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  • Articles  (18,943)
  • 1995-1999
  • 1980-1984  (18,943)
  • 1925-1929
  • 1984  (10,180)
  • 1980  (8,763)
  • Mathematics  (18,943)
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  • 1995-1999
  • 1980-1984  (18,943)
  • 1925-1929
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  • 101
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    Bulletin of mathematical biology 46 (1984), S. 295-326 
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract One particular kind of structure offers possible explanations, for long-term memory, efficient consolidation of stored information from the environment, clustering of data strings and multimodal functioning. It is a possible model for pieces of neural structure and its use offers a uniform method for both studying and constructing an extensive class of mechanisms.
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  • 102
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    Bulletin of mathematical biology 46 (1984), S. 327-332 
    ISSN: 1522-9602
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    Notes: Abstract Levenshtein dissimilarity measures are used to compare sequences in application areas including coding theory, computer science and macromolecular biology. In general, they measure sequence dissimilarity by the length of a shortest weighted sequence of insertions, deletions and substitutions required, to transform one sequence into another. Those Levenshtein dissimilarity measures based on insertions and deletions are analyzed by a model involving valuations on a partially ordered set. The model reveals structural relationships among poset, valuation and dissimilarity measure. As a consequence, certain Levenshtein dissimilarity measures are shown to be metrics characterized by betweenness properties and computable in terms of well-known measures of sequence similarity.
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  • 103
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    Bulletin of mathematical biology 46 (1984), S. 337-337 
    ISSN: 1522-9602
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  • 104
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    Bulletin of mathematical biology 46 (1984), S. 333-336 
    ISSN: 1522-9602
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    Notes: Abstract It is pointed out that the methane flux measured experimentally for certain ponds and swamps is quantitatively consistent with a commensal dependence of Methanobacteria on O2-chemotactic motile aerobic bacteria. The Methano species is thereby shielded from oxygen and provided with carbon dioxide for the anaerobic production of methane.
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  • 105
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    Bulletin of mathematical biology 46 (1984), S. 357-370 
    ISSN: 1522-9602
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    Notes: Abstract A sufficient condition is given for stochastic boundedness persistence of a top predator in generalized Lotka-Volterra-type stochastic food web models in arbitrary bounded regions of state space. The main result indicates that persistence in the corresponding deterministic system is preserved in the stochastic system if the intensities of the random fluctuations are not too large.
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  • 106
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    Bulletin of mathematical biology 46 (1984), S. 371-377 
    ISSN: 1522-9602
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    Notes: Abstract One of Bobisud's models for the evolution of cannibalism is reanalyzed by applying the method of finding evolutionarily stable strategies (or ESS's). It is demonstrated that ‘no cannibalism’ never will be an ESS if the initial rate of cannibalism is too large. It is further demonstrated that individual selection may even result in the evolution of cannibalism during food abundance. Some empirical case studies are briefly discussed in relation to this model.
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  • 107
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    Bulletin of mathematical biology 46 (1984), S. 379-387 
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    Notes: Abstract A computer algorithm is presented which equiprobably generates any member of the set of all directed trees withk labeled terminal nodes and unlabeled interior nodes. The algorithm requires roughlyk 2 /2 storage locations. The one-time initialization requiresO(k 2 ) time, while generating each tree requiresO(k) time.
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  • 108
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    Bulletin of mathematical biology 46 (1984), S. 515-527 
    ISSN: 1522-9602
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    Notes: Abstract The comparison of several sequences is central to many problems of molecular biology. Finding consensus patterns that define genetic control regions or that determine structural or functional themes are examples of these problems. Previously proposed methods, such as dynamic programming, are not adequate for solving problems of realistic size. This paper gives a new and practical solution for finding unknown patterns that occur imperfectly above a preset frequency. Algorithms for finding the patterns are given as well as estimates of statistical significance.
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  • 109
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    Bulletin of mathematical biology 46 (1984), S. 501-514 
    ISSN: 1522-9602
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    Notes: Abstract A new development is introduced here in the use of dynamic programming in finding pattern similarities in genetic sequences, as was first done by Needleman and Wunsch (1969). A condition of pattern similarity is defined and an algorithm is given which scans any set of similarities and screens out those which fail to meet the condition. When the set to be scanned contains every pair of segments, one from each of two given sequences of lengthsm andn (i.e. every possible location for a pattern similarity), then it completes the scan in a number of computational steps proportional tom·n, leaving those pairs of segments which satisfy the similarity condition. The algorithm is based on the concept of match density, as suggested by Goad and Kanehisa (1982).
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  • 110
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    Bulletin of mathematical biology 46 (1984), S. 529-543 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract This paper concerns sequences of letters in which certain “distinguished” words are of interest. Such sequences arise as data in numerous fields including genetics and neuroscience. A probability distribution is given for the number of occurrences of a chosen word in a randomized sequence of letters. Such words are considered “favored” if they occur more than expected at random. Favored words have been discovered in nerve impulse trains and may reflect a neural coding scheme.
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  • 111
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    Bulletin of mathematical biology 46 (1984), S. 545-552 
    ISSN: 1522-9602
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    Notes: Abstract As the volume of protein sequence data grows, rapid methods for searching the protein sequence database become of primary importance. Rigorous comparison of sequences is obtained with the well-known dynamic programming algorithms. However, these algorithms are not rapid enough to use for routinely searching the entire database. In this paper we discuss some methods that can be used for rapid searches.
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  • 112
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    Bulletin of mathematical biology 46 (1984), S. 553-566 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract We give algorithms for computing the extent of similarity between two or three sequences of letters. The similarity measures we consider include a penalty for inserting gaps within the sequence in order to enhance similarity. The magnitude of the penalty for gaps is assumed to be independent of their size in order to accommodate certain biological applications. Our algorithm for three sequence comparisons, which is based on solving a system of recursive equations, improves upon the efficiency of existing methods. Although the system of recursive equations utilized by the algorithm is quite complicated as it stands, it has none the less been simplified by appeal to combinatorial considerations.
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  • 113
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    Bulletin of mathematical biology 46 (1984), S. 567-577 
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    Notes: Abstract Well-known dynamic programming algorithms exist for comparing two finite sequences inO(N 2) time and storage, whereN is the common sequence length. Extensions to the comparison ofM finite sequences requireO((2N) M) time and storage, making such algorithms difficult even forM=3. A simple generalization of the sequences makes it possible to obtain some results about the geometry of sequence alignments. These ideas suggest heuristic approaches to problems of comparing several sequences. IfM sequences are known to be related by a binary tree, they can be aligned inO(MN 2) time andO(N 2+NM) storage.
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  • 114
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    Bulletin of mathematical biology 46 (1984), S. 661-672 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract Protein sequences of the Dayhoff databank of 1984 have been analyzed to evaluate the occurrences of the 400 dipeptides and 8000 tripeptides. Expected values and standard deviations for the di- and tripeptides were determined by Monte Carlo and binomial approximation. A condensed format containing this information, labeled a uniqueness diagram, is presented and made available in the form of a microfiche.
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  • 115
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    Bulletin of mathematical biology 46 (1984), S. 827-844 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract In two-state sliding filament models of muscle contraction a partial differential equation must be solved to find the cross-bridge distribution functionn(x, t). In this paper the analytical form of this function is obtained by integration along the characteristic line and special cases are presented in which the explicit expression forn(x, t) can be completely determined. These analytical solutions provide a direct mathematical connection between the microscopic contraction parameters contained in the kinetic theories and macroscopic muscle dynamics and are thus used to investigate what parameters influence the transient contractile tension in typical experimental conditions. The results of this investigation are consistent with relevant aspects of muscle physiology.
