arXiv subjects

A. N. Gorban

Publications and source records attributed to A. N. Gorban.

At least 55 records · Page 3Linked to original sources

arXiv2013

Extremal property of a simple cycle

We study systems with finite number of states $A_i$ ($i=1,..., n$), which obey the first order kinetics (master equation) without detailed balance. For any nonzero complex eigenvalue $λ$ we prove the inequality $\frac{|\Im λ|}{|\Re λ|} \leq \cot\fracπ{n}$. This bound is sharp and it becomes an equality for an eigenvalue of a simple irreversible cycle $A_1 \to A_2 \to... \to A_n \to A_1$ with equal rate constants of all transitions. Therefore, the simple cycle with the equal rate constants has the slowest decay of the oscillations among all first order kinetic systems with the same number of states.

physics.chem-ph↗

arXiv2012

Local Equivalence of Reversible and General Markov Kinetics

We consider continuous--time Markov kinetics with a finite number of states and a given positive equilibrium distribution P*. For an arbitrary probability distribution $P$ we study the possible right hand sides, dP/dt, of the Kolmogorov (master) equations. We describe the cone of possible values of the velocity, dP/dt, as a function of P and P*. We prove that, surprisingly, these cones coincide for the class of all Markov processes with equilibrium P* and for the reversible Markov processes with detailed balance at this equilibrium. Therefore, for an arbitrary probability distribution $P$ and a general system there exists a system with detailed balance and the same equilibrium that has the same velocity dP/dt at point P. The set of Lyapunov functions for the reversible Markov processes coincides with the set of Lyapunov functions for general Markov kinetics. The results are extended to nonlinear systems with the generalized mass action law.

physics.chem-ph↗

arXiv2012

Thermodynamics in the Limit of Irreversible Reactions

For many real physico-chemical complex systems detailed mechanism includes both reversible and irreversible reactions. Such systems are typical in homogeneous combustion and heterogeneous catalytic oxidation. Most complex enzyme reactions include irreversible steps. The classical thermodynamics has no limit for irreversible reactions whereas the kinetic equations may have such a limit. We represent the systems with irreversible reactions as the limits of the fully reversible systems when some of the equilibrium concentrations tend to zero. The structure of the limit reaction system crucially depends on the relative rates of this tendency to zero. We study the dynamics of the limit system and describe its limit behavior as $t \to \infty$. If the reversible systems obey the principle of detailed balance then the limit system with some irreversible reactions must satisfy the {\em extended principle of detailed balance}. It is formulated and proven in the form of two conditions: (i) the reversible part satisfies the principle of detailed balance and (ii) the convex hull of the stoichiometric vectors of the irreversible reactions does not intersect the linear span of the stoichiometric vectors of the reversible reactions. These conditions imply the existence of the global Lyapunov functionals and alow an algebraic description of the limit behavior. The thermodynamic theory of the irreversible limit of reversible reactions is illustrated by the analysis of hydrogen combustion.

cond-mat.stat-mech↗

arXiv2012

Thermodynamic Tree: The Space of Admissible Paths

Is a spontaneous transition from a state x to a state y allowed by thermodynamics? Such a question arises often in chemical thermodynamics and kinetics. We ask the more formal question: is there a continuous path between these states, along which the conservation laws hold, the concentrations remain non-negative and the relevant thermodynamic potential G (Gibbs energy, for example) monotonically decreases? The obvious necessary condition, G(x)\geq G(y), is not sufficient, and we construct the necessary and sufficient conditions. For example, it is impossible to overstep the equilibrium in 1-dimensional (1D) systems (with n components and n-1 conservation laws). The system cannot come from a state x to a state y if they are on the opposite sides of the equilibrium even if G(x) > G(y). We find the general multidimensional analogue of this 1D rule and constructively solve the problem of the thermodynamically admissible transitions. We study dynamical systems, which are given in a positively invariant convex polyhedron D and have a convex Lyapunov function G. An admissible path is a continuous curve along which $G$ does not increase. For x,y from D, x\geq y (x precedes y) if there exists an admissible path from x to y and x \sim y if x\geq y and y\geq x. The tree of G in D is a quotient space D/~. We provide an algorithm for the construction of this tree. In this algorithm, the restriction of G onto the 1-skeleton of $D$ (the union of edges) is used. The problem of existence of admissible paths between states is solved constructively. The regions attainable by the admissible paths are described.

