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Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

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At least 577 records · Page 32Linked to original sources

arXiv1999

Effect of histamine on the electric activities of cerebellar Purkinje cell

The effect of histamine (HA) on the electric activities of Purkinje cell (PC) is studied on the cerebellum slice. We find that: (1) HA's main effect on PC is excitative (72.9%); there are also a small amount of PC showing inhibitive (10.2%) or no (16.9%) response to HA. (2) Different from the conventional opinion, HA's excitative effect on PC is mutually conducted by H1 and H2 receptors; the antagonist for H1 receptor could weaken HA's excitative effect on PC, while the antagonist for H2 receptor could weaken or even block the excitative effect of HA on PC. (3) PC's reaction to HA is related to its intrinsic discharge frequency; there exists a frequency at which PC is highly sensitive to HA, and well above this frequency PC becomes stable against HA. These results indicate that the histaminergic afferent fibre can adjust PC's electric activities by releasing HA, and thereby influence the global function of the cerebellar cortex; and that just like the $γ$ region of cerebrum, cerebellum may also have some sort of characteristic frequency.

physics.bio-ph↗

arXiv1999

Locomotion and proliferation of glioblastoma cells in vitro: statistical evaluation of videomicroscopic observations

Long-term videomicroscopy and computer-aided statistical analysis were used to determine some characteristic parameters of in vitro cell motility and proliferation in three established cell lines derived from human glioblastoma tumors. Migration and proliferation activities were compared among the three cell lines since these are two features of tumor cells that strongly influence the progression of cancer. The results on these dynamical parameters of cell locomotion were compared to pathological data obtained by traditional methods. The data indicate that the analysis of cell motility provides more specific information and is potentially useful in diagnosis.

physics.bio-ph↗

arXiv1999

Statistical properties of spike trains: universal and stimulus-dependent aspects

Statistical properties of spike trains measured from a sensory neuron in-vivo are studied experimentally and theoretically. Experiments are performed on an identified neuron in the visual system of the blowfly. It is shown that the spike trains exhibit universal behavior over short time, modulated by a stimulus-dependent envelope over long time. A model of the neuron as a nonlinear oscillator driven by noise and an external stimulus, is suggested to account for these results. The model enables a theoretic distinction of the effects of internal neuronal properties from effects of external stimulus properties, and their identification in the measured spike trains. The universal regime is characterized by one dimensionless parameter, representing the internal degree of irregularity, which is determined both by the sensitivity of the neuron and by the properties of the noise. The envelope is related in a simple way to properties of the input stimulus as seen through nonlinearity of the neural response. Explicit formulas are derived for different statistical properties in both the universal and the stimulus-dependent regimes. These formulas are in very good agreement with the data in both regimes.

physics.bio-ph↗

arXiv1999

Symbols and synergy in a neural code

Understanding a neural code requires knowledge both of the elementary symbols that transmit information and of the algorithm for translating these symbols into sensory signals or motor actions. We show that these questions can be separated: the information carried by any candidate symbol in the code--- a pattern of spikes across time or across a population of cells---can be measured, independent of assumptions about what these patterns might represent. By comparing the information carried by a compound pattern with the information carried independently by its parts, we measure directly the synergy among these parts. We illustrate the use of these methods by applying them to experiments on the motion sensitive neuron H1 of the fly's visual system, where we confirm that two spikes close together in time carry far more than twice the information carried by a single spike. We analyze the sources of this synergy, and provide evidence that pairs of spikes close together in time may be special symbols in the code of H1.

physics.bio-ph↗

arXiv1999

Darwinian Aspects of Molecular Evolution at Sublinear Propagation Rates

The symmetric distribution and all other states in the symmetry sector of the frequency trajectory increase mean fitness during competitive replication at sublinear propagation rates (parabolic time course). States in the non-symmetry sector, by contrast, produce negative time variations in mean fitness. The polymorphic steady state attained in sublinear systems is destabilised by formation of a variant with above threshold fitness. Evolution in the post-steady state interval increases threshold fitness. Contrary to the proposition that 'parabolic growth invariably results in the survival of all competing species,' only species with sufficient fitness to avoid subthreshold frequencies survive.

