An analysis of the cooperative mechano-sensitive feedback between intracellular signaling, focal adhesion development, and stress fiber contractility

Cells communicate with their external environment via focal adhesions and generate activation signals that in turn trigger the activity of the intracellular contractile machinery. These signals can be triggered by mechanical loading that gives rise to a cooperative feedback loop among signaling, focal adhesion formation, and cytoskeletal contractility, which in turn equilibrates with the applied mechanical loads. We devise a signaling model that couples stress fiber contractility and mechano-sensitive focal adhesion models to complete this above mentioned feedback loop. The signaling model is based on a biochemical pathway where IP3 molecules are generated when focal adhesions grow. These IP3 molecules diffuse through the cytosol leading to the opening of ion channels that disgorge Ca2+ from the endoplasmic reticulum leading to the activation of the actin/myosin contractile machinery. A simple numerical example is presented where a one-dimensional cell adhered to a rigid substrate is pulled at one end, and the evolution of the stress fiber activation signal, stress fiber concentrations, and focal adhesion distributions are investigated. We demonstrate that while it is sufficient to approximate the activation signal as spatially uniform due to the rapid diffusion of the IP3 through the cytosol, the level of the activation signal is sensitive to the rate of application of the mechanical loads. This suggests that ad hoc signaling models may not be able to capture the mechanical response of cells to a wide range of mechanical loading events. © 2011 American Society of Mechanical Engineers.

Performance prediction of graphene nanoribbon and carbon nanotube transistors

Carbon nanotubes (CNTs) and graphene nanoribbons (GNRs) field-effect transistor (FET) can be the basis for a quasi-one- dimensional (Q1D) transistor technology. Recent experiments show that the on-off ratio for GNR devices can be improved to level exploration of transistor action is justified. Here we use the tight-binding energy dipersion approximation, to assess the performance of semiconducting CNT and GNR is qualitatively in terms of drain current drive strength, bandgap and density of states for a specified device. By reducing the maximum conductance 4e2/h by half, we observed that our model has a particularly good fit with 50 nm channel single walled carbon nanotube (SWCNT) experimental data. Given the same bandgap, CNTs outperform GNRs due to valley degeneracy. Nevertheless, the variation of the device contacts will decide which transistor will exhibit better conductivity and thus higher ON currents. © 2011 American Institute of Physics.

CHANGES IN PREDICTED MOS DEVICE CHARACTERISTICS DUE TO THE USE OF TWO DIMENSIONAL SOURCE/DRAIN PROFILES.

Two-dimensional MOS device simulation programs such as MINIMOS left bracket 1 right bracket are limited in their validity due to assumptions made in defining the initial two-dimensional source/drain profiles. The two options available to define source/drain regions both construct a two-dimensional profile from one-dimensional profiles normal to the surface. Inaccuracies in forming these source/drain profiles can be expected to effect predicted device characteristics as channel dimensions of the device are reduced. This paper examines these changes by interfacing numerically similated two dimensional source/drain profiles to MINIMOS and comparing predicted I//D-V//D characteristics with 2-D interfacing, 2-D profiles constructed from interfaced 1-D profiles and MINIMOS self generated profiles. Data obtained for simulations of 3 mu m N and P channel devices are presented.

An efficient model for the dynamic behaviour of a single pile in viscoelastic soil

This paper presents a novel, three-dimensional, single-pile model, formulated in the wavenumber domain and adapted to account for boundary conditions using the superposition of loading cases. The pile is modelled as a column in axial vibration, and a Euler-Bernoulli beam in lateral vibration. The surrounding soil is treated as a viscoelastic continuum. The response of the pile is presented in terms of the stiffness and damping coefficients, and also the magnitude and phase of the pile-head frequency-response function. Comparison with existing models shows that excellent agreement is observed between this model, a boundary-element formulation, and an elastic-continuum-type formulation. This three-dimensional model has an accuracy equivalent to a 3D boundary-element model, and a runtime similar to a 2D plane-strain analytical model. Analysis of the response of the single pile illustrates a difference in axial and lateral vibration behaviour; the displacement along the pile is relatively invariant under axial loads, but in lateral vibration the pile exhibits localised deformations. This implies that a plane-strain assumption is valid for axial loadings and only at higher frequencies for lateral loadings. © 2013 Elsevier Ltd.

A fast detailed-chemistry modelling approach for simulating the SI-HCCI transition

An established Stochastic Reactor Model (SRM) is used to simulate the transition from Spark Ignition (SI) to Homogeneous Charge Compression Ignition (HCCI) combustion mode in a four cylinder in-line four-stroke naturally aspirated direct injection SI engine with cam profile switching. The SRM is coupled with GT-Power, a one-dimensional engine simulation tool used for modelling engine breathing during the open valve portion of the engine cycle, enabling multi-cycle simulations. The mode change is achieved by switching the cam profiles and phasing, resulting in a Negative Valve Overlap (NVO), opening the throttle, advancing the spark timing and reducing the fuel mass as well as using a pilot injection. A proven technique for tabulating the model is used to create look-up tables in both SI and HCCI modes. In HCCI mode several tables are required, including tables for the first NVO, transient valve timing NVO, transient valve timing HCCI and steady valve timing HCCI and NVO. This results in the ability to simulate the transition with detailed chemistry in very short computation times. The tables are then used to optimise the transition with the goal of reducing NO x emissions and fluctuations in IMEP. Copyright © 2010 SAE International.

