Intracellular demography and the dynamics of Salmonella enterica infections.

An understanding of within-host dynamics of pathogen interactions with eukaryotic cells can shape the development of effective preventive measures and drug regimes. Such investigations have been hampered by the difficulty of identifying and observing directly, within live tissues, the multiple key variables that underlay infection processes. Fluorescence microscopy data on intracellular distributions of Salmonella enterica serovar Typhimurium (S. Typhimurium) show that, while the number of infected cells increases with time, the distribution of bacteria between cells is stationary (though highly skewed). Here, we report a simple model framework for the intensity of intracellular infection that links the quasi-stationary distribution of bacteria to bacterial and cellular demography. This enables us to reject the hypothesis that the skewed distribution is generated by intrinsic cellular heterogeneities, and to derive specific predictions on the within-cell dynamics of Salmonella division and host-cell lysis. For within-cell pathogens in general, we show that within-cell dynamics have implications across pathogen dynamics, evolution, and control, and we develop novel generic guidelines for the design of antibacterial combination therapies and the management of antibiotic resistance.

Molecular Dynamics Simulation of Thermal and Mechanical Properties of Polyimide-Carbon-Nanotube Composites

An aromatic polyimide and its mixture with randomly distributed carbon nanotubes (NTs) are simulated by using molecular dynamics, repeated energy minimization and cooling processes. The glass transition temperatures are identified through volume-temperature curves. Stress-strain curves, Young's moduli, densities and Poisson ratios are computed at different temperatures. It is demonstrated that the carbon NT reduces the softening effects of temperature on mechanical properties and increases the ability to resist deformation.

Modelling nonlinear vehicle dynamics with neural networks

The nonlinear modelling ability of neural networks has been widely recognised as an effective tool to identify and control dynamic systems, with applications including nonlinear vehicle dynamics which this paper focuses on using multi-layer perceptron networks. Existing neural network literature does not detail some of the factors which effect neural network nonlinear modelling ability. This paper investigates into and concludes on required network size, structure and initial weights, considering results for networks of converged weights. The paper also presents an online training method and an error measure representing the network's parallel modelling ability over a range of operating conditions. Copyright © 2010 Inderscience Enterprises Ltd.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

The design of an agent for modelling supply chain network dynamics

A useful insight into managerial decision making can be found from simulation of business systems, but existing work on simulation of supply chain behaviour has largely considered non-competitive chains. Where competitive agents have been examined, they have generally had a simple structure and been used for fundamental examination of stability and equilibria rather than providing practical guidance to managers. In this paper, a new agent for the study of competitive supply chain network dynamics is proposed. The novel features of the agent include the ability to select between competing vendors, distribute orders preferentially among many customers, manage production and inventory, and determine price based on competitive behaviour. The structure of the agent is related to existing business models and sufficient details are provided to allow implementation. The agent is tested to demonstrate that it recreates the main results of the existing modelling and management literature on supply chain dynamics. A brief exploration of competitive dynamics is given to confirm that the proposed agent can respond to competition. The results demonstrate that overall profitability for a supply chain network is maximised when businesses operate collectively. It is possible for an individual business to achieve higher profits by adopting a more competitive stance, but the consequence of this is that the overall profitability of the network is reduced. The agent will be of use for a broad range of studies on the long-run effect of management decisions on their network of suppliers and customers.

Dynamics of collapsing fluidized beds and its application in the simulation of pulsed fluidized beds

A new method to study collapsing process of fluidized bed was proposed. The method is based on the analysis of the pressure variation during collapse. A model is proposed to describe the pressure variation on any location of the bed during collapse. Three kind of particles were fluidized by air and the pressure variation after shutting down the gas supply was measured by pressure transducers and simulated by the proposed model. The simulated results were in good agreement with the experimental data. The parameters of the fluidized bed, such as bubble fraction alpha(b), particle fraction in dense phase alpha(p), bubble velocity u(b) and slip velocity of particle u(i), can be estimated from the measured pressure data by using the proposed model. The model was also used to calculate the pressure variation in pulsed fluidized beds with low frequency.

Forced extension of P-selectin construct using steered molecular dynamics

P-selectin, a 70-nm-long cellular adhesive molecule, possesses elastic and extensible properties when neutrophils roll over the activated endotheliam of blood vessel in inflammatory reaction. Transient formation and dissociation of P-selectin/ligand bond on applied force of blood flow induces the extension of P-selectin and relevant ligands. Steered molecular dynamics simulations were performed to stretch a single P-selectin construct consisting of a lectin (Lec) domain and an epithelial growth factor (EGF)-like domain, where P-selectin construct was forced to extend in water with pulling velocities of 0.005-0.05 nm/ps and with constant forces of 1000-2500 pN respectively. Resulting force-extension profiles exhibited a dual-peak pattern on various velocities, while both plateaus and shoulders appeared in the extension-time profiles on various forces. The force or extension profiles along stretching pathways were correlated to the conformational changes, suggesting that the structural collapses of P-selectin Lec/EGF domains were mainly attributed to the burst of hydrogen bonds within the major beta sheet of EGF domain and the disruptions of two hydrophobic cores of Lee domain. This work furthers the understanding of forced dissociation of P-selectin/ligand bond.

