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At least 109 records · Page 6Linked to original sources

arXiv2010

A ubiquitous ~62-Myr periodic fluctuation superimposed on general trends in fossil biodiversity. I. Documentation

We use Fourier analysis and related techniques to investigate the question of periodicities in fossil biodiversity. These techniques are able to identify cycles superimposed on the long-term trends of the Phanerozoic. We review prior results and analyze data previously reduced and published. Joint time-series analysis of various reductions of the Sepkoski Data, Paleobiology Database, and Fossil Record 2 indicate the same periodicity in biodiversity of marine animals at 62 Myr. We have not found this periodicity in the terrestrial fossil record. We have found that the signal strength decreases with time because of the accumulation of apparently "resistant" long-lived genera. The existence of a 62-Myr periodicity despite very different treatment of systematic error, particularly sampling-strength biases, in all three major databases strongly argues for its reality in the fossil record.

q-bio.PE↗

arXiv2011

The Quality of Oscillations in Overdamped Networks

The second law of thermodynamics implies that no macroscopic system may oscillate indefinitely without consuming energy. The question of the number of possible oscillations and the coherent quality of these oscillations remain unanswered. This paper proves the upper-bounds on the number and quality of such oscillations when the system in question is homogeneously driven and has a discrete network of states. In a closed system, the maximum number of oscillations is bounded by the number of states in the network. In open systems, the size of the network bounds the quality factor of oscillation. This work also explores how the quality factor of macrostate oscillations, such as would be observed in chemical reactions, are bounded by the smallest equivalent loop of the network, not the size of the entire system. The consequences of this limit are explored in the context of chemical clocks and limit cycles.

cond-mat.stat-mech↗

arXiv2010

The Electron Capture Hypothesis - A Challenge to Neuroscientists

Lower speed impinging ions (with hydration shells) cannot transverse ion channels once internal charge goes positive. Yet neural pulse waveforms fail to show the expected risetime distortion beginning at zero voltage. Observed waveforms cannot be explained unless electron capture is considered.

q-bio.NC↗

arXiv2010

A Review on Fish Swimming and Bird/Insect Flight

This expository review is devoted to fish swimming and bird/insect flight. (i) The simple waving motion of an elongated flexible ribbon plate of constant width, immersed in a fluid at rest, propagating a wave distally down the plate to swim forward is first considered to provide a fundamental concept on energy conservation. It is generalized to include variations in body width and thickness, vortex shedding from appended dorsal, ventral and caudal fins to closely simulate fish swimming for which a nonlinear theory is presented for large-amplitude propulsion. (ii) For bird flight, the pioneering studies on oscillating rigid wings are briefed, followed by presenting a nonlinear unsteady theory for flexible wing with arbitrary variations in shape and trajectory with a comparative study with experiments. (iii) For insect flight, more recent advances are reviewed under aerodynamic theory and modeling, computational methods, and experiments, on forward and hovering flights with producing leading-edge vortex to give unsteady high lift. (iv) Prospects are explored on extracting intrinsic flow energy by fish and bird to gain thrust for propulsion. (v) The mechanical and biological principles are drawn together for unified studies on the energetics in deriving metabolic power for animal locomotion, leading to a surprising discovery that the hydrodynamic viscous drag on swimming fish is largely associated with laminar boundary layers, thus drawing valid and sound evidences for a resolution to the fish-swim paradox proclaimed by Gray (1936, 1968).

math-ph↗

arXiv2011

The Storm and Nelson's model for polymer stretching revisited

The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical and mathematical models to quantitatively express the mechanical properties of the observed molecules. In this paper we reconsider a simple phenomenological model which reproduces the behaviour of single and double stranded DNA under tension. The problem is easily solved via the cavity method both in the small forces range and in presence of overstretching transition, so that some properties such as bending stiffness and elasticity of DNA emerge in a very clear manner. Our theoretical findings are successfully fitted to real measurements and compared to Monte Carlo simulations, confirming the quality of the approach.

physics.bio-ph↗

arXiv2010

Successful modeling of the environmental changes' influence on forests' vegetation over North Eurasia

Modeling of forests' vegetation in North Eurasia has been performed for 1982-2006 on the basis of remote sensing data. Four meteorological parameters and one parameter, characterizing geomagnetic field disturbance level, were used for this aim. It was found out that revealed formula is adequate both for coniferous evergreen and coniferous deciduous forests for accuracy to a coefficient. The most proper parameters' combination gives the correlation coefficients ~ 0.9 between modeling parameter and original data rows. These results could solve problems of climate-forests feedbacks' investigations and be useful for dendrological aims.

physics.ao-ph↗

arXiv2011

Calculation of free energy landscapes: A Histogram Reweighted Metadynamics approach

