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PubMed2002

Modeling enzyme reactivity in organic solvents and water through computer simulations.

In this article, we review how molecular modeling techniques can be used to shed light on how water and organic solvents influence the reactivity of enzymes. The application of thermodynamics-based models allowed the first qualitative predictions on the selectivity of many reaction types. However, it was with the application of quantum mechanical/molecular mechanical (QM/MM) methods that quantitative models of actual reactivity patterns could be realistically formulated.

Computer Simulation↗

PubMed1993

A survey on quantitative microdialysis: theoretical models and practical implications.

The existing methods of quantitative microdialysis are reviewed. The methods are divided into 8 groups, depending on the mathematical models and theoretical principles used to describe convective diffusion in the extracellular space of the brain. Special emphasis is made to describe each method from a historical perspective, showing its main contribution to recent knowledge, as well as its limitations and drawbacks. It is concluded that those methods based on explicitly derived equations for in vivo recovery are still too approximative and not suitable for routine application. Therefore, empirical models based on varying perfusion flow rates or concentrations of substances in the perfusion solution, found several practical implications. Methods using a reference substance as a marker of in vivo recovery are also discussed. The paper stresses the increasing importance of methods allowing the quantitative evaluation of microdialysis data whenever measuring neurotransmitter release, drug concentrations or pharmacokinetic variables.

Animals↗

PubMed2007

Both ligand- and cell-specific parameters control ligand agonism in a kinetic model of g protein-coupled receptor signaling.

G protein-coupled receptors (GPCRs) exist in multiple dynamic states (e.g., ligand-bound, inactive, G protein-coupled) that influence G protein activation and ultimately response generation. In quantitative models of GPCR signaling that incorporate these varied states, parameter values are often uncharacterized or varied over large ranges, making identification of important parameters and signaling outcomes difficult to intuit. Here we identify the ligand- and cell-specific parameters that are important determinants of cell-response behavior in a dynamic model of GPCR signaling using parameter variation and sensitivity analysis. The character of response (i.e., positive/neutral/inverse agonism) is, not surprisingly, significantly influenced by a ligand's ability to bias the receptor into an active conformation. We also find that several cell-specific parameters, including the ratio of active to inactive receptor species, the rate constant for G protein activation, and expression levels of receptors and G proteins also dramatically influence agonism. Expressing either receptor or G protein in numbers several fold above or below endogenous levels may result in system behavior inconsistent with that measured in endogenous systems. Finally, small variations in cell-specific parameters identified by sensitivity analysis as significant determinants of response behavior are found to change ligand-induced responses from positive to negative, a phenomenon termed protean agonism. Our findings offer an explanation for protean agonism reported in beta2--adrenergic and alpha2A-adrenergic receptor systems.

Algorithms↗

PubMed2005

Mechanism of transcriptional silencing in yeast.

Transcriptional silencing is a phenomenon in which the transcription of a gene by RNA polymerase II or III is repressed or not, dependent only on the gene's chromosomal location. Two prevailing models exist for silencing: (1) steric hindrance in silenced chromatin inhibits the binding of upstream activator proteins or polymerase or (2) silencing primarily blocks steps downstream of transcription preinitiation complex formation. Here, we test these models quantitatively for the case of SIR2-dependent silencing in budding yeast, using foreign and endogenous reporter proteins, at transgenic and endogenous loci. Our results contradict both models and show instead that transcriptional silencing at several URA3 transgenes, and at the naturally silenced endogenous HMRa and HMLalpha mating type genes, acts downstream of gene activator protein binding to strongly reduce the occupancy of TFIIB, RNA polymerase II, and TFIIE at the silenced promoters.

Bacterial Proteins↗

PubMed2004

Oscillatory wetting instability induced by liquid-liquid decomposition in a Ga--Pb alloy.

We present the first experimental investigation and pertinent theoretical modeling of an interfacial oscillatory instability in a binary fluid alloy, the Ga-Pb system. It is characterized by spinodal decomposition at elevated temperatures and by a complete wetting transition at liquid-liquid coexistence. For the alloy Ga(0.95)Pb(0.05) the fluid interface has been probed by second harmonic generation (SHG) under UHV conditions at temperatures between 740 and 550 K. At conditions inside the miscibility gap clear oscillations of the SHG-intensity with a period of approximately 30 min are found for different cooling cycles and also at constant temperatures. These interfacial oscillatory instabilities simultaneously induce temperature oscillations in the bulk fluid with the same period. This phenomenon can be explained by a periodic variation of the fluid interfacial emissivity. A model has been developed which describes the wetting-dewetting dynamics by hydrodynamic equations within the Reynolds approximation. It is found that the interfacial oscillatory instability is determined by capillary-gravitation instability. The model quantitatively describes the time evolution of the interfacial and temperature oscillations and gives the correct value of the oscillation period. A detailed comparison of the experimental and model results is given.

