Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces

We report the first atomistic simulation of two stacked nucleosome core particles (NCPs), with an aim to understand, in molecular detail, how they interact, the effect of salt concentration, and how different histone tails contribute to their interaction, with a special emphasis on the H4 tail, known to have the largest stabilizing effect on the NCP-NCP interaction. We do not observe specific K16-mediated interaction between the H4 tail and the H2A-H2B acidic patch, in contrast with the findings from crystallographic studies, but find that the stacking was stable even in the absence of this interaction. We perform simulations with the H4 tail (partially/completely) removed and find that the region between LYS-16 and LYS-20 of the H4 tail holds special importance in mediating the inter-NCP interaction. Performing similar tail-clipped simulations with the H3 tail removed, we compare the roles of the H3 and H4 tails in maintaining the stacking. We discuss the relevance of our simulation results to the bilayer and other liquid-crystalline phases exhibited by NCPs in vitro and, through an analysis of the histone-histone interface, identify the interactions that could possibly stabilize the inter-NCP interaction in these columnar mesophases. Through the mechanical disruption of the stacked nucleosome system using steered molecular dynamics, we quantify the strength of inter-NCP stacking in the presence and absence of salt. We disrupt the stacking at some specific sites of internucleosomal tail-DNA contact and perform a comparative quantification of the binding strengths of various tails in stabilizing the stacking. We also examine how hydrophobic interactions may contribute to the overall stability of the stacking and find a marked difference in the role of hydrophobic forces as compared with electrostatic forces in determining the stability of the stacked nucleosome system.

Measuring Receptor/Ligand Interaction at the Single-Bond Level: Experimental and Interpretative Issues

There is increased interest in measuring kinetic rates, lifetimes, and rupture forces of single receptor/ligand bonds. Valuable insights have been obtained from previous experiments attempting such measurements. However, it remains difficult to know with sufficient certainty that single bonds were indeed measured. Using exemplifying data, evidence supporting single-bond observation is examined and caveats in the experimental design and data interpretation are identified. Critical issues preventing definitive proof and disproof of single-bond observation include complex binding schemes, multimeric interactions, clustering, and heterogeneous surfaces. It is concluded that no single criterion is sufficient to ensure that single bonds are actually observed. However, a cumulative body of evidence may provide reasonable confidence. 0 2002 Biomedical Engineering Society.

Hydrodynamic interaction between two vertical cylinders in water waves

The hydrodynamic interaction between two vertical cylinders in water waves is investigated based on the linearized potential flow theory. One of the two cylinders is fixed at the bottom while the other is articulated at the bottom and oscillates with small amplitudes in the direction of the incident wave. Both the diffracted wave and the radiation wave are studied in the present paper. A simple analytical expression for the velocity potential on the surface of each cylinder is obtained by means of Graf's addition theorem. The wave-excited forces and moments on the cylinders, the added masses and the radiation damping coefficients of the oscillating cylinder are all expressed explicitly in series form. The coefficients of the series are determined by solving algebraic equations. Several numerical examples are given to illustrate the effects of various parameters, such as the separation distance, the relative size of the cylinders, and the incident angle, on the first-order and steady second-order forces, the added masses and radiation-damping coefficients as well as the response of the oscillating cylinder.

Stabilizing to disruptive transition of focal adhesion response to mechanical forces

Strong mechanical forces can, obviously, disrupt cell-cell and cell-matrix adhesions, e.g., cyclic uniaxial stretch induces instability of cell adhesion, which then causes the reorientation of cells away from the stretching direction. However, recent experiments also demonstrated the existence of force dependent adhesion growth (rather than dissociation). To provide a quantitative explanation for the two seemingly contradictory phenomena, a microscopic model that includes both integrin-integrin interaction and integrin-ligand interaction is developed at molecular level by treating the focal adhesion as an adhesion cluster. The integrin clustering dynamics and integrin-ligand binding dynamics are then simulated within one unified theoretical frame with Monte Carlo simulation. We find that the focal adhesion will grow when the traction force is higher than a relative small threshold value, and the growth is dominated by the reduction of local chemical potential energy by the traction force. In contrast, the focal adhesion will rupture when the traction force exceeds a second threshold value, and the rupture is dominated by the breaking of integrin-ligand bonds. Consistent with the experiments, these results suggest a force map for various responses of cell adhesion to different scales of mechanical force. PMID: 20542514

