| 1. |
- Abrishami, Vahid, et al.
(författare)
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Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data
- 2021
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 160, s. 43-52
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Forskningsöversikt (refereegranskat)abstract
- Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.
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| 2. |
- Adamatzky, Andrew, et al.
(författare)
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East-West paths to unconventional computing
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 131, s. 469-493
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Forskningsöversikt (refereegranskat)abstract
- Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical topics of this non-typical field include, but are not limited to physics of computation, non-classical logics, new complexity measures, novel hardware, mechanical, chemical and quantum computing. Unconventional computing encourages a new style of thinking while practical applications are obtained from uncovering and exploiting principles and mechanisms of information processing in and functional properties of, physical, chemical and living systems; in particular, efficient algorithms are developed, (almost) optimal architectures are designed and working prototypes of future computing devices are manufactured. This article includes idiosyncratic accounts of ‘unconventional computing’ scientists reflecting on their personal experiences, what attracted them to the field, their inspirations and discoveries.
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| 3. |
- Asano, Masanari, et al.
(författare)
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A model of differentiation in quantum bioinformatics
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 130, s. 88-98
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Forskningsöversikt (refereegranskat)abstract
- Differentiation is a universal process found in various phenomena of nature. As seen in the example of cell differentiation, the creation diversity on individual's character is caused by environmental interactions. In this paper, we try to explain its mechanism, which has been discussed mainly in Biology, by using the formalism of quantum physics. Our approach known as quantum bioinformatics shows that the temporal change of statistical state called decoherence fits to describe non-local phenomena like differentiation. (C) 2017 Elsevier Ltd. All rights reserved.
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| 4. |
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| 5. |
- Baladron, Carlos, et al.
(författare)
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Editorial
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 130, s. 1-1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Baladron, Carlos, et al.
(författare)
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Outline of a unified Darwinian evolutionary theory for physical and biological systems
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 130, s. 80-87
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Forskningsöversikt (refereegranskat)abstract
- The scheme of a unified Darwinian evolutionary theory for physical and biological systems is described. Every physical system is methodologically endowed with a classical information processor, which turns every system into an agent being also susceptible to evolution. Biological systems retain this structure as natural extensions of physical systems from which they are built up. Optimization of information flows turns out to be the key element to study the possible emergence of quantum behavior and the unified Darwinian description of physical and biological systems. The Darwinian natural selection scheme is completed by the Lamarckian component in the form of the anticipation of states of surrounding biophysical systems. (C) 2017 Elsevier Ltd. All rights reserved.
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| 7. |
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| 8. |
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| 9. |
- Iftikhar, Mehwish, et al.
(författare)
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AI- modelling of molecular identification and feminization of wolbachia infected Aedes aegypti
- 2020
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 150, s. 104-111
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Forskningsöversikt (refereegranskat)abstract
- Background: The genetic control strategies of vector borne diseases includes the replacement of a vector population by disease-refractory mosquitoes and the release of mosquitoes with a gene to control the vector's reproduction rates. Wolbachia are common intracellular bacteria that are found in arthropods and nematodes. Wolbachia infected male mosquitos have been used in different experimental trials around the world to suppress the target population of Aedes aegypti and this genetic control strategy has proved to be a promising alternative to other treatment strategies. Due to certain limitations, the successful application of this strategy is still awaited. Methods: Mathematical frame work for Wolbachia induced genetic control strategy has been developed in this article. With the aid of Artificial Intelligence (Al) tools, accurate parametric values are depicted. For the first time, the model is well synchronized with the experimental findings. The model is comprised of the generalized varying coefficient and multiple mating rates between infected and uninfected compartments of Aedes aegypti dengue to forecast the disease control. Results: Two mathematical models are developed in this article to demonstrate different mating rates of the genetic control strategy. The important parameters and time varying coefficients are well demonstrated with the aid of numerical computations. The resulting thresholds and forecasting may prove to be a useful tool for future experimental studies. Conclusions: From our analysis, we have concluded that the genetic control strategy is a promising technique and the role of Wolbachia infected male mosquitos, in genetic control strategies, can be better interpreted in an inexpensive manner with the aid of a theoretical model.
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| 10. |
- Igamberdiev, Abir U., et al.
