The irregular (integer) tetrahedron as a warehouse of biological information
This paper is devoted to a new classification of the twenty amino acids based on the heronian (integer) tetrahedron.
q-bio.OT↗
SEARCH · Searcharxiv
Results for “q-bio.OT”
Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Life's Solutions are Complex Fluids. A Mathematical Challenge
Classical thermodynamics and statistical mechanics describe systems in which nothing interacts with nothing. Even the highly refined theory of simple fluids does not deal very well with electrical interactions, boundary conditions, or flows, if at all. Electrical interactions, boundary conditions, and flows are essential features of living systems. Life without flow is death and so a different approach is needed to study biology alive. The theory of complex fluids deals with interactions, boundary conditions, and flows quite well as can be seen in its successful treatment of liquid crystals. I advocate treating ionic solutions in general as complex fluids, with microelements that are the solutes and components of the solution. Enzyme active sites are a special case where some solutes are reactants. Solutes are crowded into active sites of enzyme by the high density of protein charges. The electric field links chemical reactions to charges in the protein and surrounding solutions. Interactions potentiate catalysis and control biological function. I suspect that most chemical reactions that occur in liquids also need to be treated by the theory of complex fluids. The electron movements of these reactions occur in a temporary highly concentrated fluctuation, a transient spatial inhomogeneity in the bulk solution. The electron movements of these reactions (described by quantum mechanics) are coupled to the electric (and sometimes steric) fields of the bulk solution. I suspect the electron movements, inhomogeneities, and chemical reaction (in the condensed phase) need to be treated by the theory of complex fluids because everything interacts with everything else, in this system, as in so many others.
q-bio.OT↗
Evolutionary Transitions and Top-Down Causation
Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down causation -- mediated by a reversal in the flow of information from lower to higher levels of organization, to that from higher to lower levels of organization -- is a driving force for most major evolutionary transitions. We suggest that many major evolutionary transitions might therefore be marked by a transition in causal structure. We use logistic growth as a toy model for demonstrating how such a transition can drive the emergence of collective behavior in replicative systems. We then outline how this scenario may have played out in those major evolutionary transitions in which new, higher levels of organization emerged, and propose possible methods via which our hypothesis might be tested.
nlin.AO↗
Mineral bridges in nacre revisited
We confirm with high-resolution techniques the existence of mineral bridges between superposed nacre tablets. In the towered nacre of both gastropods and the cephalopod Nautilus there are large bridges aligned along the tower axes, corresponding to gaps (150-200 nm) in the interlamellar membranes. Gaps are produced by the interaction of the nascent tablets with a surface membrane that covers the nacre compartment. In the terraced nacre of bivalves bridges associated with elongated gaps in the interlamellar membrane (> 100 nm) have mainly been found at or close to the edges of superposed parental tablets. To explain this placement, we hypothesize that the interlamellar membrane breaks due to differences in osmotic pressure across it when the interlamellar space below becomes reduced at an advanced stage of calcification. In no cases are the minor connections between superimposed tablets (< 60 nm), earlier reported to be mineral bridges, found to be such.
physics.bio-ph↗
Generalized Gumbel distribution of current fluctuations in purple membrane monolayers
We investigate the nature of a class of probability density functions, say G(a), with a the shape parameter, which generalizes the Gumbel distribution. These functions appear in a model of charge transport, when applied to a metal-insulator-metal structure, where the insulator is constituted by a monolayer of bacteriorhodopsin. Current shows a sharp increase above about 3 V, interpreted as the cross-over between direct and injection sequential-tunneling regimes. In particular, we show that, changing the bias value, the probability density function changes its look from bimodal to unimodal. Actually, the bimodal distributions can be resolved in at least a couple of $G(a)$ functions with different values of the shape parameter.
cond-mat.stat-mech↗
Potential of Traditional Medicinal Plants for Treating Obesity: A Review
Obesity is a global health concern associated with high morbidity and mortality. Therapeutic strategies include synthetic drugs and surgery, which may entail high costs and serious complications. Plant-based medicinal agents offer an alternative approach. A review of the studies on accessible botanical sources for the treatment of obesity is provided, which attempts to explain how these medicinal plants act to cause weight loss, and which approach is safer and more efficient. Information was gathered for the period of 1991 to 2012. Five basic mechanisms, including stimulating thermogenesis, lowering lipogenesis, enhancing lipolysis, suppressing appetite, and decreasing the absorption of lipids may be operating. Consumption of standardized medicinal plant extracts may be a safe treatment for obesity. However, some combinations of medicinal plants may result in either lower efficacy or cause unexpected side-effects.
q-bio.OT↗
Can Resonant Oscillations of the Earth Ionosphere Influence the Human Brain Biorhythm?
