New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 25(2)

Published: Jan. 22, 2024

Abstract Bioinformatics has revolutionized biology and medicine by using computational methods to analyze interpret biological data. Quantum mechanics recently emerged as a promising tool for the analysis of systems, leading development quantum bioinformatics. This new field employs principles mechanics, algorithms, computing solve complex problems in molecular biology, drug design, protein folding. However, intersection bioinformatics, presents unique challenges. One significant challenge is possibility confusion among scientists between bioinformatics which have similar goals concepts. Additionally, diverse calculations each make it difficult establish boundaries identify purely effects from other factors that may affect processes. review provides an overview concepts their We examine challenges features this propose classification promote interdisciplinary collaboration accelerate progress. By unlocking full potential aims contribute our understanding systems.

Language: Английский

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Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology

Frontiers in Chemistry, Journal Year: 2024, Volume and Issue: 12

Published: Feb. 8, 2024

Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. nanocolloids exhibit intrinsic activity possess direct capacities comparable their counterparts. The unique metal ion architecture of these nanocolloids, including configurations, coordination environment, conductivity, the ability promote spontaneous hopping, contributes capabilities. Nano-size colloids believed be among earliest ‘oxidoreductases’ have ‘evolved’ on early Earth, playing critical systems. Representing a distinct type biocatalysts alongside metalloproteins, nanoparticles offer an alternative oxidoreductase activity. While nano-sized catalysts current Earth ecosystems intuitively significant, they remain poorly understood underestimated. Their contribution chemical biogeochemical cycles likely helped shape maintain balance our planet’s ecosystems. However, potential applications biomedical, agricultural, environmental protection sectors been fully explored or exploited. This review examines structure, properties, mechanisms from material’s evolutionary standpoint, aiming raise awareness provide innovative solutions some Earth’s sustainability challenges.

Language: Английский

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SAM-modified electrodes for understanding and harnessing the properties of redox proteins

Current Opinion in Electrochemistry, Journal Year: 2024, Volume and Issue: 46, P. 101481 - 101481

Published: March 14, 2024

Language: Английский

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Unveiling the role of inorganic nanoparticles in Earth’s biochemical evolution through electron transfer dynamics

iScience, Journal Year: 2024, Volume and Issue: 27(5), P. 109555 - 109555

Published: March 25, 2024

Language: Английский

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Universal stability of coherently diffusive one-dimensional systems with respect to decoherence

Physical review. A/Physical review, A, Journal Year: 2024, Volume and Issue: 109(4)

Published: April 24, 2024

Static disorder in a 3D crystal degrades the ideal ballistic dynamics until it produces localized regime.This Metal-Insulator Transition is often preceded by coherent diffusion.By studying three paradigmatic 1D models, namely Harper-Hofstadter-Aubry-André and Fibonacci tight-binding chains, along with power-banded random matrix model, we show that whenever diffusion present, transport exceptionally stable against decoherent noise.This completely at odds what happens for coherently dynamics, where coefficient strongly depends on environmental decoherence.A universal dependence of decoherence strength analytically derived: remains almost decoherence-independent coherence time becomes comparable mean elastic scattering time.Thus, systems quantum diffusive regime could be used to design robust wires.Moreover our results might shed new light functionality many biological systems, which operate border between regimes.

Language: Английский

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The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling

BioEssays, Journal Year: 2024, Volume and Issue: 46(5)

Published: March 9, 2024

Abstract Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well‐established lock‐and‐key model explains a ligand's recognition by receptor; however, general mechanism which receptors translate into activation, inactivation, or modulation remains elusive. Vibration Theory Olfaction was proposed in 1930s explain this subset receptor‐mediated phenomena correlating odorant molecular smell, but lacking. In 1990s, inelastic electron as plausible for translating vibration physiology. More recently, studies ligands’ vibrational spectra use deuterated analogs have provided helpful information study admittedly controversial hypothesis metabotropic other than olfactory present work, based part on published experiments from our laboratory using planarians an experimental organism, I will rationale possible approach extending idea ligand‐gated ion channels.