physics.bio-ph↗

arXiv1999

Mechanical Aspect of Chirality and its Biological Significance

Chirality is not just a structural artifact in biology but it may provide for a genuine biological advantage. This is due to the phenomenon of chiral interaction (CI) which is described here for mechanical-chiral devices. The main mechanical feature of chiral interaction is its mode of selecting one direction of rotation out of two possible and opposite ones. For example, a given chiral device such as a rotating water sprinkler, rotates in one direction. What does rotate in the opposite direction is the mirror of this given sprinkler. This mode of operation indicates space-time (PT) invariance which causes it to be also time-irreversible. This also causes a chiral device to become non-ergodic on microscopic level. This prevents certain chiral systems from readily reaching thermal equilibrium, and causes the system to act non-ergodically, which is crucial for living systems as well as for molecular evolution.

physics.bio-ph↗

arXiv1999

Molecular Evolution in Time Dependent Environments

The quasispecies theory is studied for dynamic replication landscapes. A meaningful asymptotic quasispecies is defined for periodic time dependencies. The quasispecies' composition is constantly changing over the oscillation period. The error threshold moves towards the position of the time averaged landscape for high oscillation frequencies and follows the landscape closely for low oscillation frequencies.

physics.bio-ph↗

arXiv1999

Limit Cycle Oscillations in Pacemaker Cells

In recent decades, several mathematical models describing the pacemaker activity of the rabbit sinoatrial node have been developed. We demonstrate that it is not possible to establish the existence, uniqueness, and stability of a limit cycle oscillation in those models. Instead we observe an infinite number of limit cycles. We then display numerical results from a new model, with a limit cycle that can be reached from many different initial conditions.

physics.bio-ph↗

arXiv1999

Conditions for the Formation of Axisymmetric Biconcave Vesicles

In this article, the formation of biconcave vesicle according to the minimization bending energy (Helfrich's model) is studied. We present that in order to have biconcave shape vesicle, there are necessary conditions on the parameters of the energy functional and there are implications on the geometric quantities of the vesicle. Furthermore, we also give a clear sufficient condition on the parameters to have the formation of biconcave shape vesicle.

physics.bio-ph↗

arXiv2007

Measurability of side chain rotational isomer populations: NMR and molecular mechanics of cobalt glycyl-leucine dipeptide model system

The cobalt glycyl-leucine dipeptide is a model system for studying the effects of Karplus equation calibration, molecular mechanics accuracy, backbone conformation, and thermal motions on the measurability of side chain rotational isomer populations. We analyze measurements of 8 vicinal coupling constants about the alpha to beta-carbon and beta to gamma-carbon bonds of the leucine side chain and of 10 NOESY cross relaxation rates across these bonds. Molecular mechanics and peptide and protein crystallographic databases are an essential part of this analysis because they independently suggest that the trans gauche-plus and gauche-minus trans rotational isomers of the leucine side chain predominate. They also both suggest that puckering of the cobalt dipeptide ring system reduces the gauche-plus gauche-plus rotational isomer population to less than about 10%. At the present +/- 1 Hz calibration accuracy of Karplus equations for vicinal coupling constants, the predominant trans gauche-plus and gauche-minus trans rotational isomer populations can be measured with about 5% accuracy, but the population of the gauche-plus gauche-plus rotational isomer is probably very near or just below the limit of measurability. These estimates also depend upon qualitative assessments of the accuracy of the molecular mechanics energy wells. We introduce gel graphics that are ideally suited to presenting qualitative error and measurability estimates.

physics.bio-ph↗

arXiv1999

Effects of long-range dispersion in nonlinear dynamics of DNA molecules

A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence $e^{-βr}$ on the distance, $r$, are studied. For $s$ less than some critical value, $s_{cr}$, and similarly for $β\leq β_{cr}$ there is an interval of bistability where two stable stationary states: narrow, pinned states and broad, mobile states exist at each value of the total energy. For cubic nonlinearity the bistability of the solitons occurs for dipole-dipole dispersive interaction $(s=3)$, and for the inverse radius of the dispersive interaction $β\leq β_{cr}=1.67$. For increasing degree of nonlinearity, $σ$, the critical values $s_{cr}$ and $β_{cr}$ increase. The long-distance behavior of the intrinsically localized states depends on $s$. For $s>3$ their tails are exponential while for $2<s<3$ they are algebraic. A controlled switching between pinned and mobile states is demonstrated applying a spatially symmetric perturbation in the form of a parametric kick. The mechanism could be important for controlling energy storage and transport in DNA molecules.

