Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion electrostatics is treated within the FDP model when close to the solute, and by the Coulombic model when far from the solute. The two zone model reduces computation time, but retains an accurate treatment of the ion atmosphere electrostatics near the solute. Ion compositions can be set to reproduce specific ionic strengths. The entire ion/water treatment is interfaced with the molecular dynamics package CHARMM. Using the CHARMM-ZAPI software combination, the implicit solvent model was tested on A and B form duplex DNA, and tetraloop RNA, producing stable simulations with structures remaining close to experiment. The model also reproduced the A to B duplex DNA transition. The effect of ionic strength, and the structure of the counterion atmosphere around B form duplex DNA were also examined.     

Bioinformatical evaluation of modified nucleosides as biomedical markers in diagnosis of breast cancer

It is known that patients suffering from cancer diseases excrete increased amounts of modified nucleosides with their urine. Especially methylated nucleosides have been proposed to be potential tumor markers for early diagnosis of cancer. For determination of nucleosides in randomly collected urine samples, the nucleosides were extracted using affinity chromatography and then analyzed via reversed phase high-performance liquid chromatography (HPLC) with UV-detection. Eleven nucleosides were quantified in urine samples from 51 breast cancer patients and 65 healthy women.The measured concentrations were used to train a Support Vector Machine (SVM) and a k-nearest-neighbor classifier (k-NN) to discriminate between healthy control subjects and patients suffering from breast cancer. Evaluations of the learned models by computing the leave-one-out error and the prediction error on an independent test set of 29 subjects (15 healthy, 14 breast cancer patients) showed that by using the eleven nucleosides, the occurrence of breast cancer could be forecasted with 86% specificity and 94% sensitivity when using an SVM and 86% for both specificity and sensitivity with the k-NN model.     

A hybrid phase field multiple relaxation time lattice Boltzmann method for the incompressible multiphase flow with large density contrast

A hybrid phase field multiple relaxation time lattice Boltzmann method (LBM) is presented in this paper for simulation of multiphase flows with large density contrast. In the present method, the flow field is solved by a lattice Boltzmann equation. Concurrently, the interface of two fluids is captured by solving the macroscopic Cahn‐Hilliard equation using the upwind scheme. To be specific, for simulation of the flow field, an lattice Boltzmann equation (LBE) model developed in Shao et al. (Physical Review E, 89 (2014), 033309) for consideration of density contrast in the momentum equation is used. Moreover, in the present work, the multiple relaxation time collision operator is applied to this LBE to enable simulation of problems with large viscosity contrast or high Reynolds number. For the interface capturing, instead of solving another set of LBE as in many phase field LBMs, the macroscopic Cahn‐Hilliard equation is directly solved by using a weighted essentially non‐oscillatory scheme. In this way, the present hybrid phase field LBM shares full advantages of the phase field LBM while enhancing numerical stability. The ability of the present method to simulate multiphase flow problems with large density contrast is demonstrated by several numerical examples. Copyright © 2015 John Wiley & Sons, Ltd.     

On the robustness of regularized pairwise learning methods based on kernels

Regularized empirical risk minimization including support vector machines plays an important role in machine learning theory. In this paper regularized pairwise learning (RPL) methods based on kernels will be investigated. One example is regularized minimization of the error entropy loss which has recently attracted quite some interest from the viewpoint of consistency and learning rates. This paper shows that such RPL methods and also their empirical bootstrap have additionally good statistical robustness properties, if the loss function and the kernel are chosen appropriately. We treat two cases of particular interest: (i) a bounded and non-convex loss function and (ii) an unbounded convex loss function satisfying a certain Lipschitz type condition.     

Hemodynamics of aneurysm intervention with different stents

An ideal cerebral aneurysm model with different stent forms is established. By using the single-relaxation-time (SRT) lattice Boltzmann method (LBM) to solve the flow field, the blood flow characteristics in the aneurysm under different conditions are studied numerically. The intra-arterial stenting of saccular aneurysms at different Reynolds numbers and the feasibility of new stenting forms such as double stenting and variable-spacing stenting in the aneurysms are explored. The hemodynamic factors such as velocity distribution and wall shear stress (WSS) in the aneurysm are analyzed. Numerical results show that the risk of aneurysm rupture is mainly centralized at the right corner of the aneurysm. Intervention of stents in the aneurysm can effectively reduce the intra-aneurysmal velocity and WSS, and decrease the danger of aneurysm rupture during strenuous exercise or emotional excitement. At the same time, the intervention of a double stent and the stent shape with a dense anterior part in the aneurysm has certain advantages in preventing aneurysm rupture. The intra-aneurysmal mean velocity reduction can reach 90.39% and 80.29% after the intervention of the double stent and the anterior densified stent respectively.     

