Biology is the natural science that studies life and living organisms, including their physical structure, chemical processes, molecular interactions, physiological mechanisms and evolution. Despite the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, evolution as the engine that propels the creation and extinction of species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis. Sub-disciplines of biology are defined by the research methods employed and the kind of system studied: theoretical biology uses mathematical methods to formulate quantitative models while experimental biology performs empirical experiments to test the validity of proposed theories and understand the mechanisms underlying life and how it appeared and evolved from non-living matter about 4 billion years ago through a gradual increase in the complexity of the system.
See branches of biology. The term biology is derived from the Greek word βίος, bios, "life" and the suffix -λογία, -logia, "study of." The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus used biologi in his Bibliotheca botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff; the first German use, was in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in the preface of a book, Grundzüge der Lehre van der Lebenskraft. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological and psychological perspective; the term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur by Gottfried Reinhold Treviranus, who announced: The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, the causes through which they have been effected.
The science that concerns itself with these objects we will indicate by the name biology or the doctrine of life. Although modern biology is a recent development, sciences related to and included within it have been studied since ancient times. Natural philosophy was studied as early as the ancient civilizations of Mesopotamia, the Indian subcontinent, China. However, the origins of modern biology and its approach to the study of nature are most traced back to ancient Greece. While the formal study of medicine dates back to Hippocrates, it was Aristotle who contributed most extensively to the development of biology. Important are his History of Animals and other works where he showed naturalist leanings, more empirical works that focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences into the Middle Ages. Scholars of the medieval Islamic world who wrote on biology included al-Jahiz, Al-Dīnawarī, who wrote on botany, Rhazes who wrote on anatomy and physiology.
Medicine was well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew on Aristotelian thought in upholding a fixed hierarchy of life. Biology began to develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope, it was that scholars discovered spermatozoa, bacteria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining. Advances in microscopy had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. In 1838, Schleiden and Schwann began promoting the now universal ideas that the basic unit of organisms is the cell and that individual cells have all the characteristics of life, although they opposed the idea that all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory.
Meanwhile and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735, in the 1750s introduced scientific names for all his species. Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Although he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought. Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, the first to present a coherent theory of evolution, he posited that evolution was the result of environmental stress on properties of animals, meaning that the more and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could be passed on to the animal's offspring, who would
Professor is an academic rank at universities and other post-secondary education and research institutions in most countries. Professor derives from Latin as a "person who professes" being an expert in arts or sciences, a teacher of the highest rank. In most systems of academic ranks the word "Professor" only refers to the most senior academic position, sometimes informally known as "full professor". In some countries or institutions, the word professor is used in titles of lower ranks such as associate professor and assistant professor; this colloquial usage would be considered incorrect among most other academic communities. However, the unqualified title Professor designated with a capital letter refers to a full professor in English language usage. Professors conduct original research and teach undergraduate and postgraduate courses in their fields of expertise. In universities with graduate schools, professors may mentor and supervise graduate students conducting research for a thesis or dissertation.
In many universities,'full professors' take on senior managerial roles, leading departments, research teams and institutes, filling roles such as president, principal or vice-chancellor. The role of professor may be more public facing than that of more junior staff, professors are expected to be national or international leaders in their field of expertise; the term "professor" was first used in the late 14th century to mean "one who teaches a branch of knowledge". The word comes "...from Old French professeur and directly from Latin professor'person who professes to be an expert in some art or science. As a title, "prefixed to a name, it dates from 1706"; the "hort form prof is recorded from 1838". The term "professor" is used with a different meaning: "ne professing religion; this canting use of the word comes down from the Elizabethan period, but is obsolete in England." A professor is an accomplished and recognized academic. In most Commonwealth nations, as well as northern Europe, the title professor is the highest academic rank at a university.
