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PubMedDate not supplied

Cephalo-adrenal interactions in the broader context of pragmatic and theoretical rhythm models.

Some of the literature on modeling of biological rhythms with mathematical, physical, chemical, biochemical, in vivo and in vitro oscillations is succintly annotated. The need for biologic models that account for the interaction of 3 or more periodic entities is indicated, documented and illustrated, with emphasis on the cephalo-adrenal network of rodents. Patterns of interaction, in this context, involve attenuation, no-effect and/or amplification by a third entity, the modulator, of the effect of an actor upon the reactor. Such feedsidewards lead to chronomodulation, a phenomenon accounting for qualitatively as well as quantitatively different modulatory effects of the same drug or other stimulus. Controversies of long standing can thus be resolved and novel effects uncovered.

Adrenal Glands↗
PubMedDate not supplied

Relevance of microenvironmental pH for self-organized tumor growth and invasion.

The process of tumor cell growth, invasion and metastasis involves a self-organized cascade of multiple tumor-host and tumor-immune interactions. The prediction of cancer development based exclusively on molecular evidence is still impossible because of the complex and heterogeneous control mechanisms actually acting in cellular systems. In contrast, most tumor cell systems display a limited spectrum of macroscopically observable modes of action which emerge as a result of cellular self-organization. The stability of the dynamic modes is controlled by relatively few order parameters. Their number and characteristics are different in normal and neoplastic growth. A systems-oriented analysis utilizing our method of Structured Biological Modelling (SBM) suggests that microenvironmental pH (pHme) can function as an important order parameter for self-organized cancer development. In the scope of an integrated minimal model for the multistep development of invasive tumor growth, this finding will be discussed with respect to its evolution, diagnostic relevance and possible therapeutical implications. The study underlines the necessity of minimal invasive methods for the on-line in vitro and in vivo monitoring of pH, oxygen, signal transducing molecules and essential nutrients in the microenvironment of tumor cells.

Cell Division↗
PubMed1990

Bladder cancer screening: lessons from a biologically based model of bladder cancer progression and therapeutic intervention.

The screening of asymptomatic high-risk populations has been evaluated using a biologically based model of bladder cancer. The model is built upon a mathematical representation of the induction of precursor bladder lesions with possible progression through clinical disease states. Screening strategies are based on regimens that include voided urine cytology. Diagnostic and therapeutic components of the model provide the basis for end results evaluation. Cytology screening is projected to increase average life expectancy by 1 to 3 years among those diagnosed while reducing deaths from bladder cancer by more than 50%. The additional contribution to be realized with a screening test of perfect sensitivity would be primarily in the increased identification of dysplasia and low-grade superficial papillary neoplasms, lesions that are much less life-threatening than the high-grade lesions already detectable by cytology. The theoretical potential of screening is not realizable because of diagnostic inaccuracies and treatment failures.

Adult↗
PubMed2002

Molecular modelling in structural biology.

Molecular modelling is a powerful methodology for analysing the three dimensional structure of biological macromolecules. There are many ways in which molecular modelling methods have been used to address problems in structural biology. It is not widely appreciated that modelling methods are often an integral component of structure determination by NMR spectroscopy and X-ray crystallography. In this review we consider some of the numerous ways in which modelling can be used to interpret and rationalise experimental data and in constructing hypotheses that can be tested by experiment. Genome sequencing projects are producing a vast wealth of data describing the protein coding regions of the genome under study. However, only a minority of the protein sequences thus identified will have a clear sequence homology to a known protein. In such cases valuable three-dimensional models of the protein coding sequence can be constructed by homology modelling methods. Threading methods, which used specialised schemes to relate protein sequences to a library of known structures, have been shown to be able to identify the likely protein fold even in cases where there is no clear sequence homology. The number of protein sequences that cannot be assigned to a structural class by homology or threading methods, simply because they belong to a previously unidentified protein folding class, will decrease in the future as collaborative efforts in systematic structure determination begin to develop. For this reason, modelling methods are likely to become increasingly useful in the near future. The role of the blind prediction contests, such as the Critical Assessment of techniques for protein Structure Prediction (CASP), will be briefly discussed. Methods for modelling protein-ligand and protein-protein complexes are also described and examples of their applications given.

