arXiv subjects

Rudolf Hanel

Publications and source records attributed to Rudolf Hanel.

At least 55 records · Page 3Linked to original sources

arXiv2012

A self-organized model for cell-differentiation based on variations of molecular decay rates

Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes). The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of this dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein) in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers) vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.

q-bio.MN↗

arXiv2011

What do generalized entropies look like? An axiomatic approach for complex, non-ergodic systems

Shannon and Khinchin showed that assuming four information theoretic axioms the entropy must be of Boltzmann-Gibbs type, $S=-\sum_i p_i \log p_i$. Here we note that in physical systems one of these axioms may be violated. For non-ergodic systems the so called separation axiom (Shannon-Khinchin axiom 4) will in general not be valid. We show that when this axiom is violated the entropy takes a more general form, $S_{c,d}\propto \sum_i ^W Γ(d+1, 1- c \log p_i)$, where $c$ and $d$ are scaling exponents and $Γ(a,b)$ is the incomplete gamma function. The exponents $(c,d)$ define equivalence classes for all interacting and non interacting systems and unambiguously characterize any statistical system in its thermodynamic limit. The proof is possible because of two newly discovered scaling laws which any entropic form has to fulfill, if the first three Shannon-Khinchin axioms hold. $(c,d)$ can be used to define equivalence classes of statistical systems. A series of known entropies can be classified in terms of these equivalence classes. We show that the corresponding distribution functions are special forms of Lambert-${\cal W}$ exponentials containing -- as special cases -- Boltzmann, stretched exponential and Tsallis distributions (power-laws). In the derivation we assume trace form entropies, $S=\sum_i g(p_i)$, with $g$ some function, however more general entropic forms can be classified along the same scaling analysis.

cond-mat.stat-mech↗

arXiv2011

When do generalized entropies apply? How phase space volume determines entropy

We show how the dependence of phase space volume $Ω(N)$ of a classical system on its size $N$ uniquely determines its extensive entropy. We give a concise criterion when this entropy is not of Boltzmann-Gibbs type but has to assume a {\em generalized} (non-additive) form. We show that generalized entropies can only exist when the dynamically (statistically) relevant fraction of degrees of freedom in the system vanishes in the thermodynamic limit. These are systems where the bulk of the degrees of freedom is frozen and is practically statistically inactive. Systems governed by generalized entropies are therefore systems whose phase space volume effectively collapses to a lower-dimensional 'surface'. We explicitly illustrate the situation for binomial processes and argue that generalized entropies could be relevant for self organized critical systems such as sand piles, for spin systems which form meta-structures such as vortices, domains, instantons, etc., and for problems associated with anomalous diffusion.

cond-mat.stat-mech↗

arXiv2011

Generalized entropies and the transformation group of superstatistics

Superstatistics describes statistical systems that behave like superpositions of different inverse temperatures $β$, so that the probability distribution is $p(ε_i) \propto \int_{0}^{\infty} f(β) e^{-βε_i}dβ$, where the `kernel' $f(β)$ is nonnegative and normalized ($\int f(β)d β=1$). We discuss the relation between this distribution and the generalized entropic form $S=\sum_i s(p_i)$. The first three Shannon-Khinchin axioms are assumed to hold. It then turns out that for a given distribution there are two different ways to construct the entropy. One approach uses escort probabilities and the other does not; the question of which to use must be decided empirically. The two approaches are related by a duality. The thermodynamic properties of the system can be quite different for the two approaches. In that connection we present the transformation laws for the superstatistical distributions under macroscopic state changes. The transformation group is the Euclidean group in one dimension.