In the United States and Canada, the title of professor applies to most post-doctoral academics, so a larger percentage are thus designated. In these areas, professors are scholars with doctorate degrees or equivalent qualifications who teach in four-year colleges and universities. An emeritus professor is a title given to selected retired professors with whom the university wishes to continue to be associated due to their stature and ongoing research. Emeritus professors do not receive a salary, but they are given office or lab space, use of libraries, so on; the term professor is used in the titles assistant professor and associate professor, which are not considered professor-level positions in all European countries. In Australia, the title associate professor is used in place of the term reader as used in the United Kingdom and other Commonwealth countries. Beyond holding the proper academic title, universities in many countries give notable artists and foreign dignitaries the title honorary professor if these persons do not have the academic qualifications necessary for professorship and they do not take up professorial duties.
However, such "professors" do not undertake academic work for the granting institution. In general, the title of professor is used for academic positions rather than for those holding it on honorary basis. Professors are qualified experts in their field who perform some or all the following tasks: Managing teaching and publications in their departments. Other roles of professorial tasks depend on the institution, its legacy, protocols and time. For example, professors at research-oriented universities in North America and at European universities, are promoted on the basis of research achievements and external grant-raising success. Many colleges and universities and other institutions of higher learning throughout the world follow a similar hierarchical ranking structure amongst scholars in academia. A professor earns a base salary and a range of benefits. In addition, a professor who undertakes additional roles in their institution earns additional income; some professors earn additional income by moonlighting in other jobs, such as consulting, publishing academic or popular press books, giving speeches, or coaching executives.
Some fields give professors more opportun
Assisted Model Building with Energy Refinement is a family of force fields for molecular dynamics of biomolecules developed by Peter Kollman's group at the University of California, San Francisco. AMBER is the name for the molecular dynamics software package that simulates these force fields, it is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at University of Florida, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, Junmei Wang at Encysive Pharmaceuticals. The term AMBER force field refers to the functional form used by the family of AMBER force fields; this form includes several parameters. The functional form of the AMBER force field is V = ∑ bonds k b 2 + ∑ angles k a 2 + ∑ torsions ∑ n 1 2 V n + ∑ j = 1 N − 1 ∑ i = j + 1 N f i j Despite the term force field, this equation defines the potential energy of the system; the meanings of right hand side terms are: First term: represents the energy between covalently bonded atoms.
This harmonic force is a good approximation near the equilibrium bond length, but becomes poor as atoms separate. Second term: represents the energy due to the geometry of electron orbitals involved in covalent bonding. Third term: represents the energy for twisting a bond due to bond order and neighboring bonds or lone pairs of electrons. One bond may have more than one of these terms, such that the total torsional energy is expressed as a Fourier series. Fourth term: represents the non-bonded energy between all atom pairs, which can be decomposed into van der Waals and electrostatic energies; the form of the van der Waals energy is calculated using the equilibrium well depth. The factor of 2 ensures; the energy is sometimes reformulated in terms of σ, where r 0 i j = 2 1 / 6, as used e.g. in the implementation of the softcore potentials. The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge To use the AMBER force field, it is necessary to have values for the parameters of the force field.
A large number of these parameter sets exist, are described in detail in the AMBER software user manual. Each parameter set has a name, provides parameters for certain types of molecules. Peptide and nucleic acid parameters are provided by parameter sets with names starting with "ff" and containing a two digit year number, for instance "ff99"; as of 2018 the primary protein model used by the AMBER suit is the ff14SB force field. General AMBER force field provides parameters for small organic molecules to facilitate simulations of drugs and small molecule ligands in conjunction with biomolecules; the GLYCAM force fields have been developed by Rob Woods for simulatin
Protein structure prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its folding and its secondary and tertiary structure from its primary structure. Structure prediction is fundamentally different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; every two years, the performance of current methods is assessed in the CASP experiment. A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the chain about each Cα atom, it is these conformational changes that are responsible for differences in the three dimensional structure of proteins. Each amino acid in the chain is polar, i.e. it has separated positive and negative charged regions with a free carbonyl group, which can act as hydrogen bond acceptor and an NH group, which can act as hydrogen bond donor.
