Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

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.

Modelling within-host spatiotemporal dynamics of invasive bacterial disease

Mechanistic determinants of bacterial growth, death, and spread within mammalian hosts cannot be fully resolved studying a single bacterial population. They are also currently poorly understood. Here, we report on the application of sophisticated experimental approaches to map spatiotemporal population dynamics of bacteria during an infection. We analyzed heterogeneous traits of simultaneous infections with tagged Salmonella enterica populations (wild-type isogenic tagged strains [WITS]) in wild-type and gene-targeted mice. WITS are phenotypically identical but can be distinguished and enumerated by quantitative PCR, making it possible, using probabilistic models, to estimate bacterial death rate based on the disappearance of strains through time. This multidisciplinary approach allowed us to establish the timing, relative occurrence, and immune control of key infection parameters in a true host-pathogen combination. Our analyses support a model in which shortly after infection, concomitant death and rapid bacterial replication lead to the establishment of independent bacterial subpopulations in different organs, a process controlled by host antimicrobial mechanisms. Later, decreased microbial mortality leads to an exponential increase in the number of bacteria that spread locally, with subsequent mixing of bacteria between organs via bacteraemia and further stochastic selection. This approach provides us with an unprecedented outlook on the pathogenesis of S. enterica infections, illustrating the complex spatial and stochastic effects that drive an infectious disease. The application of the novel method that we present in appropriate and diverse host-pathogen combinations, together with modelling of the data that result, will facilitate a comprehensive view of the spatial and stochastic nature of within-host dynamics. © 2008 Grant et al.

Molecular dynamics simulation on dislocation emission process

A correlative reference model for a computer simulation of molecular dynamics is proposed in this paper. Based on this model, a flexible displacement boundary scheme is naturally introduced and the dislocations emitted from a crack tip are presumed to continuously pass through the border of an inner discrete atomic region to pile up at an outer continuum region. The simulations for a Mo crystal show that the interaction between a crack and emitted dislocations results in the decrease in local stress intensity factor gradually.

Models and algorithms for tracking of maneuvering objects using variable rate particle filters

Standard algorithms in tracking and other state-space models assume identical and synchronous sampling rates for the state and measurement processes. However, real trajectories of objects are typically characterized by prolonged smooth sections, with sharp, but infrequent, changes. Thus, a more parsimonious representation of a target trajectory may be obtained by direct modeling of maneuver times in the state process, independently from the observation times. This is achieved by assuming the state arrival times to follow a random process, typically specified as Markovian, so that state points may be allocated along the trajectory according to the degree of variation observed. The resulting variable dimension state inference problem is solved by developing an efficient variable rate particle filtering algorithm to recursively update the posterior distribution of the state sequence as new data becomes available. The methodology is quite general and can be applied across many models where dynamic model uncertainty occurs on-line. Specific models are proposed for the dynamics of a moving object under internal forcing, expressed in terms of the intrinsic dynamics of the object. The performance of the algorithms with these dynamical models is demonstrated on several challenging maneuvering target tracking problems in clutter. © 2006 IEEE.

Influence of surfactant solubility on the deformation and breakup of a bubble or capillary jet in a viscous fluid

In a previous study [M. Hameed, J. Fluid Mech. 594, 307 (2008)] the authors investigated the influence of insoluble surfactant on the evolution of a stretched, inviscid bubble surrounded by a viscous fluid via direct numerical simulation of the Navier-Stokes equations, and showed that the presence of surfactant can cause the bubble to contract and form a quasisteady slender thread connecting parent bubbles, instead of proceeding directly toward pinch-off as occurs for a surfactant-free bubble. Insoluble surfactant significantly retards pinch-off and the thread is stabilized by a balance between internal pressure and reduced capillary pressure due to a high concentration of surfactant that develops during the initial stage of contraction. In the present study we investigate the influence of surfactant solubility on thread formation. The adsorption-desorption kinetics for solubility is in the diffusion controlled regime. A long-wave model for the evolution of a capillary jet is also studied in the Stokes flow limit, and shows dynamics that are similar to those of the evolving bubble. With soluble surfactant, depending on parameter values, a slender thread forms but can pinch-off later due to exchange of surfactant between the interface and exterior bulk flow. © 2009 American Institute of Physics.

A Thermodynamic Constitutive Model for Stress Induced Phase Transformation in Shape Memory Alloys

In this paper a thermodynamic constitutive model is developed for stress induced phase transformation in single crystalline and polycrystalline shape memory alloys (SMAs). Volume fractions of different martensite variants are chosen as internal variables to describe the evolution of microstructure state in the material. This model is then used in prediction the transformation behavior of a SMA (Cu-Al-Zn-Mn) under complex thermomechanical load (including complete and incomplete transformation in mechanical cycling, and proportional/non-proportional loading). (C) 2002 Elsevier Science Ltd. All rights reserved.

Cross-relaxation dynamics on anomalous saturation processes in low pressure supersonic cw HF chemical laser amplifier

It is assumed that both translational and rotational nonequilibrium cross-relaxations play a role simultaneoulsy in low pressure supersonic cw HF chemical laser amplifier. For two-type models of gas flow medium with laminar and turbulent flow diffusion mixing, the expressions of saturated gain spectrum are derived respectively, and the numerical calculations are performed as well. The numerical results show that turbulent flow diffusion mixing model is in the best agreement with the experimental result.

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.

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.

Numerical Simulation and Experimental Investigation about Internal and External Flows

In this paper, TASCflow3D is used to solve inner and outer 3D viscous incompressible turbulent flow (R-e = 5.6 X 10(6)) around axisymmetric body with duct. The governing equation is a RANS equation with standard k-epsilon turbulence model. The discrete method used is a finite volume method based on the finite element approach. In this method, the description of geometry is very flexible and at the same time important conservative properties are retained. The multi-block and algebraic multi-grid techniques are used for the convergence acceleration. Agreement between experimental results and calculation is good. It indicates that this novel approach can be used to simulate complex flow such as the interaction between rotor and stator or propulsion systems containing tip clearance and cavitation.

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.

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.

Characterising Of Internal Stresses In Duplex Coating By Fem

The internal stresses in a duplex coating involving a prequenched layer are believed to change if it is exposed to thermal loading. To characterise the internal stresses in such a duplex coating, a gradient model of finite element method is set up. The initial stress within the substrate developed in as quenching and the internal stresses due to the tempering of the prequenched layer ( TPQL) in such a duplex coating are calculated. The synthetical internal stresses in coating can be estimated by superposing uniform initial stresses developed during plating. The results indicate that the residual tensile stresses due to fabrication in coating will be decreased greatly, or even synthetical compressive internal stresses may arise in the coating.

High Aspect Ratio (L/D) Riser Viv Prediction Using Wake Oscillator Model

A two-dimensional (2-D) vortex-induced vibration (VIV) prediction model for high aspect ratio (LID) riser subjected to uniform and sheared flow is studied in this paper. The nonlinear structure equations are considered. The near wake dynamics describing the fluctuating nature of vortex shedding is modeled using classical van der Pol equation. A new approach was applied to calibrate the empirical parameters in the wake oscillator model. Compared the predicted results with the experimental data and computational fluid dynamic (CFD) results. Good agreements are observed. It can be concluded that the present model can be used as simple computational tool in predicting some aspects of VIV of long flexible structures. (C) 2008 Elsevier Ltd. All rights reserved.