cond-mat.stat-mech↗

arXiv2010

Peer-review in a world with rational scientists: Toward selection of the average

One of the virtues of peer review is that it provides a self-regulating selection mechanism for scientific work, papers and projects. Peer review as a selection mechanism is hard to evaluate in terms of its efficiency. Serious efforts to understand its strengths and weaknesses have not yet lead to clear answers. In theory peer review works if the involved parties (editors and referees) conform to a set of requirements, such as love for high quality science, objectiveness, and absence of biases, nepotism, friend and clique networks, selfishness, etc. If these requirements are violated, what is the effect on the selection of high quality work? We study this question with a simple agent based model. In particular we are interested in the effects of rational referees, who might not have any incentive to see high quality work other than their own published or promoted. We find that a small fraction of incorrect (selfish or rational) referees can drastically reduce the quality of the published (accepted) scientific standard. We quantify the fraction for which peer review will no longer select better than pure chance. Decline of quality of accepted scientific work is shown as a function of the fraction of rational and unqualified referees. We show how a simple quality-increasing policy of e.g. a journal can lead to a loss in overall scientific quality, and how mutual support-networks of authors and referees deteriorate the system.

physics.soc-ph↗

arXiv2010

A comprehensive classification of complex statistical systems and an ab-initio derivation of their entropy and distribution functions

To characterize strongly interacting statistical systems within a thermodynamical framework - complex systems in particular - it might be necessary to introduce generalized entropies, $S_g$. A series of such entropies have been proposed in the past, mainly to accommodate important empirical distribution functions to a maximum ignorance principle. Until now the understanding of the fundamental origin of these entropies and its deeper relations to complex systems is limited. Here we explore this questions from first principles. We start by observing that the 4th Khinchin axiom (separability axiom) is violated by strongly interacting systems in general and ask about the consequences of violating the 4th axiom while assuming the first three Khinchin axioms (K1-K3) to hold and $S_g=\sum_ig(p_i)$. We prove by simple scaling arguments that under these requirements {\em each} statistical system is uniquely characterized by a distinct pair of scaling exponents $(c,d)$ in the large size limit. The exponents define equivalence classes for all interacting and non interacting systems. This allows to derive a unique entropy, $S_{c,d}\propto \sum_i Γ(d+1, 1- c \ln p_i)$, which covers all entropies which respect K1-K3 and can be written as $S_g=\sum_ig(p_i)$. Known entropies can now be classified within these equivalence classes. The corresponding distribution functions are special forms of Lambert-$W$ exponentials containing as special cases Boltzmann, stretched exponential and Tsallis distributions (power-laws) -- all widely abundant in nature. This is, to our knowledge, the first {\em ab initio} justification for the existence of generalized entropies. Even though here we assume $S_g=\sum_ig(p_i)$, we show that more general entropic forms can be classified along the same lines.

physics.class-ph↗

arXiv2010

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.

cond-mat.dis-nn↗

arXiv2009

Evolutionary dynamics from a variational principle

We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic of evolutionary systems is the ongoing endogenous production of new species. These novel entities change the conditions for already existing species. Even {\em Darwin's Demon}, a hypothetical entity with exact knowledge of the abundance of all species and their fitness functions at a given time, could not pre-state the impact of these novelties on established populations. We argue that fitness is always {\it a posteriori} knowledge -- it measures but does not explain why a species has reproductive success or not. To overcome these conceptual limitations, a variational principle is proposed in a spin-model-like setup of evolutionary systems. We derive a functional which is minimized under the most general evolutionary formulation of a dynamical system, i.e. evolutionary trajectories causally emerge as a minimization of a functional. This functional allows the derivation of analytic solutions of the asymptotic diversity for stochastic evolutionary systems within a mean-field approximation. We test these approximations by numerical simulations of the corresponding model and find good agreement in the position of phase transitions in diversity curves. The model is further able to reproduce stylized facts of timeseries from several man-made and natural evolutionary systems. Light will be thrown on how species and their fitness landscapes dynamically co-evolve.

q-bio.PE↗

arXiv2009

Schumpeterian economic dynamics as a quantifiable minimum model of evolution

We propose a simple quantitative model of Schumpeterian economic dynamics. New goods and services are endogenously produced through combinations of existing goods. As soon as new goods enter the market they may compete against already existing goods, in other words new products can have destructive effects on existing goods. As a result of this competition mechanism existing goods may be driven out from the market - often causing cascades of secondary defects (Schumpeterian gales of destruction). The model leads to a generic dynamics characterized by phases of relative economic stability followed by phases of massive restructuring of markets - which could be interpreted as Schumpeterian business `cycles'. Model timeseries of product diversity and productivity reproduce several stylized facts of economics timeseries on long timescales such as GDP or business failures, including non-Gaussian fat tailed distributions, volatility clustering etc. The model is phrased in an open, non-equilibrium setup which can be understood as a self organized critical system. Its diversity dynamics can be understood by the time-varying topology of the active production networks.