These groups can therefore interact in the protein structure. The 20 amino acids can be classified according to the chemistry of the side chain which plays an important structural role. Glycine takes on a special position, as it has the smallest side chain, only one hydrogen atom, therefore can increase the local flexibility in the protein structure. Cysteine on the other hand can react with another cysteine residue and thereby form a cross link stabilizing the whole structure; the protein structure can be considered as a sequence of secondary structure elements, such as α helices and β sheets, which together constitute the overall three-dimensional configuration of the protein chain. In these secondary structures regular patterns of H bonds are formed between neighboring amino acids, the amino acids have similar Φ and Ψ angles; the formation of these structures neutralizes the polar groups on each amino acid. The secondary structures are packed in the protein core in a hydrophobic environment.
Each amino acid side group has a limited volume to occupy and a limited number of possible interactions with other nearby side chains, a situation that must be taken into account in molecular modeling and alignments. The α helix is the most abundant type of secondary structure in proteins; the α helix has 3.6 amino acids per turn with an H bond formed between every fourth residue. The alignment of the H bonds creates a dipole moment for the helix with a resulting partial positive charge at the amino end of the helix; because this region has free NH2 groups, it will interact with negatively charged groups such as phosphates. The most common location of α helices is at the surface of protein cores, where they provide an interface with the aqueous environment; the inner-facing side of the helix tends to have hydrophobic amino acids and the outer-facing side hydrophilic amino acids. Thus, every third of four amino acids along the chain will tend to be hydrophobic, a pattern that can be quite detected.
In the leucine zipper motif, a repeating pattern of leucines on the facing sides of two adjacent helices is predictive of the motif. A helical-wheel plot can be used to show this repeated pattern. Other α helices buried in the protein core or in cellular membranes have a higher and more regular distribution of hydrophobic amino acids, are predictive of such structures. Helices exposed on the surface have a lower proportion of hydrophobic amino acids. Amino acid content can be predictive of an α -helical region. Regions richer in alanine, glutamic acid and methionine and poorer in proline, glycine and serine tend to form an α helix. Proline can be present in longer helices, forming a bend. Β sheets are formed by H bonds between an average of 5–10 consecutive amino acids in one portion of the chain with another 5–10 farther down the chain. The interacting regions may be adjacent, with a short loop in between, or far apart, with other structures in between; every chain may run in the same direction to form a parallel sheet, every other chain may run in the reverse chemical direction to form an anti parallel sheet, or the chains may be parallel and anti parallel to form a mixed sheet.
The pattern of H bonding is different in the anti parallel configurations. Each amino acid in the interior strands of the sheet forms two H bonds with neighboring amino acids, whereas each amino acid on the outside strands forms only one bond with an interior strand. Looking across the sheet at right angles to the strands, more distant strands are rotated counterclockwise to form a left-handed twist; the Cα atoms alternate above and below the sheet in a pleated structure, the R side groups of the amino acids alternate above and below the pleats. The Φ and Ψ angles of the amino acids in sheets vary in one region of the Ramachandran plot, it is more difficult to predict the location of β sheets than of α helices. The situation improves somewhat when the amino acid variation in multiple sequence alignments is taken into account. Loops are regions of a protein chain that are 1) between α helices and β sheets, 2) of various lengths and three-dimensional configurations, 3) on the surface of the structure.
Hairpin loops that represent a complete turn in the polypeptide chain joining two antiparalle
University of California, San Francisco
The University of California, San Francisco is a public research university in San Francisco, California. It is part of the University of California system and it is dedicated to health science, it is a major center of teaching. UCSF was founded as Toland Medical College in 1864, in 1873 it affiliated itself with the University of California, becoming its Medical Department. In the same it incorporated the California College of Pharmacy and in 1881 it established a dentistry school. In 1964 it gained full administrative independence as a campus of the UC system headed by a chancellor, in 1970 it gained its current name. Based at Parnassus Heights and several other locations throughout the city, in the early 2000s it developed a second major campus in the newly redeveloped Mission Bay; as of October 2018, nine Nobel laureates have been affiliated with UCSF as faculty members or researchers, the University has been the site of many scientific breakthroughs. The UCSF School of Medicine, the oldest medical school in the Western United States, is the top recipient of NIH funding as of 2017.
