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.

Pull-in Instability Study of Carbon Nanotube Tweezers Under the Influence of Van der Waals Forces

The pull-in instability of two nanotubes under van der Waals force is studied. The cantilever beam with large deformation model is used. The influence of nanotube parameters such as the interior radius, the gap distance between the two nanotubes, etc, on the pull-in instability is studied. The critical nanotube length is determined for each specific set of nanotube parameters. The Galerkin method is applied to discretize the governing equations, and it shows good convergence.

Cell shape changes indicate a role for extrinsic tensile forces in Drosophila germ-band extension.

Drosophila germ-band extension (GBE) is an example of the convergence and extension movements that elongate and narrow embryonic tissues. To understand the collective cell behaviours underlying tissue morphogenesis, we have continuously quantified cell intercalation and cell shape change during GBE. We show that the fast, early phase of GBE depends on cell shape change in addition to cell intercalation. In antero-posterior patterning mutants such as those for the gap gene Krüppel, defective polarized cell intercalation is compensated for by an increase in antero-posterior cell elongation, such that the initial rate of extension remains the same. Spatio-temporal patterns of cell behaviours indicate that an antero-posterior tensile force deforms the germ band, causing the cells to change shape passively. The rate of antero-posterior cell elongation is reduced in twist mutant embryos, which lack mesoderm. We propose that cell shape change contributing to germ-band extension is a passive response to mechanical forces caused by the invaginating mesoderm.

Study on current-random wave forces acting on a framework

The forces of random wave plus current acting on a simplified offshore platform (jacket) model have been studied numerically and experimentally. The numerical results are in good agreement with experiments. The mean force can be approximated as a function of equivalent velocity parameter and the root-mean-square force as a function of equivalent significant wave height parameter.

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.

Microfabricated tissue gauges to measure and manipulate forces from 3D microtissues

Physical forces generated by cells drive morphologic changes during development and can feedback to regulate cellular phenotypes. Because these phenomena typically occur within a 3-dimensional (3D) matrix in vivo, we used microelectromechanical systems (MEMS) technology to generate arrays of microtissues consisting of cells encapsulated within 3D micropatterned matrices. Microcantilevers were used to simultaneously constrain the remodeling of a collagen gel and to report forces generated during this process. By concurrently measuring forces and observing matrix remodeling at cellular length scales, we report an initial correlation and later decoupling between cellular contractile forces and changes in tissue morphology. Independently varying the mechanical stiffness of the cantilevers and collagen matrix revealed that cellular forces increased with boundary or matrix rigidity whereas levels of cytoskeletal and extracellular matrix (ECM) proteins correlated with levels of mechanical stress. By mapping these relationships between cellular and matrix mechanics, cellular forces, and protein expression onto a bio-chemo-mechanical model of microtissue contractility, we demonstrate how intratissue gradients of mechanical stress can emerge from collective cellular contractility and finally, how such gradients can be used to engineer protein composition and organization within a 3D tissue. Together, these findings highlight a complex and dynamic relationship between cellular forces, ECM remodeling, and cellular phenotype and describe a system to study and apply this relationship within engineered 3D microtissues.

Experimental Investigation of the Velocity Effect on Adhesion Forces with an Atomic Force Microscope Atomic Force Microscope

Capillary forces are significantly dominant in adhesive forces measured with an atomic force microscope (AFM) in ambient air, which are always thought to be dependent on water film thickness, relative humidity, and the free energy of water film. We study the nature of the pull-off force on a variety of surfaces as a function of tip velocity. It is found that the capillary forces are of relatively strong dependence on tip velocity. The present experiment is expected to provide a better understanding of the work mechanism of AFM in ambient air.

Spatial repeatability of dynamic tyre forces generated by heavy vehicles

Road damage due to heavy vehicles is thought to be dependent on the extent to which lorries in normal traffic apply peak forces to the same locations along the road. A validated vehicle simulation is used to simulate 37 leaf-sprung articulated vehicles with parametric variations typical of vehicles in one weight class in the highway vehicle fleet. The spatial distribution of tyre forces generated by each vehicle is compared with the distribution generated by a reference vehicle, and the conditions are established for which repeated heavy loading occurs at specific points along the road. It is estimated that approximately two-thirds of vehicles in this class (a large proportion of all heavy vehicles) may contribute to a repeated pattern of road loading. It is concluded that dynamic tyre forces are a significant factor influencing road damage, compared to other factors such as tyre configuration and axle spacing.

Control of Mean and Fluctuating Forces on a Circular Cylinder at High Reynolds Numbers

A narrow strip is used to control mean and fluctuating forces on a circular cylinder at Reynolds numbers from 2.0 x 10(4) to 1.0 x 10(5). The axes of the strip and cylinder are parallel. The control parameters are strip width ratio and strip position characterized by angle of attack and distance from the cylinder. Wind tunnel tests show that the vortex shedding from both sides of the cylinder can be suppressed, and mean drag and fluctuating lift on the cylinder can be reduced if the strip is installed in an effective zone downstream of the cylinder. A phenomenon of mono-side vortex shedding is found. The strip-induced local changes of velocity profiles in the near wake of the cylinder are measured, and the relation between base suction and peak value in the power spectrum of fluctuating lift is studied. The control mechanism is then discussed from different points of view.