Determining the electronic structure and chemical potentials of molecules in solution

A simulation scheme is proposed for determining the excess chemical potential of a substance in solution. First, a Monte Carlo simulation is performed with classical models for solute and solvent molecules. A representative sample of these configurations is then used in a hybrid quantum/classical (QM/MM) calculation, where the solute is treated quantum-mechanically, and the average electronic structure is used to construct an improved classical model. This procedure is iterated to self-consistency in the classical model, which in practice is attained in one or two steps, depending on the quality of the initial guess. The excess free energy of the molecule within the QM/MM approach is determined relative to the classical model using thermodynamic perturbation theory with a cumulant expansion. The procedure provides a method of constructing classical point charge models appropriate for the solution and gives a measure of the importance of solvent fluctuations.

Variational Monte Carlo study of core-valence separation schemes for first-row atoms and positive ions /

All-electron partitioning of wave functions into products ^core^vai of core and valence parts in orbital space results in the loss of core-valence antisymmetry, uncorrelation of motion of core and valence electrons, and core-valence overlap. These effects are studied with the variational Monte Carlo method using appropriately designed wave functions for the first-row atoms and positive ions. It is shown that the loss of antisymmetry with respect to interchange of core and valence electrons is a dominant effect which increases rapidly through the row, while the effect of core-valence uncorrelation is generally smaller. Orthogonality of the core and valence parts partially substitutes the exclusion principle and is absolutely necessary for meaningful calculations with partitioned wave functions. Core-valence overlap may lead to nonsensical values of the total energy. It has been found that even relatively crude core-valence partitioned wave functions generally can estimate ionization potentials with better accuracy than that of the traditional, non-partitioned ones, provided that they achieve maximum separation (independence) of core and valence shells accompanied by high internal flexibility of ^core and Wvai- Our best core-valence partitioned wave function of that kind estimates the IP's with an accuracy comparable to the most accurate theoretical determinations in the literature.

Resolution of sharp fronts in the presence of model error in variational data assimilation

We show that the four-dimensional variational data assimilation method (4DVar) can be interpreted as a form of Tikhonov regularization, a very familiar method for solving ill-posed inverse problems. It is known from image restoration problems that L1-norm penalty regularization recovers sharp edges in the image more accurately than Tikhonov, or L2-norm, penalty regularization. We apply this idea from stationary inverse problems to 4DVar, a dynamical inverse problem, and give examples for an L1-norm penalty approach and a mixed total variation (TV) L1–L2-norm penalty approach. For problems with model error where sharp fronts are present and the background and observation error covariances are known, the mixed TV L1–L2-norm penalty performs better than either the L1-norm method or the strong constraint 4DVar (L2-norm)method. A strength of the mixed TV L1–L2-norm regularization is that in the case where a simplified form of the background error covariance matrix is used it produces a much more accurate analysis than 4DVar. The method thus has the potential in numerical weather prediction to overcome operational problems with poorly tuned background error covariance matrices.

Zel'dovich's method of perturbation theory in quantum mechanics

Many years ago Zel'dovich showed how the Lagrange condition in the theory of differential equations can be utilized in the perturbation theory of quantum mechanics. Zel'dovich's method enables us to circumvent the summation over intermediate states. As compared with other similar methods, in particular the logarithmic perturbation expansion method, we emphasize that this relatively unknown method of Zel'dovich has a remarkable advantage in dealing with excited stares. That is, the ground and excited states can all be treated in the same way. The nodes of the unperturbed wavefunction do not give rise to any complication.