U. S. News & World Report ranks it #5 on their "Best Medical Schools: Research" and #2 on their " "Best Medical Schools: Primary Care." The UCSF Schools of Dentistry and Pharmacy have the highest NIH funding in their respective fields. The UCSF Graduate Division offers 19 PhD programs, 11 MS programs, two certificates and a physical therapy program; the UCSF Medical Center is the nation's 6th-ranked hospital and California's highest-ranked hospital according to U. S. News & World Report. With 25,398 employees, UCSF is the second largest public agency employer in the San Francisco Bay Area. UCSF faculty have treated patients and trained residents since 1873 at the San Francisco General Hospital and for over 50 years at the San Francisco VA Medical Center; the University of California, San Francisco traces its history to Hugh Toland, a South Carolina surgeon who found great success and wealth after moving to San Francisco in 1852. A previous school, the Cooper Medical College of the University of Pacific, entered a period of uncertainty in 1862 when its founder, Elias Samuel Cooper, died.
In 1864, Toland founded a new medical school, Toland Medical College, the faculty of Cooper Medical College chose to suspend operations and join the new school. The University of California was founded in 1868, by 1870 Toland Medical School began negotiating an affiliation with the new public university. Meanwhile, some faculty of Toland Medical School elected to reopen the Medical Department of the University of the Pacific, which would become Stanford University School of Medicine. Negotiations between Toland and UC were complicated by Toland's demand that the medical school continue to bear his name, an issue on which he conceded. In March 1873, the trustees of Toland Medical College transferred it to the Regents of the University of California, it became The Medical Department of the University of California." At the same time, the University of California negotiated the incorporation of the California College of Pharmacy, the first pharmacy school in the West, established in 1872 by the Californian Pharmaceutical Society.
The Pharmacy College was affiliated in June 1873, together the Medical College and the Pharmacy College came to be known as'Affiliated Colleges'. The third college, the College of Dentistry, was established in 1881; the three Affiliated Colleges were located at different sites around San Francisco, but near the end of the 19th Century interest in bringing them together grew. To make this possible, San Francisco Mayor Adolph Sutro donated 13 acres in Parnassus Heights at the base of Mount Parnassus; the new site, overlooking Golden Gate Park, opened in the fall of 1898, with the construction of the new Affiliated Colleges buildings. The school's first female student, Lucy Wanzer, graduated in 1876, after having to appeal to the UC Board of Regents to gain admission in 1873; until 1906, the school faculty had provided care at the City-County Hospital, but did not have a hospital of its own. Following the 1906 San Francisco earthquake, more than 40,000 people were relocated to a makeshift tent city in Golden Gate Park and were treated by the faculty of the Affiliated Colleges.
This brought the school, which until was located on the western outskirts of the city, in contact with significant population and fueled the commitment of the school towards civic responsibility and health care, increasing the momentum towards the construction of its own health facilities. In April 1907, one of the buildings was renovated for outpatient care with 75 beds; this created the need to train nursing students, and, in 1907, the UC Training School for Nurses was established, adding a fourth professional school to the Affiliated Colleges. The schools continued to grow in numbers and reputation in the following year. One notable event was the incorporation of the Hooper Foundation for Medical Research in 1914, a medical research institute second only to the Rockefeller Institute; this addition bolstered the prestige of the Parnassus site during a dispute over whether the schools should consolidate at Parnassus or in Berkeley, where some of the departments had transferred. The final decision came in 1949 when the Regents of the University of California designated the Parnassus campus as the UC Medical Center in San Francisco.
