Flexible effective fragment QM/MM method: validation through the challenging tests

A new version of the QM/MM method, which is based on the effective fragment potential (EFP) methodology [Gordon, M. et al., J Phys Chem A 2001, 105, 293] but allows flexible fragments, is verified through calculations of model molecular systems suggested by different authors as challenging tests for QM/MM approaches. For each example, the results of QM/MM calculations for a partitioned system are compared to the results of an all-electron ab initio quantum chemical study of the entire system. In each case we were able to achieve approximately similar or better accuracy of the QM/MM results compared to those described in original publications. In all calculations we kept the same set of parameters of our QM/MM scheme. A new test example is considered when calculating the potential of internal rotation in the histidine dipeptide around the C(alpha)bond;C(beta) side chain bond.     

Implementation of a molecular dynamics approach with rigid fragments to simulation of chemical reactions in biomolecular systems

We describe a new implementation of the molecular dynamics method aimed at simulation of the properties of biomolecular systems in which chemical reactions are possible. The quantum mechanical/molecular mechanical method based on the effective fragment potential theory is used for calculating the energies and forces along trajectories. Due to specific features of the effective fragment theory, the behavior of the molecular mechanical subsystem is described by rigid body dynamics. The method has been applied to simulation of proton transfer along the chain of water molecules inside the gramicidin channel.     

Measurement of the beta+ and orbital electron-capture decay rates in fully ionized, hydrogenlike, and heliumlike 140Pr ions

We report on the first measurement of the beta+ and orbital electron-capture decay rates of 140Pr nuclei with the simplest electron configurations: bare nuclei, hydrogenlike, and heliumlike ions. The measured electron-capture decay constant of hydrogenlike 140Pr58+ ions is about 50% larger than that of heliumlike 140Pr57+ ions. Moreover, 140Pr ions with one bound electron decay faster than neutral 140Pr0+ atoms with 59 electrons. To explain this peculiar observation one has to take into account the conservation of the total angular momentum, since only particular spin orientations of the nucleus and of the captured electron can contribute to the allowed decay.     

Mechanisms of enzymatic hydrolysis of nucleoside triphosphates by quantum and molecular mechanics

Results of simulation of the mechanism of hydrolysis of adenosine triphosphate and guanosine triphosphate in protein matrices, as well as of deprotonated methyl triphosphate in water clusters by quantum and molecular mechanics with separation of the reaction system into conformationally flexible effective fragments are discussed.     

Solving the Stress Problem for Hollow Cylinders with Corrugated Elliptical Cross Section

The paper presents an approach based on three-dimensional elastic equations to solve boundary-value stress problems for hollow cylinders with corrugated elliptical cross section. Discrete Fourier series are used to make the problem one-dimensional and then to solve it by the stable discrete orthogonalization method. Solutions for cylinders of different thicknesses are presented     

Hybrid Equilibrium Finite Elements for Wave Diffraction Problems

Hybrid equilibrium finite elements based on the direct approximation of the domain stress and boundary displacement fields are presented. The structure is divided into a far field, which is considered as an infinite super element, and a near field, which is in turn discretized into finite elements. The displacements in the domains of typical finite elements are obtained from the assumed domain stress field by using the dynamic equilibrium equations. The Helmholtz equation is satisfied in the domain of the infinite super element, and the domain stress fields are associated with elastic and compatible displacements. The resulting governing system is symmetric, sparse, and, if well done, positive. Numerical applications are presented to illustrate the performance of the formulation     

Stress analysis of flexible noncircular cylindrical shells with hinged edges for different critical loads

An analytic nonlinear boundary-value solution is found and used in analysis of the precritical and postcritical stress states of a flexible long cylindrical shell with variable curvature and hinged longitudinal edges under nonuniform loading __________ Translated from Prikladnaya Mekhanika, Vol. 42, No. 2, pp. 43–50, February 2006.     

Analysis of the Deformation of a Hinged Flexible Noncircular Long Cylindrical Shell Under a Nonuniform Load

The nonlinear problem on deformation of a hinged flexible long noncircular cylindrical shell under nonuniform loading is solved exactly. The solution consists of two relations in terms of elementary functions. Plots are presented     

Solid mechanics 2008

Solid Mechanics 2008

Solid mechanics 2008     

Spline-approximation solution of problems of the statics of orthotropic shallow shells with variable parameters

An approach to the solution of problems of the statics of shallow orthotropic shells is proposed. It is based on reducing a two-dimensional boundary value problem to a one-dimensional one using the spline-collocation method and solution of the problem by the stable numerical method of discrete orthogonalization. Solutions are presented for problems on the stress state of orthotropic shells of double curvature for several values of the elastic constants of the material. Translated from Prikladnaya Mekhanika, Vol. 36, No. 7, pp. 60–66, July, 2000.