,1998),the first bin covers 0–3.0A˚and the distance between 3.0A ˚and 20A ˚is binned every 1A ˚.The total number of bins is 18.All 18bins with a cutoff distance of 20A ˚are used forscoring.For atomic KBP (Lu and Skolnick,2001),the distance between 1.5A˚and 14.5A ˚is binned every 1A ˚and the last bin is from 14.5A ˚to infinite.The total number of bins is 14.The first-and second-sequence neighbors are excluded whereas backbone atoms are included in counting contacts.Whenused in scoring,only the bins covering 3.5–6.5A˚are used.In all cases,contacts between atoms within a single residue are excluded from the counts and scoring.In case of zero pairs,both potentials are set to be 2h kcal/mol.No attempts were made to optimize these parameters and/or procedures presented by the original articles for possibly better performance.There are RAPDF-a ,RAPDF-b ,KBP-a ,and KBP-b ,depending on the structural database used.Multiple decoy sets for a -and b -proteinsThe database dependence of the energy functions was tested by the performance on structural discrimination.We established the decoy sets for all-a and all-b proteins from the 4state_reduced set (Park and Levitt,1996),lmds set (through conformational enumeration of loop region,Keasar and Levitt,2003),fisa set (Simons et al.,1997),fisa_casp3set (Simons et al.,1997),Rosetta (through Rosetta method;Simons et al.,1997),lattice_ssfit (through conformational enumeration on whole protein,Samudrala et al.,1999),hg_structural (through comparative modeling),LKF (through minimizing the number of violations of van der Waals constraints,Loose et al.,2004),and CASP4decoy sets (generated by numerous protein structure prediction teams using a variety of methods,Feig and Brooks,2002).There are 64and 28decoy sets for a(withFIGURE 2Energies of native states given by a -protein-trained energy functions versus those by b -protein-trained energy functions for a -proteins (s )and b -proteins (d ).The results for RAPDF,KBP,and DFIRE are shown at top,middle,and bottom panels,respectively.3352Zhang et al.Biophysical Journal 86(6)3349–3358b -content ,10%)and b (with a -content ,10%)proteins,respectively.All these 92proteins have ,30%identity to the proteins in the train-ing databases of all-a ,all-b ,a 1b ,and a /b proteins.The complete list of these proteins is shown in Table 1.Structure selections from decoysFor a given three-dimensional structure of a protein,the total potential of mean force,G ,isG ¼12+i ;ju ði ;j ;r ij Þ;(6)where the summation is over all pairs of atoms.In structure selections from decoy sets,the total potential G is calculated for each structure including native state and decoys.The native state is correctly identified if its structurehas the lowest value of G .Z-score is defined as ðÆG decoyæÿGnative Þ=ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiÆðG decoy Þ2æÿÆG decoy æ2p ;where Æædenotes the average overall FIGURE 3Z-scores given by a -pro-tein-trained energy functions versus those by b -protein-trained energy functions for a -protein (left )and b -protein (right )decoy sets.The results for RAPDF,KBP,and DFIRE are shown at top,middle,and bottom panels,respectively.Database Dependence of Potentials 3353Biophysical Journal 86(6)3349–3358decoy structures of a given native protein and G native is the total residue-residue potential of the native structure.Z-score is a measure of the bias toward the native structure.RESULTS AND DISCUSSIONWe focus first on the energy functions extracted from the databases of the all-a structures and all-b structures.Because the structural difference between all-a and all-b structures is the largest among all structural classes,the database de-pendence is likely the largest between the energy functions extracted from these two databases.It is known that a -proteins involve mostly local contacts (contacts between the residues with short sequence separations)whereas b -proteins involve mostly nonlocal contacts.Fig.1compares the performance of energy functions obtained from the databases of the all-a structures and all-b structures on structural discrimination of all-a proteins and all-b proteins.The performance is characterized by the success rate in ranking native structures within a given number of energy-ranked structures (top-ranked structures,N t ).For all three methods (RAPDF,KBP,and DFIRE),there is some degree of database dependence because an a -protein-trained energy function gives a higher success rate in structure selections of a -proteins than a b -protein-trained energy function.Similarly,a b -protein-trained energy function gives a higher success rate in structureselections of b -proteins than an a -protein-trained energy function.However,DFIRE has a substantially smaller de-pendence than either RAPDF or KBP.For example,for the top 10ranking (N t ¼10),the difference between