Within the frames of Alfvén sweep maser theory the description of morphological features of geomagnetic pulsations in the ionosphere with frequencies (0.1-10 Hz) in the vicinity of Schumann resonance (7.83 Hz) is obtained. It is shown that the related regular spectral shapes of geomagnetic pulsations in the ionosphere determined by "viscosity" and "elasticity" of magneto-plasma medium that control the nonlinear relaxation of energy and deviation of Alfvén wave energy around its equilibrium value. Due to the fact that the frequency bands of Alfvén maser resonant structures practically coincide with the frequency band delta- and partially theta-rhythms of human brain, the problem of degree of possible impact of electromagnetic "pearl" type resonant structures (0.1-5 Hz) onto the brain bio-rhythms stability is discussed.
physics.gen-ph↗
Biologists meet statisticians: A workshop for young scientists to foster interdisciplinary team work
Life science and statistics have necessarily become essential partners. The need to plan complex, structured experiments, involving elaborated designs, and the need to analyse datasets in the era of systems biology and high throughput technologies has to build upon professional statistical expertise. On the other hand, conducting such analyses and also developing improved or new methods, also for novel kinds of data, has to build upon solid biological understanding and practise. However, the meeting of scientists of both fields is often hampered by a variety of communicative hurdles - which are based on field-specific working languages and cultural differences. As a step towards a better mutual understanding, we developed a workshop concept bringing together young experimental biologists and statisticians, to work as pairs and learn to value each others competences and practise interdisciplinary communication in a casual atmosphere. The first implementation of our concept was a cooperation of the German Region of the International Biometrical Society and the Leibnitz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (short: DSMZ), Braunschweig, Germany. We collected feedback in form of three questionnaires, oral comments, and gathered experiences for the improvement of this concept. The long-term challenge for both disciplines is the establishment of systematic schedules and strategic partnerships which use the proposed workshop concept to foster mutual understanding, to seed the necessary interdisciplinary cooperation network, and to start training the indispensable communication skills at the earliest possible phase of education.
stat.OT↗
The dynamics of H-bonds of the hydration shells of ions, ATPase and NE-activated adenylyl cyclase on the coupling of energy and signal transduction
Glycerol titration distinguished from free water the local hydration shell involved in ATPase transition from active to inactive, with cooperativity for water n=16. Rat brain cortex: NE-stimulated and its basal AC in the absence of free Mg2+, allows a refractive state of AC with negative cooperativity for MgATP and ATP4-. The erythrocyte-Hb system operates as a metabolic sensor to match glucose availability with the release of Hb-carried, O2 and Mg2+ at CSF. [Mg(H2O)6](H2O)122+ by chelating either a protein or ATP4- losses most of its hydration shell. The ion pump ATPase by forming ADP3- releases an incompletely hydrated Mg2+, which could capture H2O from either [Na.(H2O)6]+ or [K.(H2O)6]+. Thus, sieve-sizing their hydration shells for fitting into Na+-pump channels. An AC refractory period may participate in STM. Mg2+ with cooperativity n=3.7 activates NE-AC. CREB-generated receptors coupled by Mg2+ may modulate hydration shells-dependent oscillations for retrieval of LTM
q-bio.OT↗
How can we improve problem-solving in undergraduate biology? Applying lessons from 30 years of physics education research
If students are to successfully grapple with authentic, complex biological problems as scientists and citizens, they need practice solving such problems during their undergraduate years. Physics education researchers have investigated student problem solving for the last three decades. Although physics and biology problems differ in structure and content, the instructional purposes align closely: explaining patterns and processes in the natural world and making predictions about physical and biological systems. In this paper, we discuss how research-supported approaches developed by physics education researchers can be adopted by biologists to enhance student problem-solving skills. First, we compare the problems that biology students are typically asked to solve with authentic, complex problems. We then describe the development of research-validated physics curricula emphasizing process skills in problem solving. We show that solving authentic, complex biology problems requires many of the same skills that practicing physicists and biologists use in representing problems, seeking relationships, making predictions, and verifying or checking solutions. We assert that acquiring these skills can help biology students become competent problem solvers. Finally, we propose how biology scholars can apply lessons from physics education in their classrooms and inspire new studies in biology education research. (To appear in Cell Biology Education - Life Sciences Education)
physics.ed-ph↗
Affine invariance of human hand movements: a direct test
Geometrical invariance, in particular affine invariance, has been recently proposed as an important principle underlying the production of hand movements. However, tests of affine invariance have traditionally been applied to the consequences of this principle rather to the principle itself. Here, we designed and performed an original, direct, test of affine invariance in a scribbling experiment. In each of the 10800 pairs of randomly-selected scribbling segments, we compared the time parameterizations obtained by transforming the first segment using four different transportation rules - affine, equi-affine, Euclidian and constant - with the experimentally-observed parameterization of the second segment. We observed that, when the two paths are affinely-similar, the affine transportation of the first segment yields the time parameterization that best matches the experimental parameterization of the second segment, which directly demonstrates the existence of affine invariance in the production of hand movements.
