A test problem for molecular dynamics integrators

We derive a test problem for evaluating the ability of time-steppingmethods to preserve the statistical properties of systems inmolecular dynamics. We consider a family of deterministic systemsconsisting of a finite number of particles interacting on acompact interval. The particles are given random initial conditionsand interact through instantaneous energy- and momentum-conservingcollisions. As the number of particles, the particle density,and the mean particle speed go to infinity, the trajectory ofa tracer particle is shown to converge to a stationary Gaussianstochastic process. We approximate this system by one describedby a system of ordinary differential equations and provide numericalevidence that it converges to the same stochastic process. Wesimulate the latter system with a variety of numerical integrators,including the symplectic Euler method, a fourth-order Runge-Kuttamethod, and an energyconserving step-and-project method. Weassess the methods' ability to recapture the system's limitingstatistics and observe that symplectic Euler performs significantlybetter than the others for comparable computational expense.     

Structural optimization with parameter-transfer finite element

A mathematical method to solve structural problems, using parameter-transfer finite elements (P-TFE) was recently proposed by the authors [1] [2] [3]. The proposed transfer finite element approach is able to create a mathematical model of a structure, taking into account directly the whole behaviour of the structure under dynamic, aerodynamic, and thermal actions, and not by assembling, in a separate fashion, the stiffness and the mass matrix on one side and the external load vector as performed by the classical finite element procedure.The purpose of this paper is to apply the above methodology to optimization problems, in particular to obtain the minimum structural weight for a beam, under primary constraints on buckling load or natural frequencies.The use of P-TFE in the field of structural optimization overcomes most difficulties of the usual techniques of solution and the element is particularly useful in the evaluation of the sensitivity matrix.The formulation of the optimization problem based on P-TFE is presented and some applications are studied. The numerical results obtained are compared with other existing methodologies and briefly discussed.

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Sommario Gli autori hanno già proposto un metodo per studiare problemi strutturali [1] [2] [3], introducendo una nuova metodologia di discretizzazione, basata sull'impiego di elementi finiti di trasferimento, funzioni esplicite di un parametro, indicati come P-TFE. Tali elementi sono in grado di rappresentare, in similitudine alla funzione di trasferimento, il comportamento completo dell'elemento strutturale in esame, soggetto ad azioni dinamiche, aerodinamiche e termiche; sono parimenti in grado di produrre, in similitudine al metodo degli elementi finiti, un modello matematico discreto di un continuo.Scopo del presente lavoro è di applicare detta metodologia a problemi di ottimizzazione, in particolare alla ricerca del minimo peso per una trave che mantenga inalterate le sue caratteristiche di carico critico o le frequenze naturali di vibrazione.Vengono quindi presentati alcuni risultati numerici dei casi esaminati e confrontati con quelli ottenuti da altri autori con l'impiego di altre metodologie.

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List of Symbols {B} _m vector of the generalized state variables - {C} _m vector of integration constants - [I] unit matrix - EI bending stiffness - A cross-sectional area - u adimensional thickness - l beam length - M,M bending moment - [N] _m shape function ofm-th order - [N*] shape function atx ₀ - P axial load - [R] _i transfer matrix of thei-th element - T,T shear force - w transverse displacement - x adimensional independent variable - x ₀ value ofx at the left of the element - {Y} vector of state variables - {Y*} imposed condition atx ₀ - _0m Kronecker delta with the first pedix always set equal to zero - normalized eigenfrequency - normalized buckling load - mass density     

Conformational analysis of 5,6-dihydropyrimidine and its derivatives

The equilibrium geometry and inversion barriers of 5,6-dihydropyrimidine, 6,7-dihydroazolopyrimidines with node nitrogen atoms and their alkyl (Me, Et, Prⁱ, Bu^t) and phenyl derivatives were calculated using a molecular mechanics approach. Annelation with azole cycles and the introduction of substituents have a slight effect on the equilibrium conformation of the dihydrocycle (distorted sofa). Alkyl substutuents at saturated carbons have an essentially equatorial orientation in 5,6-dihydropyridimine derivatives and are axial in the annelated analogs. On the other hand, the equatorial conformers are more stable in phenyl derivatives of dihydroazolopyrimidines. Factors determining the relative stability of conformers were analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 487–491, March, 1995.     

Alcohols,ethers, carbohydrates,and related compounds. II. The anomeric effect

The anomeric effect has been studied for a variety of compounds using the MM4 force field, and also using MP2/6-311++G(2d,2p) ab initio calculations and experimental data for reference purposes. Geometries and energies, including conformational, rotational barriers, and heats of formation were examined. Overall, the agreement of MM4 with the experimental and ab initio data is good, and significantly better than the agreement obtained with the MM3 force field. The anomeric effect is represented in MM4 by various explicit terms in the force constant matrix. The bond length changes are accounted for with torsion-stretch elements. The angle changes are accounted for with torsion-bend elements. The energies are taken into account with a number of torsional terms in the usual way. A torsion-torsion interaction is also of some importance. With all of these elements included in the calculation, the MM4 results now appear to be adequately accurate. The heats of formation were examined for a total of 12 anomeric compounds, and the experimental values were fit by MM4 with an RMS error of 0.42 kcal/mol.     

A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

In this paper, by capturing the atomic information and reflecting the behaviour governed by the nonlinear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes (SWCNT’s) is established to describe the nonlinear stress-strain curve of SWCNT’s and to predict both the elastic properties and breaking strain of SWCNT’s during tensile deformation. An analysis based on the virtual internal bond (VIB) model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT’s. The project supported by the National Natural Science Foundation of China (10121202, 90305015 and 10328203), the Key Grant Project of Chinese Ministry of Education (0306) and the Research Grants Council of the Hong Kong Special Administrative Region, China (HKU 7195/04E).     

Supersymmetric classical mechanics

The purpose of the paper is to construct a supersymmetric Lagrangian within the framework of classical mechanics which would be regarded as a candidate for passage to supersymmetric quantum mechanics. The authors felicitate Prof. D S Kothari on his eightieth birthday and dedicate this paper to him on this occasion.     

Lattice-BGK approach to simulating granular flows

Many continuum theories for granular flow produce an equation of motion for the fluctuating kinetic energy density (granular temperature) that accounts for the energy lost in inelastic collisions. Apart from the presence of an extra dissipative term, this equation is very similar in form to the usual temperature equation in hydrodynamics. It is shown how a lattice-kinetic model based on the Bhatnagar-Gross-Krook (BGK) equation that was previously derived for a miscible two-component fluid may be modified to model the continuum equations for granular flow. This is done by noting that the variable corresponding to the concentration of one species follows an equation that is essentially analogous to the granular temperature equation. A simulation of an unforced granular fluid using the modified model reproduces the phenomenon of clustering instability, namely the spontaneous agglomeration of particles into dense clusters, which occurs generically in all granular flows. The success of the continuum theory in capturing the gross features of this basic phenomenon is discussed. Some shear flow simulations are also presented.     

N = 4 Supersymmetric Morse Oscillator and Its Spectrum-Generating Algebra

In this paper N = 4 supersymmetry of generalized Morse oscillators in one dimension is studied. Both bound states and scattering states of its four superpartner Hamiltonians are analyzed by using unitary irreducible representations of the noncompact Lie algebra su(1,1). The spectrum-generating algebra governing the Hamiltonian of the N = 4 supersymmetric Morse oscillator is shown to be connected with the realization of Lie superalgebra osp(1,2)or B(0,1) in terms of the variables of a supersymmetric two-dimensional harmonic oscillator.