48 research outputs found
Quantum fluctuations and life
There have been many claims that quantum mechanics plays a key role in the
origin and/or operation of biological organisms, beyond merely providing the
basis for the shapes and sizes of biological molecules and their chemical
affinities. These range from the suggestion by Schrodinger that quantum
fluctuations produce mutations, to the conjecture by Hameroff and Penrose that
quantum coherence in microtubules is linked to consciousness. I review some of
these claims in this paper, and discuss the serious problem of decoherence. I
advance some further conjectures about quantum information processing in
bio-systems. Some possible experiments are suggested.Comment: 10 pages, no figures, conference pape
East-West Paths to Unconventional Computing
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.info:eu-repo/semantics/publishedVersio
Large and stable: actin aster networks formed via entropic forces
Biopolymer networks play a major role as part of the cytoskeleton. They provide
stable structures and act as a medium for signal transport. These features
encourage the application of such networks as organic computation devices.
While research on this topic is not advanced yet, previous results are very
promising. The protein actin in particular appears advantageous. It can be
arranged to various stable structures and transmit several signals. In this
study aster shaped networks were self-assembled via entropic forces by the
crowding agent methyl cellulose. These networks are characterised by a regular
and uniquely thick bundle structure, but have so far only been accounted in
droplets of 100 μm diameter. We report now regular asters in an area of a few
mm2 that could be observed even after months. Such stability outside of an
organism is striking and underlines the great potential actin aster networks
display
The Zinc Dyshomeostasis Hypothesis of Alzheimer's Disease
Alzheimer's disease (AD) is the most common form of dementia in the elderly. Hallmark AD neuropathology includes extracellular amyloid plaques composed largely of the amyloid-β protein (Aβ), intracellular neurofibrillary tangles (NFTs) composed of hyper-phosphorylated microtubule-associated protein tau (MAP-tau), and microtubule destabilization. Early-onset autosomal dominant AD genes are associated with excessive Aβ accumulation, however cognitive impairment best correlates with NFTs and disrupted microtubules. The mechanisms linking Aβ and NFT pathologies in AD are unknown. Here, we propose that sequestration of zinc by Aβ-amyloid deposits (Aβ oligomers and plaques) not only drives Aβ aggregation, but also disrupts zinc homeostasis in zinc-enriched brain regions important for memory and vulnerable to AD pathology, resulting in intra-neuronal zinc levels, which are either too low, or excessively high. To evaluate this hypothesis, we 1) used molecular modeling of zinc binding to the microtubule component protein tubulin, identifying specific, high-affinity zinc binding sites that influence side-to-side tubulin interaction, the sensitive link in microtubule polymerization and stability. We also 2) performed kinetic modeling showing zinc distribution in extra-neuronal Aβ deposits can reduce intra-neuronal zinc binding to microtubules, destabilizing microtubules. Finally, we 3) used metallomic imaging mass spectrometry (MIMS) to show anatomically-localized and age-dependent zinc dyshomeostasis in specific brain regions of Tg2576 transgenic, mice, a model for AD. We found excess zinc in brain regions associated with memory processing and NFT pathology. Overall, we present a theoretical framework and support for a new theory of AD linking extra-neuronal Aβ amyloid to intra-neuronal NFTs and cognitive dysfunction. The connection, we propose, is based on β-amyloid-induced alterations in zinc ion concentration inside neurons affecting stability of polymerized microtubules, their binding to MAP-tau, and molecular dynamics involved in cognition. Further, our theory supports novel AD therapeutic strategies targeting intra-neuronal zinc homeostasis and microtubule dynamics to prevent neurodegeneration and cognitive decline
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DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics
The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University