(författare)
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Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism
- 2019
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Ingår i: Progress in Biophysics and Molecular Biology. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0079-6107 .- 1873-1732. ; 146, s. 23-36
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Forskningsöversikt (refereegranskat)abstract
- The equilibria of coenzyme nucleotides and substrates established in plant cells generate simple rules that govern the plant metabolome and provide optimal conditions for the non-equilibrium fluxes of major metabolic processes such as ATP synthesis, CO2 fixation, and mitochondrial respiration. Fast and abundant enzymes, such as adenylate kinase, carbonic anhydrase or malate dehydrogenase, provide constant substrate flux for these processes. These "buffering" enzymes follow the Michaelis-Menten (MM) kinetics and operate near equilibrium. The non-equilibrium "engine" enzymes, such as ATP synthase, Rubisco or the respiratory complexes, follow the modified version of MM kinetics due to their high concentration and low concentration of their substrates. The equilibrium reactions serve as control gates for the non-equilibrium flux through the engine enzymes establishing the balance of the fluxes of load and consumption of metabolic components. Under the coordinated operation of buffering and engine enzymes, the concentrations of free and Mg-bound adenylates and of free Mg2+ are set, serving as feedback signals from the adenylate metabolome. Those are linked to various cell energetics parameters, including membrane potentials. Also, internal levels of reduced and oxidized pyridine nucleotides are established in the coordinated operation of malate dehydrogenase and respiratory components, with proton concentration as a feedback from pyridine nucleotide pools. Non-coupled pathways of respiration serve to equilibrate the levels of pyridine nucleotides, adenylates, and as a pH stat. This stable non-equilibrium organizes the fluxes of energy spatially and temporally, controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles.
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| 11. |
- Javed, Sana, et al.
(författare)
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Biophysics and the nonlinear dynamics instigated by a special hormone
- 2020
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 150, s. 62-66
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Forskningsöversikt (refereegranskat)abstract
- Calcitonin, a potent hypocalcemic hormone, plays a vital role in inhibiting osteoclastic activities and suppressing bone removal. The physiological characteristics of calcitonin have long been discussed, along a few recommending calcitonin as a vestigial hormone. The basis for this article is to discuss the role of low and high levels of calcitonin in normal and osteoprotic bone turnover. The effect of calcitonin on the receptor activator of nuclear factor kappa-ligand and osteoclasts has been demonstrated using numerical simulations. This behavior recommends that treatment of osteoporosis via calcitonin does not provide the required upshots. For effectiveness calcitonin must be advised along with a combined therapy like aspirin which agrees with the experimental results available in the literature.
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| 12. |
- Jensen, Per, 1956-
(författare)
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Transgenerational epigenetic effects on animal behaviour
- 2013
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 113:3, s. 447-454
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Forskningsöversikt (refereegranskat)abstract
- Over the last decade a shift in paradigm has occurred with respect to the interaction between environmentand genes. It is now clear that animal genomes are regulated to a large extent as a result of inputfrom environmental events and experiences, which cause short- and long-term modifications in epigeneticmarkings of DNA and histones. In this review, the evidence that such epigenetic modificationscan affect the behaviour of animals is explored, and whether such acquired behaviour alterations cantransfer across generation borders. First, the mechanisms by which experiences cause epigenetic modificationsare examined. This includes, for example, methylation of cytosine in CpG positions and acetylationof histones, and studies showing that this can be modified by early experiences. Secondly, theevidence that specific modifications in the epigenome can be the cause of behaviour variation isreviewed. Thirdly, the extent to which this phenotypically active epigenetic variants can be inheritedeither through the germline or through reoccurring environmental conditions is examined. A particularlyinteresting observation is that epigenetic modifications are often linked to stress, and may possibly bemediated by steroid effects. Finally, the idea that transgenerationally stable epigenetic variants may serveas substrates for natural selection is explored, and it is speculated that they may even predispose fordirected, non-random mutations.
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| 13. |
- Khalil, Mahmoud I., et al.
(författare)
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Growth or death? : Control of cell destiny by mTOR and autophagy pathways
- 2023
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 185, s. 39-55
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Forskningsöversikt (refereegranskat)abstract
- One of the central regulators of cell growth, proliferation, and metabolism is the mammalian target of rapamycin, mTOR, which exists in two structurally and functionally different complexes: mTORC1 and mTORC2; unlike m TORC2, mTORC1 is activated in response to the sufficiency of nutrients and is inhibited by rapamycin. mTOR complexes have critical roles not only in protein synthesis, gene transcription regulation, proliferation, tumor metabolism, but also in the regulation of the programmed cell death mechanisms such as autophagy and apoptosis. Autophagy is a conserved catabolic mechanism in which damaged molecules are recycled in response to nutrient starvation. Emerging evidence indicates that the mTOR signaling pathway is frequently activated in tumors. In addition, dysregulation of autophagy was associated with the development of a variety of human diseases, such as cancer and aging. Since mTOR can inhibit the induction of the autophagic process from the early stages of autophagosome formation to the late stage of lysosome degradation, the use of mTOR inhibitors to regulate autophagy could be considered a potential therapeutic option. The present review sheds light on the mTOR and autophagy signaling pathways and the mechanisms of regulation of mTOR-autophagy.
