Gotowe bibliografie tematyczne / Funnel energy landscapes

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Gotowa bibliografia na temat „Funnel energy landscapes”

Autor: Grafiati

Data publikacji: 3 czerwca 2025

Data aktualizacji: 31 lipca 2025

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Artykuły w czasopismach na temat "Funnel energy landscapes"

Wolynes, Peter G. "Energy landscapes and solved protein–folding problems." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 363, no. 1827 (2004): 453–67. http://dx.doi.org/10.1098/rsta.2004.1502.

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Energy–landscape theory has led to much progress in protein folding kinetics, protein structure prediction and protein design. Funnel landscapes describe protein folding and binding and explain how protein topology determines kinetics. Landscape–optimized energy functions based on bioinformatic input have been used to correctly predict low–resolution protein structures and also to design novel proteins automatically.

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Elenewski, Justin E., Kirill A. Velizhanin, and Michael Zwolak. "A spin-1 representation for dual-funnel energy landscapes." Journal of Chemical Physics 149, no. 3 (2018): 035101. http://dx.doi.org/10.1063/1.5036677.

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Hall, Kyle Wm, Sheelagh Carpendale, and Peter G. Kusalik. "Evidence from mixed hydrate nucleation for a funnel model of crystallization." Proceedings of the National Academy of Sciences 113, no. 43 (2016): 12041–46. http://dx.doi.org/10.1073/pnas.1610437113.

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The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological simil

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Wolynes, P. G. "Recent successes of the energy landscape theory of protein folding and function." Quarterly Reviews of Biophysics 38, no. 4 (2005): 405–10. http://dx.doi.org/10.1017/s0033583505004075.

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Protein folding and binding can be understood using energy landscape theory. When seeming deviations from the predictions of the funnel hypothesis are found, landscape theory helps us locate the cause. Sometimes the deviation reflects symmetry effects, allowing extra degeneracies to occur. Such effects seem to explain some kinetic anomalies in helical bundles. When binding processes were found to use apparently non-funneled landscapes this was traced to an inadequate understanding of biomolecular forces. The discrepancy allowed the discovery of new water-mediated forces – some of which act bet

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Müller, C. L., and I. F. Sbalzarini. "Energy Landscapes of Atomic Clusters as Black Box Optimization Benchmarks." Evolutionary Computation 20, no. 4 (2012): 543–73. http://dx.doi.org/10.1162/evco_a_00086.

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We present the energy minimization of atomic clusters as a promising problem class for continuous black box optimization benchmarks. Finding the arrangement of atoms that minimizes a given potential energy is a specific instance of the more general class of geometry optimization or packing problems, which are generally NP-complete. Atomic clusters are a well-studied subject in physics and chemistry. From the large set of available cluster optimization problems, we propose two specific instances: Cohn-Kumar clusters and Lennard-Jones clusters. The potential energies of these clusters are govern

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DOU, XIANGHUA, and JIHUA WANG. "FOLDING FREE ENERGY LANDSCAPE OF THE DECAPEPTIDE CHIGNOLIN." Modern Physics Letters B 22, no. 31 (2008): 3087–98. http://dx.doi.org/10.1142/s0217984908017606.

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Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four

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Oliveberg, Mikael, and Peter G. Wolynes. "The experimental survey of protein-folding energy landscapes." Quarterly Reviews of Biophysics 38, no. 3 (2005): 245–88. http://dx.doi.org/10.1017/s0033583506004185.

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1. Introduction 22. The macroscopic and microscopic views of protein folding 22.1 The macroscopic view: the experimental folding free-energy profile 22.2 The microscopic view: an underlying energy landscape 33. The micro to macro projection: from an energy landscape to a free-energy profile 64. Global features of the protein folding transition-state ensemble 124.1 Overall transition state location β[Dagger]: a measure of compactness 124.2 What makes folding so robust ? 135. Structural characterization of the transition-state ensemble 165.1 Insights from ϕ-value analysis 166. Deviations from id

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Stumpff-Kane, Andrew W., and Michael Feig. "A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes." Proteins: Structure, Function, and Bioinformatics 63, no. 1 (2006): 155–64. http://dx.doi.org/10.1002/prot.20853.

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Angell, C. Austen. "Energy landscapes for cooperative processes: nearly ideal glass transitions, liquid–liquid transitions and folding transitions." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 363, no. 1827 (2004): 415–32. http://dx.doi.org/10.1098/rsta.2004.1500.

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We describe basic phenomenology in the physics of supercooling liquids at constant volume (most simulations), and at constant pressure (most laboratory experiments) before focusing attention on the exceptional cases that exhibit liquid–liquid phase transitions on constant–pressure cooling. We give evidence for point defects in glasses and liquids near T g . Models based on defects predict transitions with density gaps in constant–pressure systems. We describe the energy landscape representation of such systems. Water, in these terms, is post–critical, and its nearly ideal glass formation can b

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ElSawy, Karim M., Leo S. D. Caves, and Reidun Twarock. "Polyomaviridae Assembly Polymorphism from an Energy Landscape Perspective." Computational and Mathematical Methods in Medicine 9, no. 3-4 (2008): 245–56. http://dx.doi.org/10.1080/17486700802167983.

