Chemical-equilibrium model of optimal a-Si:H growth from SiH4.
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Journal Article↗
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Darwinian selection leads to Gaia.
The Gaia hypothesis, in its strongest form, states that the Earth's atmosphere, oceans, and biota form a tightly coupled system that maintains environmental conditions close to optimal for life. According to Gaia theory, optimal conditions are intrinsic, immutable properties of living organisms. It is assumed that the role of Darwinian selection is to favor organisms that act to stabilize environmental conditions at these optimal levels. In this paper, an alternative form of Gaia theory based on more traditional Darwinian principles is proposed. In the new approach, environmental regulation is a consequence of population dynamics, not Darwinian selection. The role of selection is to favor organisms that are best adapted to prevailing environmental conditions. However, the environment is not a static backdrop for evolution, but is heavily influenced by the presence of living organisms. The resulting co-evolving dynamical process eventually leads to the convergence of equilibrium and optimal conditions. A simple Daisyworld model is used to illustrate this convergence phenomenon. Sensitivity analysis of the Daisyworld model suggests that in stable ecosystems, the convergence of equilibrium and optimal conditions is inevitable, provided there are no externally driven shocks to the system. The end result may appear to be the product of a cooperative venture, but is in fact the outcome of Darwinian selection acting upon "selfish" organisms.
Adaptation, Physiological↗
Comparison of pi-Bond Strengths in M-E (M = B, Al, Ga; E = O, N, S) Compounds. Ab Initio Calculation of Rotational Barriers.
Results of ab initio calculations of the electronic structure of compounds of the type R(2)MER'(x) and R(2)MEMR'(2) with R = H, Me, M = Al, Ga, and E = O, N, S are reported at the Hartree-Fock level with split-valence, polarization basis sets for all atoms except hydrogen where a split-valence basis set is used. Full optimizations for the equilibrium geometry and partial optimization at constrained rotational transition states have been performed to evaluate the barriers to rotation as a measure of the pi interactions in these compounds. We conclude that, although important for determining the final conformational equilibrium geometries, pi interactions are weak in these compounds as the rotational barriers are smaller than that for ethylene by 1 or 2 orders of magnitude.
Journal Article↗
A parameterized overspeeding method for the rapid attainment of low-speed sedimentation equilibrium.
The approach of a solution of dilute, monodisperse, globular macromolecules to low-speed sedimentation equilibrium in an ultracentrifuge is simulated by numerical integration of the Lamm equation. Various combinations of overspeed time and angular velocity are used to assess the conditions needed to minimize the time it takes the solution to attain sedimentation equilibrium. The optimal overspeeding time and angular velocity are determined over a wide range of values of the molecular weight (relative molar mass) of the solute and the radial distance between the meniscus and base of the solution. The results may be expressed as simple functions which allow facile calculation of (a) the optimal overspeeding time and velocity, and (b) the time required to reach sedimentation equilibrium. The results are in reasonable agreement with previous analytical solutions which were based on several simplifying assumptions. The parameterized overspeeding procedure is shown to be robust over a wide range of conditions, and typically leads to a greater than 5-fold reduction in centrifugation time.
Statistics as Topic↗
Exploring potential energy surfaces for chemical reactions: an overview of some practical methods.
Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.
Mathematical Computing↗
A neural network methodology of quadratic optimization.
According to the basic optimization principle of artificial neural networks, a novel kind of neural network model for solving the quadratic programming problem is presented. The methodology is based on the Lagrange multiplier theory in optimization and seeks to provide solutions satisfying the necessary conditions of optimality. The equilibrium point of the network satisfies the Kuhn-Tucker condition for the problem. The stability and convergency of the neural network is investigated and the strategy of the neural optimization is discussed. The feasibility of the neural network method is verified with the computation examples. Results of the simulation of the neural network to solve optimum problems are presented to illustrate the computational power of the neural network method.
