Home About us Contact
|
Home About us Contact | ||
|
|
||
Rotational Degrees (rotational + degree)
Selected AbstractsStatistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2003Vladimir Hnizdo Abstract A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical,mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical,mechanical properties corresponding to a given internal rotational degree of freedom are educed. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1172,1183, 2003 [source] Lower and upper bound estimation of isotropic and orthotropic fracture mechanics problems using elements with rotational degrees of freedomINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 5 2008Antoinette de Klerk Abstract We use Rice's path-independent J integral, as well as its dual, the I* integral, to estimate lower and upper bounds of the stress intensity factor K in linear elastic fracture mechanics problems. The elements used contain rotational degrees of freedom, and are derived from the correct energy principles to guarantee path independence of the integrals. That is, the displacement-based elements used in calculating the J integral are derived from the principle of potential energy; the assumed stress elements used in calculating the I* integral are derived from complementary energy principles. For lower bound estimation in particular, elements with drilling degrees of freedom are advantageous, due to their superior accuracy. Numerical results are presented for isotropic and orthotropic mode I and mode II fracture mechanics problems. In addition, we reflect on suitable finite element integration schemes, and applicable values for the problem dependent penalty parameter , which is used in deriving the elements. Copyright © 2006 John Wiley & Sons, Ltd. [source] A Hermite reproducing kernel approximation for thin-plate analysis with sub-domain stabilized conforming integrationINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 3 2008Dongdong Wang Abstract A Hermite reproducing kernel (RK) approximation and a sub-domain stabilized conforming integration (SSCI) are proposed for solving thin-plate problems in which second-order differentiation is involved in the weak form. Although the standard RK approximation can be constructed with an arbitrary order of continuity, the proposed approximation based on both deflection and rotation variables is shown to be more effective in solving plate problems. By imposing the Kirchhoff mode reproducing conditions on deflectional and rotational degrees of freedom simultaneously, it is demonstrated that the minimum normalized support size (coverage) of kernel functions can be significantly reduced. With this proposed approximation, the Galerkin meshfree framework for thin plates is then formulated and the integration constraint for bending exactness is also derived. Subsequently, an SSCI method is developed to achieve the exact pure bending solution as well as to maintain spatial stability. Numerical examples demonstrate that the proposed formulation offers superior convergence rates, accuracy and efficiency, compared with those based on higher-order Gauss quadrature rule. Copyright © 2007 John Wiley & Sons, Ltd. [source] Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interactionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010Ling Wang Abstract Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Singularity-Free Brownian Dynamics Analyses of Rotational Dynamics: Non-Spherical Nanoparticles in SolutionMACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2005Stine Nalum Naess Abstract Summary: From kinetic theory we have rigorously derived singularity-free Brownian dynamics analyses of nanoparticle rotational dynamics. The rigid non-spherical nanoparticles incorporate all three rotational degrees of freedom. This was achieved by using the components of Cartesian rotation vectors as the generalized coordinates describing angular orientation. The new results constitute an important advance compared to the situation when Eulerian angles specify angular orientation. Our finding eliminates one of the main longstanding obstacles to detailed studies of nanoparticle rotational dynamics in the diffusion time domain. The described formalism is applicable to a wide range of nanoparticle systems including liquid crystals, biopolymers, and colloids. [source] Does the ligand-biopolymer equilibrium binding constant depend on the number of bound ligands?,BIOPOLYMERS, Issue 11 2010Daria A. Beshnova Abstract Conventional methods, such as Scatchard or McGhee-von Hippel analyses, used to treat ligand-biopolymer interactions, indirectly make the assumption that the microscopic binding constant is independent of the number of ligands, i, already bound to the biopolymer. Recent results on the aggregation of aromatic molecules (Beshnova et al., J Chem Phys 2009, 130, 165105) indicated that the equilibrium constant of self-association depends intrinsically on the number of molecules in an aggregate due to loss of translational and rotational degrees of freedom on formation of the complex. The influence of these factors on the equilibrium binding constant for ligand-biopolymer complexation was analyzed in this work. It was shown that under the conditions of binding of "small" molecules, these factors can effectively be ignored and, hence, do not provide any hidden systematic error in such widely-used approaches, such as the Scatchard or McGhee-von Hippel methods for analyzing ligand-biopolymer complexation. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 932,935, 2010. [source] | |||||||||||||