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65-693: EMSL scientists and collaborators perform fundamental research that focuses on the biological, biogeochemical, and physical principles to predict processes occurring at the molecular and genomics-controlled smallest scales to the environmental Earth system changes at the largest scales. The Functional and Systems Biology Science Area focuses on understanding enzymes and biochemical pathways that connect protein structures and functions to phenotypic responses and interactions within cells, among cells in communities, and between cellular membrane surfaces and their environment for microbes and plants. The Environmental Transformations and Interactions Science Area focuses on

130-522: A basis set of Slater orbitals . For diatomic molecules, a systematic study using a minimum basis set and the first calculation with a larger basis set were published by Ransil and Nesbet respectively in 1960. The first polyatomic calculations using Gaussian orbitals were performed in the late 1950s. The first configuration interaction calculations were performed in Cambridge on the EDSAC computer in

195-429: A Hamiltonian. Yet, the term "empirical methods", or "empirical force fields" is usually used to describe molecular mechanics. In many cases, large molecular systems can be modeled successfully while avoiding quantum mechanical calculations entirely. Molecular mechanics simulations, for example, use one classical expression for the energy of a compound, for instance, the harmonic oscillator . All constants appearing in

260-562: A National Academy of Sciences report titled Opportunities in Chemistry . The report identified scientific challenges relating to energy and the environment that required fundamental research to achieve a solution. In response, then director of PNNL, William R. Wiley, and lab senior managers proposed a center for molecular science that would bring together researchers from the physical and life sciences and theoreticians with experience in computing and molecular process modeling. Wiley envisioned

325-915: A Web of Science search in March 2020. In June 2013, EMSL retired the Chinook computer and welcomed Cascade, a 3.4-petaflops system. EMSL celebrated its twentieth anniversary in August 2017, showcasing NWChem computational chemistry software, and advances in subsurface science and foundational biofuel production. Scientific leaders participated in the event, including internationally recognized scientists Thom Dunning, Steve Colson, and Jean Futrell. Today, EMSL focuses its scientific research in Functional and Systems Biology, Environmental Transformations and Interactions, and Computing, Analytics, and Modeling together with users from diverse scientific communities. This science

390-488: A biogeochemistry question concerning the fundamental interaction between microbes and minerals, and a study addressing the structure and function of proteins in the cell membrane. Work on these challenges led to new opportunities for the scientific community, with research campaigns designed to focus teams on a single challenge. In January 2007, EMSL celebrated its first permanent expansion: a nearly 4,000-square-foot raised floor for an 11.8-teraflop computer named Chinook, which

455-454: A facility with advanced instrumentation for the study of molecular-level chemistry in an integrated and collaborative manner. Ohio-based Battelle Memorial Institute, which operates PNNL for DOE, approved $ 8.5 million in funding over four years to build the facility; develop research programs; and obtain the equipment, facilities, scientists, and support staff. Construction began in July 1994 and

520-450: A few months to a few years. EMSL users do not have to stay on-site for the duration of their project and can visit the laboratory when needed. Much of the sample processing and analysis can be handled remotely. EMSL's user community provides the laboratory’s management team with recommendations for scientific direction and efficient operations through an elected committee of representatives. The idea that would become EMSL began in 1985 with

585-418: A hybrid approach, combining quantum mechanics for a portion of the system with classical mechanics for the remainder, quantum computational chemistry exclusively uses quantum computing methods to represent and process information, such as Hamiltonian operators. Conventional computational chemistry methods often struggle with the complex quantum mechanical equations, particularly due to the exponential growth of

650-500: A level of theory (the method) and a basis set. A basis set consists of functions centered on the molecule's atoms. These sets are then used to describe molecular orbitals via the linear combination of atomic orbitals (LCAO) molecular orbital method ansatz . A common type of ab initio electronic structure calculation is the Hartree–Fock method (HF), an extension of molecular orbital theory , where electron-electron repulsions in

715-412: A molecular dynamics simulation is a trajectory that describes how the position and velocity of particles varies with time. The phase point of a system described by the positions and momenta of all its particles on a previous time point will determine the next phase point in time by integrating over Newton's laws of motion. Monte Carlo (MC) generates configurations of a system by making random changes to

