Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site (...) of application. Moving solitons were only launched when the amide I energy was applied at one of the α-helix ends, whereas pinned solitons were produced in the α-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the α-helix through phase-modulated Gaussian pulses of amide I energy. We also compare the predicted soliton velocity based on effective soliton mass and the observed soliton velocity in computer simulations for different parameter values of the isotropy of the exciton-phonon interaction. The presented results demonstrate the capacity for explicit control of soliton velocity in protein α-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection. (shrink)

Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the (...) system of stochastic differential equations that govern the quantum dynamics of protein solitons at physiological temperature, T=310 K, for either a single isolated α-helix spine of hydrogen bonded peptide groups or the full protein α-helix comprised of three parallel α-helix spines. The simulated stochastic dynamics revealed that although the thermal noise is detrimental for the single isolated α-helix spine, the cooperative action of three amide I exciton quanta in the full protein α-helix ensures soliton lifetime of over 30 ps, during which the amide I energy could be transported along the entire extent of an 18-nm-long α-helix. Thus, macromolecular protein complexes, which are built up of protein α-helices could harness soliton-assisted energy transport at physiological temperature. Because the hydrolysis of a single adenosine triphosphate molecule is able to initiate three amide I exciton quanta, it is feasible that multiquantal protein solitons subserve a variety of specialized physiological functions in living systems. (shrink)

Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider protein solitons, whose energy is (...) lower, require heavier massive barriers for soliton reflection or trapping. Regulation of energy transport, delivery and utilization at protein active sites could thus be achieved through control of the soliton width, or of the effective mass of the protein subunits. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability (...) and mobility of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

In recent years, there are a number of proposals to consider collision-based soliton computer based on certain chemical reactions, namely Belousov-Zhabotinsky reaction, which leads to soliton solutions of coupled Nonlinear Schroedinger equations. They are called Manakov System. But it seems to us that such a soliton computer model can also be based on solitary wave solution of Maxwell-Dirac equation, which reduces to Choquard equation. And soliton solution of Choquard equation has been investigated by many researchers, therefore (...) it seems more profound from physics perspective. However, we consider both schemes of soliton computer are equally possible. More researches are needed to verify our proposition. (shrink)

The chromodielectric soliton model is Lorentz and chirally invariant. It has been demonstrated to exhibit dynamical chiral symmetry breaking and spatial confinement in the locally uniform approximation. We here study the full nonlocal quark self-energy in a color-dielectric medium modeled by a two-parameter Fermi function. Here color confinement is manifest. The self-energy thus obtained is used to calculate quark wave functions in the medium which, in turn, are used to calculate the nucleon and pion masses in the one-gluon-exchange approximation. (...) The nucleon mass is fixed to its empirical value using scaling arguments; the pion mass (for massless current quarks) turns out to be small but nonzero, depending on the model parameters. (shrink)

A new advanced systems theory concerning the emergent nature of the Social, Consciousness, and Life based on Mathematics and Physical Analogies is presented. This meta-theory concerns the distance between the emergent levels of these phenomena and their ultra-efficacious nature. The theory is based on the distinction between Systems and Meta-systems (organized Openscape environments). We first realize that we can understand the difference between the System and the Meta-system in terms of the relationship between a ‘Whole greater than the sum of (...) the parts’ and a ‘Whole less than the sum of its parts’, i.e., a whole full of holes (like a sponge) that provide niches for systems in the environment. Once we understand this distinction and clarify the nature of the unusual organization of the Meta-system, then it is possible to understand that there is a third possibility which is a whole exactly equal to the sum of its parts that is only supervenient like perfect numbers. In fact, there are three kinds of Special System corresponding to the perfect, amicable, and sociable aliquot numbers. These are all equal to the sum of their parts but with different degrees of differing and deferring in what Jacques Derrida calls “differance”. All other numbers are either excessive (systemic) or deficient (metasystemic) in this regard. The Special Systems are based on various mathematical analogies and some physical analogies. But the most important of the mathematical analogies are the hypercomplex algebras, which include the Complex Numbers, Quaternions, and Octonions, with the Sedenions corresponding to the Emergent Meta-system. However, other analogies are the Hopf fibrations between hyperspheres of various dimensions, nonorientable surfaces, soliton solutions, etc. These Special Systems have a long history within the tradition since they can be traced back to the imaginary cities of Plato. The Emergent Meta-system is a higher order global structure that includes the System with the three Special Systems as a cycle. An example of this from our tradition is in the Monadology of Gottfried Wilhelm von Leibniz. There is a conjunctive relationship between the System schema and the Special Systems that produce the Meta-system schema cycle. The Special Systems are a meta-model for the relationship between the emergent levels of Consciousness (Dissipative Ordering based on the theory of negative entropy of Prigogine), Living (Autopoietic Symbiotic based on the theory of Maturana and Varela), and Social (Reflexive based on the theory of John O’Malley and Barry Sandywell). These different special systems are related to the various existenitals identified by Martin Heidegger in Being and Time and various temporal reference frames identified by Richard M. Pico. We also relate the special systems to morphodynamic and teleodynamic systems of Terrence Deacon in Incomplete Nature to which we add sociodynamic systems to complete the series of Special Systems. (shrink)

