Experimental Test of the Pulse Perturbation Method for Determining Causal Connectivities of Chemical Species in a Reaction Network

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Perturbation Method ◽  
Stationary State ◽  
Experimental Test ◽  
Temporal Order ◽  
Reaction System ◽  
Chemical Species ◽  
Reaction Network ◽  
Quantitative Information ◽  
Pulse Perturbation ◽  
Relative Errors

For an experimental test of the pulse perturbation method we choose a part of glycolysis shown in fig. 6.1. There are similarities and some differences between the model in fig. 5.12 and the reaction system in fig. 6.1. The reaction system has reactants, enzymes, and some effectors. One point of interest in choosing this system is the test of detecting and identifying the split of the reaction chain, from glucose to F1,6BP, at the aldolase reaction into two chains, one terminating at G3P and the other at 3PG. The experiments were run in a continuous-flow stirred tank reactor (CSTR) with the reaction system at a nonequilibrium stationary state, such that the reactions run spontaneously from glucose to G3P and 3PG. The concentrations of the species at this state are close to those of physiological conditions. The metabolites G6P, F6P, F1,6BP, DHAP, G3P, and 3PG were detected and analyzed by capillary electrophoresis. Typical relative errors were 4% for G6P, 11% for F6P, 15% for F1,6BP, 9% for DHAP, 6% for 3PG, and 3% for G3P. Figure 6.3 shows the responses of the species to a pulse of G6P, in a plot of relative concentrations versus. time during the relaxation, after the pulse, back to the stationary state. Complete relaxation took about half an hour. As seen from the amplitudes of the responses in the plot, the temporal order of propagation of the pulse is: G6P, F6P, DHAP, G3P, and 3PG. The time ordering of the maximum deviations agrees with this ordering except perhaps for G3P and 3PG. In some experiments, as in this one, the species F1,6BP could not be measured adequately and is not shown. It is possible to extract qualitative information on rates but difficult to derive quantitative information. Following a pulse of F1,6BP, the temporal order of propagation in the maximum relative concentrations is F1,6BP, DHAP, and with similar amplitudes G6P (slightly higher), G3P, 3PG, and F6P (slightly lower). These small differences were within errors of measurement and are therefore not significant. In this experiment the measurements of F1,6BP are reliable.

Response of Systems to Pulse Perturbations

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Stationary State ◽  
Kinetic Equations ◽  
Reaction System ◽  
Chemical Species ◽  
Reaction Network ◽  
Transient State ◽  
First Order ◽  
Pulse Perturbation ◽  
Stable Stationary State ◽  
Mass Action Law

Consider a chemical reaction system with many chemical species; it may be in a transient state but it is easier to think of it in a stable stationary state, not necessarily but usually away from equilibrium. We wish to probe the responses of the concentrations of the chemical species to a pulse perturbation of one of the chemical species. The pulse need not be small; it can be of arbitrary magnitude. This is analogous to providing a given input to one variable of an electronic system and measuring the outputs of the other variables. The method presented in this chapter gives causal connectivities of one reacting species with another as well as regulatory features of a reaction network. Much more will be said about the responses of chemical and other systems to pulses and other perturbations in chapter 12. The effects of small perturbations on reacting systems have been investigated in a number of studies, to which we return in chapters 9 and 13. Let us begin simply: Consider a series of first-order reactions as in fig. 5.1, which shows an unbranched chain of reversible reactions. We shall not be restricted to first-order reactions but can learn a lot from this example. Let there be an influx of k0 molecules of X1 and an outflow of k8 molecules of X8 per unit time. We assume that the reaction proceeds from left to right and hence the Gibbs free energy change for each step and for the overall reaction in that direction is negative. The mass action law for the kinetic equations, say that of X2, is . . . dX2/dt = k1X1 + k−2X3 − (k−1 + k2) X2 (5.1) . . . If all the time derivatives of the concentrations are zero, then the system is in a stationary state. Suppose we perturb that stationary state with an increase in X1 by an arbitrary amount and solve the kinetic equations numerically for the variations of the concentrations as a function of time, as the system returns to the stationary state. A plot of such a relaxation is shown in fig. 5.2.

scholarly journals Dynamic Self-organization in an Open Reaction Network as a Fundamental Mechanism for the Emergence of Life

2020 ◽  
Author(s):  
Yoshiharu Mukouyama, ◽  
Yoshihiro Nakato
Keyword(s):  
Stationary State ◽  
Reaction System ◽  
Reaction Network ◽  
Self Organization ◽  
Chemical System ◽  
Irreversible Processes ◽  
Primitive Earth ◽  
Chemical Structures ◽  
Emergence Of Life ◽  
Self Organizing

