Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1,2-dihaloethanes

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables.     

Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

Effective protein conformational sampling based on predicted torsion angles

Protein structure prediction is a long‐standing problem in molecular biology. Due to lack of an accurate energy function, it is often difficult to know whether the sampling algorithm or the energy function is the most important factor for failure of locating near‐native conformations of proteins. This article examines the size dependence of sampling effectiveness by using a perfect “energy function”: the root‐mean‐squared distance from the target native structure. Using protein targets up to 460 residues from critical assessment of structure prediction techniques (CASP11, 2014), we show that the accuracy of near native structures sampled is relatively independent of protein sizes but strongly depends on the errors of predicted torsion angles. Even with 40% out‐of‐range angle prediction, 2 Å or less near‐native conformation can be sampled. The result supports that the poor energy function is one of the bottlenecks of structure prediction and predicted torsion angles are useful for overcoming the bottleneck by restricting the sampling space in the absence of a perfect energy function. © 2015 Wiley Periodicals, Inc.     

Characterizations of some homogeneous Hopf real hypersurfaces in a nonflat complex space form by extrinsic shapes of trajectories

We characterize some homogeneous Hopf real hypersurfaces in a nonflat complex space form by studying trajectories for Sasakian magnetic fields whose extrinsic shapes are tangentially of order 2.     

Evidence for a transition in deformation mechanism in nanocrystalline pure titanium processed by high-pressure torsion

Nanocrystalline titanium with an average grain size of about 60–70 nm was prepared by high-pressure torsion. The results of hardness and structural evolutions indicate that a strain-induced hardening–softening–hardening–softening behaviour occurs. For coarse-grained titanium, 〈a〉-type dislocation multiplication, twinning and a high pressure-induced α-to-ω phase transformation play major roles to accommodate deformation, leading to a significant strain hardening. As deformation proceeds, dynamic recrystallisation leads to a decrease in dislocation density, especially for 〈a〉-type dislocations, leading to a slight strain softening. The 〈c〉-component dislocation multiplication dominates the deformation when the grain size decreases to 100 nm and 〈c〉-component dislocation multiplication, grain refinement and the α-to-ω phase transformation contribute to the second strain hardening. The following strain softening is attributed to dynamic recovery.     

On the degree of Hilbert polynomials associated to the torsion functor

Let be a local, Noetherian ring and an ideal. A question of Kodiyalam asks whether for fixed , the polynomial giving the th Betti number of has degree equal to the analytic spread of minus one. Under mild conditions on , we show that the answer is positive in a number of cases, including when is divisible by or is an integrally closed -primary ideal.

     

The solution of integral equations with strongly singular kernels applied to the torsion of cracked circular cylinder

In this paper,the functions of warping displacement interruption defined on the crack lines are taken for the fundamental unknown functions.The torsion problem of cracked circular cylinder is reduced to solving a system of integral equations with strongly singular kernels.Using the numerical method of these equations,the torsional rigidities and the stress intensity factors are calculated to solve the torsion problem of circular cylinder with star-type and other different types of cracks.The numerical results are satisfactory.     

Application of an improved boundary element method on the problem of elastic torsion

An improved boundary clement method has been used in analyzing and calculating the problems of the torsion of a prismatic bar with elliptical cross-section. In this paper the calculated results correspond with the values of boundary element method. However, the quantity of data required by the improved boundary element method is much less than that required by boundary element method, and the calculating time will be greatly reduced. Therefore, the procedure of this paper is an economical and efficient numerical computational way for solving Poisson equation problem.     

S-系的扭类

假设S是有0,1的半群,τ是S-系的遗传扭论,对任意的右S-系M,Tτ（M）是M的τ-扭根。x∈Tτ（M）当且仅当存在某个τ-稠密右同余ρ,使得对任意的（S1,S2）∈ρ均有xs1=xs2,同时,当右S-系M是τ-扭自由时,M的τ-稠密同余是M的本质同余,特别,对忠实的遗传扭论τ,S的τ-稠密右同余是S