We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Due to the presence of the bias potential, it can be also used to accelerate rare events. In addition, the calculated free energy landscape is not restricted to the actual choice of collective variables and can in principle be extended to auxiliary variables of interest without further numerical effort. The applicability is shown for several examples. We present numerical results for the alanine dipeptide and the Met-Enkephalin in explicit solution to illustrate our approach. Furthermore we derive an empirical formula that allows the prediction of the computational cost for the ordinary metadynamics variant in comparison to our approach which is validated by a dimensionless representation.

physics.comp-ph↗

arXiv2010

Entropy driven aggregation of adhesion sites of supported membranes

We study, by means of mean field calculations and Monte Carlo simulations of a lattice-gas model, the distribution of adhesion sites of a bilayer membrane and a supporting flat surface. Our model accounts for the many-body character of the attractive interactions between adhesion points induced by the membrane thermal fluctuations. We show that while the fluctuation-mediated interactions alone are not sufficient to allow the formation of aggregation domains, they greatly reduce the strength of the direct interactions required to facilitate cluster formation. Specifically, for adhesion molecules interacting via a short range attractive potential, the strength of the direct interactions required for aggregation is reduced by about a factor of two to below the thermal energy $k_BT$.

cond-mat.soft↗

arXiv2010

Percolation Approach to Study Connectivity in Living Neural Networks

We study neural connectivity in cultures of rat hippocampal neurons. We measure the neurons' response to an electric stimulation for gradual lower connectivity, and characterize the size of the giant cluster in the network. The connectivity undergoes a percolation transition described by the critical exponent $β\simeq 0.65$. We use a theoretic approach based on bond.percolation on a graph to describe the process of disintegration of the network and extract its statistical properties. Together with numerical simulations we show that the connectivity in the neural culture is local, characterized by a gaussian degree distribution and not a power law on

q-bio.NC↗

arXiv2011

Optimal orientation in branched cytoskeletal networks

Actin cytoskeletal protrusions in crawling cells, or lamellipodia, exhibit various morphological properties such as two characteristic peaks in the distribution of filament orientation with respect to the leading edge. To understand these properties, using the dendritic nucleation model as a basis for cytoskeletal restructuring, a kinetic-population model with orientational-dependent branching (birth) and capping (death) is constructed and analyzed. Optimizing for growth yields a relation between the branch angle and filament orientation that explains the two characteristic peaks. The model also exhibits a subdominant population that allows for more accurate modeling of recent measurements of filamentous actin density along the leading edge of lamellipodia in keratocytes. Finally, we explore the relationship between orientational and spatial organization of filamentous actin in lamellipodia and address recent observations of a prevalence of overlapping filaments to branched filaments---a finding that is claimed to be in contradiction with the dendritic nucleation model.

q-bio.SC↗

arXiv2010

Is it Possible to Extract Metabolic Pathway Information from In Vivo H Nuclear Magnetic Resonance Spectroscopy Data?

In vivo H nuclear magnetic resonance (NMR) spectroscopy is an important tool for performing non-invasive quantitative assessments of brain tumour glucose metabolism. Brain tumours are considered fast-growth tumours because of their high rate of proliferation. In addition, tumour cells exhibit profound genetic, biochemical and histological differences with respect to the original non-transformed cell types. Therefore, there is strong interest from the clinical investigator's point of view in understanding the role of brain metabolites under normal and pathological conditions and especially in the development of early tumour detection techniques. Unfortunately, current diagnosis techniques ignore the dynamic aspects of these signals. It is largely believed that temporal variations of NMR Spectra are simply due to noise or do not carry enough information to be exploited by any reliable diagnosis procedure. Thus, current diagnosis procedures are mainly based on empirical observations extracted from single averaged spectra. In this paper, firstly a machine learning framework for the analysis of NMR spectroscopy signals which can exploit both static and dynamic aspects of these signals is introduced. Secondly, the dynamics of the signals are further analyzed using elements from chaos theory in order to understand their underlying structure. Furthermore, we show that they exhibit rich chaotic dynamics suggesting the encoding of metabolic pathway information.

physics.bio-ph↗

arXiv2011

DNA Replication via Entanglement Swapping

Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can be considered as hardware and software of living systems that are co-optimized during evolution. We try to model DNA replication in this sense as a multi-body entanglement swapping with a reliable qubit representation of the nucleotides. In our model molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits to be used to obtain intrabase entanglement and swapping protocols to be employed to obtain interbase entanglement. Finally, we discuss possible ways for computational and experimental verification of the model.

quant-ph↗

arXiv2011

Directed transport in equilibrium

We investigate a symmetry broken dimer constrained to move in a particular direction when in contact with a heat-bath at a constant temperature. The dimer is not driven by any external force. The system gains kinetic energy from the heat-bath. The symmetry broken system can use this energy in directed transport. At the hard core collision limit between the particles of the dimer, we show by exact analytic calculations and complementary numerical results that the dimer undergoes steady directed transport. Our observation, being consistent with the {\it second law of thermodynamics}, {\it detailed balance} etc leads to new physical understanding to which much attention has not been paid.