Dem analysis of soil-pipeline interaction in sand under lateral and upward movements at deep embedment

The soil-pipeline interactions under lateral and upward pipe movements in sand are investigated using DEM analysis. The simulations are performed for both medium and dense sand conditions at different embedment ratios of up to 60. The comparison of peak dimensionless forces from the DEM and earlier FEM analyses shows that, for medium sand, both methods show similar peak dimensionless forces. For dense sand, the DEM analysis gives more gradual transition of shallow to deep failure mechanisms than the FEM analysis and the peak dimensionless forces at very deep depth are higher in the DEM analysis than in the FEM analysis. Comparison of the deformation mechanism suggests that this is due to the differences in soil movements around the pipe associated with its particulate nature. The DEM analysis provides supplementary data of the soil-pipeline interaction in sand at deep embedment condition.

Fluid-structure interaction of three-dimensional magnetic artificial cilia

A numerical model is developed to analyse the interaction of artificial cilia with the surrounding fluid in a three-dimensional setting in the limit of vanishing fluid inertia forces. The cilia are modelled using finite shell elements and the fluid is modelled using a boundary element approach. The coupling between both models is performed by imposing no-slip boundary conditions on the surface of the cilia. The performance of the model is verified using various reference problems available in the literature. The model is used to simulate the fluid flow due to magnetically actuated artificial cilia. The results show that narrow and closely spaced cilia create the largest flow, that metachronal waves along the width of the cilia create a significant flow in the direction of the cilia width and that the recovery stroke in the case of the out-of-plane actuation of the cilia strongly depends on the cilia width. © 2012 Cambridge University Press.

Interaction between heavy vehicles and roads

This paper discusses road damage caused by heavy commercial vehicles. Chapter 1 presents some important terminology and a brief historical review of road construction and vehicle-road interaction, from ancient times to the present day. The main types of vehicle-generated road damage, and the methods that are used by pavement engineers to analyze them are discussed in Chapter 2. Attention is also given to the main features of the response of road surfaces to vehicle loads and mathematical models that have been developed to predict road response. Chapter 3 reviews the effects on road damage of vehicle features which can be studied without consideration of vehicle dynamics. These include gross vehicle weight, axle and tire configurations, tire contact conditions and static load sharing in axle group suspensions. The dynamic tire forces generated by heavy vehicles are examined in Chapter 4. The discussion includes their simulation and measurement, their principal characteristics, the effects of tires and suspension design on dynamic forces, and the potential benefits of using advanced suspensions for minimizing dynamic tire forces. Chapter 5 discusses methods for estimating the effects of dynamic tire forces on road damage. The two main approaches are either to examine the statistics of the forces themselves; or to calculate the response of a pavement model to the forces, and to calculate the resulting wear using a material damage model. The issues involved in assessing vehicles for 'road friendliness' are discussed in Chapter 6. Possible assessment methods include measuring strains in an instrumented pavement traversed by the vehicle, measuring dynamic tire forces, or measuring vehicle parameters such as the 'natural frequency' and 'damping ratio'. Each of these measurements involves different assumptions and analysis methods for converting the results into some measure of road damage. Chapter 7 includes a summary of the main conclusions of the paper and recommendations for tire and suspension design, road design and construction, and for vehicle regulations.