Recent improvements in prediction of protein structure by global optimization of a potential energy function

Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

High-temperature superconductivity in the two-dimensional t-J model: Gutzwiller wavefunction solution

A systematic diagrammatic expansion for Gutzwiller wavefunctions (DE-GWFs) proposed very recently is used for the description of the superconducting (SC) ground state in the two-dimensional square-lattice t-J model with the hopping electron amplitudes t (and t') between nearest (and next-nearest) neighbors. For the example of the SC state analysis we provide a detailed comparison of the method's results with those of other approaches. Namely, (i) the truncated DE-GWF method reproduces the variational Monte Carlo (VMC) results and (ii) in the lowest (zeroth) order of the expansion the method can reproduce the analytical results of the standard Gutzwiller approximation (GA), as well as of the recently proposed 'grand-canonical Gutzwiller approximation' (called either GCGA or SGA). We obtain important features of the SC state. First, the SC gap at the Fermi surface resembles a d(x2-y2) wave only for optimally and overdoped systems, being diminished in the antinodal regions for the underdoped case in a qualitative agreement with experiment. Corrections to the gap structure are shown to arise from the longer range of the real-space pairing. Second, the nodal Fermi velocity is almost constant as a function of doping and agrees semi-quantitatively with experimental results. Third, we compare the

Amplitude equations and asymptotic expansions for multi-scale problems

In this paper we introduce a new technique to obtain the slow-motion dynamics in nonequilibrium and singularly perturbed problems characterized by multiple scales. Our method is based on a straightforward asymptotic reduction of the order of the governing differential equation and leads to amplitude equations that describe the slowly-varying envelope variation of a uniformly valid asymptotic expansion. This may constitute a simpler and in certain cases a more general approach toward the derivation of asymptotic expansions, compared to other mainstream methods such as the method of Multiple Scales or Matched Asymptotic expansions because of its relation with the Renormalization Group. We illustrate our method with a number of singularly perturbed problems for ordinary and partial differential equations and recover certain results from the literature as special cases. © 2010 - IOS Press and the authors. All rights reserved.

Molecular Dynamics Simulations of Orientational Relaxation in Dipolar Lattice: Lack of Diffusive Decay for Second and Higher Rank Correlation Functions

Extensive molecular dynamics simulations have been carried out to calculate the orientational correlation functions Cl(t), G(t) = [4n/(21 + l)]Ci=-l (Y*lm(sZ(0)) Ylm(Q(t))) (where Y,,(Q) are the spherical harmonics) of point dipoles in a cubic lattice. The decay of Cl(t) is found to be strikingly different from higher l-correlation functions-the latter do not exhibit diffusive dynamics even in the long time. Both the cumulant expansion expression of Lynden-Bell and the conventional memory function equation provide very good description of the Cl(t) in the short time but fail to reproduce the observed slow, long time decay of c1 (t) .

Mathematical Modeling of Near-Wall Flows of Two-Phase Mixture with Evaporating Droplets

In the framework of the two-continuum approach, using the matched asymptotic expansion method, the equations of a laminar boundary layer in mist flows with evaporating droplets were derived and solved. The similarity criteria controlling the mist flows were determined. For the flow along a curvilinear surface, the forms of the boundary layer equations differ from the regimes of presence and absence of the droplet inertia deposition. The numerical results were presented for the vapor-droplet boundary layer in the neighborhood of a stagnation point of a hot blunt body. It is demonstrated that, due to evaporation, a droplet-free region develops near the wall inside the boundary layer. On the upper edge of this region, the droplet radius tends to zero and the droplet number density becomes much higher than that in the free stream. The combined effect of the droplet evaporation and accumulation results in a significant enhancement of the heat transfer on the surface even for small mass concentration of the droplets in the free stream. 在双连续介质理论框架下,采用匹配渐进展开方法导出并求解了具有蒸发液滴的汽雾流中层流边界层方程,给出了控制汽雾流的相似判据。对于沿曲面的流动,边界层方程的形式取决于是否存在液滴的惯性沉积。给出了热钝体验点附近蒸汽。液滴边界层的数值计算结果。它们表明：由于蒸发,在边界层内近壁处形成了一个无液滴区域；在该区上边界处,液滴半径趋于零而液滴数密度急剧增高。液滴蒸发及聚集的联合效应造成了表面热流的显著增加,甚至在自由来流中液滴质量浓度很低时此效应依然存在。

