Jeremy Smith - US grants

Climate is a major driver of forest ecosystem dynamics and operates on several spatial and temporal scales to affect tree mortality in forest communities. Large pulses of mortality can be triggered by climatic events such as prolonged and/or intense drought. Climatic influences on tree mortality are further complicated because tree mortality can be facilitated by climatically-sensitive disturbances such as bark beetle outbreaks. The goal of this doctoral research is to examine effects of climate variation on tree mortality in subalpine forests of Colorado's Front Range by integrating mortality records from permanent plots and tree-ring reconstructions of tree death dates with spatial analysis of mortality patterns related to drought and bark beetle outbreak. Ten permanent subalpine forest plots with greater than 400 trees each and thirty smaller plots with an average of 50 trees initially installed in the early 1980s were re-measured for radial growth and tree mortality. Tree species include Engelmann spruce (Picea engelmannii), subalpine fir (Abies lasiocarpa), lodgepole pine (Pinus contorta) and limber pine (Pinus flexilis). Both observed and tree-ring reconstructed tree death years from trees within the plots will be statistically compared to local and regional climate data to discern temporal associations with climate events (e.g. extreme drought). Spatial patterns of mortality within the plots will also be examined with regard to the relative location of canopy gaps, tree size and growth rate, and proximity of trees of varying sizes and growth rates. At a broader spatial scale, mortality of limber pine will be examined in relation to spatial variability of the physical environment throughout its subalpine distribution in the northern Front Range. Intensive sampling of 30 sites will provide insight into the patch size and extent of mortality directly driven by climate as well as mortality meditated by mountain pine beetle (Dendroctonus ponderosae). Cross dated tree death years will be analyzed for synchrony and quantitatively compared with local and regional climate data to test for temporal associations with climate events. A spatial logistic regression model that predicts limber pine mortality at a regional scale will be developed from topographic information, soil layers, photo-interpreted species boundaries, and historic pest information.

This study capitalizes on long-term observations from permanent plots which are crucial to an understanding of forest demography given the long timescales over which forests are shaped. In addition, analysis of climate variation and climate-related insect outbreak as agents of tree mortality situates the study within the context of current global warming trends. There are few documentary records of mountain pine beetle affecting high elevation limber pine in Colorado. This raises the possibility that the current high-level of beetle-induced mortality in limber pine is unprecedented over approximately the past 100 years and may be a harbinger of patterns associated with the current warming trend in the Colorado Rockies. Limber pine is a particularly important species for wildlife, and its populations are currently threatened by drought, beetle attack, and infection by blister rust. Thus, land managers need a better understanding of past and probable future patterns of mortality in this species to inform mitigation decisions. Data from the study will be included in a collaborative USGS initiative aimed at investigating the effects of global change on mountain regions in the western United States.

This Integrated Graduate Education and Research Training (IGERT) Program on Scalable Computing and Leading Edge Innovative Technologies (SCALE-IT) for Biology will educate future biologists in a new way of approaching biology?a seamless combination of computing expertise and research using emerging tools that can attack the most challenging problems in biology spanning sub-cellular to organismal scales. These activities will be coordinated by a team of biologists and computational scientists at the University of Tennessee and Oak Ridge National Laboratory. The goal is to endow future scientists with the expertise to work at the interface of computational and biological sciences, giving them the foundation to grasp important biological problems, understand the scope of the data needed to address them, shrewdly design comprehensive solutions, and implement them in a reasonable and efficient fashion. SCALE-IT trainees will conduct research in an environment that includes state-of-the-art instrumentation, high performance computing and worldwide distributed computing via the Tera-grid. New curricula will provide trainees with the background to work across computational and biological scales, including in-depth problem-based learning with hands-on experiences. Opportunities will be available for students to intern with major industries, institutes and other academic programs. Other broader impacts of the program include summer research experiences and curriculum development workshops for faculty and students from partner institutions. Collaborations with Delaware State University and Tennessee State University will provide pathways for underrepresented minorities to participate in this doctoral program. Training in effective communication of science will be fostered by establishing a Science Communication Center with colleagues in journalism. IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

Motions in and between proteins play key roles in the functioning of the cell. This project will provide a framework for understanding functional protein dynamics by integrating high-performance computer simulation with dynamic neutron scattering experiments on the Spallation Neutron Source at Oak Ridge National Laboratory. The complexity of biological systems is such that optimal use of next-generation neutron sources in biology will require judicious computer simulation analysis. Computational methods will be developed for obtaining simplified descriptions of protein dynamics from simulation that are suitable for direct interpretation of neutron scattering experiments designed to detect motions. Further, neutron experiments will be combined with simulation so as to probe motions between protein molecules in crystals. The research combines concepts in physics, chemistry, biophysics, structural biology and computer science to employ simulation as a stepping stone between experiments on biomolecular systems and simplified physical descriptions.