The flexibility effect of a plate according to various angles of attack in a free-stream

This paper presents a computational fluid–structure interaction analysis for a flexible plate in a free-stream to investigate the effects of flexibility and angle of attack on force generation. A Lattice Boltzmann Method with an immersed boundary technique using a direct forcing scheme model of the fluid is coupled to a finite element model with rectangular bending elements. We investigated the effects of various angles of attack of a flexible plate fixed at one of the end edges in a free-stream at a Reynolds number of 5000, which represents the wing flapping condition of insects and small birds in nature. The lift of the flexible plate is maintained at the large angle of attack, whereas the rigid plate shows the largest lift at angles of attack around 30–40° and then drastic reductions in the lift at the large angle of attack. If we consider the efficiency as the lift divided by the drag, the flexible plate shows better efficiency at angles of attack greater than 30° compared to the rigid plate. The better performance of the flexible plate at large angles of attack comes from the deformation of the plate, which produces an interaction between the trailing edge vortex and the short edge vortex. The horseshoe-shaped vortex produced by a large vortex interaction at the trailing edge side has an important role in increasing the lift, and the small projection area due to the deformation reduces the drag. Furthermore, we investigate the role of flexibility on the lift and the drag force of the rectangular plate in a free-stream as the Reynolds number increases. Whenever a large vortex interaction at the trailing edge side is shown, the efficiency of the rectangular plate is improved. Especially, the flexible plate shows better efficiency as the Reynolds number increases regardless of the angle of attack.     

On-line conveyor belts inspection based on machine vision

Under the background that mining conveyor belts are prone to failure in operation, the on-line fault detection technique based on machine vision for conveyor belts is investigated. High-brightness linear light sources arranged to a vaulted shape provide light for a line-array CCD camera to capture high-quality belt images. A fast image segmentation algorithm is proposed to deal belt images on-line. The algorithm for detecting longitudinal rip and belt deviation which are serious threat to the mine safety production from binary belt images is presented. Then, an on-line visual belt inspection system is developed. The laboratory testing results testify the validity of the visual inspection system.     

A comparison of limited-stretch models of rubber elasticity

In this paper we describe various limited-stretch models of non-linear rubber elasticity, each dependent on only the first invariant of the left Cauchy–Green strain tensor and having only two independent material constants. The models are described as limited-stretch, or restricted elastic, because the strain energy and stress response become infinite at a finite value of the first invariant. These models describe well the limited stretch of the polymer chains of which rubber is composed. We discuss Gent׳s model which is the simplest limited-stretch model and agrees well with experiment. Various statistical models are then described: the one-chain, three-chain, four-chain and Arruda–Boyce eight-chain models, all of which involve the inverse Langevin function. A numerical comparison between the three-chain and eight-chain models is provided. Next, we compare various models which involve approximations to the inverse Langevin function with the exact inverse Langevin function of the eight-chain model. A new approximate model is proposed that is as simple as Cohen׳s original model but significantly more accurate. We show that effectively the eight-chain model may be regarded as a linear combination of the neo-Hookean and Gent models. Treloar׳s model is shown to have about half the percentage error of our new model but it is much more complicated. For completeness a modified Treloar model is introduced but this is only slightly more accurate than Treloar׳s original model. For the deformations of uniaxial tension, biaxial tension, pure shear and simple shear we compare the accuracy of these models, and that of Puso, with the eight-chain model by means of graphs and a table. Our approximations compare extremely well with models frequently used and described in the literature, having the smallest mean percentage error over most of the range of the argument.     

Numerical study of the properties of the central moment lattice Boltzmann method

Central moment lattice Boltzmann method (LBM) is one of the more recent developments among the lattice kinetic schemes for computational fluid dynamics. A key element in this approach is the use of central moments to specify the collision process and forcing, and thereby naturally maintaining Galilean invariance, an important characteristic of fluid flows. When the different central moments are relaxed at different rates like in a standard multiple relaxation time (MRT) formulation based on raw moments, it is endowed with a number of desirable physical and numerical features. Because the collision operator exhibits a cascaded structure, this approach is also known as the cascaded LBM. While the cascaded LBM has been developed sometime ago, a systematic study of its numerical properties, such as the accuracy, grid convergence, and stability for well‐defined canonical problems is lacking, and the present work is intended to fulfill this need. We perform a quantitative study of the performance of the cascaded LBM for a set of benchmark problems of differing complexity, viz., Poiseuille flow, decaying Taylor–Green vortex flow, and lid‐driven cavity flow. We first establish its grid convergence and demonstrate second‐order accuracy under diffusive scaling for both the velocity field and its derivatives, that is, the components of the strain rate tensor, as well. The method is shown to quantitatively reproduce steady/unsteady analytical solutions or other numerical results with excellent accuracy. The cascaded MRT LBM based on the central moments is found to be of similar accuracy when compared with the standard MRT LBM based on the raw moments, when a detailed comparison of the flow fields are made, with both reproducing even the small scale vortical features well. Numerical experiments further demonstrate that the central moment MRT LBM results in significant stability improvements when compared with certain existing collision models at moderate additional computational cost. Copyright © 2015 John Wiley & Sons, Ltd.     

The Boltzmann–Langevin approach: A simple quantum-mechanical derivation

We present a simple quantum-mechanical derivation of correlation function of Langevin sources in the semiclassical Boltzmann–Langevin equation. The specific case of electron–phonon scattering is considered. It is shown that the assumption of weak scattering leads to the Poisson nature of the scattering fluxes.