physics.soc-ph↗

arXiv2009

Limit distributions of scale-invariant probabilistic models of correlated random variables with the q-Gaussian as an explicit example

Extremization of the Boltzmann-Gibbs (BG) entropy under appropriate norm and width constraints yields the Gaussian distribution. Also, the basic solutions of the standard Fokker-Planck (FP) equation (related to the Langevin equation with additive noise), as well as the Central Limit Theorem attractors, are Gaussians. The simplest stochastic model with such features is N to infinity independent binary random variables, as first proved by de Moivre and Laplace. What happens for strongly correlated random variables? Such correlations are often present in physical situations as e.g. systems with long range interactions or memory. Frequently q-Gaussians become observed. This is typically so if the Langevin equation includes multiplicative noise, or the FP equation to be nonlinear. Scale-invariance, i.e. exchangeable binary stochastic processes, allow a systematical analysis of the relation between correlations and non-Gaussian distributions. In particular, a generalized stochastic model yielding q-Gaussians for all q (including q>1) was missing. This is achieved here by using the Laplace-de Finetti representation theorem, which embodies strict scale-invariance of interchangeable random variables. We demonstrate that strict scale invariance together with q-Gaussianity mandates the associated extensive entropy to be BG.

cond-mat.stat-mech↗

arXiv2008

On the robustness of q-expectation values and Renyi entropy

We study the robustness of functionals of probability distributions such as the Rényi and nonadditive S_q entropies, as well as the q-expectation values under small variations of the distributions. We focus on three important types of distribution functions, namely (i) continuous bounded (ii) discrete with finite number of states, and (iii) discrete with infinite number of states. The physical concept of robustness is contrasted with the mathematically stronger condition of stability and Lesche-stability for functionals. We explicitly demonstrate that, in the case of continuous distributions, once unbounded distributions and those leading to negative entropy are excluded, both Renyi and nonadditive S_q entropies as well as the q-expectation values are robust. For the discrete finite case, the Renyi and nonadditive S_q entropies and the q-expectation values are robust. For the infinite discrete case, where both Renyi entropy and q-expectations are known to violate Lesche-stability and stability respectively, we show that one can nevertheless state conditions which guarantee physical robustness.

cond-mat.stat-mech↗

arXiv2008

Stability criteria for q-expectation values

In statistical physics lately a specific kind of average, called the q-expectation value, has been extensively used in the context of q-generalized statistics dealing with distributions following power-laws. In this context q-expectation values appear naturally. After it has been recently shown that this non-linear functional is instable, under a very strong notion of stability, it is therefore of high interest to know sufficient conditions for when the results of q-expectations are robust under small variations of the underlying distribution function. We show that reasonable restrictions on the domain of admissible probability distributions restore uniform continuity for the q-expectation. Bounds on the size of admissible variations can be given. The practical usefulness of the theorems for estimating the robustness of the q-expectation value with respect to small variations is discussed.

cond-mat.stat-mech↗

arXiv2008

Socio-economical dynamics as a solvable spin system on co-evolving networks

We consider social systems in which agents are not only characterized by their states but also have the freedom to choose their interaction partners to maximize their utility. We map such systems onto an Ising model in which spins are dynamically coupled by links in a dynamical network. In this model there are two dynamical quantities which arrange towards a minimum energy state in the canonical framework: the spins, s_i, and the adjacency matrix elements, c_{ij}. The model is exactly solvable because microcanonical partition functions reduce to products of binomial factors as a direct consequence of the c_{ij} minimizing energy. We solve the system for finite sizes and for the two possible thermodynamic limits and discuss the phase diagrams.