A detailed chemistry simulation of the SI-HCCI transition

A Stochastic Reactor Model (SRM) has been used to simulate the transition from Spark Ignition (SI) mode to Homogeneous Charge Compression Ignition (HCCI) mode in a four cylinder in-line four-stroke naturally aspirated direct injection SI engine with cam profile switching. The SRM is coupled with GT-Power, a one-dimensional engine simulation tool used for modelling engine breathing during the open valve portion of the engine cycle, enabling multi-cycle simulations. The model is initially calibrated in both modes using steady state data from SI and HCCI operation. The mode change is achieved by switching the cam profiles and phasing, resulting in a Negative Valve Overlap (NVO), opening the throttle, advancing the spark timing and reducing the fuel mass as well as utilising a pilot injection. Experimental data is presented along with the simulation results. The model is used to investigate key control parameters and their effects on parameters that are difficult to measure experimentally. The effect of the spark in the first HCCI cycles is found to have a major impact on the stability of the transition. Copyright © 2010 SAE International.

Numerical simulation of post-flame oxidation of hydrocarbons in spark ignition engines

About 50-90 percent of the hydrocarbons that escape combustion during flame passage in spark-ignition engine operation are oxidized in the cylinder before leaving the system. The process involves the transport of unreacted fuel from cold walls towards the hotter burned gas regions and subsequent reaction. In order to understand controlling factors in the process, a transient one-dimensional reactive-diffusive model has been formulated for simulating the oxidation processes taking place in the reactive layer between hot burned gases and cold unreacted air/fuel mixture, with initial and boundary conditions provided by the emergence of hydrocarbons from the piston top land crevice. Energy and species conservation equations are solved for the entire process, using a detailed chemical kinetic mechanism for propane. Simulation results show that the post-flame oxidation process takes place within a reactive layer where intermediate hydrocarbon products are formed at temperatures above 1100-1200 K, followed by a carbon monoxide conversion region closer to the hot burned gases. Model results show that most of hydrocarbons leaving the crevice are completely oxidized inside the cylinder. The largest contribution of remaining hydrocarbons are those leaving the crevice at temperatures below 1400 K. The largest fraction of non-fuel (intermediate) hydrocarbons results from hydrocarbons leaving the crevice when core temperatures are around 1400 K Copyright © 1997 Society of Automotive Engineers, Inc.

Wave propagation under vertically excited surface foundation

Recently developed equipment allows measurement of the shear modulus of soil in situ as a function of level of strain. In these field experiments, the excitation is applied on the ground surface using large scale shakers, and the response of the soil deposit is recorded through embedded receivers. The focus of this paper is on the simulation of signals which would be recorded at the receiver locations in idealized conditions to provide guidelines on the interpretation of field measurements. Discrete and finite element methods are employed to model one dimensional and three dimensional geometries, respectively, under various lateral boundary conditions. When the first times of arrival are detected by receivers under the vertical impulse, they coincide with the arrival of the P wave, related to the constrained modulus of the material, regardless of lateral boundary conditions. If one considers, on the other hand, phase differences between the motions at two receivers the picture is far more complicated and one would obtain propagation velocities, function of frequency and depth, which do not correspond to either the constrained modulus or Young's modulus. It is thus necessary to apply some care when interpreting the data from field tests based on vertical steady state vibrations. The use of inverse analysis can be considered as a way of extracting the shear modulus of soil from the field test measurements. © 2008 ASCE.

Seismic response of submarine slopes

The geological profile of submerged slopes on the continental shelf typically includes soft cohesive soils with thicknesses ranging from a few meters to tens or hundreds of meters. The response of these soils in simple shear tests is largely influenced by the presence of an initial consolidation shear stress, inducing anisotropic stress-strain-strength properties which depend also on the direction of shear. In this paper, a new simplified effective-stress-based model describing the behavior of normally to lightly overconsolidated cohesive soils is used in conjunction with a one-dimensional seismic site response analysis computer code to illustrate the importance of accounting for anisotropy and small strain nonlinearity. In particular, a simple example is carried out to compare results for different slope inclinations. Depth profiling of the maximum shear strains and permanent deformations provide insight into the mechanisms of deformation during a seismic event, and the effects of sloping ground conditions.