The emergence of life on the earth has attracted intense attention but the mechanism of it still remains an unsolved question. A key problem is that it has been left unclear why a living organism, which is regarded as an open reaction system, can demonstrate dynamic self-organization leading to highly-ordered structures and adaptive and evolutionary behavior. This paper shows by computer simulation that (1) an open reaction network is a network of irreversible processes and for this reason spontaneously reaches a stationary state and (2) a stationary state thus formed is stable against a fluctuation, namely it has self-organizing ability. Strikingly, self-organizing ability can emerge in a prebiotic chemical system with no special mechanism for overcoming disturbances by the second law of thermodynamics. The above self-organizing ability leads to adaptive and evolutionary behavior and has large potential for producing highly organized chemical structures, and is expected to have played a fundamental role in the emergence of life on the primitive earth.

Experimental Test and Applications of Correlation Metric Construction

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Time Series ◽  
Steady State ◽  
Reaction Mechanism ◽  
Experimental Test ◽  
Reaction Pathway ◽  
Chemical Species ◽  
Reaction Network ◽  
Sampling Period ◽  
The Matrix ◽  
Time Lagged

In this chapter we present an experimental test case of the deduction of a reaction pathway and mechanism by means of correlation metric construction from time-series measurements of the concentrations of chemical species. We choose as the system an enzymatic reaction network, the initial steps of glycolysis. Glycolysis is central in intermediary metabolism and has a high degree of regulation. The reaction pathway has been well studied and thus it is a good test for the theory. Further, the reaction mechanism of this part of glycolysis has been modeled extensively. The quantity and precision of the measurements reported here are sufficient to determine the matrix of correlation functions and, from this, a reaction pathway that is qualitatively consistent with the reaction mechanism established previously. The existence of unmeasured species did not compromise the analysis. The quantity and precision of the data were not excessive, and thus we expect the method to be generally applicable. This CMC experiment was carried out in a continuous-flow stirred-tank reactor (CSTR). The reaction network considered consists of eight enzymes, which catalyze the conversion of glucose into dihydroxyacetone phosphate and glyceraldehyde phosphate. The enzymes were confined to the reactor by an ultrafiltration membrane at the top of the reactor. The membrane was permeable to all low molecular weight species. The inputs are (1) a reaction buffer, which provides starting material for the reaction network to process, maintains pH and pMg, and contains any other species that act as constant constraints on the system dynamics, and (2) a set of “control species” (at least one), whose input concentrations are changed randomly every sampling period over the course of the experiment. The sampling period is chosen such that the system almost, but not quite, relaxes to a chosen nonequilibrium steady state. The system is kept near enough to its steady state to minimize trending (caused by the relaxation) in the time series, but far enough from the steady state that the time-lagged autocorrelation functions for each species decay to zero over three to five sampling periods. This long decay is necessary if temporal ordering in the network is to be analyzed.

Dynamic Self-organization in an Open Reaction Network as a Fundamental Mechanism for the Emergence of Life

2020 ◽  
Author(s):  
Yoshiharu Mukouyama, ◽  
Yoshihiro Nakato
Keyword(s):  
Stationary State ◽  
Reaction System ◽  
Reaction Network ◽  
Self Organization ◽  
Chemical System ◽  
Irreversible Processes ◽  
Primitive Earth ◽  
Chemical Structures ◽  
Emergence Of Life ◽  
Self Organizing

The emergence of life on the earth has attracted intense attention but the mechanism of it still remains an unsolved question. A key problem is that it has been left unclear why a living organism, which is regarded as an open reaction system, can demonstrate dynamic self-organization leading to highly-ordered structures and adaptive and evolutionary behavior. This paper shows by computer simulation that (1) an open reaction network is a network of irreversible processes and for this reason spontaneously reaches a stationary state and (2) a stationary state thus formed is stable against a fluctuation, namely it has self-organizing ability. Strikingly, self-organizing ability can emerge in a prebiotic chemical system with no special mechanism for overcoming disturbances by the second law of thermodynamics. The above self-organizing ability leads to adaptive and evolutionary behavior and has large potential for producing highly organized chemical structures, and is expected to have played a fundamental role in the emergence of life on the primitive earth.