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  • 116
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    Bulletin of mathematical biology 46 (1984), S. 845-857 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract Experiments on random binary, ternary, etc. (P=2, 3,…, 10) switching nets are reported. Behavioral cycle lengths are examined as functions of output variety,P, input connectance,K, and net size,N. Overall, output variety appears an influential, well-behaved net property. Strong, but well-behaved interactions appear among net variables. In high connectance nets, median cycle length grows approx. asP N/2. Other factors constant, one-connected nets show the shortest cycles, and connectance effects appear to converge asymptotically aroundN. Data for cycle length as a function of net size suggest a concavity not compatible with the Kauffman “square root law” (Kauffman, 1969). Evidence of a positive relationship between cycle length and run-in length is found in two-input nets; weaker evidence is obtained that in higher connectance nets this relationship becomes negative in sign. The “modular complexity” ofP〉2 nets is examined briefly.
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  • 117
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    Bulletin of mathematical biology 46 (1984), S. 869-877 
    ISSN: 1522-9602
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    Topics: Biology , Mathematics
    Notes: Abstract The influence of topographical situation on the spread of infection is studied. The investigation is based on a multigroup model. The population under consideration is thought to be divided into subpopulations living in regions that are separated from each other by natural barriers (mountains). Infection is carried from one region to another by migrating infectives. Migration is possible only along the river system so that the structure of the epidemiological network is that of a symmetric tree. The results allow comparison of the velocity of propagation of the epidemic for different geographical situations and allow quantification of the “channel-effect”, according to which mountainous regions are channels rather than barriers to the spread of an epidemic.
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  • 118
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    Bulletin of mathematical biology 42 (1980), S. 147-160 
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    Notes: Abstract A theory of noise fluctuations is developed which is applicable to systems of any size in which unimolecular or bimolecular reactions are occurring. The main difference between small and large reacting systems is that in the former the probability of finding a particle in a particular state does not obey a Gaussian distribution, but satisfies a distribution which reflects the mechanism of the chemical reaction. This difference is reflected in the main result of the theory: an autocorrelation function that is expressible as a sum of exponentials, the amplitudes of which are explicit functions of the moments of the distribution. Thus, by using small systems, the autocorrelation function,in principle, allows the elucidation of reaction mechanisms. Numerical simulations indicate that for reacting systems having ten or fewer particles, the deviation of the autocorrelation function from a single exponential should be easily detectable, and that estimates of the first four moments of the distribution should be possible. Accurate inference of the distribution, however, will require further mathematical and experimental advances.
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  • 119
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    Bulletin of mathematical biology 42 (1980), S. 161-172 
    ISSN: 1522-9602
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    Notes: Abstract The recent mathematical formalization of the concepts of matter and extrinsical energy, which are used for the relational representation of biological systems, is employed in the analysis of the important experimental discoveries of Comorosanet al. related to low energy electromagnetic irradiations on enzyme substrates. By means of the present analysis one of the properties inherent to the experimental phenomena is more precisely exposed, and theoretical developments corresponding to “energetical evolutions” in a biological system (Leguizamón, 1976) may now have an experimental basis. Important limitations are introduced for the validity of the commutativity and associativity of cartesian product of sets, when they represent matter and its linked extrinsical energy. In connection with this last aspect, new important knowledge is obtained for the relational mathematical representation of biological systems.
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  • 120
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    Bulletin of mathematical biology 42 (1980), S. 397-429 
    ISSN: 1522-9602
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    Notes: Abstract The structure of solutions to a simple spatially dependent population model involving growth and death is investigated. Two forms of motility of the population are considered: (1) random motion only modeled by a Fickian law, and (2) a directed component of motion (chemotaxis), included in addition to the random motion. Under certain growth conditions a traveling wave of constant speed is approached. This speed can be increased by the addition of the chemotaxis with a corresponding increase in the asymptotic population. Development of initial conditions into a wave is illustrated numerically.
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  • 121
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    Bulletin of mathematical biology 42 (1980), S. 365-396 
    ISSN: 1522-9602
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    Notes: Abstract This paper describes mechanisms of intracellular and intercellular adaptation that are due to spatial or temporal factors. The spatial mechanisms support self-regulating pattern formation that is capable of directing self-organization in a large class of systems, including examples of directed intercellular growth, transmitter production, and intracellular conductance changes. A balance between intracellular flows and counterflows causes adaptation. This balance can be shifted by environmental inputs. The decrease in Ca2+-modulated outward K+ conductance in certain molluscan nerve cells is a likely example. Examples wherein Ca2+ acts as a second messenger that shunts receptor sensitivity can also be discussed from this perspective. The systems differ in basic ways from recent diffusion models. Chemical transducers driven by membrane-bound intracellular signals can establish long-range intercellular interactions that compensate for variable intercellular distances and are invariant under developmental size changes; diffusional signals do not. The intracellular adaptational mechanisms are formally analogous to intercellular mechanisms that include cellular properties which are omitted in recent reaction-diffusion models of pattern formation. The cellular models use these properties to compute size-invariant properties despite wide variations in their intercellular signals. Mechanisms of temporal adaptation can be derived from the simplest laws of chemical transduction by using a correspondence principle. These mechanisms lead to such properties of intercellular signals as transient overshoot, antagonistic rebound, and an inverted U in sensitivity as intracellular signals or adaptation levels shift. Such effects are implicated in studies of behavioral, reinforcement, motor control, and cognitive coding.
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    Bulletin of mathematical biology 42 (1980), S. 447-459 
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    Notes: Abstract Large radiation doses to the lung can cause early death from cardiopulmonary insufficiency resulting from radiation pneumonitis and pulmonary fibrosis. A model for early death following inhalation of insoluble radioactive particles is propose. The model is based on three assumptions: (1) early death results from damage to a cluster of cells from a large number of cell clusters at risk, (2) the dose that causes early death depends on how the radiation is delivered in time and (3) the cell clusters at risk to damage are equally sensitive ro radiation. Results from asymptotic theory of extreme values, along with biophysical considerations, suggest that the cumultive distribution function for the absorbed radiation dose to the production of pulmonary injury sufficient to cause early death is best estimated by the third asymptotic distribution without a threshold. This distribution function is identical to the Weibull cumulative distribution function. Data for Beagle dogs after inhaling relatively insoluble forms of alpha- or beta-gamma-emitting particles are shown to support the Weibull model.
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    Bulletin of mathematical biology 42 (1980), S. 461-480 
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    Notes: Abstract Models of the human respiratory tract were developed based on detailed morphometric measurements of a silicone rubber cast of the human tracheobronchial airways. Emphasis was placed on the “Typical Path Lung Model” which used one typical pathway to represent a portion of the lung, such as a lobe, or to represent the whole lung. The models contain geometrical parameters, including airway segment diameters, lengths, branching angles and angles of inclination to gravity, which are needed for estimating inhaled particle deposition. Aerosol depositions for various breathing patterns and particle sizes were calculated using these lung models and the modified Findeisen-Landahl computational scheme. The results agree reasonably well with recent experimental data. Regional deposition, including lobar deposition fractions, are also calculated and compared with results based on the ICRP lung deposition model.