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780-564: A problem in the future. In the United States, basic research is funded mainly by the federal government and done mainly at universities and institutes. As government funding has diminished in the 2010s, however, private funding is increasingly important. Applied science focuses on the development of technology and techniques. In contrast, basic science develops scientific knowledge and predictions, principally in natural sciences but also in other empirical sciences, which are used as

845-467: A quantum system's wave function. Quantum computational chemistry addresses these challenges using quantum computing methods , such as qubitization and quantum phase estimation , which are believed to offer scalable solutions. Qubitization involves adapting the Hamiltonian operator for more efficient processing on quantum computers, enhancing the simulation's efficiency. Quantum phase estimation, on

910-483: A series of post-Hartree–Fock methods and combine the results. These methods are called quantum chemistry composite methods . After the electronic and nuclear variables are separated within the Born–Oppenheimer representation), the wave packet corresponding to the nuclear degrees of freedom is propagated via the time evolution operator (physics) associated to the time-dependent Schrödinger equation (for

975-722: A whole host of algorithms. Building on the founding discoveries and theories in the history of quantum mechanics , the first theoretical calculations in chemistry were those of Walter Heitler and Fritz London in 1927, using valence bond theory . The books that were influential in the early development of computational quantum chemistry include Linus Pauling and E. Bright Wilson 's 1935 Introduction to Quantum Mechanics – with Applications to Chemistry , Eyring , Walter and Kimball's 1944 Quantum Chemistry , Heitler's 1945 Elementary Wave Mechanics – with Applications to Quantum Chemistry , and later Coulson 's 1952 textbook Valence , each of which served as primary references for chemists in

1040-541: Is a tool for analyzing catalytic systems without doing experiments. Modern electronic structure theory and density functional theory has allowed researchers to discover and understand catalysts . Computational studies apply theoretical chemistry to catalysis research. Density functional theory methods calculate the energies and orbitals of molecules to give models of those structures. Using these methods, researchers can predict values like activation energy , site reactivity and other thermodynamic properties. Data that

1105-467: Is a user research facility whereby scientists, from around the world, can submit project proposals to access the laboratory’s experts and equipment at no cost. Proposals are screened through a competitive peer-review process to ensure the project is scientifically impactful and relevant to DOE's Office of Biological and Environmental Research mission. Scientists whose proposals are accepted are referred to as EMSL users. Typical user research projects can last

1170-442: Is difficult to obtain experimentally can be found using computational methods to model the mechanisms of catalytic cycles. Skilled computational chemists provide predictions that are close to experimental data with proper considerations of methods and basis sets. With good computational data, researchers can predict how catalysts can be improved to lower the cost and increase the efficiency of these reactions. Computational chemistry

1235-598: Is driving technology development and computational capabilities. Basic research Basic research , also called pure research , fundamental research , basic science , or pure science , is a type of scientific research with the aim of improving scientific theories for better understanding and prediction of natural or other phenomena. In contrast, applied research uses scientific theories to develop technology or techniques, which can be used to intervene and alter natural or other phenomena. Though often driven simply by curiosity , basic research often fuels

1300-444: Is inadequate, and several configurations must be used. The total molecular energy can be evaluated as a function of the molecular geometry ; in other words, the potential energy surface . Such a surface can be used for reaction dynamics. The stationary points of the surface lead to predictions of different isomers and the transition structures for conversion between isomers, but these can be determined without full knowledge of

1365-469: Is often not perfect, identifying issues is often easier for calculated data than experimental. Databases also give public access to information for researchers to use. They contain data that other researchers have found and uploaded to these databases so that anyone can search for them. Researchers use these databases to find information on molecules of interest and learn what can be done with those molecules. Some publicly available chemistry databases include

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1430-401: Is rigorously defined on first principles and then solved within an error margin that is qualitatively known beforehand. If numerical iterative methods must be used, the aim is to iterate until full machine accuracy is obtained (the best that is possible with a finite word length on the computer, and within the mathematical and/or physical approximations made). Ab initio methods need to define

