25,377 research outputs found
A New method for Analysis of Biomolecules Using the BSM-SG Atomic Models
Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory
explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability
to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess
some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows
uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The
resulting physical models of the atoms are characterized by the same interaction energies as the quantum mechanical
models, while the structure of the elementary particles influence their spatial arrangement in the nuclei. The resulting
atomic models with fully identifiable parameters and angular positions of the quantum orbits permit studying the physical
conditions behind the structural and bonding restrictions of the atoms connected in molecules. A new method for a
theoretical analysis of biomolecules is proposed. The analysis of a DNA molecule leads to formulation of hypotheses
about the energy storage mechanism in DNA and its role in the cell cycle synchronization. This permits shedding a light
on the DNA feature known as a C-value paradox. The analysis of a tRNA molecule leads to formulation of a hypothesis
about a binary decoding mechanism behind the 20 flavors of the complex aminoacyle-tRNA synthetases - tRNA, known
as a paradox
Erwin Schroedinger, Francis Crick and epigenetic stability
Schroedinger's book 'What is Life?' is widely credited for having played a
crucial role in development of molecular and cellular biology. My essay
revisits the issues raised by this book from the modern perspective of
epigenetics and systems biology. I contrast two classes of potential mechanisms
of epigenetic stability: 'epigenetic templating' and 'systems biology'
approaches, and consider them from the point of view expressed by Schroedinger.
I also discuss how quantum entanglement, a nonclassical feature of quantum
mechanics, can help to address the 'problem of small numbers' that lead
Schroedinger to promote the idea of molecular code-script for explanation of
stability of biological order.Comment: New and improved version of the essay, now published in the online
journal 'Biology Direct'. Contains more expanded discussion on entanglement.
18 pages, 2 figures. The file includes open reviews by E.Koonin, V.Vedral and
E.Karsent
Quantum Biology
A critical assessment of the recent developments of molecular biology is
presented. The thesis that they do not lead to a conceptual understanding of
life and biological systems is defended. Maturana and Varela's concept of
autopoiesis is briefly sketched and its logical circularity avoided by
postulating the existence of underlying {\it living processes}, entailing
amplification from the microscopic to the macroscopic scale, with increasing
complexity in the passage from one scale to the other. Following such a line of
thought, the currently accepted model of condensed matter, which is based on
electrostatics and short-ranged forces, is criticized. It is suggested that the
correct interpretation of quantum dispersion forces (van der Waals, hydrogen
bonding, and so on) as quantum coherence effects hints at the necessity of
including long-ranged forces (or mechanisms for them) in condensed matter
theories of biological processes. Some quantum effects in biology are reviewed
and quantum mechanics is acknowledged as conceptually important to biology
since without it most (if not all) of the biological structures and signalling
processes would not even exist. Moreover, it is suggested that long-range
quantum coherent dynamics, including electron polarization, may be invoked to
explain signal amplification process in biological systems in general
Proton tunneling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis
The role of proton tunneling in biological catalysis is investigated here
within the frameworks of quantum information theory and thermodynamics. We
consider the quantum correlations generated through two hydrogen bonds between
a substrate and a prototypical enzyme that first catalyzes the tautomerization
of the substrate to move on to a subsequent catalysis, and discuss how the
enzyme can derive its catalytic potency from these correlations. In particular,
we show that classical changes induced in the binding site of the enzyme
spreads the quantum correlations among all of the four hydrogen-bonded atoms
thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns
to its initial state after the binding stage, the substrate ends in a new
transition state corresponding to a quantum superposition. Open quantum system
dynamics can then naturally drive the reaction in the forward direction from
the major tautomeric form to the minor tautomeric form without needing any
additional catalytic activity. We find that in this scenario the enzyme lowers
the activation energy so much that there is no energy barrier left in the
tautomerization, even if the quantum correlations quickly decay.Comment: 15 pages, 4 figures. Authors postprint versio
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