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    Bulletin of mathematical biology 42 (1980), S. 481-488 
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    Notes: Abstract The completely symmetrical system is defined as having identical transfer coefficients between pairs of compartments and the same loss coefficient for each compartment. The eigenvalues and eigenvector are explicitly found along with the inverses of the system matrix and the matrix of eigenvectors. Many properties, special instances of more general theorems, can be seen at once from the explicit analytic solution of the initial value, washout and washin problems. The system serves as a known case for testing estimation procedures, algorithms for solutions of linear systems, eigenvalue-eigenvector and inversion routines and is of considerable tutorial value.
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    Bulletin of mathematical biology 42 (1980), S. 431-446 
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    Notes: Abstract The mathematical structures underlying the theories of organismic sets, (M, R)-systems and molecular sets are shown to be transformed naturally within the theory of categories and functors. Their natural transformations allow the comparison of distinct entities, as well as the modelling of dynamics in “organismic” structures.
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    Bulletin of mathematical biology 42 (1980), S. 489-505 
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    Notes: Abstract To explain the sodium conductance change using Wei's dipole model (Wei, 1969), we may expect that during depolarization the dipole's population difference, ΔN, is first reduced and then returns more slowly to its resting value. This paper shows that the experimental results of gating currents support this idea. Such time course of ΔN, however, is not a usual relaxation process. To account for the unusual behavior of ΔN, we propose two additional assumptions: (1) there exists a special coupling system (probably the intramolecular vibrations) whose coupling strength with the dipoles is much stronger than with the thermal bath (intermolecular vibrations), and (2) there also exist “traps” for the dipole's excitation energy so that this energy is transformed into other energy forms at a rate increasing with the increase of depolarization. Experiments suggest that the traps are proteins located at the inner membrane surface.
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    Bulletin of mathematical biology 42 (1980), S. 507-528 
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    Notes: Abstract Current research into the dynamics of iterative ecological and biological models has lead to a number of theorems concerning the existence of various types of iterative dynamical behavior. In particular, much study has been done on the dynamical behavior of the “simplest dynamical system”f b(x)=bx(1−x), which is just the canonical discrete form of logistic growth equations found in ecology, sociobiology, and population biology. In this paper, we make use of some of the techniques and concepts of topological dynamics to construct a number of generalized conjugacy theorems. These theorems are then used to demonstrate that the mappingf b has a number of conjugacy classes in which the dynamics of the iterates is equivalent to within a change of variables. The concepts of fitness and survival in logistic equations are then shown to be independent, if we follow certain intuitive definitions for these concepts. This conclusion follows from a comparison of the conjugacy classes of the functionf b and the extinction sets off b.
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  • 128
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    Notes: Abstract For chemical reactions not at equilibrium but proceeding in the forward direction in the steady state, a result found by a method first introduced by H. G. Britton (1963, 1965) is generalized to prove that if $${{\vec J} \mathord{\left/ {\vphantom {{\vec J} {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\leftarrow}$}}{J} }}} \right. \kern-\nulldelimiterspace} {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\leftarrow}$}}{J} }}$$ is the unidirectional flux ratio, $${{\vec J} \mathord{\left/ {\vphantom {{\vec J} {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\leftarrow}$}}{J} }}} \right. \kern-\nulldelimiterspace} {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\leftarrow}$}}{J} }}$$ exp (−ΔG/RT). The conditions under which the equality or inequality applies are discussed. If the unidirectional fluxes are not in the steady state, the unidirectional flux ratio is time invariant in certain specific situations. One such important case is for chemical reaction systems with an ordered sequence of reactions. For systems with more than one pathway, $${{\vec J} \mathord{\left/ {\vphantom {{\vec J} {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\leftarrow}$}}{J} }}} \right. \kern-\nulldelimiterspace} {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\leftarrow}$}}{J} }}$$ is not constant except for special cases. These results also apply to diffusional and active transport systems.
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    Bulletin of mathematical biology 42 (1980), S. 599-600 
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    Bulletin of mathematical biology 42 (1980), S. 539-549 
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    Bulletin of mathematical biology 42 (1980), S. 551-597 
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    Notes: Abstract The nonlinear second-order difference equationx n+1=axn(1-xn−1), where 0≦x nX≦1 anda ≧1, is examined from varying points of view, analytical, numerical and geometrical. An analytic expression is obtained for an invariant attracting curveC ∞ (a) in phase space, which becomes the central object of study. This basic curve, which replaces the simple parabolic shape typical of many analogous first-order models, may have a complicated geometrical structure. As the parametera increases,C ∞(a) undergoes transformations characterized by the dynamical descriptions: stable node→stable focus→stable limit cycle →chaotic attractor. Although the limited characterization ofchaos by the appearance of nonperiodic solutions and solutions of arbitrarily large period is relied upon, this appears to be only a simplified approximation of the real behavior of solutions. Trajectories (x n, xn+1),n=0,1,…, are calculated using the related nonlinear planar mapT a(x,y)=(y,ay(1−x)), and regions of persistence and escape are described for characteristic values ofa. The study of persistence, of even more fundamental interest than the associated problems of periodicity and stability, receives special attention. We introduce a geometrical model, similar in many respects to that for the well-known analoguex n+1=axn(1−x n), but having several new and important features. It appears that as the parametera increases in the chaotic regime there are infinitely many intermittent bursts of increase in the probability that any initial point (x 0, x1) will persist in the unit square under successive iterations of the mappingT a, an unexpected property that should be of interest for applications. A discussion of the applicability of these results to population dynamics theory is given, and it is suggested that such equations might find useful application to problems in developmental biology as well.
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    Bulletin of mathematical biology 42 (1980), S. 627-645 
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    Notes: Abstract Based on the principle of minimum power, a mathematical model of the functional state of the oxygen transport system is presented. The optimization model minimizes the power expenditure of the heart, bone marrow, lung and other tissues. The model is used to determine the functional parameters of the oxygen transport system in man under both normal and varying barometric pressures. Theoretical results are compared with experimental data.
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    Bulletin of mathematical biology 42 (1980), S. 601-625 
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    Notes: Abstract A quantitative model of ion binding and molecular interactions in the lipid bilayer membrane is proposed and found to be useful in examining the factors underlying such membrane characteristics as shape, sidedness, stability and vesicle size at various cation concentrations. The lipid membrane behaves as a bilayer couple whose preferential radius of curvature depends on the expansion or contraction of one monolayer relative to the other. It is proposed that molecular packing may be altered by electrostatic repulsion of adjacent like-charged phospholipid headgroups, or by bringing two headgroups closer together by divalent cation crossbridging. The surface concentrations of each type of cation-phospholipid complex can be described by simple binding equilibria and the Gouy-Chapman-Stern formulation for the surface potential in a diffuse double layer. The asymmetric distribution of acidic phospholipids in most biological membranes can account for the differential effects of identical ionic environments on either side of the bilayer. The fraction of vesicle material which tends to have a right-side-out orientation may be approximated by a normal distribution about the mean curvature. The theory generates vesicle sidedness distributions that, when fitted to experimental results from human erythrocyte membranes, provide an alternative method of estimating intrinsic cationphospholipid dissociation constants and other molecular parameters of the bilayer. The results also corroborate earlier suggestions that the Gouy-Chapman theory tends to overestimate free counter-ion concentrations at the surface under large surface potentials.
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    Bulletin of mathematical biology 42 (1980), S. 681-689 
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    Notes: Abstract The “yellow strips” on the cuticle of the Oriental Hornet (Vespa orientalis, Hymenoptera, Vespinae), present photoelectric properties. A mathematical model for the relative changes in resistance as a photoconductive process conforms to the general model for a semiconductor with traps.
