Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of long polymers (up to 8000 monomers) are monitored as they pass through nanopores. Comparison between the different pore sizes shows that wide pores can host a larger number of multiple biopolymer segments, as compared to smaller pores. The simulations provide clear evidence of folding quantization in the translocation process as the biopolymers undertake multi-folded configurations, characterized by a well-defined integer number of folds. Accordingly, the translocation time is no longer represented by a single-exponent power law dependence on the length, as it is the case for single-file translocation through narrow pores. The folding quantization increases with the biopolymer length, while the rate of translocated beads at each time step is linearly correlated to the number of resident beads in the pore. Finally, analysis of the statistics over the translocation work unravels the importance of the hydrodynamic interactions in the process.Comment: 10 pages, 6 figures, to appear in J. Stat. (2009

Mesoscopic model for soft flowing systems with tunable viscosity ratio

We propose a mesoscopic model of binary fluid mixtures with tunable viscosity ratio based on the two-range pseudo-potential lattice Boltzmann method, for the simulation of soft flowing systems. In addition to the short range repulsive interaction between species in the classical single-range model, a competing mechanism between the short range attractive and mid-range repulsive interactions is imposed within each species. Besides extending the range of attainable surface tension as compared with the single-range model, the proposed scheme is also shown to achieve a positive disjoining pressure, independently of the viscosity ratio. The latter property is crucial for many microfluidic applications involving a collection of disperse droplets with a different viscosity from the continuum phase. As a preliminary application, the relative effective viscosity of a pressure-driven emulsion in a planar channel is computed.Comment: 14page

Discrete fluidization of dense monodisperse emulsions in neutral wetting microchannels

The rheology of pressure-driven flows of two-dimensional dense monodisperse emulsions in neutral wetting microchannels is investigated by means of mesoscopic lattice simulations, capable of handling large collections of droplets, in the order of several hundreds. The simulations reveal that the fluidization of the emulsion proceeds through a sequence of discrete steps, characterized by yielding events whereby layers of droplets start rolling over each other, thus leading to sudden drops of the relative effective viscosity. It is shown that such discrete fluidization is robust against loss of confinement, namely it persists also in the regime of small ratios of the droplet diameter over the microchannel width. We also develop a simple phenomenological model which predicts a linear relation between the relative effective viscosity of the emulsion and the product of the confinement parameter (global size of the device over droplet radius) and the viscosity ratio between the disperse and continuous phases. The model shows excellent agreement with the numerical simulations. The present work offers new insights to enable the design of microfluidic scaffolds for tissue engineering applications and paves the way to detailed rheological studies of soft-glassy materials in complex geometries.Comment: 8 pages, 8 figure

On the flow of soft suspensions through orifices

The behavior of confined suspensions of soft droplets under pressure-driven flow, passing an obstacle within a planar channel, is investigated by means of a mesoscopic lattice Boltzmann model capable of simulating soft non-coalescing droplets. The simulations reveal that the threshold of the pore size, below which the flux vanishes, is between 1 and 2 droplet diameters, and increases with the packing fraction. Moreover, we show that the classical Beverloo relation between the total flux and the pore size is not suitable for the soft suspensions considered here

Michaelis-Menten dynamics in protein subnetworks

To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly, and is also more efficient computationally

An Innovative Enhanced Wall to Reduce the Energy Demand in Buildings

Energy saving in buildings is one of most important issues for European countries. The 40% of the total European energy consumption is due to building Heating and conditioning. Although in the last years many studies have been carried out in order to reach the zero-consumption house by means of passive solar heating, ventilation or thermal insulation, the energy rate due to passive solar heating could be further enhanced. This paper proposes a method for increasing the energy rate absorbed by opaque walls by using a two phase loop thermosyphon connecting the internal and the external façade of a prefabricated house wall. The evaporator zone is located on the outside face and it is irradiated by the sunlight while the condenser zone is placed on the internal face and releases heat to the domestic environment. The temperature differences between the internal and external wall facades are lower than 30 K and the heat fluxes at the evaporator change during the day from 2 up to 7 x 104 W/m2 K. The thermosyphon has been preliminary designed and implanted into a wall for a prefabricated house in Italy. A thermal model of building equipped with the thermosiphon wall has been used in order to evaluate the impact in terms of energy saving and thermal comfort in a real prefabricated low consumption house. The transient behaviour of the building has been simulated day by day during the winter period by using the EnergyPlusTM software. This solution enhances the thermal comfort of the building by keeping the indoor temperature close to the thermal comfort standard for most of the day. The annual saving on the heating energy is higher than 50% in the case of a low consumption buildin