q-bio.OT↗
Quantum Process in Living Cells
Quantum processes have been confirmed for various biological phenomena. Here we model a quantum process in cells based on coherent waves of established ultrafast energy transfers in water. We compute wave speed, ~156 km/s, and wavelength, ~9.3 nm, and determine that the waves retain local coherence. The model is compared with observations and diverse numerical applications lend support to the hypothesis that rapid energy transfers in water are characteristic of living cells. Close agreements are found for the dipole moment of water dimers, microwave radiation on yeast, and the Kleiber law of metabolic rates. We find a sphere with diameter ~20 nm is a lower bound for life in this theory. The quantum properties of the model suggest that cellular chemistry favors reactions that support perpetuation of the energy waves
physics.gen-ph↗
On Cyclic DNA Codes
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring. Cyclic codes over $R$ are designed such that their images under the mapping are also cyclic or quasi-cyclic of index 2. The additive distance and hybridization energy are functions of the neighborhood energy.
cs.IT↗
Theoretical Considerations on Compensation of the Accommodation-Vergence Mismatch by Refractive Power of Focus-Adjustable 3D Glasses
The accommodation-vergence mismatch has been considered as a cause of the visual fatigue induced in watching 3D display. We would propose the mismatch can be compensated by refractive power of adjustable-focus 3D glasses. From lens optics and geometrical considerations, we also developed equations that calculate required refractive power of the 3D glasses. The compensation we proposed is supposed to reduce the visual fatigue of 3D display.
physics.bio-ph↗
Diagonalizing the genome II: toward possible applications
In a previous paper, we showed that the orientable cover of the moduli space of real genus zero algebraic curves with marked points is a compact aspherical manifold tiled by associahedra, which resolves the singularities of the space of phylogenetic trees. In this draft of a sequel, we construct a related (stacky) resolution of a space of real quadratic forms, and suggest, perhaps without much justification, that systems of oscillators parametrized by such objects may may provide useful models in genomics.
math.AT↗
Biological Systems as Systems of Increasing Entropy: Language and Genetics
In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy) and how we think it occurs (explanatory adequacy) but also what architectural properties (in terms of matter configuration, for example) license the occurrence of certain phenomena. In the case of a biological instantiation of a physical system, justificative adequacy is to be found in the genotype-phenotype dynamics. Moreover, we will claim that such dynamics should be analyzed from a mathematical point of view, since the genotype is hypersensitive to initial conditions: a small change in a certain state of the system may have drastic effects on the output. Regarding methodology, we will use chaos theory applied to biology and also physical genetics in order to frame our research and give it theoretical weight.
nlin.CD↗
Development of Hydrogen Bonding Magnetic Reaction-based Gene Regulation through Cyclic Electromagnetic DNA Simulation in Double-Stranded DNA
The proton-magnetic reaction is commonly used in MRI machines with a strong magnetic field of over 1 T, while this study hypothesized that the electron magnetic reaction of hydrogen could affect the hydrogen bonds of double-stranded DNA (dsDNA) at a low magnetic field below 0.01 T. The goal is to develop a hydrogen bonding magnetic reaction-based gene regulation (HBMR-GR) system. The polarities of DNA base pairs are derived from the relative electrostatic charge between purines and pyrimidines, which become positively and negatively charged, respectively. The Pyu dsDNAs with pyrimidine(s)-purine(s) sequences, ds3T3A, ds3C3G, and ds3C3A, showed stronger DNA hybridization potential, increased infrared absorption at 3400-3200 cm-1, and a unique DNA conformation in HPLC analysis compared to the corresponding Puy dsDNAs. To target the three-dimensional structure of dsDNA based on the DNA base pair polarities, one can use cyclic electromagnetic DNA simulation (CEDS) with approximately 25% efficiency for randomly oriented dsDNAs. CEDS was found to induce sequence-specific hybridization of target oligo-dsDNAs in 0.005M NaCl solution and sequence-specific conformation of oligo-dsDNAs in 0.1M NaCl solution. It was found that the Pyu oligo-dsDNAs were more responsible for the hybridization and conformational changes by CEDS than the Puy oligo-dsDNAs. CEDS decreased ethidium bromide (EtBr) DNA intercalation and spermidine DNA condensation depending on CEDS time in the binding assay. The results also included that the Pyu oligo-dsDNAs were more responsible for CEDS by forming stable and unique conformation of oligo-dsDNA than the Therefore, it is postulated that the low-level HBMR-based CEDS can enhance the hybridization potential of oligo-dsDNAs and subsequently lead to the unique DNA conformation required for the initiation of various DNA functions.
q-bio.OT↗
A Broader Perspective about Organization and Coherence in Biological Systems
The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures of biological systems remains unsettled. Here, we present a broader perspective on biological organization and how quantum-like dynamics and coherence might shape the very fabric from which complex biological systems are organized. Regardless of its exact nature, a unique form of coherence seems apparent at multiple scales in biology and its better characterization may have broad consequences for the understanding of living organisms as complex systems.
q-bio.OT↗