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    Bulletin of mathematical biology 42 (1980), S. 701-718 
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    Notes: Abstract Damped nonlinear oscillations in biological and biochemical systems are investigated by the extended Krylov-Bogoliubov-Mitropolskii (KBM) method. A review on the extension made by Popov to the KBM method is given and also further improvements are presented. Applications are made to models of oscillating chemical reactions (Lefever and Nicolis, 1971), FitzHugh (1961) equations, and population dynamics (Gatto and Rinaldi, 1977). Comparison to damped oscillating physical and engineering systems is made.
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    Bulletin of mathematical biology 42 (1980), S. 719-728 
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    Notes: Abstract The conditions that will allow the lumping together of several age classes in the Leslie model are investigated. We show that if the lumping is to be valid for all population distributions, then the parameters of the model must be periodic. Lumping is valid when the population is in equilibrium, but equilibrium should be tested before the model is lumped.
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    Bulletin of mathematical biology 42 (1980), S. 647-679 
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    Notes: Abstract Catastrophe theory is a mathematical theory which, allied with a new and controversial methodology, has claimed wide application, particularly in the biological and the social sciences. These claims have recently been heatedly opposed. This article describes the debate and assesses the merits of the different arguments advanced.
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    Bulletin of mathematical biology 42 (1980), S. 765-795 
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    Notes: Abstract Estimates of capillary tracer permeability calculated using multiple indicator data depend upon the particular model adopted to describe blood tissue exchange. The model proposed by Crone (1963) is appropriate when some of the injected tracer diffuses into the tissue but does not return appreciably to the bloodstream before data collection is terminated. Under these conditions extraction of tracer by the tissue depends on a single dimensionless parameter, αcap, defined as the ratio of capillary permeability surface area to water flow. The effects of finite red cell tracer permeability on the Crone model estimate of capillary permeability are examined in the present study. The results indicate that even when back diffusion from the extravascular space is negligible, significant errors in the Crone model estimate can be expected when capillary permeability is relatively high and the ratio of red cell to capillary permeability is less than unity. However, when an aliquot of blood is equilibrated with tracer prior to injection and the dimensionless capillary permeability is relatively low (i.e. αcap ≦ 0.25 for a haematocrit≦50%), the whole blood Crone model estimate of αcap will be within 10% of the actual value, irrespective of red cell permeability. Red cell-plasma exchange for commonly used tracer-organ combinations should not significantly affect Crone estimates of capillary permeability under normal physiological conditions, but may be important in low flow situations.
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    Bulletin of mathematical biology 42 (1980), S. 807-828 
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    Notes: Abstract Assuming truncated ellipsoidal geometry for the right and left ventricles, a model is developed for the myocardium enabling biventricular mechanical behavior to be studied. Employing pressure-volume data taken from normal dog hearts and from hearts in which the pulmonary artery has been banded over periods of 2–40 weeks, it is shown that: (a) right ventricular wall stresses are higher than left ventricular stresses; (b) right ventricular wall stress increases initially to a maximum after 3–4 weeks followed by a decline to normal and even subnormal levels, attaining a minimum value at 32–33 weeks; (c) left ventricular stresses behave in a similar manner, attaining their maximum and minimum levels after 7–8 weeks and 32–33 weeks respectively. These results suggest that surgical or medical therapy in patients with hypertrophied ventricles might be more appropriate during the period of wall stress reduction.
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    Bulletin of mathematical biology 42 (1980), S. 837-845 
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    Notes: Abstract In this paper we describe a mathematical model of the oscillations of the diaphragm which limits the vitreous body from the anterior segment of the human eye after the lens has been removed in a cataract operation. We study the motion of this diaphragm driven by movements of the eye. Firstly, a mathematical statement of the problem is given and then we solve the problem exactly for a given class of eye movements. From the analysis we deduce that significant oscillations of the membrane are driven by saccades and that it is the angular acceleration of the eye which causes these types of oscillations. A numerical example is given.
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    Bulletin of mathematical biology 42 (1980), S. 871-887 
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    Notes: Abstract The Lotka-Volterra system of prey-predator equations is considered with a special type of continuous time delay. In the case of equal diffusion coefficients Hopf’s bifurcation technique is used to show the existence of travelling wave train solutions for the prey-predator system.
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    Bulletin of mathematical biology 42 (1980), S. 861-870 
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    Notes: Abstract A mathematical model of prothrombin activation is being proposed which includes the feedback mechanism of thrombin and the alteration of factor V by thrombin. This model is in good agreement with experimental data for the dependence of the rate of thrombin formation on the concentrations of factors V and X a . In particular, it correctly predicts the existence and location of a maximum in both of these cases.
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    Bulletin of mathematical biology 42 (1980), S. 847-859 
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    Notes: Abstract A new model of the upper tracheobronchial tree is proposed to account for the three-dimensional nature of the airway system. In addition to the tube length, the tube diameter, and the branching angle, the model includes information on the orientation angle of each tube relative to its parent tube. The orientation angle, defined as the angle between two successive bifurcations, is useful for calculating the gravitational inclination of each tube. The information on orientation angle is further used to construct a binary coding system for identifying individual tubes in the airway tree. The proposed model is asymmetrical, but the same principles can be readily used to construct a symmetrical one.
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    Bulletin of mathematical biology 42 (1980), S. 889-897 
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    Notes: Abstract In any control system for which the number of independent controls is smaller than the number of degrees of freedom to be controlled, our choice of control in any state is restricted to a submanifold of smaller dimension than the tangent space. This simple fact has a number of important consequences for questions of biological import; we consider its implications for adaptation, for senescent phenomena and for the determination of tertiary structures of polypeptides through control of certain average properties. We also formulate the Pontryagin Maximum Principle of Optimal control theory in such a way as to inquire whether specific biodynamic systems can be regarded as optimal with respect to rate of accumulation of particular quantities of the system. We find that if this is possible, the quantity in question must play the role of a clock.
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    Bulletin of mathematical biology 42 (1980), S. 899-900 
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    Bulletin of mathematical biology 42 (1980), S. 1-15 
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    Notes: Abstract A computational model to predict deposition of a wide variety of particulate pollutants in several species of mammals is presented. The model incorporates breathing pattern and detailed anatomical models of the respiratory tract based on extensive morphometric measurements of individual airways. The predicted deposition from this general model is in close agreement with observed deposition of monodisperse aerosols in rats. Particle size and density and respiratory breathing patterns are the critical parameters affecting regional deposition.
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    Bulletin of mathematical biology 42 (1980), S. 17-36 
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    Notes: Abstract A theory of antigen-antibody induced particulate aggregation is developed by investigating the stability of model systems of particles. Conditions for the formation of large aggregates are derived by imposing the requirement that at equilibrium a statistically significant number of redundant bonds would occur in a reduced monomer-dimer model system. A relationship is obtained which predicts the fractional agglutination in the reduced dimer system as a function of the antigen, antibody and particulate concentrations: $$\frac{g}{{2f c_0 (1 - g)^{2^ - } }} = \frac{{s_1 }}{r} + \frac{{s_1 s_2 }}{{2!r^2 }} + ... + \frac{{s_1 s_2 ...s_j }}{{j!r^j }},$$ wherec 0 is the initial concentration of monomer,f is a proximity factor,g is the fractional agglutination,s i is the average rate of formation of theith bond from an (i−1)th bound dimer, andr is the average rate of dissociation of a single antibody-antigen bond.