cond-mat.stat-mech↗

arXiv2012

Add-ons for Lattice Boltzmann Methods: Regularization, Filtering and Limiters

We describe how regularization of lattice Boltzmann methods can be achieved by modifying dissipation. Classes of techniques used to try to improve regularization of LBMs include flux limiters, enforcing the exact correct production of entropy and manipulating non-hydrodynamic modes of the system in relaxation. Each of these techniques corresponds to an additional modification of dissipation compared with the standard LBGK model. Using some standard 1D and 2D benchmarks including the shock tube and lid driven cavity, we explore the effectiveness of these classes of methods.

physics.comp-ph↗

arXiv2012

Mathematical modeling of microRNA-mediated mechanisms of translation repression

MicroRNAs can affect the protein translation using nine mechanistically different mechanisms, including repression of initiation and degradation of the transcript. There is a hot debate in the current literature about which mechanism and in which situations has a dominant role in living cells. The worst, same experimental systems dealing with the same pairs of mRNA and miRNA can provide ambiguous evidences about which is the actual mechanism of translation repression observed in the experiment. We start with reviewing the current knowledge of various mechanisms of miRNA action and suggest that mathematical modeling can help resolving some of the controversial interpretations. We describe three simple mathematical models of miRNA translation that can be used as tools in interpreting the experimental data on the dynamics of protein synthesis. The most complex model developed by us includes all known mechanisms of miRNA action. It allowed us to study possible dynamical patterns corresponding to different miRNA-mediated mechanisms of translation repression and to suggest concrete recipes on determining the dominant mechanism of miRNA action in the form of kinetic signatures. Using computational experiments and systematizing existing evidences from the literature, we justify a hypothesis about co-existence of distinct miRNA-mediated mechanisms of translation repression. The actually observed mechanism will be that acting on or changing the limiting "place" of the translation process. The limiting place can vary from one experimental setting to another. This model explains the majority of existing controversies reported.

q-bio.MN↗

arXiv2012

Quasichemical Models of Multicomponent Nonlinear Diffusion

Diffusion preserves the positivity of concentrations, therefore, multicomponent diffusion should be nonlinear if there exist non-diagonal terms. The vast variety of nonlinear multicomponent diffusion equations should be ordered and special tools are needed to provide the systematic construction of the nonlinear diffusion equations for multicomponent mixtures with significant interaction between components. We develop an approach to nonlinear multicomponent diffusion based on the idea of the reaction mechanism borrowed from chemical kinetics. Chemical kinetics gave rise to very seminal tools for the modeling of processes. This is the stoichiometric algebra supplemented by the simple kinetic law. The results of this invention are now applied in many areas of science, from particle physics to sociology. In our work we extend the area of applications onto nonlinear multicomponent diffusion. We demonstrate, how the mechanism based approach to multicomponent diffusion can be included into the general thermodynamic framework, and prove the corresponding dissipation inequalities. To satisfy thermodynamic restrictions, the kinetic law of an elementary process cannot have an arbitrary form. For the general kinetic law (the generalized Mass Action Law), additional conditions are proved. The cell--jump formalism gives an intuitively clear representation of the elementary transport processes and, at the same time, produces kinetic finite elements, a tool for numerical simulation.

cond-mat.mtrl-sci↗

arXiv2012

Simultaneously Dissipative Operators And The Infinitesimal Moore Effect In Interval Spaces