1495-453: Is to use higher order splitting. Usually, second order splitting is the most that is done because higher order splitting requires much more time to calculate and is not worth the cost. Higher order methods become too difficult to implement, and are not useful for solving differential equations despite the higher accuracy. Computational chemists spend much time making systems calculated with split operator technique more accurate while minimizing

1560-984: Is used in drug development to model potentially useful drug molecules and help companies save time and cost in drug development. The drug discovery process involves analyzing data, finding ways to improve current molecules, finding synthetic routes, and testing those molecules. Computational chemistry helps with this process by giving predictions of which experiments would be best to do without conducting other experiments. Computational methods can also find values that are difficult to find experimentally like pKa 's of compounds. Methods like density functional theory can be used to model drug molecules and find their properties, like their HOMO and LUMO energies and molecular orbitals. Computational chemists also help companies with developing informatics, infrastructure and designs of drugs. Aside from drug synthesis, drug carriers are also researched by computational chemists for nanomaterials . It allows researchers to simulate environments to test

1625-401: The Hartree–Fock method formalism, but make many approximations and obtain some parameters from empirical data. They were very important in computational chemistry from the 60s to the 90s, especially for treating large molecules where the full Hartree–Fock method without the approximations were too costly. The use of empirical parameters appears to allow some inclusion of correlation effects into

1690-436: The many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments , it can occasionally predict unobserved chemical phenomena . Computational chemistry differs from theoretical chemistry , which involves a mathematical description of chemistry. However, computational chemistry involves

1755-403: The technological innovations of applied science . The two aims are often practiced simultaneously in coordinated research and development . In addition to innovations, basic research serves to provide insights and public support of nature, possibly improving conservation efforts. Technological innovations may influence engineering concepts, such as the beak of a kingfisher influencing

1820-669: The wave packet associated to the molecular geometry are: How a computational method solves quantum equations impacts the accuracy and efficiency of the method. The split operator technique is one of these methods for solving differential equations. In computational chemistry, split operator technique reduces computational costs of simulating chemical systems. Computational costs are about how much time it takes for computers to calculate these chemical systems, as it can take days for more complex systems. Quantum systems are difficult and time-consuming to solve for humans. Split operator methods help computers calculate these systems quickly by solving

1885-682: The 1950s using Gaussian orbitals by Boys and coworkers. By 1971, when a bibliography of ab initio calculations was published, the largest molecules included were naphthalene and azulene . Abstracts of many earlier developments in ab initio theory have been published by Schaefer. In 1964, Hückel method calculations (using a simple linear combination of atomic orbitals (LCAO) method to determine electron energies of molecular orbitals of π electrons in conjugated hydrocarbon systems) of molecules, ranging in complexity from butadiene and benzene to ovalene , were generated on computers at Berkeley and Oxford. These empirical methods were replaced in

1950-500: The 1960s by semi-empirical methods such as CNDO . In the early 1970s, efficient ab initio computer programs such as ATMOL, Gaussian , IBMOL, and POLYAYTOM, began to be used to speed ab initio calculations of molecular orbitals. Of these four programs, only Gaussian, now vastly expanded, is still in use, but many other programs are now in use. At the same time, the methods of molecular mechanics , such as MM2 force field , were developed, primarily by Norman Allinger . One of

2015-527: The National Science Foundation. A worker in basic scientific research is motivated by a driving curiosity about the unknown. When his explorations yield new knowledge, he experiences the satisfaction of those who first attain the summit of a mountain or the upper reaches of a river flowing through unmapped territory. Discovery of truth and understanding of nature are his objectives. His professional standing among his fellows depends upon

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2080-544: The Reviews of Modern Physics. This paper focused largely on the "LCAO MO" approach (Linear Combination of Atomic Orbitals Molecular Orbitals). For many years, it was the second-most cited paper in that journal. A very detailed account of such use in the United Kingdom is given by Smith and Sutcliffe. The first ab initio Hartree–Fock method calculations on diatomic molecules were performed in 1956 at MIT, using

2145-461: The basis of progress and development in different fields. Today's computers, for example, could not exist without research in pure mathematics conducted over a century ago, for which there was no known practical application at the time. Basic research rarely helps practitioners directly with their everyday concerns; nevertheless, it stimulates new ways of thinking that have the potential to revolutionize and dramatically improve how practitioners deal with