Computer Simulation↗
Optimization of dose distribution for HDR brachytherapy of the prostate using Attraction-Repulsion Model.
PURPOSE: To optimize dose distribution for high-dose-rate brachytherapy for prostate cancer, we have developed a new algorithm named Attraction-Repulsion Model (ARM). In this study, we compared the ARM with geometric optimization (GO). METHODS AND MATERIALS: The ARM was used to optimize the dose distribution by finding the best dwell time combination. ARM requires grids inside the clinical target volume (CTV) and critical organs. These grids generate attraction or repulsion based on specific dose constraints. After calculations were performed repeatedly until the attraction and repulsion forces reached equilibrium, the optimal dwell time distribution was established. We compared the ARM with GO for 10 patients using dose-volume histograms. RESULTS: The CTV ranged from 23 to 48 cc, and the CTV V150 ranged from 52% to 79%, and 23% to 44% for GO and ARM, respectively. This indicates that the dose homogeneity indices, as well as the conformal indices, were higher for ARM than for GO. The urethra V150 was 0-99% and 0-1% for GO and ARM, respectively. CONCLUSION: The ARM proved to be superior to GO in minimizing the dose to normal structures and in improving dose homogeneity for the target while reducing the dose to normal tissues.
Algorithms↗
A novel neural network for variational inequalities with linear and nonlinear constraints.
Variational inequality is a uniform approach for many important optimization and equilibrium problems. Based on the sufficient and necessary conditions of the solution, this paper presents a novel neural network model for solving variational inequalities with linear and nonlinear constraints. Three sufficient conditions are provided to ensure that the proposed network with an asymmetric mapping is stable in the sense of Lyapunov and converges to an exact solution of the original problem. Meanwhile, the proposed network with a gradient mapping is also proved to be stable in the sense of Lyapunov and to have a finite-time convergence under some mild condition by using a new energy function. Compared with the existing neural networks, the new model can be applied to solve some nonmonotone problems, has no adjustable parameter, and has lower complexity. Thus, the structure of the proposed network is very simple. Since the proposed network can be used to solve a broad class of optimization problems, it has great application potential. The validity and transient behavior of the proposed neural network are demonstrated by several numerical examples.
Algorithms↗
Nickel speciation and complexation kinetics in freshwater by ligand exchange and DPCSV.
A technique of ligand exchange with DMG (dimethylglyoxime) and DPCSV was applied to determine Ni speciation in lake, river, and groundwater samples. The working conditions related to ligand-exchange equilibrium were optimized, and the ligand-exchange kinetics were examined. The observed pseudo-first-order rate, kobsd, was about 3 x 10(-5) (s-1) for Ni(DMG)2 complex formation with an excess of DMG (microM) over Ni (nM) at pH 7.1-7.7. The second-order exchange kinetic constants, kexch, were between 1.2 x 10(2) and 5.7 x 10(3) s-1 M-1 for ligand exchange of NiEDTA with DMG and between 5 x 10(2) and 7 x 10(3) s-1 M-1 for exchange of natural ligands with DMG in the freshwater samples under similar conditions. Ni ligand exchange between natural ligands and DMG occurred over days with half-lifes of 5-95 h. Total dissolved Ni concentrations in samples from various freshwater systems in Switzerland ranged from 4 nM in an oligotrophic lake to 30 nM in a small river affected by inputs from sewage effluents and agriculture. Free ionic Ni2+ concentrations were determined in the range of 10(-13)-10(-15) M (pNi = 12.2-14.7), indicating that more than 99.9% of dissolved Ni was bound by organic ligands with strong affinity (log K 12.1-14.9) and low concentrations (13-100 nM) at pH 7.2-8.2. Because of slow ligand-exchange kinetics, Ni speciation in natural waters may in many cases not reach equilibrium.
Kinetics↗
Sacral neuromodulation in lower urinary tract dysfunction.