One of shortcomings of stepwise interval methods is the following. The intervals determining the solution of a system are often expanded in the course of time irrespective of the method and step used (the {\em Moore effect}). We introduce the notion of general {\em interval spaces} and study the infinitesimal Moore effect (IME) in these spaces. We obtain the local conditions of absence of the IME in terms of Jacobi matrices field. The relation between the absence of IME and simultaneous dissipativity of the Jacobi matrices is established. We study simultaneously dissipative operators in $\Bbb{R}^n$. A linear operator $A$ is {\em dissipative} with respect to a norm $\|...\|$ if $\| \exp (At) \| \leq 1$ at all $t \geq 0$. For each norm, the dissipative operator form a closed convex cone. An operator $A$ is {\em stable dissipative} if it belongs to the interior of this cone. The family of linear operators $\{A_α\}$ is called {\em simultaneously dissipative}, if there exists a norm with respect to which all the operators are dissipative. We studied general properties of such families. For example, let the family $\{A_α\}$ be finite and generate a nilpotent Lee algebra and let for each $A_α$ there exist a norm with respect to which it is dissipative. Then $\{A_α\}$ is simultaneously dissipative. Let the family $\{A_α\}$ be compact and generate solvable Lee algebra, and let the spectrum of each operator $A_α$ lie in the open left half-plane. Then $\{A_α\}$ is simultaneously stable dissipative, i.e. there exists a norm with respect to which all $A_α$ are stable dissipative. We study the conditions of simultaneous dissipativity of the matrices of rank one and discussed their application to equations of {\em mass action law} kinetics.

physics.comp-ph↗

arXiv2011

Possibility and Impossibility of the Entropy Balance in Lattice Boltzmann Collisions

We demonstrate that in the space of distributions operated on by lattice Boltzmann methods that there exists a vicinity of the equilibrium where collisions with entropy balance are possible and, at the same time, there exist an area of nonequilibrium distributions where such collisions are impossible. We calculate and graphically represent these areas for some simple entropic equilibria using single relaxation time models. Therefore it is shown that the definition of an entropic LBM is incomplete without a strategy to deal with certain highly nonequilibrium states. Such strategies should be explicitly stated as they may result in the production of additional entropy.

physics.comp-ph↗

arXiv2011

Extended Detailed Balance for Systems with Irreversible Reactions

The principle of detailed balance states that in equilibrium each elementary process is equilibrated by its reverse process. For many real physico-chemical complex systems (e.g. homogeneous combustion, heterogeneous catalytic oxidation, most enzyme reactions etc), detailed mechanisms include both reversible and irreversible reactions. In this case, the principle of detailed balance cannot be applied directly. We represent irreversible reactions as limits of reversible steps and obtain the principle of detailed balance for complex mechanisms with some irreversible elementary processes. We proved two consequences of the detailed balance for these mechanisms: the structural condition and the algebraic condition that form together the extended form of detailed balance. The algebraic condition is the principle of detailed balance for the reversible part. The structural condition is: the convex hull of the stoichiometric vectors of the irreversible reactions has empty intersection with the linear span of the stoichiometric vectors of the reversible reaction. Physically, this means that the irreversible reactions cannot be included in oriented pathways. The systems with the extended form of detailed balance are also the limits of the reversible systems with detailed balance when some of the equilibrium concentrations (or activities) tend to zero. Surprisingly, the structure of the limit reaction mechanism crucially depends on the relative speeds of this tendency to zero.

cond-mat.stat-mech↗

arXiv2011

A Statistical Model of Aggregates Fragmentation

A statistical model of fragmentation of aggregates is proposed, based on the stochastic propagation of cracks through the body. The propagation rules are formulated on a lattice and mimic two important features of the process -- a crack moves against the stress gradient and its energy depletes as it grows. We perform numerical simulations of the model for two-dimensional lattice and reveal that the mass distribution for small and intermediate-size fragments obeys a power-law, F(m)\propto m^(-3/2), in agreement with experimental observations. We develop an analytical theory which explains the detected power-law and demonstrate that the overall fragment mass distribution in our model agrees qualitatively with that, observed in experiments.

cond-mat.stat-mech↗

arXiv2011

Principal Graphs and Manifolds

In many physical, statistical, biological and other investigations it is desirable to approximate a system of points by objects of lower dimension and/or complexity. For this purpose, Karl Pearson invented principal component analysis in 1901 and found 'lines and planes of closest fit to system of points'. The famous k-means algorithm solves the approximation problem too, but by finite sets instead of lines and planes. This chapter gives a brief practical introduction into the methods of construction of general principal objects, i.e. objects embedded in the 'middle' of the multidimensional data set. As a basis, the unifying framework of mean squared distance approximation of finite datasets is selected. Principal graphs and manifolds are constructed as generalisations of principal components and k-means principal points. For this purpose, the family of expectation/maximisation algorithms with nearest generalisations is presented. Construction of principal graphs with controlled complexity is based on the graph grammar approach.

