A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded...

Two major branches of engineering mechanics are fluid mechanics and structural mechanics, with many practical problems involving the effect of the first on the second. An example is the design of an aircraft's wings to bend within reasonable limits without breaking under the action of lift forces exerted by the air flowing over them; another is the maintenance of the structural integrity of a d...

In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the ca...

In this paper, a generalized particle system (GPS) method, a general method to describe multiple strong form representation based particle methods is described. Gradient, divergence, and Laplacian operators used in various strong form based particle method such as moving particle semi-implicit (MPS) method, smooth particle hydrodynamics (SPH), and peridynamics, can be described by the GPS metho...

The molecular electrostatic potential inside the potassium channel protein from Streptomyces liVidans has been investigated using linear scaling semiempirical quantum chemical method, for a variety of geometries, with and without solvating water molecules. The results are compared with those given by a number of popular molecular mechanics force-fields. The difference between the quantum and mo...

Graphene is a new class of two-dimensional carbon nanostructure, which holds great promise for the vast applications in many technological fields. It would be one of the prominent new materials for the next generation nano-electronic devices. In this paper the influence of various vacancy defects on the critical buckling load of a single-layered graphene nanosheet is investigated. The nanosheet...

In the light of computational chemistry, based on morpholinium cation-based Ionic Liquid, their different types of physical, chemical, and biological properties is highlighted. The physical properties are evaluated through the Density Functional Theory (DFT) of Molecular Mechanics and also examine the chemical and biological properties. The difference between Highest Occupied Molecular Orbital ...

The actin microfilament (F-actin) is a structural and functional component of the cell cytoskeleton. Notwithstanding the primary role it plays for the mechanics of the cell, the mechanical behaviour of F-actin is still not totally explored. In particular, the relationship between the mechanics of F-actin and its molecular architecture is not completely understood. In this study, the mechanical ...