Topic
Molecular models of DNA
About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.
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TL;DR: YUP is created, a general-purpose program for coarse-grained and multi-scaled models that extends the Python programming language by adding new data types and finds that objects are easy to modify, extend and redeploy.
Abstract: Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily.
110 citations
TL;DR: It is found that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules.
104 citations
TL;DR: In this paper, the Peyrard-Bishop DNA dynamic model equation is studied analytically by hyperbolic and exponential ansatz methods and numerically by finite difference method.
Abstract: In this work, we introduce a numerical and analytical study of the Peyrard-Bishop DNA dynamic model equation. This model is studied analytically by hyperbolic and exponential ansatz methods and numerically by finite difference method. A comparison between the results obtained by the analytical methods and the numerical method is investigated. Furthermore, some figures are introduced to show how accurate the solutions will be obtained from the analytical and numerical methods.
103 citations
TL;DR: In this paper, the authors studied the equilibrium formation of DNA catenanes to assess the conformational properties of supercoiled DNA as a function of ionic conditions and supercoiling density.
94 citations
TL;DR: Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's "universality class" strongly suggests the presence of an "underlying" continuous transition.
Abstract: We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's "universality class" strongly suggests the presence of an "underlying" continuous transition.
93 citations