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    Bulletin of mathematical biology 42 (1980), S. 37-56 
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    Notes: Abstract The roles of the concentrations of the three interacting constituents in the aggregation process (antibodies, antigens and particulates) are analyzed in detail. It is shown that the basic equation derived in Part I is consistent over a broad range of conditions with experimental findings previously reported.
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    Bulletin of mathematical biology 42 (1980), S. 57-78 
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    Notes: Abstract A general mathematical model describing the biochemical interactions of the hormones luteinizing hormone releasing hormone (LHRH), luteinizing hormone (LH) and testosterone (T) in the male is presented. The model structure consists of a negative feedback system of three ordinary differential equations, in which the qualitative behavior is either a stable constant equilibrium solution or oscillatory solutions. A specific realization of the model is used to describe the experimental observations of pulsatile hormone release, its experimental suppression, the onset of puberty, the effects of castration, and several other qualitative and quantitative results. This model is presented as a first step in understanding the physicochemical interactions of the hypothalamic-pituitary-gonadal axis.
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    Bulletin of mathematical biology 42 (1980), S. 79-94 
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    Notes: Abstract Based upon the transition rate equation of dipoles in the membrane, we deal with two important aspects of interaction of nerve signals: (1) conditions for nerve excitation and (2) frequency spectrum analysis of nerve impulse. Interrelations between signal amplitudes and frequencies are formulated in detail. There are several important conclusions which can be drawn from our calculations. First, toexcite the nerve, low frequencies are generally more effective than high frequencies. Second, tosedate the nerve (i.e. to suppress undesired activities), high frequencies would suit better. Third, harmonics produced through interactions of nerve signals are not necessarily weaker than the fundamental frequencies. The great significance of our theory is that it indicates in principle the feasibility to alter or rewrite the information contents of a nerve message in our body by applying stimulations of appropriate strengths and frequencies. Thus, the theory provides a physical basis and hence some understanding for a new branch of medicine—neuro therapy such as Nogier's auriculotherapy, Lamy's phonophoresis, Voll's electroacupuncture and the fast rising TENS (transcutaneous electro-neuro stimulation).
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    Bulletin of mathematical biology 42 (1980), S. 107-117 
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    Notes: Abstract A new physical property, called resonance of the B-type is hypothetically attached to the λ =546 nm irradiated crystalline (small) molecules. In this respect an up or down configuration is assumed for those states obtained through irradiation times that are multiples of 5 sec. With these assumptions, the cellular receptors that may detect these states appear to belong to three classes: the up, down and alternatively mixed up-down. Using the classic formalism of eigenvectors and eigenvalues, a simple spectroscopic type of formula is derived, through which all the possible states of the above characteristic may be obtained.
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    Bulletin of mathematical biology 42 (1980), S. 119-130 
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    Notes: Abstract A model of ecosystems with migration is proposed from the viewpoint of flow. This model explains the following two points: (1) How the density-dependent terms in population dynamics arise as a consequence of migration. (2) How the ecosystem exhibits a hierarchy in energy per unit biomass.
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    Bulletin of mathematical biology 42 (1980), S. 143-145 
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    Bulletin of mathematical biology 42 (1980), S. 95-106 
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    Notes: Abstract For precise boundary conditions of biological relevance, it is proved that the steadily propagating plane-wave solution to the Fisher equation requires the unique (eigenvalue) velocity of advance 2(Df)1/2, whereD is the diffusivity of the mutant species andf is the frequency of selection in favor of the mutant. This rigorous result shows that a so-called “wrong equation”, i.e. one which differs from Fisher's by a term that is seemingly inconsequential for certain initial conditions, cannot be employed readily to obtain approximate solutions to Fisher's, for the two equations will often have qualitatively different manifolds of exact solutions. It is noted that the Fisher equation itself may be inappropriate in certain biological contexts owing to the manifest instability of the lowerconcentration uniform equilibrium state (UES). Depicting the persistence of a mutantdeficient spatial pocket, an exact steady-state solution to the Fisher equation is presented. As an alternative and perhaps more faithful model equation for the propagation of certain species properties through a homogeneous population, we consider a reaction-diffusion equation that features a cubic-polynomial rate expression in the species concentration, with two stable UES and one intermediate unstable UES. This equation admits a remarkably simple exact analytical solution to the steadily propagating plane-wave eigenvalue problem. In the latter solution, the sign of the eigenvelocity is such that the wave propagates to yield the “preferred” stable UES (namely, the one further removed from the unstable intermediate UES) at all spatial points ast→∞. The cubic-polynomial equation also admits an exact steady-state solution for a mutant-deficient or mutant-isolated spatial pocket. Finally, the perpetuating growth of a mutant population from an arbitrary localized initial distribution, a mathematical problem analogous to that for ignition in laminar flame theory, is studied by applying differential inequality analysis, and rigorous sufficient conditions for extinction are derived here.
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    Bulletin of mathematical biology 42 (1980), S. 191-220 
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    Notes: Abstract The binding of mono-, di- and trivalent cations to negatively charged surfaces is studied within the framework of a modified Gouy-Chapman equation. For any given combination of ions of the above valences, the existence and uniqueness of the solution for the surface potential is shown. The treatment provides the surface potential and charge density. For a system containing only monovalent and divalent ions, analytical solutions are given. When trivalent ions are also present, a procedure based on numerical integration is described. The distance dependence of the electrostatic potential for planar surfaces is given. The calculations provide the amount of cations tightly bound and the amount trapped in the double layer region. The competition between cations for binding to surfaces is elucidated.
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    Bulletin of mathematical biology 42 (1980), S. 221-238 
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    Notes: Abstract This paper deals with a model describing the behavior of barium-treatedApalysia neurons. The model is represented by a dynamical system, so-called “complete system”, defined in R4 and depending on a small parameter. The study of this system under zero membrane current conditions was performed with the use of the qualitative theory of singular perturbations. We show that this system has a stable periodic solution of the discontinuous type when the small parameter tends to 0+. A reduced system defined in R3, associated to the complete system was also studied: it corresponds to a constant activation of the inward current. We demonstrate that the corresponding hypothetical cell remains silent under zero current conditions.
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    Notes: Abstract In the study of chemical modification of enzymes and other biologically active proteins, plots of fractional residual activity as a function of number of groups modified per enzyme molecule are often used to establish a correlation between the chemical modification and enzyme inactivation reactions and to determine the stoichiometry of the modification reaction. This paper presents a critical examination of the underlying theoretical framework of such graphs. Whereas these plots are usually presented as linear functions, it is shown here that the general equation describing the relationship between inactivation and modification contains an exponential term; therefore, in the general case, the plot is actually a curve. It is suggested that caution be exercised in the interpretation of such plots and that equations such as those derived in the text be used to fit theoretical curves to the data, in order to maximize the information gained from chemical modification experiments.
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    Bulletin of mathematical biology 42 (1980), S. 257-265 
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    Notes: Abstract This communiction argues that so-called “hermaphroditic” tracer systems, which are neither open nor closed, do not exist physically. The argument is based on the assumption that any observable (possibly nonhomogeneous) macroscopic compartment can be approximated by a compartmentC with a finite number of entry points for the tracer, each associated with an abstract subcompartment ofC. It is shown that the “hermaphroditic” property requires that the mean waiting time be infinite in at least one of the subcompartments, or in a subcompartment elsewhere in the system. A subcompartment with infinite mean waiting time must have some sort of memory, of infinite duration, which knows how long a given particle has been retained, however long that is, and thereby determines its probability of departure. Assuming, as seems likely, that no physical basis exists for such an infinite memory, it follows that “hermaphroditic” systems do not exist.