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Polyomaviridae assemblein vitrointo different aggregates depending on experimental conditions. We use an energy landscape approach using empirical energy calculations to quantify how the formation of these different aggregates depends on pH, the presence of bound calcium ions and disulfide linkages. Computations are carried out for SV40, a member of the Polyomaviridae family and are based on the binding free energy landscape of three distinct trimers of pentamers that correspond to the different bonding configurations between the capsid proteins observed in its crystal structure. Our computati

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Rozprawy doktorskie na temat "Funnel energy landscapes"

Cho, Samuel Sung-Il. "Energy landscapes for protein folding, binding, and aggregation simple funnels and beyond /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3244327.

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Thesis (Ph. D.)--University of California, San Diego, 2007.<br>Title from first page of PDF file (viewed February 23, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 99-106).

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Klemm, Konstantin, Christoph Flamm, and Peter F. Stadler. "Funnels in Energy Landscapes." 2008. https://ul.qucosa.de/id/qucosa%3A33087.

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Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a “folding funnel” that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a “folding funnel” as it is discussed in the protein folding literature.

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Części książek na temat "Funnel energy landscapes"

Lähteenmäki, Maria, Oona Ilmolahti, Outi Manninen, and Sari Stark. "Chapter 6. Cultural Nature in Mid-Lappish Reindeer Herding Communities." In Green Development or Greenwashing? The White Horse Press, 2023. http://dx.doi.org/10.3197/63824846758018.ch06.

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Our research task is to present and analyse features of the local human-nature and human-reindeer relations in the historical timespan of the twentieth century and in the context of cultural nature in the historical Forest Sami area of Finnish Mid-Lapland. By cultural nature we refer to the different meanings and attributes groups and individuals give and have given to their surrounding natural environment with its fauna, flora, and waterways. The question is viewed through environmental changes and the meanings connected to reindeer roundups (corrals) and roundup places as an example of human

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Succi, Sauro. "Free-Energy Funnels." In Sailing the Ocean of Complexity. Oxford University PressOxford, 2022. http://dx.doi.org/10.1093/oso/9780192897893.003.0014.

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Abstract Where we describe the structure of the free energy landscape that guides the search of the right locations of Hyperland where “things work” (the Ozland valleys). This comes through a subtle conspiracy between Order and Disorder, which shapes up funnel-like valleys where free-energy is minimised while still keeping enough order for organised structures to survive and deliver their vital functions. Where it also discussed the “miracle” by which these valleys are reached on time (they are either reached on time or invain).

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Streszczenia konferencji na temat "Funnel energy landscapes"

Chou, Chung-I., Michio Tokuyama, Irwin Oppenheim, and Hideya Nishiyama. "The Double-Funnel Energy Landscape of an Off-Lattice Model Protein: A Knowledge-Based Evolution Algorithm Approach." In COMPLEX SYSTEMS: 5th International Workshop on Complex Systems. AIP, 2008. http://dx.doi.org/10.1063/1.2897853.

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McDonald, Margot, Stacey White, Clare Olsen, et al. "The Campus as a Living Laboratory: Post-Occupancy Evaluation and a Digital Repository as a Teaching Tool." In AIA/ACSA Intersections Conference. ACSA Press, 2015. http://dx.doi.org/10.35483/acsa.aia.inter.15.5.

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In 2013-14, the California State University system funded 23 grants on 14 campuses in an effort to spur innovation in sustainability. The funding for these grants came from leveraging $250,000 of system-wide resources slated for energy efficiency improvements towards the support of educational initiatives that bridged facilities and the academy2. The intent of this initiative was to inspire applied research that tied teaching and learning to campus buildings, landscapes, and infrastructure in ways that would inform future project investments related to cost and energy savings as well as sustai

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Raporty organizacyjne na temat "Funnel energy landscapes"

Barbose, Galen L., Charles Goldman, and Jeff Schlegel. The Shifting Landscape of Ratepayer-Funded Energy Efficiency in the U.S. Office of Scientific and Technical Information (OSTI), 2009. http://dx.doi.org/10.2172/970817.

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Scarrott, Rory, Cathal O'Mahony, Michael Sweeney, et al. KETmaritime: Setting course to energise maritime uptake of Key Enabling Technologies. University College Cork, 2020. http://dx.doi.org/10.33178/10468.10928.

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Key Enabled Technologies(KETs) have the potential to impact on many aspects of society, whilst transforming European industrial competitiveness at the local, national, and global scales. Studies funded by the European Commission have shown that European advances in six technology areas would not only enhance the leadership and competitiveness of European business, but also drive advances across Europe’s business sectors and society. Despite their applicability across sectors, KETs represent a change, and a new manner of moving forward. Business and society view change both positively, welcomin

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