Computing with the actin-myosin molecular motor system

No abstract available

Effect of protein adsorption on fluid flow in a micro-channel

Abstract not available

Simulation of the motility of filaments on surfaces functionalised with molecular motors

The fundamental parameters regarding linear molecular motors have been obtained via single molecule studies for dynamic (e.g. force) and static parameters (e.g. filament flexibility). However, single molecule studies are not trivial, whereas motility assays are less demanding. A computer package––presented in this contribution with its constitutive equations––for the simulation of motility assays that allows the user to input several fundamental parameters (force exerted by the motors, flexibility of filaments, etc.); collect the predicted statistics and compare the simulated statistics with actual ones, can be then a valuable tool for a less demanding hypothesis testing of molecular motors functions

A database comprising biomolecular descriptors relevant to protein adsorption on microarray surfaces

The adsorption of biomolecules on surfaces is dependent on biomolecule molecular descriptors, surface descriptors and environment descriptors. Of these descriptors, the biomolecular-related are the most complex and arguably the most important, as being related to both adsorption and possible denaturation on surfaces. The criticality of biomolecule adsorption in the context of microarrays and microfluidics devices will increase with the advancement of proteomics that probes the functionality of proteins, which are much more responsive to surfaces than DNA - the focal biomolecule of genomics. Anticipating this development, the present contribution proposes the establishment of a biomolecular descriptors database, which could be the starting point for a depositary of data and a source of validation for predictive models for adsorption and denaturation

Models of protein linear molecular motors for dynamic nanodevices

Protein molecular motors are natural nano-machines that convert the chemical energy from the hydrolysis of adenosine triphosphate into mechanical work. These efficient machines are central to many biological processes, including cellular motion, muscle contraction and cell division. The remarkable energetic efficiency of the protein molecular motors coupled with their nano-scale has prompted an increasing number of studies focusing on their integration in hybrid micro- and nanodevices, in particular using linear molecular motors. The translation of these tentative devices into technologically and economically feasible ones requires an engineering, design-orientated approach based on a structured formalism, preferably mathematical. This contribution reviews the present state of the art in the modelling of protein linear molecular motors, as relevant to the future design-orientated development of hybrid dynamic nanodevices. © 2009 The Royal Society of Chemistry

Computing with motile bio-agents

We describe a model of computation of the parallel type, which we call 'computing with bio-agents', based on the concept that motions of biological objects such as bacteria or protein molecular motors in confined spaces can be regarded as computations. We begin with the observation that the geometric nature of the physical structures in which model biological objects move modulates the motions of the latter. Consequently, by changing the geometry, one can control the characteristic trajectories of the objects; on the basis of this, we argue that such systems are computing devices. We investigate the computing power of mobile bio-agent systems and show that they are computationally universal in the sense that they are capable of computing any Boolean function in parallel. We argue also that using appropriate conditions, bio-agent systems can solve NP-complete problems in probabilistic polynomial time

A mechanical model for the motility of actin filaments on myosin

The interaction of actin filaments with myosin is crucial to cell motility, muscular contraction, cell division and other processes. The in vitro motility assay involves the motion of actin filaments on a substrate coated with myosin, and is used extensively to investigate the dynamics of the actomyosin system. Following on from previous work, we propose a new mechanical model of actin motility on myosin, wherein a filament is modeled as a chain of beads connected by harmonic springs. This imposes a limitation on the "stretching" of the filament. The rotation of one bead with respect to its neighbours is also constrained in similar way. We implemented this model and used Monte Carlo simulations to determine whether it can predict the directionality of filament motion. The principal advantages of thismodel over our previous one are that we have removed the empirically correct but artificial assumption that the filament moves like a "worm" i.e. the head determines the direction of movement and the rest of the filament "follows" the head as well as the inclusion of dependencies on experimental rate constants (and so also on e.g. ATP concentration) via the cross-bridge cycle

Impact of protein adsorption on the geometry of microfluidics devices

'Lab-on-a-chip' microfluidics devices manipulate biological fluids, which contain significant quantities of biomolecules, in particular proteins and DNA, and even living cells. As the dimensions of these devices continue to decrease and approach the sub-micron range, and as the trend towards 'disposable' devices continues, the impact of the inevitable adsorption of biomolecules becomes more important. In this paper we estimated the protein-adsorption-related sensitivity of the geometry of a rectangular micron-sized channel. The estimation the thickness of the adsorbed protein layer versus processing parameters, i.e., protein concentration in the fluid; ionic strength of fluid; and surface tension of the walls, is based on a proposed semi-empirical model for protein adsorption. The model, derived from the data contained in a biomolecule adsorption database, uses the concept of a 'generic protein', i.e., a protein with molecular properties averaged over the range of data present in the database. The estimation of protein-adsorption-related impact on the geometry of a rectangular micron-sized channel, i.e., narrowing of the micro-channel, increases dramatically below a threshold value of approximately 1.5-2 μm

Modeling of the growth of filamentous fungi in artificial microstructures

We present a stochastic and spatial Monte Carlo model for the growth of a fungal colony in microstructures. This model is based on an 'L-system-like' representation of filaments as individual objects. Each of these can both grow in space (and be diverted by obstacles) and can send new branches. All parameters in the model such as filament dimensions, the growth speed, behavior at and around obstacles, branching angle and frequency and others are obtained from experimental studies of growth in artificial microstructures. We investigate four different possible 'strategies; the colony might use to achieve the tasks of (a) filling the available space and (2) finding its way out of the structures. The simulation results indicate that a combination of directional memory and a stop-and-branch behavior at corners gives the best results and observe that in fact this is similar to the experimentally observed behavior of the fungi. The model is expected to be of use in studying the colonization of microstructures by fungi and in the design of devices either using fungal growth or aiming to inhibit it