Language: Английский

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Universal stability of coherently diffusive 1D systems with respect to decoherence

arXiv (Cornell University), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 1, 2023

Static disorder in a 3D crystal degrades the ideal ballistic dynamics until it produces localized regime. This Metal-Insulator Transition is often preceded by coherent diffusion. By studying three paradigmatic 1D models, namely Harper-Hofstadter-Aubry-Andr\'e and Fibonacci tight-binding chains, along with power-banded random matrix model, we show that whenever diffusion present, transport exceptionally stable against decoherent noise. completely at odds what happens for coherently dynamics, where coefficient strongly depends on environmental decoherence. A universal dependence of decoherence strength analytically derived: remains almost decoherence-independent coherence time becomes comparable mean elastic scattering time. Thus, systems quantum diffusive regime could be used to design robust wires. Moreover our results might shed new light functionality many biological systems, which operate border between regimes.

Language: Английский

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Are Electrical Characterizations Consistent with the Cytochrome Structures ofGeobacter‘Nanowires’

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 12, 2023

Abstract Electrically conductive filaments from Geobacter sulfurreducens were reported to be pili with metallic-like conductivity, and yet later shown redox-active cytochromes by cryogenic electron microscopy. It has recently been argued that the simply misidentified, implying key observations formerly used refute involvement of in conductivity now must ascribed them. Herein, temperature, pH, voltage, crystallinity, charge propagation, aromatic density-related dependencies for putative are re-examined light CryoEM structures cytochrome filaments. is demonstrated that: Electrons flow through a succession redox reactions which energetics physically constrained kinetics largely independent protein identity highly conserved heme packing geometries. Computed heme-to-heme transfer rates agree, on average, within factor 10 experimentally determined other multi-heme proteins same T-stacked pairs, comprise nearly or exactly half all pairs electronic coupling-constrained bottlenecks set rate-limiting reaction µs timescale, fast enough compared typical ms enzymatic turnover. Tuning over ∼10 7 -fold range G. strains variants seems both implausible physiologically irrelevant if those supposed cytochromes. The protein-limited flux conduction 300-nm filament T- slip-stacked predicted ∼0.1 pA; cell discharging ∼1 pA/s would need at least filaments, consistent experimental estimates abundance. currents Omc- S Z relevant 0.1 V bias, however, pA nA, respectively. Some discrepancy attributable conditions dehydrated adsorbed bear Au- electrode contacts 2 hemes, case conducting probe atomic force microscopy, crushed under forces known deform change transport mechanism more highly-structured proteins. Previously observed hallmarks synthetic organic inconsistent structurally resolved physiological conditions, including (I) increased crystallinity promoting delocalization, (II) carbon nanotube-like (III) an exponential increase-then-decrease upon cooling, was only explain model potentials false. Furthermore, spectroscopic structural characterizations OmcZ attest huge acid-induced transition crystalline state enhancing either strongly disagree analyses higher pH values give inconclusive results can overly interpreted. Overall, significant currently exists— not between theory experiment —but structure one hand functional ‘nanowires’ other. structures, theoretical models, biological experiments, kinetic agreement about nature rate architectures stand opposed solid-state date. relevance and/or physical plausibility some experiments should examined further.

Language: Английский

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Quantum Tunneling in Natural Product Biosynthesis

Natural Product Communications, Journal Year: 2024, Volume and Issue: 19(4)

Published: April 1, 2024

Language: Английский

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Quantum Physics, Digital Computers, and Life from a Holistic Perspective

Foundations of Physics, Journal Year: 2024, Volume and Issue: 54(4)

Published: Aug. 1, 2024

Abstract Quantum physics is a linear theory, so it somewhat puzzling that can underlie very complex systems such as digital computers and life. This paper investigates how this possible. Physically, are necessarily modular hierarchical structures, with number of key features. Firstly, they cannot be described by single wave function: only local functions exist, rather than function for living cell, cat, or brain. Secondly, the quantum to classical transition characterised contextual wave-function collapse shaped macroscopic elements classically. Thirdly, downward causation occurs in physical hierarchy two ways: influence time dependent constraints, creation, modification, deletion lower level elements. Fourthly, there also logical structures supported ones, algorithms computer programs, They able support arbitrary operations, which outcomes aided design 3-d printing. Finally, open systems, heat baths playing role their dynamics providing arrows agree cosmological direction established evolution universe.

Language: Английский

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