Vesico-urethral dysfunction is a major problem in daily medical practice due to its psychological disturbances, its social costs and its high impact on quality of life. Recently, sacral neuromodulation, namely the electrical stimulation of the sacral nerves, appears to have become an alternative for radical bladder surgery particularly in cases of idiopathic bladder overactivity. The mechanism of action is only partially understood but it seems to involve a modulation in the spinal cord due to stimulation of inhibitory interneurons. Temporary sacral nerve stimulation is the first step. It comprises the temporary application of neuromodulation as a diagnostic test to determine the best location for the implant and to control the integrity of the sacral root. If test stimulation is successful, a permanent device is implanted. This procedure is safe in experienced hands. So-called idiopathic bladder overactivity still the major indication for this technique. Patients not likely to benefit from the procedure were those with complete or almost complete spinal lesions, but incomplete spinal lesions seemed to be a potential indication. This technique is now also indicated in the case of idiopathic chronic retention and chronic pelvic pain syndrome. When selection is performed, more than three-quarters of the patients showed a clinically significant response with 50% or more reduction in the frequency of incontinent episodes, but the results vary according to the author's mode of evaluation. From the economic point of view, the initial investment in the device is amortized in the mid-term by savings related to lower urinary tract dysfunction. Finally, this technique requires an attentive follow-up and adjustments to the electric parameters so as to optimize the equilibrium between the neurological systems.
Afferent Pathways↗
Evidence for involvement of the carboxy terminus of helix 1 of growth hormone in receptor binding: use of charge reversal mutagenesis to account for calcium dependence of binding and for design of higher affinity analogues.
In this study we have demonstrated that the C-terminus of helix 1 of porcine GH (pGH) is a receptor-interactive region, thus extending the current binding site model of GH. This was achieved by introducing charge reversal mutations into this region of pGH, which influenced receptor affinity and Ca2+ dependence of binding. The first mutant (R34E pGH, conversion of Arg 34 to Glu) introduced a putative Ca2+ binding site which is present in human GH (hGH) [Barnard et al. (1989) J. Theor. Biol. 140, 355-367] and sits opposite E220 of receptor subunit 1. This mutant exhibited increased Ca2+ dependence of receptor binding but even at optimal Ca2+ did not display higher than wild-type affinity. Introduction of a second Ca2+ binding site adjacent to the first by a second charge reversal (K30E R34E pGH) further increased Ca2+ dependence of binding and also increased affinity for the rabbit GH receptor (2.4 +/- 0.4)-fold relative to wild-type pGH at optimal Ca2+. Equilibrium dialysis and Scatchard analysis of binding of 45Ca2+ to pGH and K30E R34E pGH revealed two Ca2+ binding sites on wild-type pGH and an additional two Ca2+ binding sites on the K30E R34E pGH mutant (Kd 0.5-0.8 mM), as predicted. A third partial charge reversal mutant in the fourth helix (H170D) also led to enhanced Ca2+ dependence of binding, supporting our proposal that E34 and D170 are responsible for the Ca2+ dependence of hGH binding to the rabbit GH receptor. Examination of the crystal structure shows that E34 and D170 are in close proximity and would interact repulsively with a cluster of acidic residues on the receptor consisting of E126, E127, and E220 unless neutralized by Ca2+ or an introduced basic residue. Accordingly, charge reversal at the adjacent pGH residue E33 (E33K pGH) led to a Ca2+ independent (3.0 +/- 0.4)-fold increase in affinity of binding. As well as extending the binding site model of GH, these studies provide a mechanistic explanation for the unique Ca2+ dependence of hGH binding to the rabbit GH receptor. They also indicate that charge reversal can be used to design higher affinity GH analogues and could assist in the mapping of interactive regions in ligand-receptor complexes generally.
Animals↗
Industrial input-output analysis: implications for industrial ecology.