Journal Article↗

PubMed2000

[Column efficiency prediction of two dimensional chromatography by artificial neural network].

This paper used artificial neural network (ANN) modeling method to study the relationship between the column efficiency and the operating conditions. This method solved the problem that it is not easy to establish a quantitative model between the column efficiency and its main effecting factors using those traditional modeling methods, as the relationship is usually quite complex and non-linear in fact. The varied-pace BP (back-propagation) learning algorithm was adopted, and a three-layer weight-connected ANN model for a typical dual column system was established. The effective plate number representing the column efficiency acted as the output vectors, while the temperature of the pre-column, the temperature of the main column, the pressure difference between the columns and the vent rate acted as the input vectors. Then the model acquired was used to predict column efficiency (characterized by "effective plate number") under different operating conditions. The results showed that the model predicting value was in consistent with the value found. This work proved that ANN modeling method was suitable for the study on the relationship between the column efficiency of two-dimensional column chromatography system and the operating conditions.

Algorithms↗

PubMed1991

Differences in response in vivo to amphotericin B among Candida albicans strains.

A group of ten Candida albicans strains previously determined to be resistant or susceptible to topical amphotericin B in vivo and in vitro were exposed to treatment with different concentrations of the drug in a quantitative model of candidal keratitis in Dutch-belted rabbits. After 5 days of topical treatment with amphotericin B eye drops in concentrations of 0.3%, 0.03%, or 0.003%, quantitative isolate recovery in treated animals was compared with that of untreated controls. A dose response was observed for all five susceptible strains. The two strains that were most sensitive to amphotericin B in vitro also were the most susceptible in vivo. At each dose level there was a two- to eightfold reduction in isolate recovery among highly susceptible strains compared with less susceptible strains (P less than 0.05). The five resistant strains remained so even when the 0.3% concentration was used. Among strains of C. albicans susceptible to amphotericin B, there appeared to be a variation in degree of susceptibility in vivo that correlated with the minimum inhibitory concentration.

Administration, Topical↗

PubMed2004

Resolving within- and between-population variation in feeding ecology with a biomechanical model.

Studies of phenotypic plasticity have emphasized the effect of the environment on the phenotype, but plasticity can also be used as a tool to study the functional significance of key traits. By inducing variation in phenotypes and testing quantitative models that predict performance based on biological mechanisms, we can develop functionally general models of performance. Pumpkinseed sunfish from lakes with high snail availability have large levator posterior muscles (which are used to crush snail shells), whereas fish from lakes with few snails have relatively small muscles. Here we: (1) quantify differences in the feeding ability of an ontogenetic series of pumpkinseed from two populations; and (2) evaluate whether a biomechanical model can resolve the observed ontogenetic and between-population variation in feeding ecology. Mass, but not length, of the levator posterior muscle in fish from Three Lakes (a lake rich in snails) was greater than for comparably sized fish from Wintergreen Lake (a lake with few snails). Handling times were shorter, crushing strengths were 71% greater, and foraging rate (snail tissue mass consumed per time) and the fraction of thick-shelled snails in the diet were approximately 100% greater for fish from Three Lakes compared to comparably sized fish from Wintergreen. These between-lake differences were not significant after adjusting for variation in pharyngeal morphology, suggesting that the biomechanical model of snail crushing resolved observed ontogenetic and population-level variation in the feeding ecology of pumpkinseed.

Analysis of Variance↗

PubMed2004

Quantification of glycine crystallinity by near-infrared (NIR) spectroscopy.

The object of this investigation was to use near-infrared (NIR) spectroscopy for quantification of glycine crystallinity. Glycine samples, with different degrees of crystallinity, were obtained by physically mixing different proportions of crystalline beta-glycine with amorphous glycine. NIR spectra were obtained, directly from samples in glass vials, over the wavelength range of 1100-2500 nm. A partial least squares (PLS) model was developed to correlate the NIR spectral changes with the degree of crystallinity. Using this model, a standard error of calibration (SEC) of 2.1% was obtained with an r(2) value of 0.996. Cross validation was used to test the precision of the quantitative model, resulting in a standard error of prediction (SEP) of 3.2%. These results indicate that NIR spectroscopy is well suited to the measurement of glycine crystallinity in lyophilized products. Employing the PLS model, the crystallinity of glycine in freeze-dried sucrose-glycine mixtures was evaluated. At a sucrose to glycine ratio >4, glycine crystallization during lyophilization was inhibited. Conversely, at ratios < or =0.67, glycine remained substantially crystalline. At intermediate compositions, the glycine was partially crystalline.