2210-564: The behavior of atomic and molecular systems under the framework of quantum mechanics, as defined by the Schrödinger equation. To obtain exact agreement with the experiment, it is necessary to include specific terms, some of which are far more important for heavy atoms than lighter ones. In most cases, the Hartree–Fock wave function occupies a single configuration or determinant. In some cases, particularly for bond-breaking processes, this

2275-416: The complete surface. A particularly important objective, called computational thermochemistry , is to calculate thermochemical quantities such as the enthalpy of formation to chemical accuracy. Chemical accuracy is the accuracy required to make realistic chemical predictions and is generally considered to be 1 kcal/mol or 4 kJ/mol. To reach that accuracy in an economic way, it is necessary to use

2340-421: The computational cost. Calculating methods is a massive challenge for many chemists trying to simulate molecules or chemical environments. Density functional theory (DFT) methods are often considered to be ab initio methods for determining the molecular electronic structure, even though many of the most common functionals use parameters derived from empirical data, or from more complex calculations. In DFT,

2405-784: The coupling of terrestrial and atmospheric processes. Rhizosphere Function investigates interactions between genes and the environment at the molecular level to understand, predict and control plant and ecosystem traits at the systems scale. Structural Biology gains structural, biochemical, and dynamic information about proteins, protein complexes, and other biomolecules at nanoscale spatial and temporal resolutions to understand function. Systems Modeling uses computational models of protein structure and function, metabolic modeling, and machine learning approaches to associate genotype with phenotype and to understand biological processes that control nutrient flux, and enable predictive approaches to biodesign and biofuel/bioproduct production. EMSL

2470-449: The decades to follow. With the development of efficient computer technology in the 1940s, the solutions of elaborate wave equations for complex atomic systems began to be a realizable objective. In the early 1950s, the first semi-empirical atomic orbital calculations were performed. Theoretical chemists became extensive users of the early digital computers. One significant advancement was marked by Clemens C. J. Roothaan's 1951 paper in

2535-527: The design of a high-speed bullet train. Basic research advances fundamental knowledge about the world. It focuses on creating and refuting or supporting theories that explain observed phenomena. Pure research is the source of most new scientific ideas and ways of thinking about the world. It can be exploratory , descriptive , or explanatory; however, explanatory research is the most common. Basic research generates new ideas, principles, and theories, which may not be immediately utilized but nonetheless form

2600-407: The effectiveness and stability of drug carriers. Understanding how water interacts with these nanomaterials ensures stability of the material in human bodies. These computational simulations help researchers optimize the material find the best way to structure these nanomaterials before making them. Databases are useful for both computational and non computational chemists in research and verifying

2665-464: The equations must be obtained beforehand from experimental data or ab initio calculations. The database of compounds used for parameterization, i.e. the resulting set of parameters and functions is called the force field , is crucial to the success of molecular mechanics calculations. A force field parameterized against a specific class of molecules, for instance, proteins, would be expected to only have any relevance when describing other molecules of

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2730-535: The first mentions of the term computational chemistry can be found in the 1970 book Computers and Their Role in the Physical Sciences by Sidney Fernbach and Abraham Haskell Taub, where they state "It seems, therefore, that 'computational chemistry' can finally be more and more of a reality." During the 1970s, widely different methods began to be seen as part of a new emerging discipline of computational chemistry . The Journal of Computational Chemistry

2795-453: The following. The programs used in computational chemistry are based on many different quantum-chemical methods that solve the molecular Schrödinger equation associated with the molecular Hamiltonian . Methods that do not include any empirical or semi-empirical parameters in their equations – being derived directly from theory, with no inclusion of experimental data – are called ab initio methods . A theoretical approximation

2860-416: The full molecular Hamiltonian ). In the complementary energy-dependent approach, the time-independent Schrödinger equation is solved using the scattering theory formalism. The potential representing the interatomic interaction is given by the potential energy surfaces . In general, the potential energy surfaces are coupled via the vibronic coupling terms. The most popular methods for propagating