Global analysis of dynamical decision-making models through local computation around the hidden saddle

Bistable dynamical switches are frequently encountered in mathematical modeling of biological systems because binary decisions are at the core of many cellular processes. Bistable switches present two stable steady-states, each of them corresponding to a distinct decision. In response to a transient signal, the system can flip back and forth between these two stable steady-states, switching between both decisions. Understanding which parameters and states affect this switch between stable states may shed light on the mechanisms underlying the decision-making process. Yet, answering such a question involves analyzing the global dynamical (i.e., transient) behavior of a nonlinear, possibly high dimensional model. In this paper, we show how a local analysis at a particular equilibrium point of bistable systems is highly relevant to understand the global properties of the switching system. The local analysis is performed at the saddle point, an often disregarded equilibrium point of bistable models but which is shown to be a key ruler of the decision-making process. Results are illustrated on three previously published models of biological switches: two models of apoptosis, the programmed cell death and one model of long-term potentiation, a phenomenon underlying synaptic plasticity. © 2012 Trotta et al.

Material point method for coupled hydromechanical problems

This paper describes a new formulation of the material point method (MPM) for solving coupled hydromechanical problems of fluid-saturated soil subjected to large deformation. A soil-pore fluid coupled MPM algorithm based on Biot's mixture theory is proposed for solving hydromechanical interaction problems that include changes in water table location with time. The accuracy of the proposed method is examined by comparing the results of the simulation of a one-dimensional consolidation test with the corresponding analytical solution. A sensitivity analysis of the MPM parameters used in the proposed method is carried out for examining the effect of the number of particles per mesh and mesh size on solution accuracy. For demonstrating the capability of the proposed method, a physical model experiment of a large-scale levee failure by seepage is simulated. The behavior of the levee model with time-dependent changes in water table matches well to the experimental observations. The mechanisms of seepage-induced failure are discussed by examining the pore-water pressures, as well as the effective stresses computed from the simulations © 2013 American Society of Civil Engineers.

Effects of electron-electron interactions on the electronic Raman scattering of graphite in high magnetic fields

We report the observation of strongly temperature (T)-dependent spectral lines in electronic Raman-scattering spectra of graphite in a high magnetic field up to 45 T applied along the c axis. The magnetic field quantizes the in-plane motion, while the out-of-plane motion remains free, effectively reducing the system dimension from 3 to 1. Optically created electron-hole pairs interact with, or shake up, the one-dimensional Fermi sea in the lowest Landau subbands. Based on the Tomonaga-Luttinger liquid theory, we show that interaction effects modify the spectral line shape from (ω-Δ)-1/2 to (ω-Δ)2α-1/2 at T = 0. At finite T, we predict a thermal broadening factor that increases linearly with T. Our model reproduces the observed T-dependent line shape, determining the electron-electron interaction parameter α to be ∼0.05 at 40 T. © 2014 American Physical Society.

A framework for the analysis of thermal losses in reciprocating compressors and expanders

This article presents a framework that describes formally the underlying unsteady and conjugate heat transfer processes that are undergone in thermodynamic systems, along with results from its application to the characterization of thermodynamic losses due to irreversible heat transfer during reciprocating compression and expansion processes in a gas spring. Specifically, a heat transfer model is proposed that solves the one-dimensional unsteady heat conduction equation in the solid simultaneously with the first law in the gas phase, with an imposed heat transfer coefficient taken from suitable experiments in gas springs. Even at low volumetric compression ratios (of 2.5), notable effects of unsteady heat transfer to the solid walls are revealed, with thermally induced thermodynamic cycle (work) losses of up to 14% (relative to the work input/output in equivalent adiabatic and reversible compression/expansion processes) at intermediate Péclet numbers (i.e., normalized frequencies) when unfavorable solid and gas materials are selected, and closer to 10-12% for more common material choices. The contribution of the solid toward these values, through the conjugate variations attributed to the thickness of the cylinder wall, is about 8% and 2% points, respectively, showing a maximum at intermediate thicknesses. At higher compression ratios (of 6) a 19% worst-case loss is reported for common materials. These results suggest strongly that in designing high-efficiency reciprocating machines the full conjugate and unsteady problem must be considered and that the role of the solid in determining performance cannot, in general, be neglected. © 2014 Richard Mathie, Christos N. Markides, and Alexander J. White. Published with License by Taylor & Francis.

Minimalistic models of an energy efficient vertical hopping robot

The use of free vibration in elastic structure can lead to energy efficient robot locomotion, since it significantly reduces the energy expenditure if properly designed and controlled. However, it is not well understood how to harness the dynamics of free vibration for the robot locomotion, because of the complex dynamics originated in discrete events and energy dissipation during locomotion. From this perspective, this paper explores three minimalistic models of free vibration that can characterize the basic principle of robot locomotion. Since the robot mainly exhibits vertical hopping, three one-dimensional models are examined that contain different configurations of simple spring-damper-mass components. The self-stability of these models are also investigated in simulation. The real-world and simulation experiments show that one of the models best characterizes the robot hopping, through analyzing the basic kinematics and negative works in actuation. Based on this model, the control parameters are analyzed for the energy efficient hopping. © 2013 IEEE.