By Prof. Shaofan Li, Prof. Bohua Sun (auth.)
"Advances in smooth topic Mechanics" is a compilation and choice of contemporary works in delicate topic mechanics by way of a bunch of lively researchers within the box. the most goals of this e-book are first to disseminate the most recent advancements in tender topic mechanics within the box of utilized and computational mechanics, and moment to introduce delicate topic mechanics as a sub-discipline of soppy topic physics. As a massive department of soppy topic physics, tender subject mechanics has built swiftly in recent times. the various novel techniques mentioned during this ebook are certain, similar to the coarse grained finite aspect strategy for modeling colloidal adhesion, entropic elasticity, meshfree simulations of liquid crystal elastomers, simulations of DNA, and so forth. The ebook is meant for researchers and graduate scholars within the box of mechanics, condensed topic physics and biomaterials.
Dr. Shaofan Li is a professor of the collage of California-Berkeley, U.S.A; Dr. Bohua sunlight is a professor of Cape Peninsula college of expertise, South Africa.
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Color plot at the end of the book) practically unaffordable to investigate the DNA looping behavior. Therefore, the continuum descriptions are preferred to simulate the configuration and free energy of the DNA loop. In this study, we constructed a three-dimensional hyperelastic beam model of the DNA loop with 76 base pairs long composed of regularly repeating G – C sequences. 1, and the DNA loop is modeled by 100 Hughes-Liu beam elements[77] in DYNA3D[78] . The lac repressor itself is treated as a rigid coupler and the boundary conditions of the beam are obtained from the crystal structure of the lac repressor DNA complex[79] .
Phys Rev A, 31: 1695-1697, 1985. [69] Luty B A, Tironi I G, Vangunsteren W F. Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J Chem Phys, 103: 30143021, 1995. [70] Fukunaga H, Takimoto J, Masao D. A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions. J Chem Phys, 116: 8183-8190, 2002.
5 Multiscale homogenization for simulation of DNA molecules 29 among these superatoms, which is a function of superatom positions r. 67) ¯b and U ¯nb denotes the effective (coarse-grained) bonded and nonwhere U bonded potential functions, respectively, and other parameters with superposed bars are the parameters of coarse-grained potentials. These parameters of the effective force fields for the coarse-grained DNA model are characterized by performing the multiscale wavelet projection onto the fine-scale solutoins obtained from the full MD simulation.