Industrial ecology will need to develop fundamentally new approaches to reducing, reusing, and recycling wastes. Industrial ecology will also require an analytic framework for examining the implications for the economic system as a whole of each potential web of industrial changes. A suitable framework is furnished by structural economics, which situates the economy within the physical world. This approach is based on dynamic analysis rather than static concepts of equilibrium, and optimization assumptions are used selectively rather than as the general solution mechanism. Input-output economics, an important formal model within structural economics, can trace the stocks and flows of energy and other materials from extraction through production and consumption to recycling or disposal. An input-output computation, including wastes, is presented; it illustrates the separate but integrated analysis of physical stocks and flows and of prices and costs. This paper also describes the major advances that have been made in the last decade in the extension of input-output economics to address increasingly complex questions, notably the fully dynamic physical/price/income model and the engineering/input-output data base. Economists need to be able to assess the costs of cleaning up and to develop incentive schemes to increase the likelihood this will happen. To do this, economists need to take on the difficult "how" questions that concern industrial ecologists since the cost, and indeed the wider implications, of cleaning up depends upon how it is done. Structural economics, and modern input-output models and data bases, in particular, can help meet this challenge.
Journal Article↗
Administered activity optimization in patients studied by equilibrium gated radionuclide ventriculography using pyrophosphate and technetium-99m.
Equilibrium gated radionuclide ventriculography is one of the most important fields of work in nuclear cardiology. The in vivo labelled method utilizing 99mTc and red cells labelled with pyrophosphate is one of the most widely used. In the present work determination of the optimum 99mTc activity was studied. A sample of 30 patients was divided into five groups which received various amounts of radioactivity: 303 MBq, 444 MBq, 617 MBq, 803 MBq and 1020 MBq. The image quality of each study was assessed qualitatively and by using a method based on the construction of an image quality discriminant function. The number of counts in regions of interest in the heart, liver, lung and spleen, and the background, were processed as variables. The best results for the selected variables were obtained with 803 MBq.
Adult↗
Q learning in the minority game.
We present a numerical investigation of the minority game model, where the dynamics of the agents is described by the Q-learning algorithm. The numerical results show that the Q-learning dynamics is suppressing the "crowd effect," which is characteristic of the minority game with standard inductive dynamics, and it converges to a stationary state that is close to the optimal Nash equilibrium of the game.
Journal Article↗
Constructing a statistical mechanics for Beck-Cohen superstatistics.
The basic aspects of both Boltzmann-Gibbs (BG) and nonextensive statistical mechanics can be seen through three different stages. First, the proposal of an entropic functional (S(BG)=-k Sigma(i)p(i)ln p(i) for the BG formalism) with the appropriate constraints (Sigma(i)p(i)=1 and Sigma(i)p(i)E(i)=U for the BG canonical ensemble). Second, through optimization, the equilibrium or stationary-state distribution (p(i)=e(-betaE(i))/Z(BG) with Z(BG)= Sigma(j)e(-betaE(j)) for BG). Third, the connection to thermodynamics (e.g., F(BG)=-(1/beta)ln Z(BG) and U(BG)=-(partial differential/partial differential beta)ln Z(BG)). Assuming temperature fluctuations, Beck and Cohen recently proposed a generalized Boltzmann factor B(E)= integral (infinity)(0)dbetaf(beta)e(-betaE). This corresponds to the second stage described above. In this paper, we solve the corresponding first stage, i.e., we present an entropic functional and its associated constraints which lead precisely to B(E). We illustrate with all six admissible examples given by Beck and Cohen.
Journal Article↗
In situ amplification of oestrogen receptor alpha mRNA in breast cancer cell lines and tumours.
