Local synaptic signaling enhances the stochastic transport of\ud motor-driven cargo in neurons

The tug-of-war model of motor-driven cargo transport is formulated as an intermittent trapping process. An immobile trap, representing the cellular machinery that sequesters a motor-driven cargo for eventual use, is located somewhere within a microtubule track. A particle representing a motor-driven cargo that moves randomly with a forward bias is introduced at the beginning of the track. The particle switches randomly between a fast moving phase and a slow moving phase. When in the slow moving phase, the particle can be captured by the trap. To account for the possibility the particle avoids the trap, an absorbing boundary is placed at the end of the track. Two local signaling mechanisms—intended to improve the chances of capturing the target—are considered by allowing the trap to affect the tug-of-war parameters within a small region around itself. The first is based on a localized adenosine triphosphate (ATP) concentration gradient surrounding a synapse, and the second is based on a concentration of tau—a microtubule-associated protein involved in Alzheimer’s disease—coating the microtubule near the synapse. It is shown that both mechanisms can lead to dramatic improvements in the capture probability, with a minimal increase in the mean capture time. The analysis also shows that tau can cause a cargo to undergo random oscillations, which could explain some experimental observations

Stochastic models of intracellular transport

The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an over-damped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of ATP hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review we present a wide range of analytical methods and models of intracellular transport. In the case of diffusive transport, we consider narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion. In the case of active transport, we consider Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean field approximations. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self–organization of subcellular structures

Dynamics and pragmatics for high performance concurrency

This thesis is concerned with support at all levels for building highly concurrent and dynamic parallel processing systems. The CSP model of concurrency, as (largely) embodied in the occam programming language is used due to its simplicity, expressiveness, architecture- independent nature, and potential for high performance. Additionally, occam provides guarantees regarding freedom from aliasing and race-hazard error. This thesis addresses one of the grand challenges of present day computer science: providing a software technology that offers the dynamic flexibility and performance of mainstream object oriented environments with the level of safety, formal analysis, modularity and lightweight concurrency offered by CSP/occam. Two approaches to this challenge are possible: do something to make the mainstream languages (e.g. Java, C++) safe, or make occam dynamic -- without compromising its existing good properties. This thesis follows the latter route. The first part of this thesis concentrates on enhancing the occam language and run-time system, on a commodity platform (IBM PC) running the freely available Linux operating system. After a brief introduction to the various components of the kroc occam system, additions and extensions to the occam programming language and supporting run-time system are examined. These provide a greater degree of programming flexibility in occam (for example, by adding support for dynamic allocation, mobile semantics and dynamic network construction), without compromising the safety of programs which use them. Benchmarks are reported that demonstrate significant improvements in performance (for example, channel communication in tens of nano-seconds). The second part concentrates on improving the level of interaction between occam programs and the OS environment. Providing easy access to sockets and networking, for example. This thesis concludes with a discussion of the work presented herein, with consideration given to parallels with object-oriented languages. Also described are details of ongoing and potential future research. The modified language grammar, details of new compiler generated code, and miscellany are provided in the appendices.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Dynamics and pragmatics for high performance concurrency

This thesis is concerned with support at all levels for building highly concurrent and dynamic parallel processing systems. The CSP model of concurrency, as (largely) embodied in the occam programming language is used due to its simplicity, expressiveness, architecture- independent nature, and potential for high performance. Additionally, occam provides guarantees regarding freedom from aliasing and race-hazard error. This thesis addresses one of the grand challenges of present day computer science: providing a software technology that offers the dynamic flexibility and performance of mainstream object oriented environments with the level of safety, formal analysis, modularity and lightweight concurrency offered by CSP/occam. Two approaches to this challenge are possible: do something to make the mainstream languages (e.g. Java, C++) safe, or make occam dynamic -- without compromising its existing good properties. This thesis follows the latter route. The first part of this thesis concentrates on enhancing the occam language and run-time system, on a commodity platform (IBM PC) running the freely available Linux operating system. After a brief introduction to the various components of the kroc occam system, additions and extensions to the occam programming language and supporting run-time system are examined. These provide a greater degree of programming flexibility in occam (for example, by adding support for dynamic allocation, mobile semantics and dynamic network construction), without compromising the safety of programs which use them. Benchmarks are reported that demonstrate significant improvements in performance (for example, channel communication in tens of nano-seconds). The second part concentrates on improving the level of interaction between occam programs and the OS environment. Providing easy access to sockets and networking, for example. This thesis concludes with a discussion of the work presented herein, with consideration given to parallels with object-oriented languages. Also described are details of ongoing and potential future research. The modified language grammar, details of new compiler generated code, and miscellany are provided in the appendices