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| 14. |
- Khrennikov, Andrei, et al.
(författare)
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Automaton model of protein : Dynamics of conformational and functional states
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 130:A, s. 2-14
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Tidskriftsartikel (refereegranskat)abstract
- In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory of automata to model the latter dynamics. In our model protein's behavior is modeled with the aid of two dynamical systems, ontic and epistemic, which describe evolution of conformational and functional states of proteins, respectively. The epistemic automaton is constructed from the ontic automaton on the basis of functional (observational) equivalence relation on the space of ontic states. This reminds a few approaches to emergent quantum mechanics in which a quantum (epistemic) state is treated as representing a class of prequantum (ontic) states. This approach does not match to the standard protein structure-function paradigm. However, it is perfect for modeling of behavior of intrinsically disordered proteins. Mathematically space of protein's ontic states (conformational states) is modeled with the aid of p-adic numbers or more general ultrametric spaces encoding the internal hierarchical structure of proteins. Connection with theory of p-adic dynamical systems is briefly discussed.
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| 15. |
- Melkikh, Alexey V., et al.
(författare)
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Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 130, s. 61-79
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Forskningsöversikt (refereegranskat)abstract
- A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. (C) 2017 Elsevier Ltd. All rights reserved.
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| 16. |
- Melkikh, Alexey V., et al.
(författare)
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Nontrivial quantum and quantum-like effects in biosystems : Unsolved questions and paradoxes
- 2015
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 119:2, s. 137-161
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Forskningsöversikt (refereegranskat)abstract
- Non-trivial quantum effects in biological systems are analyzed. Some unresolved issues and paradoxes related to quantum effects (Levinthal's paradox, the paradox of speed, and mechanisms of evolution) are addressed. It is concluded that the existence of non-trivial quantum effects is necessary for the functioning of living systems. In particular, it is demonstrated that classical mechanics cannot explain the stable work of the cell and any over-cell structures. The need for quantum effects is generated also by combinatorial problems of evolution. Their solution requires a priori information about the states of the evolving system, but within the framework of the classical theory it is not possible to explain mechanisms of its storage consistently. We also present essentials of so called quantum-like paradigm: sufficiently complex bio-systems process information by violating the laws of classical probability and information theory. Therefore the mathematical apparatus of quantum theory may have fruitful applications to describe behavior of bio-systems: from cells to brains, ecosystems and social systems. In quantum-like information biology it is not presumed that quantum information bio-processing is resulted from quantum physical processes in living organisms. Special experiments to test the role of quantum mechanics in living systems are suggested. This requires a detailed study of living systems on the level of individual atoms and molecules. Such monitoring of living systems in vivo can allow the identification of the real potentials of interaction between biologically important molecules. (C) 2015 Elsevier Ltd. All rights reserved.
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| 17. |
- Melkikh, Alexey V., et al.
(författare)
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Quantum-like model of partially directed evolution
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 125, s. 36-51
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Tidskriftsartikel (refereegranskat)abstract
- The background of this study is that models of the evolution of living systems are based mainly on the evolution of replicators and cannot explain many of the properties of biological systems such as the existence of the sexes, molecular exaptation and others. The purpose of this study is to build a complete model of the evolution of organisms based on a combination of quantum-like models and models based on partial directivity of evolution. We also used optimal control theory for evolution modeling. We found that partial directivity of evolution is necessary for the explanation of the properties of an evolving system such as the stability of evolutionary strategies, aging and death, the presence of the sexes. The proposed model represents a systems approach to the evolution of species and will facilitate the understanding of the evolution and biology as a whole.
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| 18. |
- Pedersen, Morten Gram, et al.
(författare)
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Mathematical modeling and statistical analysis of calcium-regulated insulin granule exocytosis in beta-cells from mice and humans.