This project involves a strong graduate and undergraduate teaching component in a highly international research group, and will provide tools for general use by the neutron and biosimulation communities. Outreach activities will include lectures in the local community and web-based press articles. A number of applied scientific disciplines will benefit from the research in that a physical understanding of protein dynamics is a prerequisite for the rational design of biofuels, bionanomaterials, catalysts for environmental science and other useful systems.

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Smith

The motion, metabolic, and force analysis system requested would benefit research, research training, and education in the Biomechanics Lab and Rocky Mountain Cancer Rehabilitation Institute (RMCRI) at the University of Northern Colorado (UNC). Understanding mechanisms associated with the structural characteristics of the prosthesis, the higher energetic costs of amputee locomotion, and common walking asymmetries in lower extremity amputees could impact prosthetic design and rehabilitation programs. Two new research projects involving lower extremity amputees would benefit from the acquisition of the requested equipment. One project would investigate the effect of increasing prosthesis mass on the mechanics and energetics of amputee locomotion. The second would focus on improving models of the prosthetic ankle by creating a method for identifying the instant center of rotation of prosthetic ankles. Current research in the Biomechanics Lab has been limited to 2-D analyses, but with acquisition of the requested equipment, the proposed research would expand to 3-D analyses.

This award in the Chemical Synthesis (SYN) program in the Division of Chemistry at NSF supports a project by Professor Jeremy Smith from the Department of Chemistry and Biochemistry at New Mexico State University to carry out fundamental studies aimed at uncovering new reactivity of high-valent iron complexes. The project involves the use of tris(carbene)borate ligands to prepare novel iron(IV) complexes and the use of a range of simple transition metal carbonyl and nitrosyl complexes to systematically probe their electronic structures. The project is interdisciplinary in nature and involves synthetic inorganic chemistry, a variety of spectroscopic techniques, and the measurement of magnetic properties.

The project could lead to the discovery of new reactivity patterns in iron(IV) complexes of potential relevance to nitrogen fixation (i.e., the conversion of atmospheric nitrogen to derivatives that can be assimilated by living organisms). In addition, this project will provide excellent interdisciplinary training of students, from undergraduate to post-doctoral, including those from groups historically underrepresented in the sciences.

In this project funded by the Chemical Synthesis Program of the Chemistry Division, Professor Jeremy M. Smith, Department of Chemistry and Biochemistry, Indiana University, investigates how well-defined manganese catalysts convert water into oxygen. Nature has learned to convert water to oxygen using visible light. This process is called photosynthesis and uses manganese in a complicated biological protein. In this project, smaller managanese compounds are being studied both to provide basic information on photosynthetic oxygen formation and to provide new catalysts, based on inexpensive, abundant metals, for use in the laboratory or by the chemical industry. An important part of the project involves the training of students in bioinorganic and energy chemistry.

This project utilizes synthetic, spectroscopic and physical studies to investigate the mechanism of water oxidation by manganese macrocyclic complexes. The modular catalyst design allows for the introduction of functional groups, enabling systematic studies into the effect of proton and hydrogen atom transport as well as metal cofactors on catalyst performance. A family of manganese pyridinophane compounds serve as functional models for the oxygen evolving complex of Photosystem II. This work sets out to: (1) experimentally validate a computationally-proposed mechanism for water oxidation by these complexes, (2) determine the impact of pyridinophane stereoelectronic properties on catalytic selectivity and activity, and (3) delineate the effect of the second coordination sphere on catalytic activity, including the presence of proton and hydrogen atom relays, and redox-innocent metals. Spectroscopic, reactivity and mechanistic investigations of these species provide insights relevant to the biological water oxidation mechanism, particularly the key O-O bond forming step. Compounds are characterized by standard physical methods of X-ray diffraction, NMR, EPR, and IR, while catalytic behavior is investigated by a combination of electrochemical measurements and standard mechanistic probes.

This workshop will discuss the progress and prospects in the field of neutron scattering as a vital tool in biological research that could provide elusive and critical, unique information about complex biological systems. Special emphasis of the workshop will be on combining high-performance computation with neutron scattering. Education and broader impact activities to enable better access to neutron scattering methodologies will also be a focus of the discussion. The workshop will provide a road-map by defining the scientific, engineering and data challenges required to use neutron scattering as a tool to study biological systems.