A computational fluid-structure interaction study of inflation cycles of a tension cone decelerator

Inflatable aerodynamic decelerators present potential advantages for planetary entry in missions of robotic and human exploration. The design of these structures face many engineering challenges, including complex deformable geometries, anisotropic material response, and coupled shockturbulence interactions. In this paper, we describe a comprehensive computational fluid-structure interaction study of an inflation cycle of a tension cone decelerator in supersonic flow and compare the simulations with earlier published experimental results. The aeroshell design and flow conditions closely match recent experiments conducted at Mach 2.5. The structural model is a 16-sided polygonal tension cone with seams between each segment. The computational model utilizes adaptive mesh refinement, large-eddy simulation, and shell mechanics with self-contact modeling to represent the flow and structure interaction. This study focuses on the dynamics of the structure as the inflation pressure varies gradually, and the behavior of forces experienced by the flexible and rigid (the payload capsule) structures. © 2011 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Interaction of linear waves with an array of infinitely long horizontal circular cylinders in a two-layer fluid of infinite depth

The linear water wave scattering and radiation by an array of infinitely long horizontal circular cylinders in a two-layer fluid of infinite depth is investigated by use of the multipole expansion method. The diffracted and radiated potentials are expressed as a linear combination of infinite multipoles placed at the centre of each cylinder with unknown coefficients to be determined by the cylinder boundary conditions. Analytical expressions for wave forces, hydrodynamic coefficients, reflection and transmission coefficients and energies are derived. Comparisons are made between the present analytical results and those obtained by the boundary element method, and some examples are presented to illustrate the hydrodynamic behavior of multiple horizontal circular cylinders in a two-layer fluid. It is found that for two submerged circular cylinders the influence of the fluid density ratio on internal-mode wave forces is more appreciable than surface-mode wave forces, and the periodic oscillations of hydrodynamic results occur with the increase of the distance between two cylinders; for four submerged circular cylinders the influence of adding two cylinders on the wave forces of the former cylinders is small in low and high wave frequencies, but the influence is appreciable in intermediate wave frequencies.

Interaction of linear waves with infinitely long horizontal cylinders studied by boundary element method

The two-dimensional problems concerning the interaction of linear water waves with cylinders of arbitrary shape in two-layer deep water are investigated by use of the Boundary Integral Equation method (BIEM). Simpler new expressions for the Green functions are derived, and verified by comparison of results obtained by BIEM with these by an analytical method. Examined are the radiation and scattering of linear waves by two typical configurations of cylinders in two-layer deep water. Hydrodynamic behaviors including hydrodynamic coefficients, wave forces, reflection and transmission coefficients and energies are analyzed in detail, and some interesting physical phenomena are observed.

Properties of proto-neutron star and effect of three-body forces

Within the Brueckner-Hartree-Fock framework, the equation of state and the properties of newborn neutron stars are investigated by adopting a realistic nucleon-nucleon interaction AV(18) supplemented with a microscopic three-body force or a phenomenological three-body force. The maximum mass of newborn neutron star and the proton fraction in the newborn beta-stable neutron-star matter are calculated. The neutrino-trapping and the three-body force effects are discussed, and the interplay between the effects of the trapped neutrino and the three-body force are especially explored. It is shown that neutrino trapping considerably affects the proton abundance and the equation of state of the newborn neutron star in both cases with and without the three-body forces. The effect of neutrino trapping remarkably enhances the proton abundance, and the contribution of the three-body force makes the equation of state of the newborn neutron star much stiffer at high densities and consequently increases the proton abundance strongly. The trapped neutrinos significantly reduce the influence of the three-body force on the proton abundance in newborn neutron stars.

Numerical modeling of water wave interaction with a soft mud bed

A vertical 2-D numerical model is presented for simulating the interaction between water waves and a soft mud bed. Taking into account nonlinear rheology, a semi-empirical rheological model is applied to this water-mud model, reflecting the combined visco-elasto-plastic properties of soft mud under such oscillatory external forces as water waves. In order to increase the resolution of the flow in the neighborhood of both sides of the inter-surface, a logarithmic grid in the vertical direction is employed for numerical treatment. Model verifications are given through comparisons between the calculated and the measured mud mass transport velocities as well as wave height changes.