- 2011
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 1873-1732 .- 0079-6107. ; 107:2, s. 257-264
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Tidskriftsartikel (refereegranskat)abstract
- Insulin is released from pancreatic beta-cells as a result of Ca(2+)-evoked exocytosis of dense-core granules. Secretion is biphasic, which has been suggested to correspond to the release of different granule pools. Here we review and carefully reanalyze previously published patch-clamp data on depolarization-evoked Ca(2+)-currents and corresponding capacitance measurements. Using a statistical mixed-effects model, we show that the data indicate that pool depletion is negligible in response to short depolarizations in mouse beta-cells. We then review mathematical models of granule dynamics and exocytosis in rodent beta-cells and present a mathematical description of Ca(2+)-evoked exocytosis in human beta-cells, which show clear differences to their rodent counterparts. The model suggests that L- and P/Q-type Ca(2+)-channels are involved to a similar degree in exocytosis during electrical activity in human beta-cells.
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| 19. |
- Pylkkänen, Paavo
(författare)
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The quantum epoché
- 2015
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 119:3, s. 332-340
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Tidskriftsartikel (refereegranskat)abstract
- The theme of phenomenology and quantum physics is here tackled by examining some basic interpretational issues in quantum physics. One key issue in quantum theory from the very beginning has been whether it is possible to provide a quantum ontology of particles in motion in the same way as in classical physics, or whether we are restricted to stay within a more limited view of quantum systems, in terms of complementary but mutually exclusive phenomena. In phenomenological terms we could describe the situation by saying that according to the usual interpretation of quantum theory (especially Niels Bohr's), quantum phenomena require a kind of epoche (i.e. a suspension of assumptions about reality at the quantum level). However, there are other interpretations (especially David Bohm's) that seem to re-establish the possibility of a mind-independent ontology at the quantum level. We will show that even such ontological interpretations contain novel, non-classical features, which require them to give a special role to “phenomena” or “appearances”, a role not encountered in classical physics. We will conclude that while ontological interpretations of quantum theory are possible, quantum theory implies the need of a certain kind of epoche even for this type of interpretations. While different from the epoche connected to phenomenological description, the “quantum epoche” nevertheless points to a potentially interesting parallel between phenomenology and quantum philosophy.
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| 20. |
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| 21. |
- Rorsman, Patrik, et al.
(författare)
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Electrophysiology of pancreatic beta-cells in intact mouse islets of Langerhans
- 2011
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 1873-1732 .- 0079-6107. ; 107:2, s. 224-235
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Forskningsöversikt (refereegranskat)abstract
- When exposed to intermediate glucose concentrations (6-16 mol/l), pancreatic beta-cells in intact islets generate bursts of action potentials (superimposed on depolarised plateaux) separated by repolarised electrically silent intervals. First described more than 40 years ago, these oscillations have continued to intrigue beta-cell electrophysiologists. To date, most studies of beta-cell ion channels have been performed on isolated cells maintained in tissue culture (that do not burst). Here we will review the electrophysiological properties of beta-cells in intact, freshly isolated, mouse pancreatic islets. We will consider the role of ATP-regulated K+-channels (K-ATP-channels), small-conductance Ca2+-activated K+-channels and voltage-gated Ca2+-channels in the generation of the bursts. Our data indicate that K-ATP-channels not only constitute the glucose-regulated resting conductance in the beta-cell but also provide a variable K+- conductance that influence the duration of the bursts of action potentials and the silent intervals. We show that inactivation of the voltage-gated Ca2+-current is negligible at voltages corresponding to the plateau potential and consequently unlikely to play a major role in the termination of the burst. Finally, we propose a model for glucose-induced beta-cell electrical activity based on observations made in intact pancreatic islets. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.
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| 22. |
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| 23. |
- Stålhand, Jonas, et al.
