Acoustic wave interaction with a laminated transversely isotropic spherical shell with imperfect bonding

An exact analysis is carried out to study interaction of a time-harmonic plane-progressive sound field with a multi-layered elastic hollow sphere made of spherically isotropic materials with interlaminar bonding imperfections. A modal state equation with variable coefficients is set up in terms of appropriate displacement and stress functions and their spherical harmonics, ultimately leading to calculation of a global transfer matrix. A linear spring model is adopted to describe the interlaminar adhesive bonding whose effects are incorporated into the global transfer matrix by introduction of proper interfacial transfer matrices. The solution is first used to correlate the perturbation in the material elastic constants of an evacuated and water submerged steel (isotropic) spherical shell to the sensitivity of resonances appearing in the backscattered amplitude spectrum. The backscattering form function, in addition to the acoustic radiation force acting on selected transversely isotropic spherical shells with distinct degrees of material anisotropy, is subsequently calculated and discussed. An illustrative numerical example is given for a multi-layered hollow sphere with two distinct interlaminar interface conditions (i.e., perfectly and imperfectly bonded layers). Limiting cases are considered and fair agreements with solutions available in the literature are established.     

Numerical analysis of ossicular chain lesion of human ear

Abstract Lesion of ossicular chain is a common ear disease impairing the sense of hearing. A comprehensive numerical model of human ear can provide better understanding of sound transmission. In this study, we propose a three-dimensional finite element model of human ear that incorporates the canal, tympanic membrane, ossicular bones, middle ear suspensory ligaments/muscles, middle ear cavity and inner ear fluid. Numerical analysis is conducted and employed to predict the effects of middle ear cavity, malleus handle defect, hypoplasia of the long process of incus, and stapedial crus defect on sound transmission. The present finite element model is shown to be reasonable in predicting the ossicular mechanics of human ear.     

A novel virtual samples-based sparse representation method for face recognition

A limited training set usually limits the performance of face recognition in practice. Even sparse representation-based methods which outperform in face recognition cannot avoid such situation. In order to effectively improve recognition accuracy of sparse representation-based methods on a limited training set, a novel virtual samples-based sparse representation (VSSR) method for face recognition is proposed in this paper. In the proposed method, virtual training samples are constructed to enrich the size and diversity of a training set and a sparse representation-based method is used to classify test samples. Extensive experiments on different face databases confirm that VSSR is robust to illumination variations and works better than many representative representation-based face recognition methods.     

Discovery of potential inhibitors targeting the kinase domain of polynucleotide kinase/phosphatase (PNKP): Homology modeling,virtual screening based on multiple conformations,and molecular dynamics simulation

In recent years, the level of interest has been increased in developing the DNA-repair inhibitors, to enhance the cytotoxic effects in the treatment of cancers. Polynucleotide kinase/phosphatase (PNKP) is a critical human DNA repair enzyme that repairs DNA strand breaks by catalyzing the restoration of 5’-phosphate and 3’-hydroxyl termini that are required for subsequent processing by DNA ligases and polymerases. PNKP is the only protein that repairs the 3′-hydroxyl group and 5′-phosphate group, which depicts PNKP as a potential therapeutic target. Besides, PNKP is the only DNA-repair enzyme that contains the 5′-kinase activity, therefore, targeting this kinase domain would motivate the development of novel PNKP-specific inhibitors. However, there are neither crystal structures of human PNKP nor the kinase inhibitors reported so far. Thus, in this present study, a sequential molecular docking-based virtual screening with multiple PNKP conformations integrating homology modeling, molecular dynamics simulation, and binding free energy calculation was developed to discover novel PNKP kinase inhibitors, and the top-scored molecule was finally submitted to molecular dynamics simulation to reveal the binding mechanism between the inhibitor and PNKP. Taken together, the current study could provide some guidance for the molecular docking based-virtual screening of novel PNKP kinase inhibitors.     