the success rates of selecting a -proteins given by an energy function trained by the two structural databases is 6%for RAPDF and 14%for KBP,but only 2%for DFIRE.For the structure selection of b -proteins,the corresponding difference is 17%for RAPDF,18%for KBP,and 0%for DFIRE.Fig.1shows that at every number of top-ranked structures,DFIRE consistently gives the smallest difference between the two success rates among RAPDF,KBP,and DFIRE.The difference between the energy functions trained by different structural databases can also be visualized by comparing the total energies of the native structures of 64a -proteins and 28b -proteins given by the energy functions.Fig.2compares the energy given by the a -protein-trained potentials with that given by the b -protein-trained potentials.The root mean-squared deviations between the two energy values for the 64a -proteins are 0.296for RAPDF,1.07for KBP,and 0.132for DFIRE,respectively.(The relative difference is used,i.e.,the energy difference is divided by the average energy predicted by two energy functions.)The corresponding root mean-squared deviation values for the 28b -proteins are 0.342for RAPDF,0.694for KBP,and 0.068for DFIRE,respectively.Thus,the DFIRE gives the smallest database dependence in native energy.In fact,both RAPDF and KBP show a systematic deviation.An a -protein-trained energy function always gives a lower energy to a -proteins than a b -protein-trained energy function does.Similarly,a b -protein-trained energy function always gives a lower energy to b -proteins than an a -protein-trained energy function does.The lower the energy,the stronger the systematic deviation.In contrast,the correlation slope between the energy given by the a -protein-trained DFIRE potential and that given by the b -protein-trained DFIRE potential is very close to 1for either a -proteins or b -proteins.To further illustrate the database dependence,the Z-scores given by energy functions trained by different databases are shown in Fig.3.It is clear that DFIRE has the smallest database dependence on Z-scores.For a -protein decoys,the root mean-square deviation values of Z-scores between two database-trained energy functions are 1.95for RAPDF,1.07for KBP,and 0.387for DFIRE,respectively.The corre-sponding values for b -protein decoys are 0.767for RAPDF,0.457for KBP,and 0.257for DFIRE,respectively.For a -proteins,there is one significant outlier for DFIRE at high Z-score value where the Z-score given by DFIRE-b is lower than that given by DFIRE-a .This is contributed by 1beo in the lattice_ssfit decoy set.We found that the energy differences given by DFIRE-a and DFIRE-b are in fact quite small for both decoys and native states (,10%).The large difference in Z-score resulted from an artificially narrow range of DFIRE energies of decoys relative to the energy difference between native state anddecoys.FIGURE 4As in Fig.1but for the comparison of success rates given by the energy functions trained by a -proteins,b -proteins,a /b proteins,a 1b proteins,and all proteins.The test sets are the decoy sets for 92proteins.3354Zhang et al.Biophysical Journal 86(6)3349–3358Thus,the ranks of native state energies (or success rates),the energies of native states,and Z-scores predicted by the energy functions extracted from all-a and all-b structures all indicate that DFIRE has a significantly smaller database dependence than either RAPDF or KBP.In addition to the databases of all-a and all-b structures,we also built the database of a 1b and a /b structures.Because a 1b and a /b structures contain the structural features of both a -helices and b -strands,one expects that the results based on the energy functions extracted from mixed a -and b -structural elements are closer to the results extracted from the structures of all proteins.Indeed,as Fig.4shows,the success rates predicted by the DFIRE potential extracted from the original database (1011proteins,DFIRE-all;Zhou and Zhou,2002)are closer to those by the potential extracted from a 1b and a /b structures than those by the potentials from a -and b -databases.For example,at the top-10ranking,the differences between the average success rates over rankings 1–10are 2.4%between DFIRE-all and DFIRE-a ,2.4%between DFIRE-all and DFIRE-b , 1.1%between DFIRE-all and DFIRE-a 1b ,and 0.2%between DFIRE-all and DFIRE-a /b .The difference between the success rate given by DFIRE-all and that by DFIRE-a /b is the smallest.This is somewhat expected because the a /b structural class contains mixed elements of a -helices and b -strands whereas a 1b structures do not mix these two structuralelements.FIGURE 5The distance-dependent pair potential trained with the databases of a -proteins (dotted lines ),b -proteins (dashed lines ),and all proteins (solid lines ).The left panel is between C b -atoms of Leu and ASP and the