Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Density Functional Theoretical Modeling, Electrostatic Surface Potential and Surface Enhanced Raman Spectroscopic Studies on Biosynthesized Silver Nanoparticles: Observation of 400 pM Sensitivity to Explosives

Interaction of adsorbate on charged surfaces, orientation of the analyte on the surface, and surface enhancement aspects have been studied. These aspects have been explored in details to explain the surface-enhanced Raman spectroscopic (SERS) spectra of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (HNIW or CL-20), a well-known explosive, and 2,4,6-trinitrotoluene (TNT) using one-pot synthesis of silver nanoparticles via biosynthetic route using natural precursor extracts of clove and pepper. The biosynthesized silver nanoparticles (bio Ag Nps) have been characterized using UV-vis spectroscopy, scanning electron microscopy and atomic force microscopy. SERS studies conducted using bio Ag Nps on different water insoluble analytes, such as CL-20 and TNT, lead to SERS signals at concentration levels of 400 pM. The experimental findings have been corroborated with density functional computational results, electrostatic surface potential calculations, Fukui functions and potential measurements.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data (sin theta/lambda)(max) = 1.1 angstrom(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H center dot center dot center dot N and N-H center dot center dot center dot O hydrogen bonds, in which the N3-H3B center dot center dot center dot N1 and N3-H3A center dot center dot center dot O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N center dot center dot center dot H and O center dot center dot center dot H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the pi-electron cloud.

Charge density distribution and electrostatic interactions of ethionamide: an inhibitor of the enoyl acyl carrier protein reductase (inhA) enzyme of Mycobacterium tuberculosis

An experimental charge density analysis of an anti-TB drug ethionamide was carried out from high resolution X-ray diffraction at 100 K to understand its charge density distribution and electrostatic properties. The experimental results were validated from periodic theoretical charge density calculations performed using CRYSTAL09 at the B3LYP/6-31G** level of theory. The electron density rho(bcp)(r) and the Laplacian of electron density del(2)(rho bcp)(r) of the molecule calculated from both the methods display the charge density distribution of the ethionamide molecule in the crystal field. The electrostatic potential map shows a large electropositive region around the pyridine ring and a large electronegative region at the vicinity of the thiol atom. The calculated experimental dipole moment is 10.6D, which is higher than the value calculated from theory (8.2D). The topological properties of C-H center dot center dot center dot S, N-H center dot center dot center dot N and N-H center dot center dot center dot S hydrogen bonds were calculated, revealing their strength. The charge density analysis of the ethionamide molecule determined from both the experiment and theory gives the topological and electrostatic properties of the molecule, which allows to precisely understand the nature of intra and intermolecular interactions.

Numerical and Analytical Study on the Pull-in Instability of Micro-Structure under Electrostatic Loading

The one-mode analysis method on the pull-in instability of micro-structure under electrostatic loading is presented. Taylor series are used to expand the electrostatic loading term in the one-mode analysis method, which makes analytical solution available. The one-mode analysis is the combination of Galerkin method and Cardan solution of cubic equation. The one-mode analysis offers a direct computation method on the pull-in voltage and displacement. In low axial loading range, it shows little difference with the established multi-mode analysis on predicting the pull-in voltages for three different structures (cantilever, clamped-clamped beams and the plate with four edges simply-supported) studied here. For numerical multi-mode analysis, we also show that using the structural symmetry to select the symmetric mode can greatly reduce both the computation effort and the numerical fluctuation.

Electrostatic Interactions Between Glycosaminoglycan Molecules

The electrostatic interactions between nearest-neighbouring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains are obtained on the bottle brush conformation of proteoglycan aggrecan based on an asymptotic solution of the Poisson-Boltzmann equation the CS-GAGs satisfy under the physiological conditions of articular cartilage. The present results show that the interactions are associated intimately with the minimum separation distance and mutual angle between the molecular chains themselves. Further analysis indicates that the electrostatic interactions are not only expressed to be purely exponential in separation distance and decrease with the increasing mutual angle but also dependent sensitively on the saline concentration in the electrolyte solution within the tissue, which is in agreement with the existed relevant conclusions.

Modeling Nonlinear Peeling of Ductile Thin Films-Critical Assessment of Analytical Bending Models Using FE Simulations

Three analytical double-parameter criteria based on a bending model and a two-dimensional finite element analysis model are presented for the modeling of ductile thin film undergoing a nonlinear peeling process. The bending model is based on different governing parameters: (1) the interfacial fracture toughness and the separation strength, (2) the interfacial fracture toughness and the crack tip slope angle, and (3) the interfacial fracture toughness and the critical Mises effective strain of the delaminated thin film at the crack tip. Thin film nonlinear peeling under steady-state condition is solved with the different governing parameters. In addition, the peeling test problem is simulated by using the elastic-plastic finite element analysis model. A critical assessment of the three analytical bending models is made by comparison of the bending model solutions with the finite element analysis model solutions. Furthermore, through analyses and comparisons for solutions based on both the bending model and the finite element analysis model, some connections between the bending model and the finite element analysis model are developed. Moreover, in the present research, the effect of different selections for cohesive zone shape on the ductile film peeling solutions is discussed.