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    Bulletin of mathematical biology 42 (1980), S. 273-274 
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    Bulletin of mathematical biology 42 (1980), S. 275-275 
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    Bulletin of mathematical biology 42 (1980), S. 277-281 
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    Bulletin of mathematical biology 42 (1980), S. 267-272 
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    Notes: Abstract The implication of state space structure on the existence of a repeatable experimentE designed to determine if a states∈L has propertyP or notP is investigated. It is shown that if a state spaceL is connected, then no experimentE is repeatable. This formalism is used to demonstrate that if a propertyP has an associated set of points inL which is dense with dense complement inL, then there exists no repeatable experimentE which can be used to test whethers has propertyP or notP. Other consequences of this formalization are discussed.
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    Bulletin of mathematical biology 42 (1980), S. 282-282 
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    Bulletin of mathematical biology 42 (1980), S. 283-294 
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    Notes: Abstract It has been shown that the resistance of flow and the wall shear increase with the size of the stenosis but these increases are comparatively small due to non-Newtonian behaviour of the blood indicating the usefulness of its rheological character in the functioning of the diseased arterial circulation.
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    Bulletin of mathematical biology 42 (1980), S. 327-337 
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    Notes: Abstract The modern theory of generalized Hamiltonian systems is used to construct a unified canonical description of the linear Lagrangian biodynamics introduced by Kerner.
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    Bulletin of mathematical biology 42 (1980), S. 305-325 
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    Notes: Abstract The purpose of this paper is to justify an asymptotic method developed for the study of peristaltic transport in a tube of arbitrary cross section. Within the framework of long wave approximation, the three-dimensional nonlinear Navier-Stokes equations are reduced to a sequence of two-dimensional linear boundary value problems of Laplace and biharmonic operators. It is shown that, if a Reynolds number is less than some constant, the solution of the approximate equations is indeed an asymptotic approximation to the exact solution of the problem as the ratio of the maximum radius of the tube to the wave length of the peristaltic motion of the wall tends to zero, and the error estimates are expressed inL 2 norms. Furthermore, under the same condition the exact solution is shown to be unique and stable under arbitrary perturbation of spatially periodic disturbance. Application of the stability condition to peristaltic transport in a tube of circular cross section is given.
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    Bulletin of mathematical biology 42 (1980), S. 295-304 
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    Notes: Abstract A mathematical analysis, including existence and uniqueness, is given for some boundary value problems which model the flow of a fluid-solute mixture in a tube which is placed in an interstitium. The model permits an interchange of fluid and solute across the tube walls.
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    Bulletin of mathematical biology 42 (1980), S. 339-364 
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    Notes: Abstract The vertebrate nervous system has topographic interconnections in many parts, known for example as retinotopy, somatotopy, etc. It is plausible that modifiable synapses play an important role in forming and refining these connections together with the sensory experiences. To elucidate the mechanism of topographic organization, we propose a simple model consisting of two nerve fields connected by modifiable excitatory synapses. The model also includes modifiable inhibitory synapses. The behavior of the model is described by a set of simultaneous non-linear integro-differential equations. By analyzing the equations, we obtain the equilibrium solution of topographic connections. It is also proved that a part of the presynaptic field which is frequently stimulated comes to be mapped on a large area of the postsynaptic field so that it has a good resolution.
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    Bulletin of mathematical biology 42 (1980), S. 691-700 
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    Notes: Abstract The steady-state solution of the equations governing substrate exchange between vascular and extravascular compartments separated by a membrane with finite, symmetrical substrate permeability is presented. Substrate removal from the extravascular compartment by Michaelis-Menten saturation type kinetics with negligible diffusion in the axial and instantaneous diffusion in the transverse directions in both compartments are assumed. It is shown that the solution degenerates into known expressions for special linearized and asymptotic cases. The method of solution is also applied to an extension of the original model incorporating autoregulatory feedback effects upon the process responsible for substrate removal.
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    Bulletin of mathematical biology 42 (1980), S. 729-737 
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    Notes: Abstract Global asymptotic stability and equilibrium coexistence is established in two species Lotka-Volterra-type competition when there are time delays in interspecific interaction terms and the intraspecies competition is stronger than the interspecies competition.
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    Bulletin of mathematical biology 42 (1980), S. 739-746 
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    Notes: Abstract The realized (observed) value of Landau’s dominance hierarchy index is examined. Under a model of constant pairwise dominance probabilities, the observed index is shown to be a strongly consistent estimator of the underlying (true) index. However, a large number of encounters between animals is shown to be required in order to reduce bias and variance to practical levels except when the pairwise dominance probabilities are near one.
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    Bulletin of mathematical biology 42 (1980), S. 747-748 
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    Bulletin of mathematical biology 42 (1980), S. 749-749 
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    Bulletin of mathematical biology 42 (1980), S. 751-763 
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    Notes: Abstract The steady state potassium conductance as a function of measured membrane potential difference (p.d.) ϕ of the squid giant axon is corrected for the effect of accumulation of potassium in the periaxonal space. This correction is made on the assumption that several mathematical models of the axon are valid. These are (i) the McIlroy (1975), McIlroy-Hahn (1978) model of membrane conductanceg i(i=K, Na) which is a detailed model of passive transport of ions across the axonal membrane with the aid of mobile, negatively-charged carriers, (ii) the Adelmanet al. (1973) compartmental model of the periaxonal and external bathing-solution spaces, (iii) the enzymatic theory of nervous conduction due to McIlroy (1970 a, b, c), (iv) the Wien dissociative effect of the axolemmic electric field on the weak membrane buffer proposed by Bass and Moore (1968) as a trigger mechanism in nervous excitation and (v) the model (McIlroy, 1979) of the interfacial double-layer p.d.s. which are assumed to exist at the membrane’s surfaces because of the presence of a fixed surface charge. From the correctedg k (ϕ) curves the values of the double-layer p.d.s. of model (v) are deduced and these are shown to lead to a consistent, physically reasonable solution for the distance (approx. 6.8Å) between the fixed surface charges and for the dissociation constants of these sites in their interactions with the ions of the extra-membrane electrolytes. Assuming that the selectivity coefficint of the potassium conducting system for the squid giant axon is approx. 52 it is deduced that the potassium permeability,P ks , of the periaxonal barrier ≈1.37(±0.5)×10−4 cm sec−1 and the thickness of the periaxonal space ≈451±159Å.
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    Bulletin of mathematical biology 42 (1980), S. 797-805 
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    Notes: Abstract The effects of peripheral layer viscosity on physiological characteristics of blood flow through the artery with mild stenosis have been studied. It has been shown that the resistance to flow and the wall shear decrease as the peripheral layer viscosity decreases.
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    Bulletin of mathematical biology 42 (1980), S. 829-836 
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    Notes: Abstract A study was made of Higgins’ model of glycolysis incorporating molecular diffusion of intermediates, utilizing an earlier conjecture due to Landau. Conditions for the existence of asymptotically stable spatio-temporal periodic solutions are obtained.
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    Bulletin of mathematical biology 46 (1984), S. 81-102 
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    Notes: Abstract The temperature regulation in homothermic animals is an example of a negative feedback system. It shows sudden changes of parameter values, and therefore suggests the use of catastrophe theory for its description. This paper reports on work done on the human temperature regulation mechanism to shows that the five-dimensional dual butterfly catastrophe model is sufficient for its description. Nearly all experiments reported in the literature overlook the dynamic multiparametric nature of the process. Use of catastrophe theory, on the other hand, shows that one cannot find a model with fewer than five parameters for such a system. From work by Benzinger and Kitzinger, the exact shape of part of the corresponding bifurcation set is determined.