Crystallization↗

PubMed2006

A novel quantitative cross-validation of different cortical surface reconstruction algorithms using MRI phantom.

Cortical surface reconstruction is important for functional brain mapping and morphometric analysis of the brain cortex. Several methods have been developed for the faithful reconstruction of surface models which represent the true cortical surface in both geometry and topology. However, there has been no explicit comparison study among those methods because each method has its own procedures, file formats, coordinate systems, and use of the reconstructed surface. There has also been no explicit evaluation method except visual inspection to validate the whole-cortical surface models quantitatively. In this study, we presented a novel phantom-based validation method of the cortical surface reconstruction algorithm and quantitatively cross-validated the three most prominent cortical surface reconstruction algorithms which are used in Freesurfer, BrainVISA, and CLASP, respectively. The validation included geometrical accuracy and mesh characteristics such as Euler number, fractal dimension (FD), total surface area, and local density of points. CLASP showed the best geometric/topologic accuracy and mesh characteristics such as FD and total surface area compared to Freesurfer and BrainVISA. In the validation of local density of points, Freesurfer and BrainVISA showed more even distribution of points on the cortical surface compared to CLASP.

Algorithms↗

PubMed2002

Toward a pharmacophore for drugs inducing the long QT syndrome: insights from a CoMFA study of HERG K(+) channel blockers.

In this paper, we present a pharmacophore for QT-prolonging drugs, along with a 3D QSAR (CoMFA) study for a series of very structurally variegate HERG K(+) channel blockers. The blockade of HERG K(+) channels is one of the most important molecular mechanisms through which QT-prolonging drugs increase cardiac action potential duration. Since QT prolongation is one of the most undesirable side effects of drugs, we first tried to identify the minimum set of molecular features responsible for this action and then we attempted to develop a quantitative model correlating the 3D stereoelectronic characteristics of the molecules with their HERG blocking potency. Having considered an initial set of 31 QT-prolonging drugs for which the HERG K(+) channel blocking activity was measured on mammalian transfected cells, we started the construction of a theoretical screening tool able to predict whether a new molecule can interact with the HERG channel and eventually induce the long QT syndrome. This in silico tool might be useful in the design of new drug candidates devoid of the physicochemical features likely to cause the above-mentioned side effect.

Anti-Arrhythmia Agents↗

PubMed2005

Transient and steady state CO oxidation kinetics on nanolithographically prepared supported Pd model catalysts: experiments and simulations.

Applying molecular-beam methods to a nanolithographically prepared planar PdSiO2 model catalyst, we have performed a detailed study of the kinetics of CO oxidation. The model catalyst was prepared by electron-beam lithography, allowing individual control of particle size and position. The sample was structurally characterized by atomic force microscopy and scanning electron microscopy before and after reaction. In the kinetic experiments, the O-rich and CO-rich regimes were investigated systematically with respect to their transient and steady-state behaviors, both under bistable and monostable reaction conditions. Separate molecular beams were used in order to supply the reactants, allowing individual control over the reactant fluxes. The desorbing CO2 was detected by both angle-resolved and angle-integrated mass spectrometries. The experimental results were analyzed using different types of microkinetic models, including a detailed reaction-diffusion model, which takes into account the structural parameters of the catalyst as well as scattering of the reactants from the support. The model quantitatively reproduces the results as a function of the reactant fluxes and the surface temperature. Various kinetic effects observed are discussed in detail on the basis of the model. Specifically, it is shown that under conditions of limited oxygen mobility, the switching behavior between the kinetic regimes is largely driven by the surface mobility of CO.

Journal Article↗

PubMed2002

Conformational change of the actomyosin complex drives the multiple stepping movement.

Actin-myosin (actomyosin) generates mechanical force by consuming ATP molecules. We apply the energy landscape perspective to address a controversial issue as to whether the myosin head moves with multiple steps after a single ATP hydrolysis or only a single mechanical event of the lever-arm swinging follows a single ATP hydrolysis. Here we propose a theoretical model in which the refolding of the partially unfolded actomyosin complex and the movement of the myosin head along the actin filament are coupled. A single ATP hydrolysis is followed by the formation of a high free-energy partially unfolded actomyosin complex, which then gradually refolds with a concomitant multiple stepping movement on the way to the lowest free-energy rigor state. The model quantitatively explains the single-molecular observation of the multiple stepping movement and is consistent with structural observations of the disorder in the actomyosin-binding process. The model also explains the observed variety in dwell time before each step, which is not accounted for by previous models, such as the lever-arm or ratchet models.

Actins↗

PubMed2002

hairy: A quantitative trait locus for drosophila sensory bristle number.

