Coarse Grained Model
Mostrando 13-24 de 36 artigos, teses e dissertações.
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13. Coarse-grained microscopic model of glass formers
We introduce a coarse-grained model for atomic glass formers. Its elements are physically motivated local microscopic dynamical rules parameterized by observables. Results of the model are established and used to interpret the measured behaviors of supercooled fluids approaching glass transitions. The model predicts the presence of a crossover from hiera
National Academy of Sciences.
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14. Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
Coarse-grained models have been extremely valuable in promoting our understanding of protein folding. However, the quantitative accuracy of existing simplified models is strongly hindered either from the complete removal of frustration (as in the widely used Gō-like models) or from the compromise with the minimal frustration principle and/or realistic prote
National Academy of Sciences.
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15. Defining Coarse-Grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models
Coarse-grained (CG) models of large biomolecular complexes enable simulations of these systems over long timescales that are not accessible for atomistic molecular dynamics (MD) simulations. A systematic methodology, called essential dynamics coarse-graining (ED-CG), has been developed for defining coarse-grained sites in a large biomolecule. The method vari
The Biophysical Society.
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16. REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics
The REACH (realistic extension algorithm via covariance Hessian) coarse-grained biomolecular simulation method is a self-consistent multiscale approach directly mapping atomistic molecular dynamics simulation results onto a residue-scale model. Here, REACH is applied to calculate the dynamics of protein-protein interactions. The intra- and intermolecular flu
The Biophysical Society.
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17. An embedded network approach for scale-up of fluctuation-driven systems with preservation of spike information
To address computational “scale-up” issues in modeling large regions of the cortex, many coarse-graining procedures have been invoked to obtain effective descriptions of neuronal network dynamics. However, because of local averaging in space and time, these methods do not contain detailed spike information and, thus, cannot be used to investigate, e.g.,
National Academy of Sciences.
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18. A coarse-grained model for a nanometer-scale molecular pump
A theory for a nanometer-scale pump based on the ratchet concept is presented. A lattice gas model with a set of moves that satisfy hydrodynamic equations is used to describe an asymmetric nanometer channel connecting two reservoirs of fluid. The channel, which is coupled to an external oscillatory (or stochastic) driving force, pumps fluid from one reservoi
National Academy of Sciences.
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19. Coarse-Grained Brownian Dynamics Simulations of the 10-23 DNAzyme
Deoxyribozymes (DNAzymes) are single-stranded DNA that catalyze nucleic acid biochemistry. Although a number of DNAzymes have been discovered by in vitro selection, the relationship between their tertiary structure and function remains unknown. We focus here on the well-studied 10-23 DNAzyme, which cleaves mRNA with a catalytic efficiency approaching that o
The Biophysical Society.
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20. Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model
The mixed-resolution elastic network model was introduced previously for computing the motions of a structure, which is described at different levels of detail in different parts, for example, with atomistic and residue-level regions. This method has proved to be an efficient tool to explore the collective dynamics of proteins with some atomistic details, wh
The Biophysical Society.
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21. A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments
Proteins fold through a variety of mechanisms. For a given protein, folding routes largely depend on the protein's stability and its native-state geometry, because the landscape is funneled. These ideas are corroborated for cytochrome c by using a coarse-grained topology-based model with a perfect funnel landscape that includes explicit modeling of the heme.
National Academy of Sciences.
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22. From residue matching patterns to protein folding topographies: General model and bovine pancreatic trypsin inhibitor
A coarse-grained model for protein-folding dynamics is introduced based on a discretized representation of torsional modes. The model, based on the Ramachandran map of the local torsional potential surface and the class (hydrophobic/polar/neutral) of each residue, recognizes patterns of both torsional conformations and hydrophobic-polar contacts, with tolera
The National Academy of Sciences.
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23. Rapid compaction during RNA folding
We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and
The National Academy of Sciences.
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24. Three-body interactions improve the prediction of rate and mechanism in protein folding models
Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Cα-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō -like Hamiltonian with native pairwise interactions only, we have found (i)
National Academy of Sciences.