(författare)
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Smooth muscle contraction : Mechanochemical formulation for homogeneous finite strains
- 2008
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 96:1-3, s. 465-481
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Forskningsöversikt (refereegranskat)abstract
- Chemical kinetics of smooth muscle contraction affect mechanical properties of organs that function under finite strains. In an effort to gain further insight into organ physiology, we formulate a mechanochemical finite strain model by considering the interaction between mechanical and biochemical components of cell function during activation. We propose a new constitutive framework and use a mechanochemical device that consists of two parallel elements: (i) spring for the cell stiffness; (ii) contractile element for the sarcomere. We use a multiplicative decomposition of cell elongation into filament contraction and cross-bridge deformation, and suggest that the free energy be a function of stretches, four variables (free unphosphorylated myosin, phosphorylated cross-bridges, phosphorylated and dephosphorylated cross-bridges attached to actin), chemical state variable driven by Ca2+-concentration, and temperature. The derived constitutive laws are thermodynamically consistent. Assuming isothermal conditions, we specialize the mechanical phase such that we recover the linear model of Yang et al. [2003a. The myogenic response in isolated rat cerebrovascular arteries: smooth muscle cell. Med. Eng. Phys. 25, 691-709]. The chemical phase is also specialized so that the linearized chemical evolution law leads to the four-state model of Hai and Murphy [ 1988. Cross-bridge phosphorylation and regulation of latch state in smooth muscle. Am. J. Physiol. 254, C99-C106]. One numerical example shows typical mechanochemical effects and the efficiency of the proposed approach. We discuss related parameter identification, and illustrate the dependence of muscle contraction (Ca (2+)-concentration) on active stress and related stretch. Mechanochemical models of this kind serve the mathematical basis for analyzing coupled processes such as the dependency of tissue properties on the chemical kinetics of smooth muscle.
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| 24. |
- Söderberg, Per G.
(författare)
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Optical radiation and the eyes with special emphasis on children
- 2011
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 107:3, s. 389-392
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Forskningsöversikt (refereegranskat)abstract
- The Sun is the most abundant source of optical radiation for the child eye. New hand-held visible lasers are a threat to the child eye. Some scientific data suggest that near infrared radiation may cause cumulative damage in the ocular lens. The child eye usually is exposed to ambient solar radiation, gazing at the horizon. Ambient Sun ultraviolet radiation (UVR) exposure to the child is complex due to atmospheric scattering and strong dependence on background reflection. Solar exposure causes biological damage, only by photochemical mechanisms. UVR exposure to a child eye is mainly a threat to the anterior segment of the eye, but also age dependently to the retina. Above threshold exposure to UVR, for short delay onset of damage, causes a toxic reaction on the surface of the eye, snow blindness, and cataract. Sub-threshold daily exposure to UVR over decades is associated with several ocular surface pathologies and eye lid cancer. Visible radiation is a threat to the retina. A single above threshold exposure, for short delay onset of damage to the retina causes immediate photochemical Type II retinal damage. Sun blindness. A single exposure of the retina to a very high intensity laser beam may cause thermal or thenno-mechanical damage in the retina. In environments with high irradiance of optical radiation, the child eye should be protected. Legislation and public information is required for avoidance of damage from high intensity laser systems. More research is urgently needed to exclude the potential hazard of near infrared radiation.
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| 25. |
- Turner, Philip, et al.
(författare)
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New insights into the physical processes that underpin cell division and the emergence of different cellular and multicellular structures
- 2020
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier BV. - 0079-6107 .- 1873-1732. ; 150, s. 13-42
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Forskningsöversikt (refereegranskat)abstract
- Despite decades of focused research, a detailed understanding of the fundamental physical processes that underpin biological systems (structures and processes) remains an open challenge. Within the present paper we report on biomimetic studies, which offer new insights into the process of cell division and the emergence of different cellular and multicellular structures. Experimental studies specifically investigated the impact of including different concentrations of charged bio-molecules (cytokinin and gibberellic acid) on the growth of BaCO3 - SiO2 based structures. Results highlighted the role of charge density on the emergence of long-range order, underpinned by a negentropic process. This included the growth of synthetic cell-like structures, with the intrinsic capacity to divide and change morphology at cellular and multicellular scales. Detailed study of dividing structures supports a hypothesis that cell division is dependent on the establishment of a charge-induced macroscopic quantum potential and cell-scale quantum coherence, which allows a description in terms of a macroscopic Schrodinger-like equation, based on a constant different from the Planck constant. Whilst the system does not reflect full correspondence with standard quantum mechanics, many of the phenomena that we typically associate with such a system are recovered. In addition to phenomena normally associated with the Schrodinger equation, we also unexpectedly report on the emergence of intrinsic spin as a macroscopic quantum phenomena, whose origins we account for within a four-dimensional fractal space-time and a macroscopic Pauli equation, which represents the non-relativistic limit of the Dirac equation.
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| 26. |
- Yamato, Ichiro, et al.