2925-619: The mechanistic and predictive understanding of the environmental (physiochemical, hydrological, biogeochemical), microbial, plant, and ecological processes in above and belowground ecosystems, the atmosphere, and their interfaces. The Computing, Analytics, and Modeling Science Area focuses on using state-of-the-art experimental data to develop a predictive understanding of biological and environmental systems through advanced data analytics, visualization, and computational modeling and simulation. EMSL uses Integrated Research Platforms to uncover critical information for understanding and predicting

2990-541: The methods. Primitive semi-empirical methods were designed even before, where the two-electron part of the Hamiltonian is not explicitly included. For π-electron systems, this was the Hückel method proposed by Erich Hückel , and for all valence electron systems, the extended Hückel method proposed by Roald Hoffmann . Sometimes, Hückel methods are referred to as "completely empirical" because they do not derive from

3055-896: The molecular functions of biological and ecosystem processes. Biogeochemical Transformations investigates how molecular interactions at the Earth’s land, water, and air interfaces transform and transport nutrients and contaminants within the environment. Biomolecular Pathways investigates the translation of genomic information into functional relationships among biomolecules within cells in response to changes in their internal or external environment. Cell Signaling and Communications reveals dynamic interactions and trafficking of molecular signals within and between cells, populations, and communities to understand complex inter-relationships between organisms in response to their environment. Terrestrial-Atmospheric Processes investigates molecular transformations, physical processes that control them, and

3120-578: The molecule are not specifically taken into account; only the electrons' average effect is included in the calculation. As the basis set size increases, the energy and wave function tend towards a limit called the Hartree–Fock limit. Many types of calculations begin with a Hartree–Fock calculation and subsequently correct for electron-electron repulsion, referred to also as electronic correlation . These types of calculations are termed post-Hartree–Fock methods. By continually improving these methods, scientists can get increasingly closer to perfectly predicting

3185-468: The originality and soundness of his work. Creativeness in science is of a cloth with that of the poet or painter. It conducted a study in which it traced the relationship between basic scientific research efforts and the development of major innovations, such as oral contraceptives and videotape recorders. This study found that basic research played a key role in the development in all of the innovations. The number of basic science research that assisted in

3250-773: The other hand, assists in accurately determining energy eigenstates, which are critical for understanding the quantum system's behavior. While these techniques have advanced the field of computational chemistry, especially in the simulation of chemical systems, their practical application is currently limited mainly to smaller systems due to technological constraints. Nevertheless, these developments may lead to significant progress towards achieving more precise and resource-efficient quantum chemistry simulations. The computational cost and algorithmic complexity in chemistry are used to help understand and predict chemical phenomena. They help determine which algorithms/computational methods to use when solving chemical problems. This section focuses on

3315-404: The positions of its particles, together with their orientations and conformations where appropriate. It is a random sampling method, which makes use of the so-called importance sampling . Importance sampling methods are able to generate low energy states, as this enables properties to be calculated accurately. The potential energy of each configuration of the system can be calculated, together with

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3380-766: The production of a given innovation peaked between 20 and 30 years before the innovation itself. While most innovation takes the form of applied science and most innovation occurs in the private sector, basic research is a necessary precursor to almost all applied science and associated instances of innovation. Roughly 76% of basic research is conducted by universities. A distinction can be made between basic science and disciplines such as medicine and technology. They can be grouped as STM (science, technology, and medicine; not to be confused with STEM [science, technology, engineering, and mathematics]) or STS (science, technology, and society). These groups are interrelated and influence each other, although they may differ in

3445-428: The same class. These methods can be applied to proteins and other large biological molecules, and allow studies of the approach and interaction (docking) of potential drug molecules. Molecular dynamics (MD) use either quantum mechanics , molecular mechanics or a mixture of both to calculate forces which are then used to solve Newton's laws of motion to examine the time-dependent behavior of systems. The result of

3510-457: The scientific foundation for applied science. Basic science develops and establishes information to predict phenomena and perhaps to understand nature, whereas applied science uses portions of basic science to develop interventions via technology or technique to alter events or outcomes. Applied and basic sciences can interface closely in research and development . The interface between basic research and applied research has been studied by

3575-634: The specifics such as methods and standards. The Nobel Prize mixes basic with applied sciences for its award in Physiology or Medicine . In contrast, the Royal Society of London awards distinguish natural science from applied science. Computational chemistry Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate

3640-403: The structures and properties of molecules , groups of molecules, and solids. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion ( dihydrogen cation ), achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in

3705-410: The sub problems in a quantum differential equation . The method does this by separating the differential equation into two different equations, like when there are more than two operators. Once solved, the split equations are combined into one equation again to give an easily calculable solution. This method is used in many fields that require solving differential equations, such as biology . However,

3770-634: The technique comes with a splitting error. For example, with the following solution for a differential equation. e h ( A + B ) {\textstyle e^{h(A+B)}} The equation can be split, but the solutions will not be exact, only similar. This is an example of first order splitting. e h ( A + B ) ≈ e h A e h B {\textstyle e^{h(A+B)}\approx e^{hA}e^{hB}} There are ways to reduce this error, which include taking an average of two split equations. Another way to increase accuracy

3835-501: The total energy is expressed in terms of the total one- electron density rather than the wave function. In this type of calculation, there is an approximate Hamiltonian and an approximate expression for the total electron density. DFT methods can be very accurate for little computational cost. Some methods combine the density functional exchange functional with the Hartree–Fock exchange term and are termed hybrid functional methods. Semi-empirical quantum chemistry methods are based on

3900-602: The usage of computer programs and additional mathematical skills in order to accurately model various chemical problems. In theoretical chemistry, chemists, physicists, and mathematicians develop algorithms and computer programs to predict atomic and molecular properties and reaction paths for chemical reactions. Computational chemists, in contrast, may simply apply existing computer programs and methodologies to specific chemical questions. Historically, computational chemistry has had two different aspects: These aspects, along with computational chemistry's purpose, have resulted in

3965-739: The validity of computational methods. Empirical data is used to analyze the error of computational methods against experimental data. Empirical data helps researchers with their methods and basis sets to have greater confidence in the researchers results. Computational chemistry databases are also used in testing software or hardware for computational chemistry. Databases can also use purely calculated data. Purely calculated data uses calculated values over experimental values for databases. Purely calculated data avoids dealing with these adjusting for different experimental conditions like zero-point energy. These calculations can also avoid experimental errors for difficult to test molecules. Though purely calculated data

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4030-519: The values of other properties, from the positions of the atoms. QM/MM is a hybrid method that attempts to combine the accuracy of quantum mechanics with the speed of molecular mechanics. It is useful for simulating very large molecules such as enzymes . Quantum computational chemistry aims to exploit quantum computing to simulate chemical systems, distinguishing itself from the QM/MM (Quantum Mechanics/Molecular Mechanics) approach. While QM/MM uses

4095-677: Was completed in August 1997. EMSL opened October 1, 1997 for full operation. During its first five years, EMSL leaders built capabilities, recruited scientific leadership, and attracted users. The leaders then expanded the scientific focus to include biology, particularly the study of naturally occurring microbes for environmental cleanup, alternative energy, and carbon dioxide reduction in the atmosphere. EMSL's early user program focused on single investigator studies that crossed scientific areas and quickly reached more than 1,000 users per year, representing every state and several foreign countries. During this period, EMSL focused on two Grand Challenges:

4160-717: Was first published in 1980. Computational chemistry has featured in several Nobel Prize awards, most notably in 1998 and 2013. Walter Kohn , "for his development of the density-functional theory", and John Pople , "for his development of computational methods in quantum chemistry", received the 1998 Nobel Prize in Chemistry. Martin Karplus , Michael Levitt and Arieh Warshel received the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems". There are several fields within computational chemistry. These fields can give rise to several applications as shown below. Computational chemistry

4225-611: Was then the fifth-fastest system in the world. In April 2008, EMSL dedicated a new office pod to distinguished user J. Mike White that houses nearly 100 staff and users PNNL. In early 2012, EMSL opened its Quiet Wing housing a suite of ultrasensitive high-resolution microscopy and scanning instruments. In October 2010, EMSL’s premier computational chemistry software package, NWChem went open source, allowing computer scientists worldwide to contribute to its future development and making it available to more researchers and students. The code has been cited over 3760 times since 2010, according to

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