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Register a new userA pH-based bio-rheostat: a proof-of-concept
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New science and new technology need new materials and new concepts. In this respect, biological matter can play a primary role because it is a material with interesting and innovative features which has found several applications in technology, from highly sensitive sensors for medical treatments to devices for energy harvesting. Furthermore, most of its phenomenology remains unclear thus giving new hints for speculative investigations. In this letter, we explore the possibility to use a well-known photosensitive protein, the Reaction Center of Rhodobacter Sphaeroides, to build up an electrical pH sensor, i.e., a device able to change its resistance depending on the pH of the solution in which it crystalizes. By using a microscopic model successfully tested on analogue proteins, we investigate the electrical response of the Reaction Center single protein under different conditions of applied bias, showing the feasibility of the bio-rheostat hypothesis. As a matter of facts, the calculated resistance of this protein grows of about 100% when going from a pH = 10 to a pH = 6.5. Moreover, calculations of the conductance response in a wide range of applied bias point out interesting deviations from the linear regime. All findings are in qualitative agreement with the known role of pH in biochemical activities of Reaction Center and similar proteins, therefore supporting a proof-of-concept for the development of new electron devices based on biomaterials
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A core goal of functional neuroimaging is to study how the environment is processed in the brain. The mainstream paradigm involves concurrently measuring a broad spectrum of brain responses to a small set of environmental features preselected with reference to previous studies or a theoretical framework. As a complement, we invert this approach by allowing the investigator to record the modulation of a preselected brain response by a broad spectrum of environmental features. Our approach is optimal when theoretical frameworks or previous empirical data are impoverished. By using a prespecified closed-loop design, the approach addresses fundamental challenges of reproducibility and generalisability in brain research. These conditions are particularly acute when studying the developing brain, where our theories based on adult brain function may fundamentally misrepresent the topography of infant cognition and where there are substantial practical challenges to data acquisition. Our methodology employs machine learning to map modulation of a neural feature across a space of experimental stimuli. Our method collects, processes and analyses EEG brain data in real-time; and uses a neuro-adaptive Bayesian optimisation algorithm to adjust the stimulus presented depending on the prior samples of a given participant. Unsampled stimuli can be interpolated by fitting a Gaussian process regression along the dataset. We show that our method can automatically identify the face of the infants mother through online recording of their Nc brain response to a face continuum. We can retrieve model statistics of individualised responses for each participant, opening the door for early identification of atypical development. This approach has substantial potential in infancy research and beyond for improving power and generalisability of mapping the individual cognitive topography of brain function.
The new multipurpose event-generation framework SHERPA, acronym for Simulation for High-Energy Reactions of PArticles, is presented. It is entirely written in the object-oriented programming language C++. In its current form, it is able to completely simulate electron--positron and unresolved photon--photon collisions at high energies. Also, fully hadronic collisions, such as, e.g., proton--anti-proton, proton--proton, or resolved photon--photon reactions, can be described on the signal level.
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experimental averages are to be retrieved, data are described by a Boltzmann-like distribution ($propto e^{F/T}$) where $F$ is a linear combination of fluxes and the `temperature parameter $Tgeq 0$ allows for fluctuations. The zero-temperature limit corresponds to a Flux Balance Analysis scenario, where an objective function ($F$) is maximized. As a test, we have inverse modeled, by means of Boltzmann learning, the catabolic core of Escherichia coli in glucose-limited aerobic stationary growth conditions. Empirical means are best reproduced when $F$ is a simple combination of biomass production and glucose uptake and the temperature is finite, implying the presence of fluctuations. The scheme presented here has the potential to deliver new quantitative insight on cellular metabolism. Our implementation is however computationally intensive, and highlights the major role that effective algorithms to sample the high-dimensional solution space of metabolic networks can play in this field.
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed, or to provide abstraction of some behavior of the system resulting more compact models. In this paper we enrich the stochastic process algebra Bio-PEPA, with the possibility of assigning delays to actions, yielding a new non-Markovian process algebra: Bio-PEPAd. This is a conservative extension meaning that the original syntax of Bio-PEPA is retained and the delay specification which can now be associated with actions may be added to existing Bio-PEPA models. The semantics of the firing of the actions with delays is the delay-as-duration approach, earlier presented in papers on the stochastic simulation of biological systems with delays. These semantics of the algebra are given in the Starting-Terminating style, meaning that the state and the completion of an action are observed as two separate events, as required by delays. Furthermore we outline how to perform stochastic simulation of Bio-PEPAd systems and how to automatically translate a Bio-PEPAd system into a set of Delay Differential Equations, the deterministic framework for modeling of biological systems with delays. We end the paper with two example models of biological systems with delays to illustrate the approach.
The term In Silico Trial indicates the use of computer modelling and simulation to evaluate the safety and efficacy of a medical product, whether a drug, a medical device, a diagnostic product or an advanced therapy medicinal product. Predictive models are positioned as new methodologies for the development and the regulatory evaluation of medical products. New methodologies are qualified by regulators such as FDA and EMA through formal processes, where a first step is the definition of the Context of Use (CoU), which is a concise description of how the new methodology is intended to be used in the development and regulatory assessment process. As In Silico Trials are a disruptively innovative class of new methodologies, it is important to have a list of possible CoUs highlighting potential applications for the development of the relative regulatory science. This review paper presents the result of a consensus process that took place in the InSilicoWorld Community of Practice, an online forum for experts in in silico medicine. The experts involved identified 46 descriptions of possible CoUs which were organised into a candidate taxonomy of nine CoU categories. Examples of 31 CoUs were identified in the available literature; the remaining 15 should, for now, be considered speculative.
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