Designing generalized statistical ensembles for numerical simulations of biopolymers.
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Summary
The study of the structural properties of two simple models: a bead-and-spring model of polyethylene with independent hindered torsions and an all-atom model of alanine and glycine oligomers with 12 amino acids in vacuum are presented.
- Type
- dissertation
- Published
- 2004-11-15
- Cited by
- 25
- References
- 53
- OpenAlex
- https://openalex.org/W15549958
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:17858056
Keywords
Winery, Cape, Effluent, Geography, Environmental protection
References
- The Explicit Density Functional and Its Connection with Entropy Maximization
- Theory of helix-coil transitions in biopolymers
- Conformation of Carbohydrates
- Conformational Theory of Large Molecules: The Rotational Isomeric State Model in Macromolecular Systems
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- Encyclopedia of Optimization
- Introduction to protein structure
- Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence
- Principles of Nucleic Acid Structure
- Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
- Review of "Adaptation in Natural and Artificial Systems by John H. Holland", The U. of Michigan Press, 1975
- A constrained maximum entropy method in polymer statistics
- All-atom generalized-ensemble simulations of small proteins.
- Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
- Determination of a transition state at atomic resolution from protein engineering data.
- Multioverlap simulations for transitions between reference configurations.
- Statistical mechanics of chain molecules
- Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes
- Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations.
- Global optimization by energy landscape paving.
Cited by
- Ab initio simulations of Cu binding sites on the N-terminal region of prion protein
- THE HATSOPOULOS–GYFTOPOULOS RESOLUTION OF THE SCHRÖDINGER–PARK PARADOX ABOUT THE CONCEPT OF "STATE" IN QUANTUM STATISTICAL MECHANICS
- Modeling of the Zn2+ binding in the 1-16 region of the amyloid beta peptide involved in Alzheimer's disease.
- Combined EPR and molecular modeling study of PPI dendrimers interacting with copper ions: effect of generation and maltose decoration.
- Is Cu involved in prion oligopeptide stability? Experiments and numerical simulations
- Molecular statistics of cytochrome c: structural plasticity and molecular environment
- Modeling H3 histone N-terminal tail and linker DNA interactions.
- Zn induced structural aggregation patterns of β-amyloid peptides by first-principle simulations and XAS measurements.
- Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels.
- The Notion of Scientific Knowledge in Biology
- Insights into the mechanisms of amyloid formation of Zn(II)-Ab11-28: pH-dependent zinc coordination and overall charge as key parameters for kinetics and the structure of Zn(II)-Ab11-28 aggregates.
- Modelling protein-DNA interactions in chromatin
- Structural Insights into the Osteopontin-Aptamer Complex by Molecular Dynamics Simulations
- Towards High-Throughput Modelling of Copper Reactivity Induced by Structural Disorder in Amyloid Peptides.
- Computational models explain how copper binding to amyloid-β peptide oligomers enhances oxidative pathways.
- SARS-CoV-2 Virion Stabilization by Zn Binding
- Implementations of replica-permutation and replica sub-permutation methods into LAMMPS
- Modelling Protein Plasticity: The Example of Frataxin and Its Variants
- Probing protein stability: towards a computational atomistic, reliable, affordable, and improvable model
- PROCEEDINGS OF THE 3RD INTERNATIONAL CONFERENCE ON MOLECULAR SIMULATION Learning chemistry with multiple first-principles simulations
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