cs.LG↗

arXiv2011

Elastic principal manifolds and their practical applications

Principal manifolds serve as useful tool for many practical applications. These manifolds are defined as lines or surfaces passing through "the middle" of data distribution. We propose an algorithm for fast construction of grid approximations of principal manifolds with given topology. It is based on analogy of principal manifold and elastic membrane. The first advantage of this method is a form of the functional to be minimized which becomes quadratic at the step of the vertices position refinement. This makes the algorithm very effective, especially for parallel implementations. Another advantage is that the same algorithmic kernel is applied to construct principal manifolds of different dimensions and topologies. We demonstrate how flexibility of the approach allows numerous adaptive strategies like principal graph constructing, etc. The algorithm is implemented as a C++ package elmap and as a part of stand-alone data visualization tool VidaExpert, available on the web. We describe the approach and provide several examples of its application with speed performance characteristics.

cond-mat.dis-nn↗

arXiv2011

Reciprocal Relations Between Kinetic Curves

We study coupled irreversible processes. For linear or linearized kinetics with microreversibility, $\dot{x}=Kx$, the kinetic operator $K$ is symmetric in the entropic inner product. This form of Onsager's reciprocal relations implies that the shift in time, $\exp (Kt)$, is also a symmetric operator. This generates the reciprocity relations between the kinetic curves. For example, for the Master equation, if we start the process from the $i$th pure state and measure the probability $p_j(t)$ of the $j$th state ($j\neq i$), and, similarly, measure $p_i(t)$ for the process, which starts at the $j$th pure state, then the ratio of these two probabilities $p_j(t)/p_i(t)$ is constant in time and coincides with the ratio of the equilibrium probabilities. We study similar and more general reciprocal relations between the kinetic curves. The experimental evidence provided as an example is from the reversible water gas shift reaction over iron oxide catalyst. The experimental data are obtained using Temporal Analysis of Products (TAP) pulse-response studies. These offer excellent confirmation within the experimental error.

cond-mat.stat-mech↗

arXiv2011

Kinetic Path Summation, Multi--Sheeted Extension of Master Equation, and Evaluation of Ergodicity Coefficient

We study the Master equation with time--dependent coefficients, a linear kinetic equation for the Markov chains or for the monomolecular chemical kinetics. For the solution of this equation a path summation formula is proved. This formula represents the solution as a sum of solutions for simple kinetic schemes (kinetic paths), which are available in explicit analytical form. The relaxation rate is studied and a family of estimates for the relaxation time and the ergodicity coefficient is developed. To calculate the estimates we introduce the multi--sheeted extensions of the initial kinetics. This approach allows us to exploit the internal ("micro")structure of the extended kinetics without perturbation of the base kinetics.

physics.comp-ph↗

arXiv2010

Correlations, Risk and Crisis: From Physiology to Finance

We study the dynamics of correlation and variance in systems under the load of environmental factors. A universal effect in ensembles of similar systems under the load of similar factors is described: in crisis, typically, even before obvious symptoms of crisis appear, correlation increases, and, at the same time, variance (and volatility) increases too. This effect is supported by many experiments and observations of groups of humans, mice, trees, grassy plants, and on financial time series. A general approach to the explanation of the effect through dynamics of individual adaptation of similar non-interactive individuals to a similar system of external factors is developed. Qualitatively, this approach follows Selye's idea about adaptation energy.

physics.bio-ph↗

arXiv2010

Principal manifolds and graphs in practice: from molecular biology to dynamical systems

We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.

cs.NE↗

arXiv2010

Asymptotology of Chemical Reaction Networks

The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit approximations of eigenvalues and eigenvectors of kinetic matrix. Accuracy of estimates is proven. Performance of the algorithms is demonstrated on simple examples. Application of algorithms to nonlinear systems is discussed.

physics.chem-ph↗