The medical facilities were updated, the departments returned to San Francisco from Berkeley. During this period a number of research institutes were established, many new facilities were
Stony Brook University
The State University of New York at Stony Brook known as Stony Brook University and SUNY Stony Brook, is a public sea-grant and space-grant research university in Stony Brook, New York. It is one of four university centers of the State University of New York system; the institution was founded 62 years ago in 1957 in Oyster Bay as State University College on Long Island, moved to Stony Brook in 1962. The university has expanded to include 220 major buildings with a combined area of more than 12.2 million gross square feet across 1,454 acres of land. In 2001, Stony Brook was elected to the Association of American Universities, it is a member of the larger Universities Research Association. The university's health science and medical component, collectively referred to as Stony Brook Medicine, includes the Schools of Medicine, Dental Medicine, Health Technology and Management and Pharmaceutical Sciences, Social Welfare, as well as the Hospital, major centers and institutes, programs and community-based healthcare settings, the Long Island State Veterans Home.
Stony Brook University, part of the management team of Brookhaven National Laboratory – a national laboratory of the United States Department of Energy – acquired land for a Research & Development Park adjacent to its main campus in 2004, has four business incubators across the region. The university's impact on the Long Island economy amounts to $7.38 billion in increased output, research expenditures have surpassed the $230 million mark annually. Stony Brook is the largest single-site employer on Long Island. Stony Brook's intercollegiate athletic teams are the Seawolves. Since 1994, they have competed in Division I of the NCAA, are members of the America East Conference and the Colonial Athletic Association; the State University of New York at Stony Brook was established in Oyster Bay in 1957 as the State University College on Long Island, by the governor and state of New York. Established a decade after the creation of New York's public higher education system, the institution was envisioned as a college for the preparation of secondary school teachers.
Leonard K. Olson was appointed as the first dean of the institution and was instrumental in the recruitment of faculty staff and planning of the Stony Brook campus. SUCOLI opened with an inaugural class of 148 students, on the grounds of the William Robertson Coe Planting Fields estate; these first students were admitted on a tuition-free basis. 1961 was a year of firsts as thirty students were conferred degrees in the first commencement and the University was appointed its first president, John Francis Lee. Lee left that year due to political and bureaucratic matters regarding the future of the University and the central administration at Albany. Lee fulfilled his primary task of reshaping the university from a technical science and engineering college of limited degree options to a full-scale university featuring liberal arts programs. In 1960 the Heald Report, commissioned by Governor Nelson Rockefeller, recommended a major new public university be built on Long Island to "stand with the finest in the country", a report that would shape most of the University's growth for years to come.
Ward Melville, a philanthropist and businessman from the Three Village area in western Suffolk County donated over 400 acres of land to the state for the development of a state university and in 1962 the institution relocated to Stony Brook and renamed as the State University of New York at Stony Brook. However, the name has fallen out of favor, since 2005, has been replaced with Stony Brook University; the campus had 782 students enrolled in 1962, but enrollment had increased more than tenfold by 1969, surpassing the 8,000 mark, fueled by the large funding of public higher education in the Sputnik era. In 1963, only three years after the release of the Heald Report, the Governor commissioned the "Education of Health Professions" report; the report outlined the need for expansion of the university system to prepare medical professionals for the future needs of the state. The report was important for Stony Brook as it recommended creation of a Health Science Center and academic hospital at the campus to serve the need of the fastest-growing counties in New York at the time.
In 1965, the State University appointed John S. Toll, a renowned physicist from the University of Maryland as the second president of Stony Brook. In 1966, the University set forth initial timetables for the development of the Health Science Center, which would house the University's health programs and hospital. Despite the budgetary concerns and challenges from Albany, the University released a formalized plan early in 1968 and funding for recruitment of faculty was provided. At the same time, residential housing was expanded to 3,000, the Stony Brook Union opened in 1970, in 1971, the massive expansion project for the campus library was completed. Despite the fast-paced growth, campus infrastructure struggled to keep pace: overcrowding, landscaping and safety were persistent problems at the University, which led to multiple protests and growing tension between the student body and the administration. In January 1968, the infamous “Operation Stony Brook” drug raid resulted in the arrest of twenty nine students and in the fall of 1968, tension climaxed as the administration and students decided on a three-day moratorium to bring together the entire university with the goal of improving communicati