cond-mat.stat-mech↗

arXiv2008

Physics of Evolution: Selection without Fitness

Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish. Survival probability is typically associated with the 'fitness' of a particular variation. In this paper we argue that the notion of fitness is an a posteriori concept, in the sense that one can assign higher fitness to species that survive but one can generally not derive or even measure fitness - or fitness landscapes - per se. For this reason we think that in a 'physical' theory of evolution such notions should be avoided. In this spirit, here we propose a random matrix model of evolution where selection mechanisms are encoded in the interaction matrices of species. We are able to recover some key facts of evolution dynamics, such as punctuated equilibrium, i.e. the existence of intrinsic large extinctions events, and, at the same time, periods of dramatic diversification, as known e.g. from fossil records. Further, we comment on two fundamental technical problems of a 'physics of evolution', the non-closedness of its phase space and the problem of co-evolving boundary conditions, apparent in all systems subject to evolution.

q-bio.PE↗

arXiv2008

Parkinson's Law Quantified: Three Investigations on Bureaucratic Inefficiency

We formulate three famous, descriptive essays of C.N. Parkinson on bureaucratic inefficiency in a quantifiable and dynamical socio-physical framework. In the first model we show how the use of recent opinion formation models for small groups can be used to understand Parkinson's observation that decision making bodies such as cabinets or boards become highly inefficient once their size exceeds a critical 'Coefficient of Inefficiency', typically around 20. A second observation of Parkinson - which is sometimes referred to as Parkinson's Law - is that the growth of bureaucratic or administrative bodies usually goes hand in hand with a drastic decrease of its overall efficiency. In our second model we view a bureaucratic body as a system of a flow of workers, which enter, become promoted to various internal levels within the system over time, and leave the system after having served for a certain time. Promotion usually is associated with an increase of subordinates. Within the proposed model it becomes possible to work out the phase diagram under which conditions bureaucratic growth can be confined. In our last model we assign individual efficiency curves to workers throughout their life in administration, and compute the optimum time to send them to old age pension, in order to ensure a maximum of efficiency within the body - in Parkinson's words we compute the 'Pension Point'.

physics.soc-ph↗

arXiv2008

A fast and efficient gene-network reconstruction method from multiple over-expression experiments

Reverse engineering of gene regulatory networks presents one of the big challenges in systems biology. Gene regulatory networks are usually inferred from a set of single-gene over-expressions and/or knockout experiments. Functional relationships between genes are retrieved either from the steady state gene expressions or from respective time series. We present a novel algorithm for gene network reconstruction on the basis of steady-state gene-chip data from over-expression experiments. The algorithm is based on a straight forward solution of a linear gene-dynamics equation, where experimental data is fed in as a first predictor for the solution. We compare the algorithm's performance with the NIR algorithm, both on the well known E.Coli experimental data and on in-silico experiments. We show superiority of the proposed algorithm in the number of correctly reconstructed links and discuss computational time and robustness. The proposed algorithm is not limited by combinatorial explosion problems and can be used in principle for large networks of thousands of genes.

q-bio.MN↗

arXiv2008

Pruning the Tree of Life: k-core Percolation as Selection Mechanism

We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known to be of power law type. The model incorporates both species-species interactions and ancestral relationships. The main novelty of this work is to show the feasibility of k-core percolation as a selection mechanism. We give theoretical predictions for the observable distributions, confirm their validity by computer simulation and report good agreement with the fossil data. A key feature of the proposed model is a co-evolving fitness landscape determined by the topology of the underlying species interactions, ecological niches emerge naturally. The predicted distributions are independent of the rate of speciation, i.e. whether one adopts an gradualist or punctuated view of evolution.

q-bio.PE↗

arXiv2008

Maximum entropy approach to central limit distributions of correlated variables

Hilhorst and Schehr recently presented a straight forward computation of limit distributions of sufficiently correlated random numbers \cite{hilhorst}. Here we present the analytical form of entropy which --under the maximum entropy principle (with ordinary constraints)-- provides these limit distributions. These distributions are not $q$-Gaussians and can not be obtained with Tsallis entropy.

cond-mat.stat-mech↗