Databases, Protein↗
PubMed2005

Empirical nanotube model for biological applications.

An empirical model is developed to capture the electrostatics of finite-length single-walled armchair carbon nanotubes for biological applications. Atomic partial charges are determined to match the electrostatic potential field computed at the B3LYP/6-31G* level of density functional theory, and a tight-binding Hamiltonian is selected which permits one to reproduce the dielectric properties in good agreement with density functional theory results. The new description is applied to study movement of a water molecule through a finite-length nanotube channel in order to demonstrate the method's feasibility. We find that atomic partial charges on the tube edges dominate the interaction between the nanotube and the entering water molecule, while the polarization of the nanotube lowers the electrostatic energy of the water molecule inside the tube.

Electrons↗
PubMed1988

Period-doubling bifurcations leading to chaos in discrete models of biology.

Elementary methods are used to analyse periodic bifurcations associated with discrete models of the reaction-diffusion type motivated by population genetics. In particular, the existence and stability of temporal bifurcations of periods 1, 2, and 3 are discussed. The study of the route to chaos due to diffusive effects is initiated.

Biometry↗
PubMed2005

Binding affinities for models of biologically available potential Cu(II) ligands relevant to Alzheimer's disease: an ab initio study.

A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.

Alzheimer Disease↗
PubMed2002

Time-dependent extinction rate and species abundance in a tangled-nature model of biological evolution.

We present a model of evolutionary ecology consisting of a web of interacting individuals, a tangle-nature model. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and the macroevolutionary mode of the dynamics are emergent properties. The macrodynamics exhibit intermittent two-mode switching with a gradually decreasing extinction rate. The generated ecologies become gradually better adapted as well as more complex in a collective sense. The form of the species abundance curve compares well with observed functional forms. The model's error threshold can be understood in terms of the characteristics of the two dynamical modes of the system.

Biological Evolution↗
PubMed1981

Approximate solution of a model of biological immune responses incorporating delay.

A model of the humoral immune response, proposed by Dibrov, Livshits and Volkenstein (1977b), in which the antibody production by a constant target cell population depends on the antigenic stimulation at earlier times, is considered from an analytic standpoint. A method of approximation based on a consideration of the asymptotic limit of "large" delay in the antibody response is shown to be applicable, and to give results similar to those obtained numerically by the above authors. The relevance of this type of approximation to other systems exhibiting "outbreak" phenomena is discussed.

Animals↗
PubMedDate not supplied

Children's and adults' models for predicting teleological action: the development of a biology-based model.

Understanding that only living things must act to gain self-beneficial goals is important for developing a theory-like understanding of the living world. This research studied the models that preschoolers, fifth graders, and adults use to guide their predictions of self-beneficial, goal-directed (i.e., teleological) action. Four possible models have been suggested: finalist, complexity based, biology based, and animal based. In Study 1, participants (N = 104) were assigned to one of two conditions that differed in whether a beneficial or neutral object was pictured; they were asked to predict whether animals, plants, machines, and simple artifacts would modify their movement in the direction of that object. Preschoolers' predictions were consistent with an animal-based model, fifth graders' predictions were consistent with biology-based and complexity-based models, and adults' predictions were consistent with a biology-based model. Analysis of both individual response patterns and explanations supported these findings, but also showed that a significant number of preschoolers and fifth graders were finalist, and that very few individual fifth graders followed a complexity-based teleology. In Study 2, participants (N = 84) reported whether the animals, plants, machines, and simple artifacts in Study 1 had psychological capacities. All age groups attributed psychological capacities to animals at levels higher than other domains and at above-chance levels. The evidence from these two studies suggests that preschoolers, unlike fifth graders and adults, predict teleological action for plants and animals on the basis of these entities' inferred psychological capacities.

Adult↗
PubMed2005

Simulations of a mortality plateau in the sexual Penna model for biological aging.