Calculi for higher order communicating systems

This thesis develops two Calculi for Higher Order Communicating Systems. Both calculi consider sending and receiving processes to be as fundamental as nondeterminism and parallel composition. The first calculus called CHOCS is an extension of Milner's CCS in the sense that all the constructions of CCS are included or may be derived from more fundamental constructs. Most of the mathematical framework of CCS carries over almost unchanged. The operational semantics of CHOCS is given as a labelled transition system and it is a direct extension of the semantics of CCS with value passing. A set of algebraic laws satisfied by the calculus is presented. These are similar to the CCS laws only introducing obvious extra laws for sending and receiving processes. The power of process passing is underlined by a result showing that the recursion operator is unnecessary in the sense that recursion can be simulated by means of process passing and communication. The CHOCS language is also studied by means of a denotational semantics. A major result is the full abstractness of this semantics with respect to the operational semantics. The denotational semantics is used to provide an easy proof of the simulation of recursion. Introducing processes as first class objects yields a powerful metalanguage. It is shown that it is possible to simulate various reduction strategies of the untyped λ-Calculus in CHOCS. As pointed out by Milner, CCS has its limitations when one wants to describe unboundedly expanding systems, e.g. an unbounded number of procedure invocations in an imperative concurrent programming language P with recursive procedures. CHOCS may neatly describe both call-by-value and call-by-reference parameter mechanisms for P. We also consider call-by-name and lazy parameter mechanisms for P. The second calculus is called Plain CHOCS. Essential to the new calculus is the treatment of restriction as a static binding operator on port names. This calculus is given an operational semantics using labelled transition systems which combines ideas from the applicative transition systems described by Abramsky and the transition systems used for CHOCS. This calculus enjoys algebraic properties which are similar to those of CHOCS only needing obvious extra laws for the static nature of the restriction operator. Processes as first class objects enable description of networks with changing interconnection structure and there is a close connection between the Plain CHOCS calculus and the π-Calculus described by Milner, Parrow and Walker: the two calculi can simulate one another. Recently object oriented programming has grown into a major discipline in computational practice as well as in computer science. From a theoretical point of view object oriented programming presents a challenge to any metalanguage since most object oriented languages have no formal semantics. We show how Plain CHOCS may be used to give a semantics to a prototype object oriented language called 0.Open Acess

Water in cratonic lithosphere : calibrating laboratory-determined models of electrical conductivity of mantle minerals using geophysical and petrological observations

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q06010, doi:10.1029/2012GC004055.Measurements of electrical conductivity of “slightly damp” mantle minerals from different laboratories are inconsistent, requiring geophysicists to make choices between them when interpreting their electrical observations. These choices lead to dramatically different conclusions about the amount of water in the mantle, resulting in conflicting conclusions regarding rheological conditions; this impacts on our understanding of mantle convection, among other processes. To attempt to reconcile these differences, we test the laboratory-derived proton conduction models by choosing the simplest petrological scenario possible – cratonic lithosphere – from two locations in southern Africa where we have the most complete knowledge. We compare and contrast the models with field observations of electrical conductivity and of the amount of water in olivine and show that none of the models for proton conduction in olivine proposed by three laboratories are consistent with the field observations. We derive statistically model parameters of the general proton conduction equation that satisfy the observations. The pre-exponent dry proton conduction term (σ0) and the activation enthalpy (ΔHwet) are derived with tight bounds, and are both within the broader 2σ errors of the different laboratory measurements. The two other terms used by the experimentalists, one to describe proton hopping (exponent r on pre-exponent water content Cw) and the other to describe H2O concentration-dependent activation enthalpy (term αCw1/3 added to the activation energy), are less well defined and further field geophysical and petrological observations are required, especially in regions of higher temperature and higher water content.The SAMTEX data were acquired through funding provided by the Continental Dynamics program of the U.S. National Science Foundation (grant EAR0455242 to RLE), the South African Department of Science and Technology (grant to South African Council for Geoscience), and Science Foundation Ireland (grant 05/RGP/GEO001 to AGJ) plus financial and/or logistical support provided by all members of the SAMTEX consortium. JF was initially supported by an IRCSET grant to AGJ for the TopoMed project (TopoMed: Plate reorganization in the western Mediterranean: Lithospheric causes and topographic consequences) within the European Science Foundation’s TOPOEUROPE EUROCORES (http://www.esf.org/activities/eurocores/ running-programmes/topo-europe.html), and subsequently by an SFI PI grant (10/IN.1/I3022) to AGJ for IRETHERM (www.iretherm.ie).2012-12-1

Contributions to unsupervised and supervised learning with applications in digital image processing

311 p. : il.[EN]This Thesis covers a broad period of research activities with a commonthread: learning processes and its application to image processing. The twomain categories of learning algorithms, supervised and unsupervised, have beentouched across these years. The main body of initial works was devoted tounsupervised learning neural architectures, specially the Self Organizing Map.Our aim was to study its convergence properties from empirical and analyticalviewpoints.From the digital image processing point of view, we have focused on twobasic problems: Color Quantization and filter design. Both problems have beenaddressed from the context of Vector Quantization performed by CompetitiveNeural Networks. Processing of non-stationary data is an interesting paradigmthat has not been explored with Competitive Neural Networks. We have statesthe problem of Non-stationary Clustering and related Adaptive Vector Quantizationin the context of image sequence processing, where we naturally havea Frame Based Adaptive Vector Quantization. This approach deals with theproblem as a sequence of stationary almost-independent Clustering problems.We have also developed some new computational algorithms for Vector Quantizationdesign.The works on supervised learning have been sparsely distributed in time anddirection. First we worked on the use of Self Organizing Map for the independentmodeling of skin and no-skin color distributions for color based face localization. Second, we have collaborated in the realization of a supervised learning systemfor tissue segmentation in Magnetic Resonance Imaging data. Third, we haveworked on the development, implementation and experimentation with HighOrder Boltzmann Machines, which are a very different learning architecture.Finally, we have been working on the application of Sparse Bayesian Learningto a new kind of classification systems based on Dendritic Computing. This lastresearch line is an open research track at the time of writing this Thesis