Protein molecular motors, which convert chemical energy into kinetic energy, are prime candidates for use in nanodevice in which active transport is required. To be able to design these devices it is essential that the properties of the cytoskeletal filaments propelled by the molecular motors are well established. Here we used micro-contact printed BSA to limit the amount of HMM that can adsorb creating a tightly confined pathway for the filaments to travel. Both the image and statistical analysis of the movement of the filaments through these structures have been used to new insights into the motility behaviour of actomyosin on topographically homogenous, but motor-heterogeneous planar systems. It will be shown that it is possible to determine the persistence length of the filaments and that it is related to the amount of locally adsorbed HMM. This provides a basis that can be used to optimize the design of future nanodevices incorporating the actomyosin system for the active transport.
The prediction of protein adsorption to surfaces from solution is a perennial unsolved problem in biomedicine, physical
chemistry and other fields. Here we used neural networks and the previously developed Biomolecular Adsorption
Database (BAD) to predict the amount of protein adsorbed by a set of five descriptors of the protein, surface and
solution. We find a moderately good predictive ability if very large adsorption values are present and a good fit if these
few outliers are eliminated. With a growing number of entries in the BAD, we expect the accuracy of the predicted
values to increase substantially. This paper presents for the first time a universal and stand-alone quantitative predictor of
protein adsorption.
One the major difficulties of microarray technology relate to the processing of large and - importantly - error-loaded
images of the dots on the chip surface. Whatever the source of these errors, those obtained in the first stage of
data acquisition - segmentation - are passed down to the subsequent processes, with deleterious results. As it has been
demonstrated recently that biological systems have evolved algorithms that are mathematically efficient, this
contribution attempts to test an algorithm that mimics a bacterial-"patented" algorithm for the search of available space
and nutrients to find, "zero-in" and eventually delimitate the features existent on the microarray surface.
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.
Self-segregation and compartimentalisation are observed experimentally to occur spontaneously on live membranes as well as reconstructed model membranes. It is believed that many of these processes are caused or supported by anomalous diffusive behaviours of biomolecules on membranes due to the complex and heterogeneous nature of these environments. These phenomena are on the one hand of great interest in biology, since they may be an important way
for biological systems to selectively localize receptors, regulate signaling or modulate kinetics; and on the other, they provide an inspiration for engineering designs that mimick natural systems. We present an interactive software package we are developing for the purpose of simulating such processes numerically using a fundamental Monte Carlo approach. This program includes the ability to simulate kinetics and mass transport in the presence of either mobile or immobile obstacles and other relevant structures such as liquid-ordered lipid microdomains. We also present preliminary
simulation results regarding the selective spatial localization and chemical kinetics modulating power of immobile obstacles on the membrane, obtained using the program.
In earlier work, we proposed “computing with bio-agents”, a new model of computation, of the distributed parallel type, based on the notion that motions of biological objects such as bacteria or protein molecular motors in confined spaces can be regarded as computations. Beginning with the observation that the geometric nature of the
physical structures in which model biological objects move modulates the motions of the latter, we inferred that by altering the geometry, one can control the characteristic trajectories of the objects and thus perform meaningful computations. In the present work we describe designed geometries and structures that can be used to achieve various
computational tasks in this framework. Specifically, we describe methods for solving difficult combinatorial problems from graph and number theory in an efficient way using bio-agents.
The immobilization and hybridization processes of DNA strands on poly-l-lysine (PL) covered surfaces have been studied using the atomic force microscopy (AFM) in a topographic mode. The statistical analysis of topographic surfaces showed an increase in the Z-threshold with additions of single strand DNA (ssDNA) and the complimentary DNA (ccDNA). Also no drastic change of statistical fractal dimension (slope of the log-log perimeter-area plot) is
observed when comparing the PL-surfaces coated with ssDNA and ccDNA. These two results suggest that ssDNA strands are successfully immobilized and spatially hybridized with ccDNA on the PL surface and the growth of hybridized ccDNA occurs mainly in the vertical dimension. The methods described here are good candidates for the
detection of DNA hybridization, especially in the context of DNA nanoarrays.
The identification and differentiation of colours is a relatively problematic task for colour-impaired and partially vision-impaired persons and an impossible one for completely blind. In various contexts, this leads to a loss of independence or an increased risk of harm. The identification of colour using optoelectronic devices, on the other hand, can be done precisely and inexpensively. Additionally, breakthroughs in miniaturising and integrating colour sensors into biological systems may lead to significant advances in electronic implants for alleviating blindness. Here we present a functional handheld device developed for the identification of colour, intended for use by the vision-impaired. We discuss the features and limitations of the device and describe in detail one target application - the identification of different banknote denominations by the blind.
KEYWORDS: Motion models, Head, Acquisition tracking and pointing, Molecules, Monte Carlo methods, Proteins, In vitro testing, Stochastic processes, Polymers, Control systems
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 this
model 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.
The non-invasive or minimally invasive real-time spectral analysis of tissue and biological fluids in vivo would be of great assistance for diagnosis and monitoring of a wide range of diseases. We propose here a novel microdevice capable of determining the reflectance spectrum of a sample using a set of micrometer-sized light emitting diodes and a patch of photosensitive material. The purported device would be wireless and remote-powered via RF magnetic fields and due to its dimensions would be suitable as a long-term implant, for example for monitoring glucose levels in diabetics. We present a design for this device, discuss its limitations and suggest some applications, including its use for in vivo biochemical assays.
Investigation of protein-polymeric surface interaction requires reliable practical techniques for evaluation of the efficiency of protein immobilization. In this study the efficiency of protein immobilization was evaluated using three different techniques: (1) protein-binding assay with fluorescent detection and (2) quantification, and (3) atomic force microscopy. This approach enables us to rapidly analyse the adsorption properties of different proteins. The comparative physico-chemical adsorption of α-chymotrypsin, human serum albumin, human immunoglobulin, lysozyme, and myoglobin in the micro-wells fabricated via a localized laser ablation of a protein-blocked thin gold layer (50 nm) deposited on a Poly(methyl ethacrylate) film has been studied. Correlations were observed between the quantitative and qualitative differences depending on both protein and polymeric surface hydrophobicity.
Lab-on-a-chip microfluidic devices commonly manipulate biological fluids, which contain significant quantities of biomolecules, in particular proteins and DNA. This inevitably leads to the adsorption of these biomolecules to the surfaces of the devices through which the fluid flows. As the dimensions of these devices continue to decrease and approach the sub-micron range, this phenomenon will become more and more important. In this paper, we model the effect of protein adsorption on the flow of fluid through a microchannel, under the assumption that classical hydrodynamics applies. We predict that the adsorption of a thin layer of protein on the walls of a thin microchannel can significantly decrease the effective flow rate and velocity through the channel. Finally, we briefly mention the possibility that the increased wall roughness and modified wall chemistry, attributable to the deposition of the protein, could also lead to the modification of the flow, and in particular, may render the crucial “no-slip” wall condition invalid.
We propose a new, biologically-inspired model of computation, based on the motion of actin filaments on a myosin substrate, as used in motility assays, noting that this represents a marriage of the fields of natural computing and computing with agents. A highly simplified model of actin motility is presented and used to simulate the simultaneous motion of identical filaments. We show that using some simple formal definitions, we can regard this motion as a continuous computation. We demonstrate using a computer simulation, how actin filaments can be used to solve a traditional maze in a highly parallel fashion, with obvious implications for attacking computationally difficult graph problems. Briefly, we mention the limitations of our model and possibilities for the physical implementation of such a system.
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