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Virtual Cell (virtual + cell)

Distribution by Scientific Domains

Engineering	50%

Selected Abstracts

Topology of the Mitochondrial Inner Membrane: Dynamics and Bioenergetic Implications

IUBMB LIFE, Issue 3-5 2001
Carmen A. Mannella
Abstract Electron tomography indicates that the mitochondrial inner membrane is not normally comprised of baffle-like folds as depicted in textbooks. In actuality, this membrane is pleomorphic, with narrow tubular regions connecting the internal compartments (cristae) to each other and to the membrane periphery. The membrane topologies observed in condensed (matrix contracted) and orthodox (matrix expanded) mitochondria cannot be interconverted by passive folding and unfolding. Instead, transitions between these morphological states likely involve membrane fusion and fission. Formation of tubular junctions in the inner membrane appears to be energetically favored, because they form spontaneously in yeast mitochondria following large-amplitude swelling and recontraction. However, aberrant, unattached, vesicular cristae are also observed in these mitochondria, suggesting that formation of cristae junctions depends on factors (such as the distribution of key proteins and/or lipids) that are disrupted during extreme swelling. Computer modeling studies using the "Virtual Cell" program suggest that the shape of the inner membrane can influence mitochondrial function. Simulations indicate that narrow cristae junctions restrict diffusion between intracristal and external compartments, causing depletion of ADP and decreased ATP output inside the cristae. [source]

The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3-D cell

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2009
Yose Y. Widjaja
Abstract Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40,000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real-time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein "twins" when they occur in multiple locations. Since the Interactorium permits multi-level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net. [source]

Improvement of mass source/sink for an immersed boundary method

INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 11 2007
Wei-Xi Huang
Abstract An improved immersed boundary method using a mass source/sink as well as momentum forcing is developed for simulating flows over or inside complex geometries. The present method is based on the Navier,Stokes solver adopting the fractional step method and a staggered Cartesian grid system. A more accurate formulation of the mass source/sink is derived by considering mass conservation of the virtual cells in the fluid crossed by the immersed boundary. Two flow problems (the decaying vortex problem and uniform flow past a circular cylinder) are used to validate the proposed formulation. The results indicate that the accuracy near the immersed boundary is improved by introducing the accurate mass source/sink. Copyright © 2006 John Wiley & Sons, Ltd. [source]

Virtual Shop Clusters: A New Layout Concept for a Ship Repair and Maintenance Facility

NAVAL ENGINEERS JOURNAL, Issue 2 2008
BRIAN MAYER
Organic ship maintenance facilities and depots of the Navy are mostly organized as trade-specific shops rather than by product (or process) families. For example, welders are in the weld shop, machinists are in the machine shop, pipe-fitters are in the pipe shop, etc. There is a belief that this guild-type organizational structure is what enables a repair facility to do almost anything, albeit at the cost of moving product all over the "factory." This skill-based organizational structure is identical to the functional (or department) layout that is preferred by most jobshops in the commercial manufacturing sectors. But, any company that has successfully implemented Lean Thinking has almost always replaced a Functional (or Process Village) Layout by a Cellular Layout. At the Navy's Southeast Regional Maintenance Center (SERMC), a typical repair job must visit multiple shops that pass work back and forth between them. For example, a pipe job may be sent by the pipe shop to the machine shop for re-threading, then routed to the weld shop where it is welded to a frame, after which the welded sub-assembly returns to the pipe shop for inspection and final assembly. Thereby, significant delays and operational wastes occur because people have to walk between the shops, discuss matters at daily production meetings, and e-mail/phone each other to make sure that their schedules match. If activities are not completed as per schedule, the jobs get further delayed because they queue at the shops, waiting to be served. This lack of detailed (and accurate) planning and scheduling, combined with poor schedule visibility and shop floor control, is the curse of the Functional Layout that currently exists at SERMC. This paper will describe a pilot project to assess the feasibility of cellular manufacturing at SERMC. The fundamental hypothesis that was tested is that even in a repair and maintenance facility there could exist several families of repair jobs where jobs grouped into a family require similar combinations of processes, equipment, materials, etc. that can be provided by a small group of shops. In fact, several potential families of repair jobs, and the appropriate cluster of shops for each family of repair jobs, were identified using the Production Flow Analysis and Simplification Toolkit (PFAST) software. Based on these results, it was decided to implement a shop cluster (or focused factory, or repair cell) to complete any repair jobs done by the dive shop. It was recommended that the dive shop be merged with a few other shops, and be provided the necessary tools, cross-trained personnel, equipment, and other support systems to become an autonomous multi-function shop. Simulation using the SimCAD software from CreateAsoft Inc. (http://www.createasof.com) was used to verify the results expected from making the proposed changes. The primary analysis was intended to evaluate the benefits of implementing a focused factory in the dive shop. The secondary analysis was intended to evaluate the advantages of implementing a virtual shop cluster (or focused factory, or repair cell) in any ship repair facility like SERMC. The simulation results showed that implementing either physical cells or virtual cells based on the different families of repair jobs identified by PFAST could improve job turnaround times at any Navy ship repair facility like SERMC. Both the types of delays as well as the time values of these delays differed significantly across the existing and alternative shop configurations that were proposed. [source]