A crack perpendicular to and terminating at a bimaterial interface

Using dislocation simulation approach, the basic equation for a finite crack perpendicular to and terminating at a bimaterial interface is formulated. A novel expansion method is proposed for solving the problem. The complete solution to the problem, including the explicit formulae for the T stresses ahead of the crack tip and the stress intensity factors are presented. The stress held characteristics are analysed in detail. It is found that normal stresses sigma(x) and sigma(y) ahead of the crack tip, are characterised by Q fields if the crack is within a stiff material and the parameters \p(T)\ and \q(T)\ are very small, where Q is a generalised stress intensity factor for a crack normal to and terminating at the interface. If the crack is within a weak material, the normal stresses sigma(x) and sigma(y) are dominated by the Q field plus T stress.

Stress state in front of a crack perpendicular to bimaterial interface

Using a dislocation simulation approach, the basic equation for a crack perpendicular to a bimaterial interface is formulated in this paper. A novel expansion method is proposed for solving the problem. The complete solution for the problem, including the T stress ahead of the crack tip and the stress intensity factors are presented. The stress field characteristics are analyzed in detail. It is found that ahead of the crack tip and near the interface the normal stress, perpendicular to the crack plane, sigma(x), is characterized by the K fields and the normal stress sigma(y) is dominated by the K field plus T stress in the region of 0 < r/b < 0.4 for b/a(0) less than or equal to 0.1, where b is the distance from the crack tip to the interface.

Two-time scales inner solutions and motion of a geostrophic vortex

Based on the authors' previous work, in this paper the systematical analyses on the motion and the inner solutions of a geostrophic vortex have been presented by means of thematched asymptotic expansion method with multiple time scales (S/gh001/2 and α S/gh001/2) and space scales. It has been shown that the leading inner solutions to the core structure in two-time scales analyses are identified with the results in normal one-time scale analyses. The time averages of the first-order solutions on short time variable τ are the same as the first-order solutions obtained in one normal time scale analyses. The geostrophic vortex induces an oscillatory motion in addition to moving with the background flow. The period, amplitude andthe deviation from the mean trajectory depend on the core structure and the initial conditions. The velocity of the motion of vortex center varies periodically and the time average of the velocity on short time variable τ is equal to the value of the local mean velocity.

The motion and the core structure of a geostrophic vortex - one-time scale inner solution and the motion of the vortex

By means of the matched asymptotic expansion method with one-time scale analysis we have shown that the inviscid geostrophic vortex solution represents our leading solution away from the vortex. Near the vortex there is a viscous core structure, with the length scale O(a). In the core the viscous stresses (or turbulent stresses) are important, the variations of the velocity and the equivalent height are finite and dependent of time. It also has been shown that the leading inner solutions of the core structure are the same for two different time scales of S/(ghoo)1/2 and S/a (ghoo)1/2. Within the accuracy of O(a) the velocity of a geostrophic vortex center is equal to the velocity of the local background flow, where the vortex is located, in the absence of the vortex. Some numerical examples demonstrate the contributions of these results.

Numerical experiments on one-dimensional model of turbulence

The initial-value problem of a forced Burgers equation is numerically solved by the Fourier expansion method. It is found that its solutions finally reach a steady state of 'laminar flow' which has no randomness and is stable to disturbances. Hence, strictly speaking, the so-called Burgers turbulence is not a turbulence. A new one-dimensional model is proposed to simulate the Navier-Stokes turbulence. A series of numerical experiments on this one-dimensional turbulence is made and is successful in obtaining Kolmogorov's (1941) k exp(-5/3) inertial-range spectrum. The (one-dimensional) Kolmogorov constant ranges from 0.5 to 0.65.

Analytical calculations of Eulerian and Lagrangian time correlations in turbulent shear flows

The Taylor series expansion method is used to analytically calculate the Eulerian and Lagrangian time correlations in turbulent shear flows. The short-time behaviors of those correlation functions can be obtained from the series expansions. Especially, the propagation velocity and sweeping velocity in the elliptic model of space-time correlation are analytically calculated and further simplified using the sweeping hypothesis and straining hypothesis. These two characteristic velocities mainly determine the space-time correlations.