Buffer capacity in multiple chemical reaction systems involving solid phases

2006 ◽  
Vol 84 (8) ◽  
pp. 1036-1044 ◽  
Author(s):  
Ilie Fishtik ◽  
Igor Povar
Keyword(s):  
Chemical Reaction ◽  
Buffer Capacity ◽  
Reaction System ◽  
Chemical Species ◽  
Abundant Species ◽  
Stoichiometric Coefficient ◽  
Reaction Systems ◽  
Chemical Reaction Systems ◽  
Chemical Reaction System ◽  
Multiple Chemical

The buffer capacity of a chemical species in a multiple chemical reaction system is discussed in terms of a special class of stoichiometrically unique reactions referred to as response reactions (RERs). More specifically, it is shown that the buffer capacity may be partitioned into a sum of contributions associated with RERs. This finding provides a deeper understanding of the factors that determine the buffer capacity. In particular, the main contributions to the buffer capacity come from the RERs involving the most abundant species. Concomitantly, the RERs approach provides a simple stoichiometric algorithm for the derivation and analysis of the buffer capacity that may be easily implemented into a computer software.Key words: buffer capacity, response reaction, heterogeneous system, stoichiometric coefficient.

Rheo-Optiics for Multicomponent Liquids

1991 ◽  
Vol 248 ◽  
Author(s):  
G. Fuller ◽  
J. van Egmond ◽  
J. Zawada ◽  
L. Archer
Keyword(s):  
Light Scattering ◽  
Structure Factor ◽  
Uniaxial Extension ◽  
Chemical Species ◽  
Polymer Melt ◽  
Orientation Distribution ◽  
Quantitative Information ◽  
Dioctyl Phthalate ◽  
Multicomponent Systems ◽  
Relaxation Dynamics

AbstractThe application of techniques in optical rheometry for the study of multicomponent systems is reviewed. Small angle light scattering (SALS) patterns are related to the structure of concentration fluctuations with length scales of the order of the wavelength of light. Scattering techniques such as SALS and scattering dichroism have been applied to monitor the transient evolution of anisotropic concentration fluctuation enhancement during simple shear induced phase separation in a semi-dilute solution of polystyrene (PS) in dioctyl phthalate(DOP). Furthermore, the Onuki- Doi theory relating scattering dichroism and structure factor has been used to verify the consistency between scattering dichroism and anisotropy in structure factor. Infrared polarimetry is a useful technique in probing the transient microstructural orientation of individual chemical species in multicomponent systems. The simultaneous measurement of intrinsic infrared dichroism and birefringence is particularly effective and has been employed to monitor component relaxation dynamics in miscible blends of poly(ethylene oxide) and poly(methyl methacrylate). Polarization Modulated Laser Raman Scattering (PMLRS) has been successfully employed to study the orientation dynamics of a polymer melt subjected to transient uniaxial extension. PMLRS provides quantitative information about the time evolution of both the second and fourth moments of the orientation distribution function of molecular segments.

scholarly journals Pulse perturbation technique for determination of piroxicam in pharmaceuticals using an oscillatory reaction system

2013 ◽  
Vol 11 (2) ◽  
pp. 180-188 ◽  
Author(s):  
Nataša Pejić ◽  
Nataša Sarap ◽  
Jelena Maksimović ◽  
Slobodan Anić ◽  
Ljiljana Kolar-Anić
Keyword(s):  
Perturbation Technique ◽  
Kinetic Method ◽  
Reaction System ◽  
Direct Determination ◽  
Pharmaceutical Formulations ◽  
Oscillatory Reaction ◽  
Reaction Conditions ◽  
Good Sample ◽  
Pulse Perturbation

AbstractA simple and reliable novel kinetic method for the determination of piroxicam (PX) was proposed and validated. For quantitative determination of PX, the Bray-Liebhafsky (BL) oscillatory reaction was used in a stable non-equilibrium stationary state close to the bifurcation point. Under the optimized reaction conditions (T = 55.0°C, [H2SO4]0 = 7.60×10−2 mol L−1, [KIO3]0 = 5.90×10−2 mol L−1, [H2O2]0 = 1.50×10−1 mol L−1 and j 0 = 2.95×10−2 min−1), the linear relationship between maximal potential shift ΔE m , and PX concentration was obtained in the concentration range 11.2–480.5 µg mL−1 with a detection limit of 9.9 µg mL−1. The method had a rather good sample throughput of 25 samples h−1 with a precision RSD = 4.7% as well as recoveries RCV ≤ 104.4%. Applicability of the proposed method to the direct determination of piroxicam in different pharmaceutical formulations (tablets, ampoules and gel) was demonstrated.

The Physico-Psycho-Galvanic Reflex in the Neuroses and Psychoses. (Essay for which was awarded the Bronze Medal of the Royal Medico-Psychological Association, 1926.)

