المؤلفون: Alexander L. Tournier, Paul W. Fitzjohn, Paul A. Bates

المصدر: Algorithms for Molecular Biology
Algorithms for Molecular Biology, Vol 1, Iss 1, p 25 (2006)

مصطلحات موضوعية: lcsh:QH426-470, Process (engineering), Computer science, Research, Applied Mathematics, Function (mathematics), Interval (mathematics), Complex network, computer.software_genre, Set (abstract data type), lcsh:Genetics, lcsh:Biology (General), Computational Theory and Mathematics, Diffusion process, Structural Biology, Simple (abstract algebra), Data mining, Statistical physics, Diffusion (business), lcsh:QH301-705.5, Molecular Biology, computer

الوصف: Background Simulation methods can assist in describing and understanding complex networks of interacting proteins, providing fresh insights into the function and regulation of biological systems. Recent studies have investigated such processes by explicitly modelling the diffusion and interactions of individual molecules. In these approaches, two entities are considered to have interacted if they come within a set cutoff distance of each other. Results In this study, a new model of bimolecular interactions is presented that uses a simple, probability-based description of the reaction process. This description is well-suited to simulations on timescales relevant to biological systems (from seconds to hours), and provides an alternative to the previous description given by Smoluchowski. In the present approach (TFB) the diffusion process is explicitly taken into account in generating the probability that two freely diffusing chemical entities will interact within a given time interval. It is compared to the Smoluchowski method, as modified by Andrews and Bray (AB). Conclusion When implemented, the AB & TFB methods give equivalent results in a variety of situations relevant to biology. Overall, the Smoluchowski method as modified by Andrews and Bray emerges as the most simple, robust and efficient method for simulating biological diffusion-reaction processes currently available.

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f487d4d466f451c91dcff4c7081dc05d
https://doi.org/10.1186/1748-7188-1-25

المؤلفون: Alexander L. Tournier, Jeremy C. Smith

المصدر: Physical Review Letters. 91

مصطلحات موضوعية: Models, Molecular, Physics, Principal Component Analysis, Quantitative Biology::Biomolecules, Myoglobin, Protein Conformation, Water, General Physics and Astronomy, Motion (geometry), Molecular physics, Displacement (vector), Molecular dynamics, chemistry.chemical_compound, Nonlinear system, Models, Chemical, chemistry, Principal component analysis, Computer Simulation, Statistical physics

الوصف: Proteins exhibit a solvent-driven dynamical transition at 180--220 K, manifested by nonlinearity in the temperature dependence of the average mean-square displacement. Here, molecular dynamics simulations of hydrated myoglobin show that the onset of the transition at $\ensuremath{\sim}180\text{ }\text{ }\mathrm{K}$ is characterized by the appearance of a single double-well principal component mode involving a global motion of two groups of helices. As the temperature is raised a few more quasiharmonic and multiminimum components successively appear. The results indicate an underlying simplicity in the protein dynamical transition.

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9cf0048ba8d96027f29b9c3726b736eb
https://doi.org/10.1103/physrevlett.91.208106

المؤلفون: M. Ullmann, Stefan Fischer, Jeremy C. Smith, T. Becker, Frank Noé, Alexander L. Tournier

المصدر: Advances in Solid State Physics ISBN: 9783540401506

مصطلحات موضوعية: Materials science, Protein dynamics, Thermodynamics, Function (mathematics), Statistical physics, Glass transition

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::3b4e76de4fa7490730880124adcbea26
https://doi.org/10.1007/978-3-540-44838-9_48