Advances in Soft Matter Mechanics by Prof. Shaofan Li, Prof. Bohua Sun (auth.)

By Prof. Shaofan Li, Prof. Bohua Sun (auth.)

"Advances in smooth subject Mechanics" is a compilation and choice of modern works in gentle topic mechanics by way of a gaggle of lively researchers within the box. the most pursuits of this booklet are first to disseminate the most recent advancements in tender topic mechanics within the box of utilized and computational mechanics, and moment to introduce smooth topic mechanics as a sub-discipline of sentimental topic physics. As a big department of soppy subject physics, delicate topic mechanics has built quickly lately. the various novel techniques mentioned during this publication are distinct, comparable to the coarse grained finite aspect procedure for modeling colloidal adhesion, entropic elasticity, meshfree simulations of liquid crystal elastomers, simulations of DNA, and so forth. The e-book 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 solar is a professor of Cape Peninsula college of expertise, South Africa.

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2 Homogenization of potential function from molecular dynamics simulation The potential functions of the coarse-grained DNA model are constructed in such a way that the coarse-grained molecule is able to represent the same configuration space as the atomistic model. , the number of particles N , the volume of the system V , and the temperature T are kept constant during the MD simulation. The Nose-Hoover method[67,68] is applied to keep the temperature of the system at 300 K, while the long-range electrostatic interactions are evaluated using Ewald sum technique[69] .

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.

48] Villa E, Balaeff A, Mahadevan L, et al. Multiscale method for simulating protein-DNA complexes. Multiscale Model Simul, 2: 527-553, 2004. [49] Starostin E L. Symmetric equilibria of a thin elastic rod with self-contacts. Phil Trans R Soc Lond A, 362: 1317-1334, 2004. [50] Chamekh M, Mani-Aouadi S, Moakher M. Modeling and numerical treatment of elastic rods with frictionless self-contact. Comput Mehtods Appl Mech Eng, 198: 3751-3764, 2009. [51] Coleman B D, Swigon D. Theory of self-contact in Kirchhoff rods with applications to supercoiling of knotted and unknotted DNA plasmids.

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