Recent world-wide research and development activities have created an opportunity to use neutron scattering as another vital tool in biological research. This technology offers excellent potential to provide previously elusive information about complex biological systems unobtainable with other measurement tools. Neutrons are ideal for studying multi-scale phenomena intrinsic to biological processes. With no charge, they cause little radiation damage and are highly penetrating, enabling use of complex sample environments. Also, neutrons have energies similar to atomic motions, and their spin can be coupled to magnetic fields in spin echo measurements, allowing the study of dynamic processes over a wide range of timescales, from picoseconds to microseconds. Moreover, a particularly desirable property of neutrons for biology has to do with hydrogen (H), the most abundant element in biological systems. Photons and electrons interact with the atomic electric field. With just one electron, hydrogen is all but invisible to x-rays or light. Neutrons, on the other hand, interact with nuclei, and protons have a relatively strong and negative scattering length. The isotope deuterium (D) has an even stronger scattering length, which is positive. This different sensitivity of neutrons to H and D allows for enhanced visibility of specific parts of complex biological systems through isotopic substitution. These properties are the foundation by which neutron scattering can be used to obtain precise information on the location and dynamics of H at the atomic level, as well as truly unique information on large, dynamic, multi-domain complexes at longer length and time scales. The workshop will discuss neutron crystallography, small angle scattering, diffraction, reflectometry and imaging for studying soft matter structure from the atomic to micrometer length scales and, via spectroscopic measurements, self and collective motions and excitations from sub-picosecond to microsecond timescales.

This workshop is co-funded by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate, and by the Chemistry of Life Processes Program in the Division of Chemistry and the Physics of Living Systems Program in the Division of Physics, both in the Mathematical and Physical Sciences Directorate.

Very small molecules common in interstellar space are often unstable and very reactive. For example, the compound that contains a phosphorus atom (P) bonded to a single nitrogen atom (N) was the first phosphorus compound to be detected in space, but this molecule has only fleeting existence on earth because it easily reacts with other molecules. Nonetheless, this P-N species has been proposed as a starting materials for electronic and magnetic materials. Because these molecules are so simple, but so reactive, a very important research topic is focused on how to prepare and stabilize them. In this project, funded by the Chemical Synthesis Program of the Chemistry Division, Professor Jeremy Smith of the Department of Chemistry at Indiana University, is developing a new strategy to make a variety of simple, yet highly reactive molecules. The strategy involves individually attaching two atoms (P and N) to two different metals. These species are then brought into contact and the P and N then to bind each other, while being stabilized by the metals. In addition to training students for entry into the technological workforce, the team develops materials to assist teachers and the general public in reading and interpreting scientific research.


In this project a combination of synthetic, spectroscopic and computational methods are used to assemble and characterize diatomic molecules as ligands in transition metal complexes. The modular nature of the building block strategy allows a range of diatomic molecules to be accessed, with the resulting compounds displaying unusual magnetic and reactivity properties. In collaboration with the Indiana University College of Arts and Science Office of Science Outreach, publications resulting from the research are deconstructed to assist teachers and the general public to understand and interpret the concepts, assumptions, and methods of scientific papers.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

This award is supported by the Major Research Instrumentation and the Chemistry Instrumentation Programs. Professor Michael Brown from Indiana University and colleagues Nicola Pohl, Amar Flood, Jeremy Smith and Silas Cook are acquiring a 500 MHz nuclear magnetic resonance (NMR) spectrometer. This spectrometer allows research in a variety of fields such as those that accelerate chemical reactions of significant economic importance, as well as facilitating studies of biologically relevant species. In general, NMR spectroscopy is one of the most powerful tools available to chemists for the elucidation of the structure of molecules. It is used to identify unknown substances, to characterize specific arrangements of atoms within molecules, and to study the dynamics of interactions between molecules in solution or in the solid state. Access to state-of-the-art NMR spectrometers is essential to chemists who are carrying out frontier research. The NMR studies improve understanding of synthetic organic/inorganic chemistry, materials chemistry and biochemistry. This instrument is an integral part of teaching as well as research. This broadly accessible instrumentation strengthens the regional NMR analytical infrastructure and help advance the scientific careers of many undergraduate and graduate researchers, postdocs and visiting scholars in several research groups. The spectrometer enriches the education and training experience of underrepresented undergraduate students in several NSF supported science, technology, engineering and mathematics (STEM) programs and is used to enrich activities at a local children's museum.