physics.bio-ph↗

arXiv1999

Models for energy and charge transport and storage in biomolecules

Two models for energy and charge transport and storage in biomolecules are considered. A model based on the discrete nonlinear Schrodinger equation with long-range dispersive interactions (LRI's) between base pairs of DNA is offered for the description of nonlinear dynamics of the DNA molecule. We show that LRI's are responsible for the existence of an interval of bistability where two stable stationary states, a narrow, pinned state and a broad, mobile state, coexist at each value of the total energy. The possibility of controlled switching between pinned and mobile states is demonstrated. The mechanism could be important for controlling energy storage and transport in DNA molecules. Another model is offered for the description of nonlinear excitations in proteins and other anharmonic biomolecules. We show that in the highly anharmonic systems a bound state of Davydov and Boussinesq solitons can exist.

physics.bio-ph↗

arXiv1999

Serine Proteases: an Ab Initio Molecular Dynamics Study

In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.

physics.bio-ph↗

arXiv1999

Some Exact Results of Hopfield Neural Networks and Applications

A set of fixed points of the Hopfield type neural network was under investigation. Its connection matrix is constructed with regard to the Hebb rule from a highly symmetric set of the memorized patterns. Depending on the external parameter the analytic description of the fixed points set had been obtained. And as a conclusion, some exact results of Hopfield neural networks were gained.

physics.bio-ph↗

arXiv1999

Microarrays for Amino Acid Analysis and Protein Sequencing

A method is described where the aminoacyl-tRNA synthetase system is used to create very small devices for quantitative analysis of the amino acids that occur in proteins. The basis of the method is that each of the 20 synthetases and/or a tRNA specific for a different amino acid is separated spatially (e.g. in tiny chambers or on a surface). The reactions catalyzed by all 20 synthetases are monitored in a spatially resolved manner. Each separately positioned synthetase or tRNA will signal its cognate amino acid. The synthetase reactions can be monitored using continuous spectroscopic assays. Alternatively, since elongation factor Tu;GTP (EF-Tu;GTP) specifically binds all AA-tRNAs, the aminoacylation reactions catalyzed by the synthetases can be monitored using ligand assays. Microarrays for amino acid analysis are suggested. Additionally, it is possible that amino acid analysis arrays can be integrated with aminopeptidase or carboxypeptidase digestions to produce miniaturized enzymatic sequenators capable of generating either N- or C-terminal sequence data at femtomole-attomole levels. The possibility of parallel processing of many samples in an automated manner is discussed.

physics.bio-ph↗

arXiv1999

Physical Parameters for Biconcave Shape Vesicles

The Helfrich's shape equation of axisymmetric vesicles is studied. A sufficient condition on the physical parameters and some geometric properties are discovered for the biconcave shape.

physics.bio-ph↗

arXiv1999

Evolutionary implications of a power-law distribution of protein family sizes

Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in a family can grow over time as genetic information is duplicated through evolution. We explore how evolution directs the size distribution of these families. Theoretical predictions for family sizes are obtained from two models, one in which individual genes duplicate and a second in which the entire genome duplicates. Predictions from these models are compared with the family size distributions for several organisms whose complete genome sequence is known. We find that protein family size distributions in nature follow a power-law distribution. Comparing these results to the model systems, we conclude that genome duplication is the dominant mechanism leading to increased genetic material in the species considered.

physics.bio-ph↗

arXiv2000

Scale Specific and Scale Independent Measures of Heart Rate Variability as Risk Indicators

We study the Heart Rate Variability (HRV) using scale specific variance and scaling exponents as measures of healthy and cardiac impaired individuals. Our results show that the variance and the scaling exponent are uncorrelated. We find that the variance measure at certain scales is well suited to separate healthy subjects from heart patients. However, for cumulative survival probability the scaling exponents outperform the variance measure. Our risk study is based on a database containing recordings from 428 individuals after myocardial infarct (MI) and on database containing 105 healthy subjects and 11 heart patients. The results have been obtained by applying three recently developed methods (DFA - Detrended Fluctuation Analysis, WAV - Multiresolution Wavelet Analysis, and DTS - Detrended Time Series analysis) which are shown to be highly correlated.

physics.med-ph↗