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At least 487 records · Page 27Linked to original sources

arXiv2001

Non-Linear Dynamics In Patients With Stable Angina Pectoris

We investigate the clinical and prognostic significance of fractal dimension and detrended fluctuation analysis by comparing the group of patients with stable angina pectoris without previous myocardial infarction with the group of age-matched healthy controls. The fractal dimension of the R-R series was determined using the rescaled range (R/S) analysis technique. To quantify fractal longe-range-correlation properties of heart rate variability, the detrended fluctuation analysis (DFA) technique was used. The heart rate variability was characterized by a scaling exponent $α$, separately for short-term ($<$ 11 beats), and for long-term ($>$ 11 beats) time scales. The results of data sets show the existence of crossover phenomena between short-time scales. The short-term fractal scaling exponent was significantly lower in patients with stable angina pectoris.

physics.med-ph↗

arXiv2001

Hamming distance geometry of a protein conformational space. Application to the clustering of a 4 ns molecular dynamics trajectory of the HIV-1 integrase catalytic core

Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space in two halves. Thus, the information encoded in the binary sequences is also used to characterize the regions of conformational space visited by the system. We apply this distance and their associated geometric structures, to the clustering and analysis of conformations sampled during a 4 ns molecular dynamics simulation of the HIV-1 integrase catalytic core. The cluster analysis of the simulation shows a division of the trajectory into two segments of 2.6 and 1.4 ns length, which are qualitatively different: the data points to the fact that equilibration is only reached at the end of the first segment. Some length of the paper is devoted to compare the Hamming distance to the r.m.s. deviation measure. The analysis of the cases studied so far, shows that under the same conditions the two measures behave quite differently, and that the Hamming distance appears to be more robust than the r.m.s. deviation.

physics.bio-ph↗

arXiv2001

Zipf's law in human heartbeat dynamics

It is shown that the distribution of low variability periods in the activity of human heart rate typically follows a multi-scaling Zipf's law. The presence or failure of a power law, as well as the values of the scaling exponents, are personal characteristics depending on the daily habits of the subjects. Meanwhile, the distribution function of the low-variability periods as a whole discriminates efficiently between various heart pathologies. This new technique is also applicable to other non-linear time-series and reflects these aspects of the underlying intermittent dynamics, which are not covered by other methods of linear- and nonlinear analysis.

physics.med-ph↗

arXiv2001

Sucrose Solutions as Prospective Medium to Study the Vesicle Structure: SAXS and SANS study

The possibility to use sucrose solutions as medium for X-ray and neutron small-angle scattering experiments has been explored for dimyristoylphosphatidylcholine (DMPC) vesicles and mixed DMPC/C_(12)E_(8) aggregates. The influence of sucrose concentration on phospholipid vesicles size and polydispersity has been investigated by complimentary X-ray and neutron scattering. Sucrose solutions decreased vesicle size and polydispersity and increased a contrast between phospholipid membrane and bulk solvent sufficiently for X-rays. 40% sucrose in H2O increased X-ray contrast by up to 10 times compared to pure H2O. The range of sucrose concentration 30%-40% created the best experimental conditions for the X-ray small-angle experiment with phospholipid vesicles.

physics.bio-ph↗

arXiv2001

Correlated noise induced control of prey extinction

We study the steady state properties of a phenomenological two-state predator model in presence of correlated Gaussian white noise. Based on the corresponding Fokker-Planck equation for probability distribution function the steady state solution of the probability distribution function and its extrema have been investigated. We show for a typical value of noise correlation there is a giant loss of bistability which in turn prevents the prey population from going into extinction.

physics.bio-ph↗

arXiv2001

On the "barcode" functionality of the DNA, or The phenomenon of Life in the physical Universe

The information contained in the genome is insufficient for the control of organism development. Thus, the whereabouts of actual operational directives and workings of the genome remain obscure. In this work, it is suggested that the genome information plays a role of a "barcode". The DNA structure presents a pseudo-random number(PRN)with classification tags, so organisms are characterized by DNA as library books are characterized by catalogue numbers. Elaboration of the "barcode" interpretation of DNA implicates the infrastructure of the physical Universe as a seat of biological information processing. Thanks to the PRNs provided by DNA, biological objects can share these facilities in the Code Division Multiple Access (CDMA) mode, similarly to cellular phone communications. Figuratively speaking, populations of biological objects in the physical Universe can be seen as a community of users on the Internet with a wireless CDMA connection. The phenomenon of Life as a collective information processing activity has little to do with physics and is to be treated with the methodology of engineering design. The concept of the "barcode" functionality of DNA confronts the descriptive scientific doctrines with a unique operational scheme of biological information control. Recognition of this concept would require sacrificing the worldview of contemporary cosmology.