right panel is between backbone atom N of Val and O of Trp.The results for RAPDF,atomic KBP,and DFIRE are shown in top,middle,and bottom panels,respectively.Database Dependence of Potentials 3355Biophysical Journal 86(6)3349–3358The database for all proteins should be more similar to a random mixture of a-and b-structural elements.The database independence of DFIRE potential further confirms the previousfinding that the performance of DFIRE potential in structure selection is insensitive to the number of proteins used in the database(200or more)and whether or not the target proteins are contained in training structural databases (Zhou and Zhou,2002).It should be emphasized that the DFIRE potential is not only mostly database independent but also has higher success rates than RAPDF and KBP in either a-protein decoys or b-protein decoys.Fig.5provides two examples of the pair potentials given by RAPDF,KBP,and DFIRE methods using three different structural databases.One is the potential between C b atoms of Leu and Asp and the other is between backbone N atom of Val and O atom of Trp.It is difficult,however,to judge the difference between the potentials extracted from different structural databases from the individual pair potential.To further understand the source for the difference between the three methods,one can compare the reducedreference states½N expðrÞ¼+ij N expði;j;rÞ given by themethods.For both RAPDF and KBP,N expðrÞ¼+ij N expði;j;rÞ¼N obsðrÞ:For DFIRE,N exp(r)¼(r/r cut)a(D r/D r cut)N obs(r cut).Thus,the database dependence of the reduced reference state in the DFIRE only comes from N obs(r)at r¼r cut,whereas it is N obs(r)at all distance for RAPDF and KBP.Fig.6plots the ratio of N exp(r)obtained from the a-protein database or the b-protein database to that from the1011-protein database.Even though all reference states have the database dependence,the database de-pendencies of RAPDF and KBP are significantly larger than that of DFIRE.It should be noted that the database dependence of N obs(r cut)is normal because the number of pairs at a certain distance is strongly dependent on the number of proteins.This dependence is apparently canceled by the database dependence of N obs(i,j,r)in DFIRE.We emphasize that the distance dependence of the reduced reference state[N exp(r)]is the same for RAPDF and KBP, but,the dependence of N exp(i,j,r)on atomic types for RAPDF and KBP is different(see Eqs.2and3). CONCLUDING REMARKSThe examination of the database dependence of statistical energy functions is important for an accurate prediction of protein structures.An accurate energy function should be capable of folding proteins with a,b,or any other structural topologies.This requires the statistical energy function to be independent of the structural database used for energy extraction.Here,the database dependences of RAPDF, atomic KBP,and DFIRE are examined based on their performance on structure selections.It is shown that the DFIRE potential is the least dependent on the structural database used for energy derivation,compared to RAPDF and atomic KBP.The significant database dependence of all-atom KBP/RAPDF statistical potentials confirms the previous finding for the database dependence of the residue-level Sippl potential with smaller databases of different structural classes (Furuichi and Koehl,1998).The origin of significant database dependence for RAPDF and atomic KBP is likely due to significant database dependence of their reference states.This highlights the importance of choosing an appropriate reference state for deriving statistical energy function.The mostly independent DFIRE energy function on the structural database,together with the independence of its performance for the systems with various amino-acid compositions (surface vs.core,monomer vs.dimeric interface;Zhou and Zhou,2002,2003;Liu et al.,2004),indicates that a physical reference state produces not only a physically but also a quantitatively more accurate statistical energy function. We thank Professor Charles L.Brooks and Professor Michael Feig for the CASP4decoy sets.This work is supported by the National Institutes of Health(R01GM 966049and R01GM068530);a grant from the Howard Hughes Medical Institute to the State University of New York,Buffalo;and by the Center for Computational Research and the Keck Center for Computational Biology at the State University of New York,Buffalo. REFERENCESAltuvia,Y.,O.Schueler,and H.Margalit.1995.Ranking potential binding peptides to MHC molecules by a computational threading approach. J.Mol.Biol.249:244–250.Bryant,S.H.,and wrence.1993.An empirical energy function for threading protein sequence through the folding motif.Proteins.16:92–112. Casari,G.,and M.J.Sippl.1992.Structure-derived hydrophobic potential. 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