A Molecular Dynamics Simulation: the Effect of Finite Size on the Thermal Conductivity in a Single Crystal Silicon

Non-equilibrium molecular dynamics (NEMD) simulations are performed to calculate thermal conductivity. The environment-dependent interatomic potential (EDIP) potential on crystal silicon is adopted as a model system. The issues are related to nonlinear response, local thermal equilibrium and statistical averaging. The simulation results by non-equilibrium molecular dynamics show that the calculated thermal conductivity decreases almost linearly as the film thickness reduced at the nanometre scale. The effect of size on the thermal conductivity is also obtained by a theoretic analysis of the kinetic theory and formulas of the heat capacity. The analysis reveals that the contributions of phonon mean free path (MFP) and phonon number in a finite cell to thermal conductivity are very important.

A Constrained Particle Dynamics for Continuum-Particle Hybrid Method in Micro- and Nano-Fluidics

A hybrid method of continuum and particle dynamics is developed for micro- and nano-fluidics, where fluids are described by a molecular dynamics (MD) in one domain and by the Navier-Stokes (NS) equations in another domain. In order to ensure the continuity of momentum flux, the continuum and molecular dynamics in the overlap domain are coupled through a constrained particle dynamics. The constrained particle dynamics is constructed with a virtual damping force and a virtual added mass force. The sudden-start Couette flows with either non-slip or slip boundary condition are used to test the hybrid method. It is shown that the results obtained are quantitatively in agreement with the analytical solutions under the non-slip boundary conditions and the full MD simulations under the slip boundary conditions.

Dynamics Of Fine Particles In Liquid-Solid Fluidized Beds

On the basis of the Local Equilibrium Model (LEM), fine particles with large Richardson-Zaki exponent n show, under certain conditions during bed expansion and collapse, different dynamic behavior from particles with small n. For an expansion process there may be a concentration discontinuity propagating upward from the distributor, and, on the contrary, for a collapse process there may be a progressively broadening and upward-propagating continuous transition zone instead of discontinuity. The predictions of the bed height variation and the discontinuity trace have been validated experimentally. (c) 2007 Chinese Society of Particuology and Institute of Process Engineering, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Tolman Effect On Fluid Dynamics In Carbon Nanotubes

The numerical solutions of or(R) given by two different methods (Samsonov et al., 2003; and Lu et al., 2005) are compared with the result that they are coincident closely (the difference is within 4%). We conclude that it is necessary to consider the Tolman correction in the calculation of fluid dynamics in carbon nanotubes. Although our conclusion is the same as that of Prylutskyy et al. (2005), the sign of our Tolman correction is opposite to theirs, and the difference can be attributed to the errors appeared in the paper of Prylutskyy et al.

Molecular Dynamics And Density Functional Studies Of A Body-Centered-Tetragonal Polymorph Of Zno

We report a previously unknown body-centered-tetragonal structure for ZnO. This structure results from a phase transformation from wurtzite in [0001]-oriented nanorods during uniaxial tensile loading and is the most stable phase for ZnO when stress is above 7 GPa. The stress-induced phase transformation has important implications for the electronic, piezoelectric, mechanical, and thermal responses of ZnO. The discovery of this polymorph brings about a more complete understanding of the extent and nature of polymorphism in ZnO. A crystalline structure-load triaxiality map is developed to summarize the relationship between structure and loading.

Size-Dependent Elastic Properties Of Ni Nanofilms By Molecular Dynamics Simulation

Size-dependent elastic properties of Ni nanofilms are investigated by molecular dynamics ( MD) simulations with embedded atom method (EAM). The surface effects are considered by calculating the surface relaxation, surface energy, and surface stress. The Young's modulus and yield stress are obtained as functions of thickness and crystallographic orientation. It is shown that the surface relaxation has important effects on the the elastic properties at nanoscale. When the surface relaxation is outward, the Young's modulus decreases with the film thickness decreasing, and vice versa. The results also show that the yield stresses of the films increase with the films becoming thinner. With the thickness of the nanofilms decreasing, the surface effects on the elastic properties become dominant.

Molecular Dynamics Simulation Of Adhesion Forces In A Dipalmitoylphosphatidylcholine Membrane

Adhesion forces of Dipalmitoylphosphatidylcholine ( DPPC) membrane in the gel phase are investigated by molecular dynamics ( MD) simulation. In the simulations, individual DPPC molecules are pulled out of DPPC membranes with different rates and we get the maximum adhesion forces of DPPC membrane. We find that the maximum adhesion forces increase with pull rate, from about 400 to 700 pN when pull rates are from 0.001 to 0.03 nm/ps. We analyze the relationship between pull rate and adhesion forces of different origins using Brownian dynamics and notice that viscosity of solvent plays an important role in adhesion forces. Then we simulate the motion of a single DPPC molecule in solvent and it elucidates that the maximum drag force is almost linear with respect to the pull rate. We use Stokes' relation to describe the motion of a single DPPC molecule and deduce the effective length of a DPPC molecule. Conformational analyses indicate that the free energy variation of a DPPC molecule inside and outside of the DPPC membrane is an essential part of adhesion energy.