The award is aimed at enhancing research and education at all levels. The spectrometer is especially used for developing reactions for the preparation of organic molecules to be further studied for potential therapeutic activity and for determining the affinity of host-guest complexes. It is also employed by researchers interested in obtaining mechanistic insight into electrochemical nitrogen oxides reduction which is relevant in the production of ammonia and other industrially and physiologically important products as well as for carrying out natural product structure determination on microscale. The nuclear magnetic resonance spectrometer and associated instrumentation is also used for characterization of products obtained from high-throughput microscale reactions involving biocatalytic carbon-hydrogen functionalization and for studying NMR in catalytic design. It is also used by researchers carrying out high-throughput evaluation of glycosylation reactions which are controlled enzymatic modifications of organic molecules (especially proteins) by addition of sugar molecules.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

With the support of the Chemical Catalysis program in the Division of Chemistry, Professor Yulia Pushkar of Purdue University, Professor Jeremy Smith of Indiana University and Associate Professor Elena Jakubikova of North Carolina State University are studying catalysts that will use electrical energy for the conversion of aqueous nitrate to useful or benign products such as ammonia. Nitrate is a water pollutant that occurs largely as a result of agricultural fertilizer use. The proposed research takes a first step to addressing this problem through the development of robust and efficient electrocatalysts that to convert nitrate to desirable compounds via reductive chemistry. Scientific insights gained through these studies will likely impact the development of other electrocatalysts for other useful electrochemical conversions. Outreach activities include a partnership with the public radio program “A Moment of Science” and the development of YouTube videos on the nitrogen cycle.

This project combines the expertise of three research groups in synthetic, electrochemical, spectroscopic, and computational studies on the development of environmentally relevant electrocatalysts. A modular class of graphite-conjugated macrocyclic complexes will be characterized by a range of physical methods, including synchrotron-based X-ray spectroscopy. Together with experimentally calibrated electronic structure calculations, these data will provide information on the coordination environment, structure, and electron configuration of the metal ion. Redox properties will be characterized by electrochemical measurements, with computational methods providing detailed insights into the electronic structures of different oxidation states. In addition to standard electrochemical and computational methods for mechanistic interrogation, in situ spectroscopic characterization is expected to provide detailed information on the nature of intermediates in the catalytic cycle. Mechanistic investigations into materials that are selective for nitrate reduction will provide insight that is expected to aid in the rational design of catalysts having improved activity. Outreach activities are to including a partnership with a public radio broadcast and the development of publicly accessible educational videos are expected to reach a wide audience and inform the public broadly about electrocatalysis and its utility in developing environmentally beneficial reductive nitrogen chemistry.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

The Alabama Department of Labor has identified Diesel Technicians as a high demand occupation and estimates that 3000 technicians will be hired over the next six years. Wallace State Community College will help to meet this need by revising and enhancing its Diesel Technician program to align with industrial needs and to put students on the path to quickly earn a credential that will result in employment. The college will leverage partnerships to build new virtual training opportunities that will make the program more accessible to students who need flexible learning options. An additional partnership with the National Institute of Women in Trades, Technology, and Sciences will increase the diversity of students entering the Diesel Technology program, ultimately providing more opportunities and jobs for women and adult learners. This project has the potential to establish a pathway to employment for individuals in communities that have been disproportionately impacted by the COVID-19 pandemic in Alabama. In addition, the project can decrease the potential negative impacts on supply-chain logistics that heavily rely on diesel technology for the transportation of groceries and farming supplies.

The revised Diesel Technician program will be designed to (1) improve student learning outcomes by aligning the curriculum with National Automotive Technicians Education Foundation standards, (2) implement a hybrid online content delivery model that will enable students to complete up to 75% of their coursework from remote locations, and (3) increase the number of graduates who are women and/or from populations that are not yet equitably represented in diesel technology fields. A Diesel Technology Business and Industry Leadership Team will work with college faculty to align the curriculum with the needs of employers. Students enrolled in the program will use virtual reality training to give them access to on-the-job training that would otherwise take place in a technical workshop. A digital coach in the virtual training modules will provide immediate feedback through Conversational Artificial Intelligence. Information gathered from this project will be shared and replicated among ten Wallace State STEM Career and Technical Education workforce programs. This project is funded by the Advanced Technological Education program that focuses on the education of technicians for the advanced-technology fields that drive the nation's economy.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.