12 research outputs found
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Modeling RNA, protein, and synthetic molecules using coarse-grained and all-atom representations
The aim of computational chemistry is to depict and understand the dynamics and interactions of molecular systems. In addition to increased comprehension in the physical and life sciences, this insight yields important applications to therapeutic design and materials science. In computational chemistry, molecules can be modeled in a number of representations depending on the molecular system and phenomena of interest. In this work, both simplified, coarse-grained representations and all-atom representations are used to model the interactions of RNA, cucurbituril host-guest chemistry, and cadmium selenide quantum dot binding to the Src homology 3 domain.
For RNA, a coarse-grained model was developed termed RACER (RnA CoarsE-gRained) to accurately predict RNA structure and folding free energy. After optimization to statistical potentials, RACER accurately predicted the structures of 14 RNAs with an average 4.15Å root mean square deviation (RMSD) to the experimental structure. Further, RACER captured the sequence-specific variation in folding free energy for a set of 6 RNA hairpins and 5 RNA duplexes, with a R² correlation of 0.96 to experiment.
The binding free energies of a cucurbituril host with 14 guests were computed using a polarizable force field and the free energy techniques of Bennett acceptance ratio and the orthogonal space random walk. The polarizable force field captured binding accurately, yet unexpectedly, the orthogonal space random walk method converged slowly, albeit at still reduced computational expense to the Bennett acceptance ratio.
Lastly, the nanotoxicity effects of trioctylphosphine oxide coated cadmium selenide quantum dots are investigated with the model Src homology 3 protein domain in complex with its native proline rich motif ligand. With increasing quantum dot concentration, there is an increasing preference for the quantum dots to bind to the proline rich motif active site, inhibiting Src homology 3 function.Biomedical Engineerin
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field
Program and Proceedings: The Nebraska Academy of Sciences 1880-2010
PROGRAM
FRIDAY, APRIL 23, 2010
REGISTRATION FOR ACADEMY, Lobby of Lecture wing, Olin Hall
Aeronautics and Space Science, Session A, Olin 249
Aeronautics and Space Science, Session B, Olin 224
Chemistry and Physics, Section A, Chemistry, Olin A
Collegiate Academy, Biology Session A, Olin B
Collegiate Academy, Chemistry and Physics, Session A, Olin 324
Biological and Medical Sciences, Session A, Olin 112
Biological and Medical Sciences, Session B, Smith Callen Conference Center
Chemistry and Physics, Section B, Physics, Planetarium
History and Philosophy of Science, Olin 325
Junior Academy, Judges Check-In, Olin 219
Junior Academy, Senior High REGISTRATION, Olin Hall Lobby
NWU Health and Sciences Graduate School Fair, Olin and Smith Curtiss Halls
Junior Academy, Senior High Competition, Olin 124, Olin 131
Aeronautics and Space Science, Poster Session, Olin 249
Teaching of Science and Math, Olin 325
MAIBEN MEMORIAL LECTURE, OLIN B
Dr. Mark Greip, Vice-Chair, Department of Chemistry, University of Nebraska-Lincoln
LUNCH, PATIO ROOM, STORY STUDENT CENTER
(pay and carry tray through cafeteria line, or pay at NAS registration desk)
Aeronautics Group, Conestoga Room
Anthropology, Olin 111
Biological and Medical Sciences, Session C, Olin 112
Biological and Medical Sciences, Session D, Smith Callen Conference Center
Chemistry and Physics, Section A, Chemistry, Olin A
Chemistry and Physics, Section B, Physics, Planetarium
Collegiate Academy, Biology Session A, Olin B
Collegiate Academy, Biology Session B, Olin 249
Collegiate Academy, Chemistry and Physics, Session A, Olin 324
Junior Academy, Judges Check-In, Olin 219
Junior Academy, Junior High REGISTRATION, Olin Hall Lobby
Junior Academy, Senior High Competition, (Final), Olin 110
Earth Science, Olin 224
Junior Academy, Junior High Competition, Olin 124, Olin 131
NJAS Board/Teacher Meeting, Olin 219
Junior Academy, General Awards Presentations, Smith Callen Conference Center
BUSINESS MEETING, OLIN B
SOCIAL HOUR for Members, Spouses, and Guests
First United Methodist Church, 2723 N 50th Street, Lincoln, NE
ANNUAL BANQUET and Presentation of Awards and Scholarships
First United Methodist Church, 2723 N 50th Street, Lincoln, N
Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems
We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.Peer ReviewedPostprint (published version
Microscopy Conference 2021 (MC 2021) - Proceedings
Das Dokument enthält die Kurzfassungen der Beiträge aller Teilnehmer an der Mikroskopiekonferenz "MC 2021"