1926 ◽  
Vol 72 (299) ◽  
pp. 492-503 ◽  
Author(s):  
P. K. McCowan
Keyword(s):  
Electrical Conductivity ◽  
Experimental Test ◽  
Experimental Methods ◽  
Quantitative Information ◽  
Medical Superintendent ◽  
Yield Information ◽  
Valuable Method ◽  
Bronze Medal

Discussing experimental psychiatry Kraepelin observes that lack of comprehension of the experimental test, lack of ability to execute it, lack of interest, of co-operation, and of endurance, all conspire to increase the task of the experimenter and to modify the value of the results. The consequent demand for trustworthy experimental methods, which without too complicated technique and too unusual demands on the patient shall yield information of significant variations from the normal in quantitative terms, voices at once the need and the embarrassment of the experimental psychiatrist. The determination of the electrical conductivity of the skin is undoubtedly one valuable method of approach in this search after quantitative information, and this paper is the result of some months' investigation which I carried out at the Maudsley Hospital, when, through the kindness of the Medical Superintendent, Dr. E. Mapother, I had put at my disposal cases of psycho-neuroses and early psychoses.

scholarly journals Noise control for molecular computing

2018 ◽  
Vol 15 (144) ◽  
pp. 20180199 ◽  
Author(s):  
Tomislav Plesa ◽  
Konstantinos C. Zygalakis ◽  
David F. Anderson ◽  
Radek Erban
Keyword(s):  
Stochastic Dynamics ◽  
Noise Control ◽  
Reaction System ◽  
Reaction Network ◽  
Intrinsic Noise ◽  
Biochemical Networks ◽  
Mass Action ◽  
Mass Action Kinetics ◽  
Interdisciplinary Field ◽  
Biochemical Systems

Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement in nucleic-acid-based technology in general, and strand-displacement DNA computing in particular, a large class of abstract biochemical networks may be physically realized using nucleic acids. Methods for systematic design of the abstract systems with prescribed behaviours have been predominantly developed at the (less-detailed) deterministic level. However, stochastic effects, neglected at the deterministic level, are increasingly found to play an important role in biochemistry. In such circumstances, methods for controlling the intrinsic noise in the system are necessary for a successful network design at the (more-detailed) stochastic level. To bridge the gap, the noise-control algorithm for designing biochemical networks is developed in this paper. The algorithm structurally modifies any given reaction network under mass-action kinetics, in such a way that (i) controllable state-dependent noise is introduced into the stochastic dynamics, while (ii) the deterministic dynamics are preserved. The capabilities of the algorithm are demonstrated on a production–decay reaction system, and on an exotic system displaying bistability. For the production–decay system, it is shown that the algorithm may be used to redesign the network to achieve noise-induced multistability. For the exotic system, the algorithm is used to redesign the network to control the stochastic switching, and achieve noise-induced oscillations.

Introduction

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Reaction Mechanism ◽  
Chemical Kinetics ◽  
Chemical Engineering ◽  
Reaction Pathway ◽  
Reaction System ◽  
Chemical Species ◽  
Pulse Method ◽  
Elementary Reaction ◽  
Elementary Reactions ◽  
Arbitrary Strength

Chemical kinetics as a science has existed for more than a century. It deals with the rates of reactions and the details of how a given reaction proceeds from reactants to products. In a chemical system with many chemical species, there are several questions to be asked: What species react with what other species? In what temporal order? With what catalysts? And with what results? The answers constitute the macroscopic reaction mechanism. The process can be described macroscopically by listing the reactants, intermediates, products, and all the elementary reactions and catalysts in the reaction system. The present book is a treatise and text on the determination of complex reaction mechanisms in chemistry and in chemical reaction systems that occur in chemical engineering, biochemistry, biology, biotechnology, and genomics. A basic knowledge of chemical kinetics is assumed. Several approaches are suggested for the deduction of information on the causal chemical connectivity of the species, on the elementary reactions among the species, and on the sequence of the elementary reactions that constitute the reaction pathway and the reaction mechanism. Chemical reactions occur by the collisions of molecules, and such an event is called an elementary reaction for specified reactant and product molecules. A balanced stoichiometric equation for an elementary reaction yields the number of each type of molecule according to conservation of atoms, mass, and charge. Figure 1.1 shows a relatively simple reaction mechanism for the decomposition of ozone by light, postulated to occur in a series of three elementary steps. (The details of collisions of molecules and bond rearrangements are not discussed.) All approaches are based on the measurements of the concentrations of chemical species in the whole reaction system, not on parts, as has been the practice. One approach is called the pulse method, in which a pulse of concentration of one or more species of arbitrary strength is applied to a reacting system and the responses of as many species as possible are measured. From these responses causal chemical connectivities may be inferred. The basic theory is explained, demonstrated on a model mechanism, and tested in an experiment on a part of glycolysis.

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