High-throughput virtual screening and microsecond MD simulations to identify potential sugar mimic of the solute-binding protein BlAXBP of the ABC transporter from Bifidobacterium animalis subsp. Lactis

Xylotetraose is a prebiotic oligosaccharide can be utilized by the ABC transporter of the gut microbiota Bifidobacteria. BlAXBP is the solute binding protein of the ABC transporter, and its complex with xylotetraose has been solved by X-ray crystallography. Here, we have identified novel sugar mimic of BlAXBP by applying a high-throughput virtual screening of ZINC database containing a huge library with ∼22 M compounds. To begin with, we identified 18,571 ligands by a ligand-based virtual screening. Further, a total of 3968 compounds were selected for molecular docking due to their Tanimoto coefficient’s value were larger than a cutoff of 0.08. The molecular mechanics-generalized born surface area was used to evaluate the binding free energies, and the top 10 ligands with free energies below an energy threshold of -35.22 kcal/mol were selected. ZINC13783511 formed the most stable complex with BlAXBP and its recognition mechanism were further explored by microsecond MD simulations in explicit solvent. Free energy landscapes were used to evaluate conformational changes of BlAXBP in its ligand free and binding states. Collectively, this work identified potential novel sugar mimics to BlAXBP, providing novel atomic-level understanding of the binding mechanism.     

Identification of novel anti cancer agents by applying insilico methods for inhibition of TSPO protein

Cancer is a genomic disease characterised as impaired cellular energy metabolism. Cancer cells derive most of their energy from oxidative phosphorylation unlike normal ones during cell progression TSPO protein present in external mitochondrial membrane, is involved in various cellular functions like Cell proliferation, mitochondrial respiration, synthesis of steroids and also participates in import of cholesterol into the inner mitochondrial membrane from outside of the membrane of mitochondria.The 3D model of TSPO protein is built using comparative homology modelling techniques and validated by proSA, Ramachandran plot and ERRAT in the present work. Active site prediction is carried out using SiteMap and literature, which allows the prediction of the important binding pockets for the identification of putative active site. New molecular entities as TSPO inhibitors were obtained from Virtual screening using MS Spectrum databank in Schrodinger suite and were prioritised based on Glide Score. Docking was performed using Autodock to identify molecules with different scaffolds and were prioritised based on binding energy and RMSD values. Qikprop is used to calculate pharmacokinetic properties of the screened molecules which are found to be in permissible range as possible novel inhibitors of TSPO protein to supress cell proliferation.     

Inverse dynamics of the HALF parallel manipulator with revolute actuators

Recursive matrix relations for kinematics and dynamics of the HALF parallel manipulator are presented in this paper. The prototype of this robot is a spatial mechanism with revolute actuators, which has two translation degrees of freedom and one rotation degree of freedom. The parallel manipulator consists of a base plate, a movable platform and a system of three connecting legs, having wide application in the fields of industrial robots, simulators, parallel machine tools and any other manipulating devices where high mobility is required. Supposing that the position and the motion of the moving platform are known, an inverse dynamics problem is solved using the principle of virtual powers. Finally, some iterative matrix relations and graphs of the torques and powers for all actuators are analysed and determined. It is shown that this approach is an effective means for kinematics and dynamics modelling of parallel mechanisms.     

A principle of virtual work for combined electrostatic and mechanical loading of materials

The equations governing mechanics and electrostatics are formulated for a system in which the material deformations and electrostatic polarizations are arbitrary. A mechanical/electrostatic energy balance is formulated for this situation in terms of the electric enthalpy, in which the electric potential and the electric field are the independent variables, and charge and electric displacement, respectively, are the conjugate thermodynamic forces. This energy statement is presented in the form of a principle of virtual work (PVW), in which external virtual work is equated to internal virtual work. The resulting expression involves an internal material virtual work in which (1) material polarization is work-conjugate to increments of electric field, and (2) a combination of Cauchy stress, Maxwell stress and a product of polarization and electric field is work-conjugate to increments of strain. This PVW is valid for all material types, including those that are conservative and those that are dissipative. Such a virtual work expression is the basis for a rigorous formulation of a finite element method for problems involving the deformation and electrostatic charging of materials, including electroactive polymers and switchable ferroelectrics. The internal virtual work expression is used to develop the structure of conservative constitutive laws governing, for example, electroactive elastomers and piezoelectric materials, thereby determining the form of the Maxwell or electrostatic stress. It is shown that the Maxwell or electrostatic stress has a form fully constrained by the constitutive law and cannot be chosen independently of it. The structure of constitutive laws for dissipative materials, such as viscoelastic electroactive polymers and switchable ferroelectrics, is similarly determined, and it is shown that the Maxwell or electrostatic stress for these materials is identical to that for a material having the same conservative response when the dissipative processes in the material are shut off. The form of the internal virtual work is used further to develop the structure of dissipative constitutive laws controlled by rearrangement of material internal variables.