physics.bio-ph↗

arXiv2001

Intercellular Communication Via Intracellular Calcium Oscillations

In this letter we present the results of a simple model for intercellular communication via calcium oscillations, motivated in part by a recent experimental study. The model describes two cells (a "donor" and "sensor") whose intracellular dynamics involve a calcium-induced, calcium release process. The cells are coupled by assuming that the the input of the sensor cell is proportional to the output of the donor cell. As one varies the frequency of calcium oscillations of the donor cell, the sensor cell passes through a sequence of N:M phase locked regimes and exhibits a "Devil's staircase" behavior. Such a phase locked response has been seen experimentally in pulsatile stimulation of single cells. We also study a stochastic version of the coupled two cell model. We find that phase locking holds for realistic choices for the cell volume.

physics.bio-ph↗

arXiv2001

What is the optimal anthropoid primate diet?

Following Socrates' advice "You should learn all you can from those who know. Everyone should watch himself throughout his life, and notice what sort of meat and drink and what form of exercise suit his constitution, and he should regulate them in order to enjoy good health." Based on biological, chemical and physical considerations I have attempted to synthesize guide lines for an optimal diet from the vast literature. For an offshoot of the primate line it may be wise not to stray too far from the line's surprisingly uniform predominantly frugi- and herbi-vorous diet that is only lightly supplemented by hunted small mammals, eggs, nuts, insects, etc. By dry weight raw wild fruit contains fats, proteins, carbohydrates, digested and undigested fiber in the approximate proportions 5 : 7 : 14 : 17 : 17. The fat component contains both essential fatty acids, about 23% linoleic and 16% alpha-linolenic, the latter severely lacking in Western diets. The practical problem is how to as best as possible, but not religiously, approximate this diet with super-market items.

physics.bio-ph↗

arXiv2003

What does the correlation dimension of the human heart rate measure?

It is shown that in the case of human heart rate, the scaling behaviour of the correlation sum (calculated by the Grassberger-Procaccia algorithm) is a result of the interplay of various factors: finite resolution of the apparatus (finite-size effects), a wide dynamic range of mean heart rate, the amplitude of short-time variability being a decreasing function of the mean heart rate. The value of the scaling exponent depends on all these factors and is a certain measure of short-time variability of the signal.

physics.med-ph↗

arXiv2002

The control of phenotype: connecting enzyme variation to physiology

Metabolic control analysis (Kacser & Burns (1973). Symp. Soc. Exp. Biol. 27, 65-104; Heinrich & Rapoport (1974). Eur. J. Biochem. 42, 89-95) was developed for the understanding of multi-enzyme networks. At the core of this approach is the flux summation theorem. This theorem implies that there is an invariant relationship between the control coefficients of enzymes in a pathway. One of the main conclusions that has been derived from the summation theorem is that phenotypic robustness to mutation (e.g. dominance) is an inherent property of metabolic systems and hence does not require an evolutionary explanation (Kacser & Burns (1981). Genetics. 97, 639-666; Porteous (1996). J. theor. Biol. 182, 223-232). Here we show that for mutations involving discrete changes (of any magnitude) in enzyme concentration the flux summation theorem does not hold. The scenarios we examine are two-enzyme pathways with a diffusion barrier, two enzyme pathways that allow for enzyme saturation and two enzyme pathways that have both saturable enzymes and a diffusion barrier. Our results are extendable to sequential pathways with any number of enzymes. The fact that the flux summation theorem cannot hold in sequential pathways casts serious doubts on the claim that robustness with respect to mutations is an inherent property of metabolic systems.

physics.bio-ph↗

arXiv2002

Translocation Properties of Primitive Molecular Machines and Their Relevance to the Structure of the Genetic Code

We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the translocation properties of primitive molecular machines, which capture basic features of ribosomal/messenger RNA interactions, while operating under prebiotic conditions. Our model consists of a short one-dimensional chain of charged particles(rRNA antecedent) interacting with a polymer (mRNA antecedent) via electrostatic forces. The chain is subject to external forcing that causes it to move along the polymer which is fixed in a quasi one dimensional geometry. Our numerical and analytic studies of statistical properties of random chain/polymer potentials suggest that, under very general conditions, a dynamics is attained in which the chain moves along the polymer in steps of three monomers. By adjusting the model in order to consider present day genetic sequences, we show that the above property is enhanced for coding regions. Intergenic sequences display a behavior closer to the random situation. We argue that this dynamical property could be one of the underlying causes for the three base codon structure of the genetic code.

physics.bio-ph↗

arXiv2002

Pattern Propagation Speed in Synfire Chains with Excitatory-Inhibitory Couplings

The speed of firing pattern propagation in a synfire chain, composed of non-leaky integrate-and-fire neurons, and assuming homogenous connection delays, is studied. An explicit relation, relating the propagation speed to the connecting weights distribution and other network parameters, is derived. The analytic results are then checked with a computer simulation. When the network is fed with a fully synchronized input pattern, the pattern propagation speed is independent of the weight parameters. When the fed input is asynchronous, depending on the weight parameters, the propagation speed is more than or less than the synchronous case. In this case the propagation speed increases by increasing the mean or standard deviation of connecting weights. The biological relevance of these findings and their relevance to the notion of synfire chains are discussed.