It has been known for long time that the cosmic sound wave was there since the early epoch of the Universe. Signatures of its existence are abound. However, such a sound wave model of cosmology is rarely developed fully into a complete framework. This paper can be considered as our second attempt towards such a complete description of the Universe based on soliton wave solution of cosmological KdV equation. Then we advance further this KdV equation by virtue of Cellular (...) Automaton method to solve the PDEs. We submit wholeheartedly Robert Kurucz’s hypothesis that Big Bang should be replaced with a finite cellular automaton universe with no expansion. Nonetheless, we are fully aware that our model is far from being complete, but it appears the proposed cellular automaton model of the Universe is very close in spirit to what Konrad Zuse envisaged long time ago. It is our hope that the new proposed method can be verified with observation data. But we admit that our model is still in its infancy, more researches are needed to fill all the missing details. (shrink)

Unifying physics by describing a variety of interactions – or even all interactions – within a common framework has long been an alluring goal for physicists. One of the most ambitious attempts at unification was made in the 1910s by Gustav Mie. Mie aimed to derive electromagnetism, gravitation, and aspects of the emerging quantum theory from a single variational principle and a well-chosen Lagrangian. Mie’s main innovation was to consider nonlinear field equations to allow for stable particle-like solutions (now called (...) solitons), and he clarified the use of variational principles in the context of special relativity. The following brief introduction to Mie’s work has three main objectives. The first is to explain how Mie’s project fit into the contemporary development of the electromagnetic world view. Part of Mie’s project was to develop a relativistic theory of gravitation as a consequence of his generalized electromagnetic theory, and our second goal is to briefly assess this work, which reflects the conceptual resources available for developing a new account of gravitation by analogy with electromagnetism. Finally, Mie was a vocal critic of other approaches to the problem of gravitation. Mie’s criticisms of Einstein, in particular, bring out the subtlety and novelty of the ideas that Einstein used to guide his development of general relativity. (shrink)

The paper considers a new type of objects – blinking fractals – that are not covered by traditional theories studying dynamics of self-similarity processes. It is shown that the new approach allows one to give various quantitative characteristics of the newly introduced and traditional fractals using infinite and infinitesimal numbers proposed recently. In this connection, the problem of the mathematical modelling of continuity is discussed in detail. A strong advantage of the introduced computational paradigm consists of its well-marked numerical character (...) and its own instrument – Infinity Computer – able to execute operations with infinite and infinitesimal numbers. (shrink)

Very often traditional approaches studying dynamics of self-similarity processes are not able to give their quantitative characteristics at infinity and, as a consequence, use limits to overcome this difficulty. For example, it is well know that the limit area of Sierpinski’s carpet and volume of Menger’s sponge are equal to zero. It is shown in this paper that recently introduced infinite and infinitesimal numbers allow us to use exact expressions instead of limits and to calculate exact infinitesimal values of areas (...) and volumes at various points at infinity even if the chosen moment of the observation is infinitely faraway on the time axis from the starting point. It is interesting that traditional results that can be obtained without the usage of infinite and infinitesimal numbers can be produced just as finite approximations of the new ones. (shrink)