The Penna model is a strategy to simulate the genetic dynamics of age-structured populations, in which the individual genomes are represented by bit strings. It provides a simple metaphor for the evolutionary process in terms of the mutation accumulation theory. In its original version, an individual dies due to inherited diseases when its current number of accumulated mutations, n, reaches a threshold value T. Since the mean number of diseases increases with age, the probability to die is zero for very young ages (n < T) and equals 1 for the old ones (n > or = T). Here, instead of using a step function to determine the genetic death age, we test several other functions that may or may not slightly increase the death probability at young ages (n < T), but that decrease this probability at old ones. Our purpose is to study the oldest old effect, that is, a plateau in the mortality curves at advanced ages. By imposing certain conditions, it has been possible to obtain a clear plateau using the Penna model. However, a more realistic one appears when a modified version, that keeps the population size fixed without fluctuations, is used. We also find a relation between the birth rate, the age structure of the population, and the death probability.

Aging↗
PubMed2006

QxDB: a generic database to support mathematical modelling in biology.

QxDB (quantitative x-modelling database) is a web-based generic database package designed especially to house quantitative and structural information. Its development was motivated by the need for centralized access to such results for development of mathematical models, but its usefulness extends to the general research community of both modellers and experimentalists. Written in PHP (Hyper Preprocessor) and MYSQL, the database is easily adapted to new fields of research and ported to Apache-based web servers. Unlike most existing databases, experimental and observational results curated in QxDB are supplemented by comments from the experts who contribute input to the database, giving their evaluations of experimental techniques, breadth of validity of results, experimental conditions, and the like, thus providing the visitor with a basis for gauging the quality (or appropriateness) of each item for his/her needs. QxDB can be easily customized by adapting the contents of the database table containing the descriptors that characterize each data record according to an informal ontology of the research domain. We will illustrate this adaptability of QxDB by presenting two examples, the first dealing with modelling in oncology and the second with mechanical properties of cells and tissues.

Biology↗
PubMed1989

First and second moments and the mean Hamming distance in a stochastic replication-mutation model for biological macromolecules.

In this work first and second moments for a many species Moran model are calculated. The model describes by means of a time-continuous birth- and death process the evolution of an ensemble of N macromolecules out of n possible species. The molecules may replicate (correct or erroneous, in the latter case producing mutants) and may undergo elimination. Replication and elimination will be coupled in order to keep population size constant. In the case of arbitrary replication rates an expansion of the moments in powers of 1/N is found. For equal replication rates exact calculation of the moments is possible. In the case of a v-cube model (binary macromolecules) the second moments may be used to find a simple expression for the mean Hamming distance in the system. This quantity provides a measure for the localization of the ensemble.

Biopolymers↗
PubMed2003

Toward rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic T-cell maturation.

One of the problems biologists face is a data set too large to comprehend in full. Experimenters generate data at an ever-growing pace, each from their own niche of interest. Current theories are each able, at best, to capture and model only a small part of the data. We aim to develop a general approach to modeling that will help broaden biological understanding. T-cell maturation in the thymus is a telling example of the accumulation of experimental data into a large disconnected data set. The thymus is responsible for the maturation of stem cells into mature T cells, and its complexity divides research into different fields, for example, cell migration, cell differentiation, histology, electron microscopy, biochemistry, molecular biology, and more. Each field forms its own viewpoint and its own set of data. In this study we present the results of a comprehensive integration of large parts of this data set. The integration is performed in a two-tiered visual manner. First, we use the visual language of Statecharts, which makes specification precise, legible, and executable on computers. We then set up a moving graphical interface that dynamically animates the cells, their receptors, the different gradients, and the interactions that constitute thymic maturation. This interface also provides a means for interacting with the simulation.

Cell Communication↗
PubMed1985

The repair-misrepair model in radiobiology: comparison to other models.

Biological phenomena related to the inactivation of eukaryotic cells by noxious agents have been formulated mathematically in the repair-misrepair (RMR) model by separately quantitating the initial submicroscopic production of molecular lesions and the later, macroscopic expression of effects in the course of cell progression and repair. This paper presents some conceptual and quantitative similarities and differences between the RMR and seven other models proposed for cellular radiobiology including: the linear-quadratic, three-lambda, cubic-survival, target theory, hit-size probability, cybernetic, and lethal-potentially lethal models. The comparison of the various approaches has shown that the RMR model can be generalized to show relationships with each.

Animals↗