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    Bulletin of mathematical biology 46 (1984), S. 103-114 
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    Notes: Abstract This paper is an analytical study on the pulse wave velocities in the aorta. In conformity to a physiologic state of loading, the distensibility of the vessel wall has been accounted for. The wall material is treated by using the theory of large elastic deformations. The orthotropicity of wall tissues and the effect of the surrounding tissues have been incorporated in the analysis which is based on the use of the strain energy function suggested by Vaishnavet al. Numerical values of the wave velocities of the canine middle descending thoracic aorta are computed by using the derived analytical expressions.
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    Bulletin of mathematical biology 46 (1984), S. 41-80 
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    Notes: Abstract The theory of a symmetrical 3-barrier, 4-site, single-filing ionic channel is developed. The model goes beyond earlier models by including additional sites, as well as barriers which need not be symmetrical in the applied field, and contains the earlier models as special cases. It is itself a special case of the most general 4-site model, which has 5 barriers. By considering the barriers at the mouth and middle of the channel to be sufficiently larger than the barriers separating the sites in each channel half, these barriers can be neglected; thus this case reduces to a 3-barrier model where the sites in each channel half can then be assumed to be in equilibrium with each other. The alternative 3-barrier, 4-site case, where the barrier between the sites is considered to be larger than that at the mouth of the channel, is considered elsewhere. Pure cation permeation is considered and only single-salt properties of the system are analyzed, namely occupancy, conductance, flux ratio exponent and current-voltage relation. The concentration dependences of these properties are computed and interrelated and, where possible, also given in analytical form. The mathematical relations are obtained for a channel which is symmetrical around its middle, which is the appropriate assumption for the gramicidin channel. However, the barriers themselves are allowed to be asymmetric with respect to the potential dependence, which has been found to be essential for gramicidin. Mathematically, a straight-forward matrix formulation is used; but a general theoretical method is presented for reducing a complex model (with more than 2 sites) to a simpler cases when equilibrium exists across one or several barriers, as is often the cases. This method is a prototype which makes analytical solutions of complex barrier models possible in many cases.
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    Bulletin of mathematical biology 46 (1984), S. 219-227 
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    Notes: Abstract A chain-like arrangement of four urns (a catenary system) into which different color balls (white, corresponding to radio atoms, and black, corresponding to stable atoms) are being transferred is used to simulate the transport of atoms down the GI tract of man and animals. Into the first urn (stomach) are placedw o white balls andr black balls while in the 2nd (small intestines) and 3rd (large intestines) urn, onlyr blacks are put in, with no whites. A sample of sizer is transferred from the 1st, 2nd and 3rd urns to the 2nd, 3rd and 4th (infinite universe) urns. From the random variable difference equations the first and second moments for the distribution of the number of radio atoms present in each urn are obtained. The variance of the contents of radioatoms in the excretion urn is
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    Bulletin of mathematical biology 46 (1984), S. 229-234 
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    Notes: Abstract A power series solution is presented which describes the steady-state concentration profiles for substrate and product molecules in immobilized enzyme systems. Diffusional effects and product inhibition are incorporated into this model. The kinetic consequences of diffusion limitation and product inhibition for immobilized enzymes are discussed and are compared to kinetic behavior characteristic of other types of effects, such as substrate inhibition and substrate activation.
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    Bulletin of mathematical biology 46 (1984), S. 205-217 
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    Notes: Abstract The use of spheroids as a tumor model has become commonplace since it was discovered that many cell lines can form spheroids when grown on a surface to which the cells cannot attach. This culture system complicates experiments which depend on oxygen supply because the oxygen concentration in the vicinity of a stationary spheroid has not been well defined. We present in this paper solutions to the oxygen diffusion equation for simple geometries: a spheroid in an infinite stationary medium and in a finite spherical stationary medium. Comparison of these solutions provides an estimate of the oxygen supply to a spheroid in a Petri dish. We show that typical spheroids can be expected to cause a substantial depletion of the oxygen in the nearby medium. Any disturbance of the medium or the spheroids will temporarily increase the oxygen supply. We provide a method for estimating the rate of return to equilibrium in the finite cases. These results indicate that the oxygen supply to stationary spheroids can be altered temporarily by small movements or changes in temperature which cause convection currents, or permanently by changes in the depth of the medium.
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    Bulletin of mathematical biology 46 (1984), S. 235-246 
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    Notes: Abstract Alternative sufficient conditions are derived that guarantee the stability of spatially heterogenous steady-state distributions of motile aerobic bacterial populations attracted chemotactically by oxygen, motile anaerobic populations repelled by oxygen, and the oxygen concentration itself through a stationary aqueous medium. In particular, it follows from the latter criteria that the heterogeneous steady-state distributions for cylindrical regions with arbitrary cross-sections, uniform depth and mixed Dirichlet-Neumann boundary conditions on the oxygen concentration (appropriate to certain still-water bodies in nature) are stable with respect to arbitrary perturbations in the bacteria cell and the oxygen distributions.
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    Bulletin of mathematical biology 46 (1984), S. 339-355 
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    Notes: Abstract Closed positive feedback loops of catalytic reactions between macromolecules, or hypercycles, provide a kinetic mechanism whereby each Species serves to catalyze selfreproduction of its successor in the loop. Hypercycles of five members or more evolve into limit cycles characteristic of a biochemical clock. Computer study of the coupled non-linear differential equations which describe these systems shows that the periodT n of then-species limit cycle is given byT n=nτn, where τn is an elemental repeat period reflecting translational time invariance. Analytic solutions of the equations are developed so that the time evolution of elementaryn-hypercycles can be traced in dynamical detail. It is shown that the magnitude of τn is, to good approximation, a linear function ofn. For a givenn, τn is a very sensitive function of the relative concentration a given member of the loop has at the time its predecessor dominates the state of the hypercycle. These concentrations decrease with increasingn. Aroundn=15 they become so small that elementary hypercycles become unstable against disruptive concentration fluctuations. Species concentrations for more realistic hypercycles tend not to be as small, so that the present estimate of a maximum number of components is a lower bound.
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    Bulletin of mathematical biology 46 (1984), S. 399-406 
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    Notes: Abstract The technique of the probability generating function is used to derive the stochastic differential equations for a nonlinear model based on Eigen and Schuster's theory of biomolecular selection and evolution. The stabilities of various steady states are analyzed by using the linear stability approximation. The instability of a small starting population is investigated numerically. The minimum starting populations required for steady-state survival are then estimated for a wide range of parameters.
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    Bulletin of mathematical biology 46 (1984), S. 389-398 
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    Notes: Abstract Some morphological features of the human bronchial tree were simulated by computergenerated trees. The trees were ordered by the methods of Horsfield and Strahler. Delta, the difference between the Horsfield orders of the two branches at a bifurcation, was determined by pseudorandom numbers generated according to a distribution of probabilities defined on input. By trial and error a distribution was found which resulted in trees being generated with average Strahler order branching ratios of 2.82, similar to a real bronchial tree. Branching angles and length ratio could also be defined on input. By varying these input parameters it was found that the form of the tree was quite sensitive to them, and that by a suitable choice the intrasegmental part of the bronchial tree could be simulated. It is concluded that branching ratio, length ratio, mean branching angles and distribution of delta are controlled within tight limits in the bronchial tree, and this may support the concept of optimal design.