cond-mat.stat-mech↗

arXiv2010

Attractor Dynamics with Synaptic Depression

Neuronal connection weights exhibit short-term depression (STD). The present study investigates the impact of STD on the dynamics of a continuous attractor neural network (CANN) and its potential roles in neural information processing. We find that the network with STD can generate both static and traveling bumps, and STD enhances the performance of the network in tracking external inputs. In particular, we find that STD endows the network with slow-decaying plateau behaviors, namely, the network being initially stimulated to an active state will decay to silence very slowly in the time scale of STD rather than that of neural signaling. We argue that this provides a mechanism for neural systems to hold short-term memory easily and shut off persistent activities naturally.

cond-mat.dis-nn↗

arXiv2010

A closed-form solution of the three-dimensional contact problem for biphasic cartilage layers

A three-dimensional unilateral contact problem for articular cartilage layers is considered in the framework of the biphasic cartilage model. The articular cartilages bonded to subchondral bones are modeled as biphasic materials consisting of a solid phase and a fluid phase. It is assumed that the subchondral bones are rigid and shaped like elliptic paraboloids. The obtained analytical solution is valid over long time periods and can be used for increasing loading conditions.

physics.bio-ph↗

arXiv2010

Recent Progress in Chirality Research Using Circularly Polarized Light

(abridged) We review recent studies of chirality using circularly polarized light, along with the birth and evolution of life and planetary systems. Terrestrial life consists almost exclusively of one enantiomer, left-handed amino acids. This characteristic feature is called homochirality, whose origin is still unknown. The route to homogeneity of chirality would be connected with the origin and development of life on early Earth along with evolution of the solar system. Detections of enantiomeric excess in several meteorites support the possibility that the seed of life was injected from space, considering the possible destruction and racemization in the perilous environment on early Earth. Circularly polarized light could bring the enantiomeric excess of prebiotic molecules in space. Recent experimental works on photochemistry under ultraviolet circularly polarized light are remarkable. Recent astronomical observations by imaging polarimetry of star-forming regions are now revealing the distribution of circularly polarized light in space. Astrobiological view on chirality of life would contribute to understanding of the origin and development of life, from the birth and the end of stars and planetary systems in space. Deep insights on terrestrial life, extrasolar life, and the origin of life in the universe, would be brought by consideration of both of the place where life is able to live, the "habitable" zone, and the place where life is able to originate, what we shall call the "originable" zone.

astro-ph.GA↗

arXiv2011

Comment on "Quantum Control and Entanglement in a Chemical Compass"

In this comment we show that the avian compass entanglement considerations of J. Cai, G. G. Guerreschi and H. J. Briegel (Phys. Rev. Lett. 104, 220502 (2010)) result in unphysical predictions on the magnetic sensitivity of this biochemical sensor. As well known from a series of papers on precision measurements and detailed derivations of standard quantum limits, not taking into account decoherence results in an overestimate of the entanglement lifetime, and this is the case at hand. The entanglement lifetime is wrongly assumed by the authors to be independent of the reaction time (the inverse of the recombination rate) and hence it is grossly overestimated. This is so because the spin coherence lifetime is limited by the reaction time, and the entanglement lifetime cannot be any longer.

quant-ph↗

arXiv2010

Variational principles in chemical equilibria: Complex chemical systems with interacting subsystems

The goal of the paper is to derive a revised condition of global equilibrium in complex chemical systems as variational principle in formalism of recently developed discrete thermodynamics (DTD) of chemical equilibria. In classical approach the problem of complex equilibrium is solved by minimization of the system Gibbs' free energy subject to logistic constraints. DTD demands any isolated system to comprise smaller subentities, which individual equilibria are based on the balance of internal and external thermodynamic forces, acting against them. The internal forces are equal to the subsystems thermodynamic affinities, while external forces originate from subsystems mutual interactions. Those interactions impose additional constraints on the mother system Gibbs' free energy minimum. Basic expression of discrete thermodynamics, being multiplied by subsystems deviations from their "true" thermodynamic equilibria, is naturally identical to d'Alembert's principle. A thermodynamic version of d'Alembert's principle in combination with derived from it thermodynamic version of the principle of virtual work, allowed us to express the interactive constraints as a condition, that the sum of all subsystems thermodynamic affinities, multiplied by their deviations from their "true" equilibria, must be equal to zero. The revised formula of global equilibrium condition in complex chemical systems contains three terms - system Gibbs' free energy, logistic constraints, identical to their classical version, and interactive constraints, originated from the subsystems mutual interactions.

physics.chem-ph↗