Design of equipment safety & reliability for an aseptic liquid food packaging line through maintenance engineering

The organisation of maintenance, in the Aseptic Liquid Food (ALF) industry, represents an important management task that enables a company to pursue higher manufacturing effectiveness and improved market share. This research is concerned with the process to design and implement maintenance tasks. These two complementary processes (design and implementation) have been thought and designed to answer the particular needs of food industry regarding product safety and equipment reliability. Numerous maintenance engineering researchers have focused on maintenance engineering and reliability techniques highlighting the contribution of maintenance in achieving world class manufacturing and competitive advantage. Their outcome emphasizes that maintenance is not a “necessary evil” because of costs associated, but it can be considered an “investment” that produces an added value which generates a real company profit. The existing maintenance engineering techniques pursue equipment reliability at minimum cost; but in food industry, food safety represents the most critical issue to address and solve. The research methodology chosen is based on case studies coming from ALF industries. These show that low maintenance effectiveness could have dramatic effects on final consumers and on the company’s image and underline the need of a maintenance design and implementation process that takes into consideration all critical factors relevant to liquid food industry. The analysis of measurable indicators available, represents a tool necessary to show the status of critical performance indicators and reveals the urgency of a research necessary to address and solve the maintenance problems in food industry. The literature review underlines the increasing regulations in place in food industry and that no literature is available to define a maintenance design and implementation process for ALF and in general for food industry. The literature review enabled also the gap existing between theory and real maintenance status, in the ALF, to be identified and the aim of the research was to explore this gap. The analysis of case studies and Key Performance Indicators (KPI’s) available highlights the problem and the literature review provides the knowledge necessary to identify the process to design and implement maintenance procedures for ALF industry. The research findings provide a useful guide to identify the process to design maintenance tasks able to put under control food safety and equipment reliability issues. Company’s restraining forces and cultural inertia, that work against new maintenance procedures, have been analysed and a maintenance implementation process have been designed to avoid losing the benefits produced by the design phase. The analysis of condition monitoring systems shows devices and techniques useful to improve product safety, equipment reliability, and then maintenance effectiveness. This research aimed to fill the gap in the existing literature showing the solution to manage both food safety and production effectiveness issues in food industry. It identifies a maintenance design process able to capture all conceivable critical factors in food industry and to provide the solution to design reliable task lists. Furthermore, the maintenance implementation process shows the way to maximize the maintenance design outcome through the empowerment of equipment operators and close cooperation with maintenance and quality specialists. The new maintenance design and implementation process represents the answer to the research problem and a reliable solution that allows the food industry to improve food safety and production effectiveness.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Modeling realistic multiphase flows using a non-orthogonal multiple-relaxation-time lattice Boltzmann method

In this paper, we develop a three-dimensional multiple-relaxation-time lattice Boltzmann method (MRT-LBM) based on a set of non-orthogonal basis vectors. Compared with the classical MRT-LBM based on a set of orthogonal basis vectors, the present non-orthogonal MRT-LBM simplifies the transformation between the discrete velocity space and the moment space, and exhibits better portability across different lattices. The proposed method is then extended to multiphase flows at large density ratio with tunable surface tension, and its numerical stability and accuracy are well demonstrated by some benchmark cases. Using the proposed method, a practical case of a fuel droplet impacting on a dry surface at high Reynolds and Weber numbers is simulated and the evolution of the spreading film diameter agrees well with the experimental data. Furthermore, another realistic case of a droplet impacting on a super-hydrophobic wall with a cylindrical obstacle is reproduced, which confirms the experimental finding of Liu \textit{et al.} [``Symmetry breaking in drop bouncing on curved surfaces," Nature communications 6, 10034 (2015)] that the contact time is minimized when the cylinder radius is comparable with the droplet cylinder.Comment: 19 pages, 11 figure