The aim of this work was to develop a direct in situ reverse transcription polymerase chain reaction (in situ RT-PCR) assay for the detection of oestrogen receptor alpha (ERalpha) mRNA on in vitro cell lines and breast tumour cell smears. ERalpha mRNA amplification was performed on MCF-7 (ERalpha positive) and MDA-MB-231 (ERalpha negative) cell lines as well as on 51 cytological smears of breast tumour samples from patients. The in situ amplification of mRNA in cell lines and ex vivo breast tumours was successful. However, finding an equilibrium between optimal cell morphology and PCR performance varied with each tumour, leading to difficulty in standardisation for daily practice. Nonetheless, in situ RT-PCR is a useful tool for the detection of ERalpha mRNA in selected cases, both in vitro and ex vivo. J Clin PATHOL: Mol Pathol
Breast Neoplasms↗
Early functional differentiation in the chick embryonic disc: interaction between mechanical activity and extracellular matrix.
The mechanical behaviour of ectodermal cells in the area opaca and the supracellular organization of fibronectin in the adjacent extracellular matrix were studied in whole chick blastoderms developing in vitro. The pattern of spontaneous mechanical activity and its modification by immunoglobulins against fibronectin were determined using a real-time image-analysis system. The pattern of fibronectin was studied using immunocytochemical techniques. It was found that the ectodermal cells in the area opaca actively develop a radially oriented contraction, which leads to a distension of the area pellucida from which the embryo develops. Abnormally increased tension resulted in perturbations of gastrulation and neurulation. An optimized mechanical equilibrium within the blastoderm seems to be necessary for normal development. Anti-fibronectin antibodies applied to the basal side of the blastoderm led rapidly and reversibly to an increase of tension in the contracted cells. This observation indicates that modifications of the extracellular matrix can be transmitted to cytoskeletal elements within adjacent cells. The extracellular matrix of the area opaca contains fibronectin arranged in radially oriented fibrils. This orientation corresponds to the direction of migration of the mesodermal cells. Interestingly, the radial pattern of fibronectin is found in the regions where the ectodermal cells are contracted and develop radially oriented forces. This observation suggests that the supracellular assembly of the extracellular materials could be influenced by the mechanical activity of adjacent cells. Possible modulations of the supracellular organization of extracellular matrix by other factors, e.g. diffusible metabolites, is also discussed. The presence of characteristically organized extracellular matrix components, of spatially differentiated cell activities and of reciprocal interactions between them makes the young chick blastoderm an excellent system for physiological studies of the coordinated cellular activities that lead to changes in form, complexity and function.
Animals↗
Ryanodine induces persistent inactivation of the Ca2+ release channel from skeletal muscle sarcoplasmic reticulum.
Junctional sarcoplasmic reticulum (SR) membranes isolated from rabbit skeletal muscle were pretreated with 0.1-500 microM ryanodine under equilibrium conditions optimal for receptor binding, followed by the removal of bound alkaloid by several washes in Ca(2+)- and ryanodine-free buffer. Pretreatment with > 100 nM ryanodine results in a concentration-dependent decrease in the Bmax of the high affinity sites and a complete loss of measurable low affinity binding sites that persist for > 48 hr. Quantitative analysis of residual ryanodine using three different methods demonstrates that the inhibition is not the result of residual ryanodine bound to its receptor. Ca2+ transport measurements made with antipyrylazo III show that actively loaded ryanodine-pretreated SR exhibits a persistent insensitivity to ryanodine- and daunomycin-induced Ca2+ release that is not seen with washed control vesicles. Lipid bilayer membranes fused with SR vesicles exhibit rapidly fluctuating single-channel events with a conductance of 468 pS in asymmetric CsCl solutions. Ryanodine (10 microM) produces a unidirectional transition to a slowly fluctuating half-conductance state that is not reversed by perfusion of the bilayer with Ca(2+)-free buffer and subsequent addition of dithiothreitol. However, dithiothreitol added in the ryanodine pretreatment medium offers marked protection against ryanodine-induced loss of binding sites and allows complete restoration of native gating behavior of single channels in bilayer lipid membrane. Using three different experimental approaches, the data demonstrate that the alkaloid at micromolar concentration persistently alters SR Ca2+ release channel function, perhaps by uncoupling four negatively cooperative binding sites. The oxidation of critical receptor thiols is implicated in the process.
Animals↗