Influence of Electrostatic Interaction on Fibrinogen Adsorption on Gold Studied by Imaging Ellipsometry Combined with Electrochemical Methods

Imaging ellipsometry was combined with electrochemical methods for studying electrostatic interactions of protein and solid surfaces. The potential of zero charge for gold-coated silicon wafer/solution interfaces wad determined by AC impedance method. The potential of the gold-coated silicon wafer was controlled at the potential of zero charge, and the adsorption of fibrinogen on the potential-controlled and non-controlled surfaces was measured in real time at the same time by imaging ellipsometry The effect of electrostatic interaction was studied by comparing the difference between the potential of controlled adsorption and the Potential of noncontrolled adsorption. It was shown that the rate of fibrinogen adsorption on the potentiostatic surface was faster than that on the nonpotentiostatic surface. The electrostatic influence on fibrinogen adsorption on the gold-coated silicon wafer was weak, so the hydrophobic interaction should be the major affinity.

Influence of van der Waals and Casimir Forces on Electrostatic Torsional Actuators

The influence of van der Waals (vdW) and Casimir forces on the stability of the electrostatic torsional nanoelectromechanical systems (NEMS) actuators is analyzed in the paper. With the consideration of vdW and Casimir effects, the dependence of the critical tilting angle and pull-in voltage on the sizes of structure is investigated. And the influence of vdW torque is compared with that of Casimir torque. The modified coefficients of vdW and Casimir torques on the pull-in voltage are, respectively, calculated. When the gap is sufficiently small, pull-in can still take place with arbitrary small angle perturbation because of the action of vdW and Casimir torques even if there is not electrostatic torque. And the critical pull-in gaps for two cases are, respectively, derived.

Stability and Bifurcation Bahaviour of Electrostatic Torsional NEMS Varactor Influenced by Dispersion Forces

The influences of Casimir and van der Waals forces on the nano-electromechanical systems (NEMS) electrostatic torsional varactor are studied. A one degree of freedom, the torsional angle, is adopted, and the bifurcation behaviour of the NEMS torsional varactor is investigated. There are two bifurcation points, one of which is a Hopf bifurcation point and the other is an unstable saddle point. The phase portraits are also drawn, in which periodic orbits are around the Hopf bifurcation point, but the periodic orbit will break into a homoclinic orbit when meeting the unstable saddle point.

Dynamic Stability of Electrostatic Torsional Actuators with van Der Waals Effect

electrostatic torsional nano-electro-mechanical systems (NEMS) actuators is analyzed in the paper. The dependence of the critical tilting angle and voltage is investigated on the sizes of structure with the consideration of vdW effects. The pull-in phenomenon without the electrostatic torque is studied, and a critical pull-in gap is derived. A dimensionless equation of motion is presented, and the qualitative analysis of it shows that the equilibrium points of the corresponding autonomous system include center points, stable focus points, and unstable saddle points. The Hopf bifurcation points and fork bifurcation points also exist in the system. The phase portraits connecting these equilibrium points exhibit periodic orbits, heteroclinic orbits, as well as homoclinic orbits.

Numerical Simulation on the Micro-Scale Bending Induced by Pulsed Laser Beam

利用自行研制的含热传导、冲击动力学大、变形有限元程序,模拟了小尺寸梁在脉冲激光加热条件下的变形过程。在此基础上,利用商用程序模拟了冷却及残余应力的产生,研究了激光参数（强度及分布）等对于微弯曲的影响。数值模拟结果与文献中的实验观察相吻合。

Static Study of Cantilever Beam stiction under Electrostatic Force Influence

The model and analysis of the cantilever beam adhesion problem under the action of electrostatic force are given. Owing to the nonlinearity of electrostatic force, the analytical solution for this kind of problem is not available. In this paper, a systematic method of generating polynomials which are the exact beamsolutions of the loads with different distributions is provided. The polynomials are used to approximate the beam displacement due to electrostatic force. The equilibrium equation offers an answer to how the beam deforms but no information about the unstuck length. The derivative of the functional with respect to the unstuck length offers such information. But to compute the functional it is necessary to know the beam deformation. So the problem is iteratively solved until the results are converged. Galerkin and Newton-Raphson methods are used to solve this nonlinear problem. The effects of dielectric layer thickness and electrostatic voltage on the cantilever beamstiction are studied.The method provided in this paper exhibits good convergence. For the adhesion problem of cantilever beam without electrostatic voltage, the analytical solution is available and is also exactly matched by the computational results given by the method presented in this paper.

Size Effects in Micro-bending Deformation of MEMS Devices Based on the Discrete Dislocation Theory

In the present research, the discrete dislocation theory is used to analyze the size effect phenomena for the MEMS devices undergoing micro-bending load. A consistent result with the experimental one in literature is obtained. In order to check the effectiveness to use the discrete dislocation theory in predicting the size effect, both the basic version theory and the updated one are adopted simultaneously. The normalized stress-strain relations of the material are obtained for different plate thickness or for different obstacle density. The prediction results are compared with experimental results.

Quasi-static three-point bending of carbon fiber sandwich beams with square honeycomb cores

Sandwich beams comprising identical face sheets and a square honeycomb core were manufactured from carbon fiber composite sheets. Analytical expressions were derived for four competing collapse mechanisms of simply supported and clamped sandwich beams in three-point bending: core shear, face microbuckling, face wrinkling, and indentation. Selected geometries of sandwich beams were tested to illustrate these collapse modes, with good agreement between analytic predictions and measurements of the failure load. Finite element (FE) simulations of the three-point bending responses of these beams were also conducted by constructing a FE model by laying up unidirectional plies in appropriate orientations. The initiation and growth of damage in the laminates were included in the FE calculations. With this embellishment, the FE model was able to predict the measured load versus displacement response and the failure sequence in each of the composite beams. © 2011 American Society of Mechanical Engineers.