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    Bulletin of mathematical biology 46 (1984), S. 407-422 
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    Notes: Abstract In this paper perturbation methods are used for the mathematical analysis of coupled relaxation oscillators. This study covers entrainment by an external periodic stimulus as well as mutual entrainment of coupled oscillators with different limit cycles. The oscillators are of a type one meets in the modeling of biological oscillators by chemical reactions and electronic circuits. Special attention is given to entrainment different from 1∶1. The results relate to phenomena occurring in physiological experiments, such as the periodic stimulation of neural and cardiac cells, and in the non-regular functioning of organs and organisms, such as the AV-block in the heart.
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    Bulletin of mathematical biology 46 (1984), S. 423-446 
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    Notes: Abstract A new, more realistic model of the action of ionizing radiation on mammalian cells growingin vitro is presented. Although this model requires a large number of parameters, these are linked to biologically observable quantities rather than being abstract sensitivities, as had previously been the case. Three different stochastic processes are required: {X(t);t ∈ [0, τ]}, representing damage alterations during irradiation; {(X(t), S(t));t ∈ [τ, τ+T D]}, representing changes in both damageX(t) and cell cycle positionS(t) during the post-irradiation cell cycle; and {N x(t);t ∈ [0,T G]}, representing the subsequent colony growth process conditioned on the value ofX(τ+T D). The assumptions used to define these processes extend a previous model of short term DNA damage formation and repair (Nelson S. J. 1982,Radiat. Res. 92, 120–145) to include the influence of cell cycle progression on damage in the irradiated cell and the effect of permanent inherited damage on the daughter cells' colony growth pattern. Expressions corresponding to commonly measured radiation effects are derived from the model and compared with predictions from previous models. It is found that these previous models oversimplified the mechanism of radiation action because they did not adequately represent repair during irradiation, the influence of radiation-induced cycle delays and damage inheritance by any daughter cells. Suggestions are then made for ways in which the new model can be used to test the importance of these effects.
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    Bulletin of mathematical biology 46 (1984), S. 461-465 
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    Bulletin of mathematical biology 46 (1984), S. 467-472 
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    Bulletin of mathematical biology 46 (1984), S. 447-460 
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    Notes: Abstract A stochastic approach is utilized to develop a model equation capable of describing the time course of germination in a sample of bacterial spores. The time required by a spore to complete the change characteristic of germination consists of an initial interval of no change followed immediately by the duration of the change itself. The experimental basis of the proposed model is the observation that each of these time intervals is distributed over a range of values in a spore sample. Mixed continuous and discrete probabilities are employed in arriving at an average single-spore germination curve which, to a different scale, describes the sample in time.
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    Bulletin of mathematical biology 46 (1984), S. 473-500 
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    Notes: Abstract Mathematical methods for comparison of nucleic acid sequences are reviewed. There are two major methods of sequence comparison: dynamic programming and a method referred to here as the regions method. The problem types discussed are comparison of two sequences, location of long matching segments, efficient database searches and comparison of several sequences.
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    Bulletin of mathematical biology 46 (1984), S. 579-590 
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    Notes: Abstract An algorithm for nucleic acid and protein sequence alignment is presented. It is a non-metric local similarity minimal-difference algorithm and in the current implementation, assembles the matching regions found into a pseudo-global format. Its strengths are its speed of execution and the especially convenient presentation of its output. The algorithm is intended for use in sequence melding and local (small-region) similarity searching. It is not designed to replace a metric Needleman-Wunsch-Sellers-type similarity algorithm. The program is written in FORTRAN and is designed to be easily transportable to a variety of computer systems.
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    Bulletin of mathematical biology 46 (1984), S. 591-621 
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    Notes: Abstract This is a review of past and present attempts to predict the secondary structure of ribonucleic acids (RNAs) through mathematical and computer methods. Related areas covering classification, enumeration and graphical representations of structures are also covered. Various general prediction techniques are discussed, especially the use of thermodynamic criteria to construct an optimal structure. The emphasis in this approach is on the use of dynamic programming algorithms to minimize free energy. One such algorithm is introduced which comprises existing ones as special cases.
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    Bulletin of mathematical biology 46 (1984), S. 641-659 
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    Notes: Abstract It is shown that the concepts of grammar complexity and syntactic structure provide a useful mathematical framework for the investigation of some current problems in protein structure. Grammar complexity gives a measure of the degree of aperiodicity of a sequence and also an optimization criterion for evaluating amino acid categorizations. Three systems of amino acid categorization are compared in relation to their value for describing molecular architecture.
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    Bulletin of mathematical biology 46 (1984), S. 623-639 
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    Notes: Abstract A scheme for representing amino acids as vectors in the plane is presented and justified. The two dimensions of the plane are size and hydrophobicity. The vector representation is then applied to generate a consensus sequence for some sets of homologous proteins. A figure of merit for the degree of homology of a set of sequences results from the analysis. Some other applications of the scheme are considered also. This work grew from ideaseeds planted by Margaret Dayhoff's work in theAtlas of Protein Structure and Sequence. It is with gratitude that I dedicate this paper to her memory.
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    Bulletin of mathematical biology 46 (1984), S. I 
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    Bulletin of mathematical biology 46 (1984), S. 699-744 
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    Notes: Abstract An annotated bibliography of mathematical and computer analyses of protein and nucleic acid sequences is presented. The major subject areas represented are the determination of sequences, restriction mapping, similarity searching, sequence alignment, codon utilization, statistical analysis, information theoretic analysis, the construction of secondary and tertiary structure and DNA topology.
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    Notes: Abstract DISGEO is a new implementation of a distance geometry algorithm which has been specialized for the calculation of macromolecular conformation from distance measurements obtained by two-dimensional nuclear Overhauser enhancement spectroscopy. The improvements include (1) a decomposition of the complete embedding process into two successive, more tractable calculations by the use of “substructures”, (2) a compact data structure for storing incomplete distance information on a structure, (3) a more efficient shortest-path algorithm for computing the triangle inequality limits on all distances from this information, (4) a new algorithm for selecting random metric spaces from within these limits, (5) the use of chirality constraints to obtain good covalent geometry without the use ofad hoc weights or excessive optimization. The utility of the resultant program with nuclear magnetic resonance data is demonstrated by embedding complete spatial structures for the protein basic pancreatic trypsin inhibitor vs all 508 intramolecular, interresidue proton-proton contacts shorter than 4.0 Å that were present in its crystal structure. The crystal structure could be reproduced from this data set to within 1.3 Å minimum root mean square coordinate difference between the backbone atoms. We conclude that the information potentially available from nuclear magnetic resonance experiments in solution is sufficient to define the spatial structure of small proteins.
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    Bulletin of mathematical biology 46 (1984), S. 765-783 
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    Notes: Abstract Recent evidence suggests that the cyclic nucleotides play a central role in the intracellular processing of neural signals. The dynamics of this system may be seen as a realization of the enzymatic neuron model. Enzymatic neurons are formal neurons which map binary afferent signals into patterns of excitation across an abstract membrane. The distribution of enzyme-like elements called excitases enables a set of local threshold functions to determine the firing activity of the neuron. This paper analyzes the basic properties of enzymatic neurons in a simple continuous-time framework, and shows how they may be presented as reaction-diffusion networks which model the cyclic nucleotide system. We present the results of computer simulations of this neuron and discuss its implications for selectional learning and its relation to conventional two-factor systems. One fundamental property of the reaction-diffusion neuron is its so-called “double-dynamics” property; examination of this property and its contribution to the computing power of the neuron provides some insight into the obscure relation between microscopic and macroscopic models of computation.
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