(författare)
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Energy and information flows in biological systems : Bioenergy transduction of V-1-ATPase rotary motor and dynamics of thermodynamic entropy in information flows
- 2017
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Ingår i: Progress in Biophysics and Molecular Biology. - : Elsevier. - 0079-6107 .- 1873-1732. ; 130, s. 33-38
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Forskningsöversikt (refereegranskat)abstract
- We classify research fields in biology with respect to flows of materials, energy, and information. We investigate energy transducing mechanisms in biology, using as a representative the typical molecular rotary motor Vi-ATPase from a bacterium Enterococcus hirae. The structures of several intermediates of the rotary motor are described and the molecular mechanism of the motor converting chemical energy into mechanical energy is discussed. Comments and considerations on the information flows in biology, especially on the thermodynamic entropy in quantum physical and biological systems, are presented in section 3 in a biologist friendly manner. (C) 2017 Elsevier Ltd. All rights reserved.
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| 27. |
- Zhu, CH, et al.
(författare)
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Diversity in S-layers
- 2017
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Ingår i: Progress in biophysics and molecular biology. - : Elsevier BV. - 1873-1732 .- 0079-6107. ; 123, s. 1-15
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Tidskriftsartikel (refereegranskat)
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| 28. |
- Al-Karadaghi, Salam, et al.
(författare)
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A decade of progress in understanding the structural basis of protein synthesis
- 2000
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Ingår i: Progress in Biophysics and Molecular Biology. - 1873-1732. ; 73:2, s. 167-193
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Forskningsöversikt (refereegranskat)abstract
- The key reaction of protein synthesis, peptidyl transfer, is catalysed in all living organisms by the ribosome - an advanced and highly efficient molecular machine. During the last decade extensive X-ray crystallographic and NMR studies of the three-dimensional structure of ribosomal proteins, ribosomal RNA components and their complexes with ribosomal proteins, and of several translation factors in different functional states have taken us to a new level of understanding of the mechanism of function of the protein synthesis machinery. Among the new remarkable features revealed by structural studies, is the mimicry of the tRNA molecule by elongation factor G, ribosomal recycling factor and the eukaryotic release factor 1. Several other translation factors, for which three-dimensional structures are not yet known, are also expected to show some form of tRNA mimicry. The efforts of several crystallographic and biochemical groups have resulted in the determination by X-ray crystallography of the structures of the 30S and 50S subunits at moderate resolution, and of the structure of the 70S subunit both by X-ray crystallography and cryo-electron microscopy (EM). In addition, low resolution cryo-EM models of the ribosome with different translation factors and tRNA have been obtained. The new ribosomal models allowed for the first time a clear identification of the functional centres of the ribosome and of the binding sites for tRNA and ribosomal proteins with known three-dimensional structure. The new structural data have opened a way for the design of new experiments aimed at deeper understanding at an atomic level of the dynamics of the system.
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| 29. |
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| 30. |
- Gerlee, Philip, 1980, et al.
(författare)
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Evolving homeostatic tissue using genetic algorithms
- 2011
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Ingår i: Progress in Biophysics & Molecular Biology. - : Elsevier BV. - 0079-6107. ; 106:2, s. 414-425
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Tidskriftsartikel (refereegranskat)abstract
- Multicellular organisms maintain form and function through a multitude of homeostatic mechanisms. The details of these mechanisms are in many cases unknown, and so are their evolutionary origin and their link to development. In order to illuminate these issues we have investigated the evolution of structural homeostasis in the simplest of cases, a tissue formed by a mono-layer of cells. To this end, we made use of a 3-dimensional hybrid cellular automaton, an individual-based model in which the behaviour of each cell depends on its local environment. Using an evolutionary algorithm (EA) we evolved cell signalling networks, both with a fixed and an incremental fitness evaluation, which give rise to and maintain a mono-layer tissue structure. Analysis of the solutions provided by the EA shows that the two evaluation methods gives rise to different types of solutions to the problem of homeostasis. The fixed method leads to almost optimal solutions, where the tissue relies on a high rate of cell turnover, while the solutions from the incremental scheme behave in a more conservative manner, only dividing when necessary. In order to test the robustness of the solutions we subjected them to environmental stress, by wounding the tissue, and to genetic stress, by introducing mutations. The results show that the robustness very much depends on the mechanism responsible for maintaining homeostasis. The two evolved cell types analysed present contrasting mechanisms by which tissue homeostasis can be maintained. This compares well to different tissue types found in multicellular organisms. For example the epithelial cells lining the colon in humans are shed at a considerable rate, while in other tissue types, which are not as exposed, the conservative type of homeostatic mechanism is normally found. These results will hopefully shed light on how multicellular organisms have evolved homeostatic mechanisms and what might occur when these mechanisms fail, as in the case of cancer. (C) 2011 Published by Elsevier Ltd.
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