physics.bio-ph↗

arXiv2002

Long range correlations in DNA sequences

The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested earlier has been applied to extract slope parameters that characterize the correlation properties for several intron containing and intron less DNA sequences. An important aspect of all the DNA sequences is the properties of complimentarity by virtue of which any two complimentary distributions (like GA is complimentary to TC or G is complimentary to ATC) have identical fluctuations at all scales although their distribution functions need not be identical. Due to this complimentarity, the famous DNA walk representation whose statistical interpretation is still unresolved is shown to be a special case of the present formalism with a density distribution corresponding to a purine or a pyrimidine group. Another interesting aspect of most of the DNA sequences is that the factorial moments as a function of length exceed unity around a region where the variance versus length in a log-log plot shows a bending. This is a pure phenomenological observation which is found for several DNA sequences with a few exception. Therefore, this length scale has been used as an approximate measure to exclude the bending regions from the slope analyses. The asymmetries in the nucleotide contents or the patchy structure as a possible origin of the long range correlations has also been investigated.

physics.bio-ph↗

arXiv2002

FAST CARS: Engineering a Laser Spectroscopic Technique for Rapid Identification of Bacterial Spores

Airborne contaminants, e.g., bacterial spores, are usually analyzed by time consuming microscopic, chemical and biological assays. Current research into real time laser spectroscopic detectors of such contaminants is based on e.g. resonant Raman spectroscopy. The present approach derives from recent experiments in which atoms and molecules are prepared by one (or more) coherent laser(s) and probed by another set of lasers. The connection with previous studies based on "Coherent Anti-Stokes Raman Spectroscopy" (CARS) is to be noted. However generating and utilizing maximally coherent oscillation in macromolecules having an enormous number of degrees of freedom is much more challenging. This extension of the CARS technique is called FAST CARS (Femtosecond Adaptive Spectroscopic Techniques for Coherent Anti-Stokes Raman Spectroscopy), and the present paper proposes and analyses ways in which it could be used to rapidly identify pre-selected molecules in real time.

physics.optics↗

arXiv2002

Characteristics of Molecular-biological Systems and Process-network Synthesis

Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property excursions. The scaling apparent in biological systems is shown. Applications to evolution and reverse engineering are construed. The use of several programs, such as the Synprops, Design of molecules, Therm and Knapsack are suggested as instruments to study biological process network synthesis. The properties of robust self-assembly and Self-Organizing synthesis are important contributors to the discussion. The bar code of life and intelligent design is reviewed. The need for better data in biological systems is emphasized.

physics.bio-ph↗

arXiv2002

Geometry of compact tubes and protein structures

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures the well-known characteristics of polymers and their phases but also provides a natural explanation for many of the key features of protein behavior. There are two natural length scales associated with a tube subject to compaction -- the thickness of the tube and the range of the attractive interactions. For short tubes, when these length scales become comparable, one obtains marginally compact structures, which are relatively few in number compared to those in the generic compact phase of polymers. The motifs associated with the structures in this new phase include helices, hairpins and sheets. We suggest that Nature has selected this phase for the structures of proteins because of its many advantages including the few candidate strucures, the ability to squeeze the water out from the hydrophobic core and the flexibility and versatility associated with being marginally compact. Our results provide a framework for understanding the common features of all proteins.

physics.bio-ph↗

arXiv2002

Collective Properties of the Exactly Solvable Model of Ion-Channel Assemblies in a Biological Cell Membrane

The behaviour of a system of ion channels formed across the cell membrane is presented. The infinite number of channels with an infinite coupling is introduced first as a reference point for the detailed derivation of the thermal-equilibrium probability distribution and the classification of the phase transitions. Fluctuations in a finite system are discussed next. We propose a new, step-like model of the ion channel switching, for which we provide the analytical results. The relation of this model to experiment is also provided. Finally, the master equation for the finite channel-number membrane is analysed numerically with the help of an exact-diagonalization technique. In particular, the decay-time of a metastable solution is estimated. The results do not agree with those obtained perturbationally, the difference is explained by the proposed frozen-diffusion approach.

physics.bio-ph↗

arXiv2002

The Loss of Multifractality in Migraines

We study the middle cerebral artery blood flow velocity (MCAfv) in humans using transcranial Doppler ultrasonography (TCD). The time series of the axial flow velocity averaged over a cardiac beat interval is found to exhibit clear multifractal properties for healthy subjects. We observe a loss of multifractality for subjects with migraine.

physics.bio-ph↗