Advances in medicine, agriculture, and an understanding of evolution depend on resolving the genetic architecture of quantitative traits, which is challenging since variation for complex traits is caused by multiple interacting quantitative trait loci (QTL) with small and conditional effects. Here, we show that the key developmental gene, hairy (h), is a QTL for Drosophila sternopleural bristle number, a model quantitative trait. Near-isoallelic lines (NIL) for the h gene region exhibited significant variation in bristle number and failed to complement a hairy mutation. Sequencing 10 h alleles from a single population revealed 330 polymorphic sites in approximately 10 kb. Genotypes for 25 of these and 14 additional sites in the flanking regions were determined for the 57 NIL and associated with variation in bristle number in four genetic backgrounds. A highly significant association was found for a complicated insertion/deletion polymorphism upstream of the transcription start site. This polymorphism, present in 17.5% of the h alleles, was associated with an increase of 0.5 bristle and accounted for 31% of the genetic variance in bristle number in the NIL.

Animals↗

PubMed2006

Teaching from classic papers: Hill's model of muscle contraction.

A. V. Hill's 1938 paper "The heat of shortening and the dynamic constants of muscle" is an enduring classic, presenting detailed methods, meticulous experiments, and the model of muscle contraction that now bears Hill's name. Pairing a simulation based on Hill's model with a reading of his paper allows students to follow his thought process to discover key principles of muscle physiology and gain insight into how to develop quantitative models of physiological processes. In this article, the experience of the author using this approach in a graduate biomedical engineering course is outlined, along with suggestions for adapting this approach to other audiences.

History, 20th Century↗

PubMed1989

A quantitative analysis of chain-schedule performance.

Six pigeons were trained with a chain variable-interval variable-interval schedule on the left key and with reinforcers available on the right key on a single variable-interval schedule arranged concurrently with both links of the chain. All three schedules were separately and systematically varied over a wide range of mean intervals. During these manipulations, the obtained reinforcer rates on constant arranged schedules also frequently changed systematically. Increasing reinforcer rates in Link 2 of the chain increased response rates in both links and decreased response rates in the variable-interval schedule concurrently available with Link 2. Increasing Link-1 reinforcer rates increased Link-1 response rates and decreased Link-2 response rates. Increasing reinforcer rates on the right-key schedule decreased response rates in Link 1 of the chain but did not affect the rate in Link 2. The results extend and amplify previous analyses of chain-schedule performance and help define the effects that a quantitative model must describe. However, the complexity of the results, and the fact that constant arranged reinforcer schedules did not necessarily lead to constant obtained reinforcer rates, precluded a quantitative analysis.

Journal Article↗

PubMed2004

Forces during bacteriophage DNA packaging and ejection.

The conjunction of insights from structural biology, solution biochemistry, genetics, and single-molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this article we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure.

Bacteriophages↗

PubMed2002

Kinetic modeling in positron emission tomography.

Most PET kinetic modeling approaches have at their basis a compartmental model that has first-order, constant coefficients. The present article outlines the one-, two-, and three-compartment models used to measure cerebral blood flow, cerebral glucose metabolism, and receptor binding, respectively. The number of compartments of each model is based on specific knowledge of the physiological and/or biochemical compartments into which the tracer distributes. Additional physical and biochemical properties of the tracer distribution are considered in specifying the use of first-order rate constants. For example, in cerebral blood flow and receptor binding studies transport across the blood-brain barrier by diffusion can be modeled as a first-order process. A saturable carrier-mediated process or saturable enzyme catalyzed reaction, when tracer doses of the labeled substrate are used and the natural substrate is in steady-state, also results in first-order rate constants, as in glucose metabolism studies. The rate of ligand binding, on the other hand, depends on the concentrations of both substrate and available receptors. In order to appropriately model the reaction as pseudo first-order during a specified experimental interval, protocols are carefully designed to assure that the number of available binding sites remains approximately constant throughout the given interval. A broad array of scanning protocols is employed for kinetic analyses. These include single-scan approaches, which function like their autoradiographic counterparts in animal studies and are often called "autoradiographic" methods, which allow estimation of a single parameter. Dynamic scanning to obtain the time course of tissue activity allows simultaneous estimation of multiple parameters. Scanning may be conducted during a period of tracer uptake or after attainment of steady-state conditions. All quantitative modeling approaches share the common requirement that an arterial input function be measured or an appropriate surrogate be found. A vast array of methods is available for estimation of model parameters, both micro and macro. In the final analysis, it is the interaction among all elements of the PET study, including careful tracer selection, model specification, experimental protocol design, and sound parameter estimation methods, that determines the quantitative accuracy of the estimates of the physiological or biochemical process under study.

Animals↗