Development and validation of Fluid Structure Interaction Methods for an Oscillating Wave Surge Converter

The term fatigue loads on the Oyster Oscillating Wave Surge Converter (OWSC) is used to describe hydrostatic loads due to water surface elevation with quasi-static changes of state. Therefore a procedure to implement hydrostatic pressure distributions into finite element analysis of the structure is desired. Currently available experimental methods enable one to measure time variant water surface elevation at discrete locations either on or around the body of the scale model during tank tests. This paper discusses the development of a finite element analysis procedure to implement time variant, spatially distributed hydrostatic pressure derived from discretely measured water surface elevation. The developed method can process differently resolved (temporal and spatial) input data and approximate the elevation over the flap faces with user defined properties. The structural loads, namely the forces and moments on the body can then be investigated by post processing the numerical results. This method offers the possibility to process surface elevation or hydrostatic pressure data from computational fluid dynamics simulations and can thus be seen as a first step to a fluid-structure interaction model.

Environmental and track perturbations on multiple pantograph interaction with catenaries in high-speed trains

The top velocity of high-speed trains is generally limited by the ability to supply the proper amount of energy through the pantograph-catenary interface. The deterioration of this interaction can lead to the loss of contact, which interrupts the energy supply and originates arcing between the pantograph and the catenary, or to excessive contact forces that promote wear between the contacting elements. Another important issue is assessing on how the front pantograph influences the dynamic performance of the rear one in trainsets with two pantographs. In this work, the track and environmental conditions influence on the pantograph-catenary is addressed, with particular emphasis in the multiple pantograph operations. These studies are performed for high speed trains running at 300 km/h with relation to the separation between pantographs. Such studies contribute to identify the service conditions and the external factors influencing the contact quality on the overhead system. (C) 2013 Elsevier Ltd. All rights reserved.

Numerical Investigations on Soil Structure Interaction of Multistorey Frames

Frames are the most widely used structural system for multistorey buildings. A building frame is a three dimensional discrete structure consisting of a number of high rise bays in two directions at right angles to each other in the vertical plane. Multistorey frames are a three dimensional lattice structure which are statically indeterminate. Frames sustain gravity loads and resist lateral forces acting on it. India lies at the north westem end of the Indo-Australian tectonic plate and is identified as an active tectonic area. Under horizontal shaking of the ground, horizontal inertial forces are generated at the floor levels of a multistorey frame. These lateral inertia forces are transferred by the floor slab to the beams, subsequently to the columns and finally to the soil through the foundation system. There are many parameters that affect the response of a structure to ground excitations such as, shape, size and geometry of the structure, type of foundation, soil characteristics etc. The Soil Structure Interaction (SS1) effects refer to the influence of the supporting soil medium on the behavior of the structure when it is subjected to different types of loads. Interaction between the structure and its supporting foundation and soil, which is a complete system, has been modeled with finite elements. Numerical investigations have been carried out on a four bay, twelve storeyed regular multistorey frame considering depth of fixity at ground level, at characteristic depth of pile and at full depth. Soil structure interaction effects have been studied by considering two models for soil viz., discrete and continuum. Linear static analysis has been conducted to study the interaction effects under static load. Free vibration analysis and further shock spectrum analysis has been conducted to study the interaction effects under time dependent loads. The study has been extended to four types of soil viz., laterite, sand, alluvium and layered.The structural responses evaluated in the finite element analysis are bending moment, shear force and axial force for columns, and bending moment and shear force for beams. These responses increase with increase in the founding depth; however these responses show minimal increase beyond the characteristic length of pile. When the soil structure interaction effects are incorporated in the analysis, the aforesaid responses of the frame increases upto the characteristic depth and decreases when the frame has been analysed for the full depth. It has been observed that shock spectrum analysis gives wide variation of responses in the frame compared to linear elastic analysis. Both increase and decrease in responses have been observed in the interior storeys. The good congruence shown by the two finite element models viz., discrete and continuum in linear static analysis has been absent in shock spectrum analysis.