Frank, Till D.
Frank, Till D.
Frank, Till D.
Now showing 1 - 9 of 9
- PublicationRate of Entropy Production as a Physical Selection Principle for Mode-Mode Transitions in Non-Equilibrium Systems: With an Application to a Non-Algorithmic Dynamic Message Buffer(EuroJournals, 2011-06)We examine a generic set of amplitude equations proposed earlier by Haken that describes the emergence and bifurcations of modes and spatio-temporal patterns of selforganizing non-equilibrium systems. We relate feedback parameters occurring in the amplitude equations to pumping processes associated with entropy production. In doing so, we show that the rate of entropy production determines which mode-mode transitions are allowed and which not. Roughly speaking, transitions occur from modes of low rate of entropy production towards modes of high rate of entropy production (selection principle). In line with the recent efforts in the field of physical intelligence, we outline how physical, non-algorithmic, self-organizing systems satisfying Haken’s amplitude equations may be used to design a dynamic input-output message buffer. The functioning of such a dynamic buffer again follows the aforementioned selection principle: the buffer switches between input and output modes in order to select modes with relatively high rates of entropy production. Moreover, only mode-mode transitions are allowed that increase the rate of entropy production of the active mode.
- PublicationNegative hysteresis in affordance experiments(Taylor & Francis, 2011)
;To perceive an affordance is to perceive what the current layout of surfaces affords with respect to one’s body size and action capabilities (Gibson, 1979). Affordance experiments have demonstrated that the shift from one mode of behavior to another exhibits the features typical of a self-organized dynamic system (Fitzpatrick et al., 1994; Richardson et al., 2007; van der Kamp et al., 1998), where stable patterns of behavior emerge from the lawful interaction between components of the animal-environment-task system. 109
- PublicationNAMBU BRACKET FORMULATION OF NONLINEAR BIOCHEMICAL REACTIONS BEYOND ELEMENTARY MASS ACTION KINETICS(Informa UK (Taylor & Francis), 2012-01)We develop a Nambu bracket formulation for a wide class of nonlinear biochemical reactions by exploiting previous work that focused on elementary biochemical mass action reactions. To this end, we consider general reaction mechanisms including for example enzyme kinetics. Furthermore, we go beyond elementary reactions and account for reactions involving stoichiometric coefficients different from unity. In particular, we show that the stoichiometric matrix of biochemical reactions can be expressed in terms of Nambu brackets. Finally, we solve the sign problem that arises in the context of coupled biochemical reactions.
360Scopus© Citations 4
- PublicationOscillatory nonequilibrium Nambu systems: the canonical-dissipative Yamaleev oscillator(Springer-Verlag, 2012-03-07)
; ;We study the emergence of oscillatory self-sustained behavior in a nonequilibrium Nambu system that features an exchange between different kinetical and potential energy forms. To this end, we study the Yamaleev oscillator in a canonical-dissipative framework. The bifurcation diagram of the nonequilibrium Yamaleev oscillator is derived and different bifurcation routes that are leading to limit cycle dynamics and involve pitchfork and Hopf bifurcations are discussed. Finally, an analytical expression for the probability density of the stochastic nonequilibrium oscillator is derived and it is shown that the shape of the density function is consistent with the oscillator properties in the deterministic case. 340Scopus© Citations 16
- PublicationVersatility of Cooperative Transcriptional Activation: A Thermodynamical Modeling Analysis for Greater-Than-Additive and Less-Than-Additive Effects(Public Library of Science, 2012-04-10)
; ; ;We derive a statistical model of transcriptional activation using equilibrium thermodynamics of chemical reactions. We examine to what extent this statistical model predicts synergy effects of cooperative activation of gene expression. We determine parameter domains in which greater-than-additive and less-than-additive effects are predicted for cooperative regulation by two activators. We show that the statistical approach can be used to identify different causes of synergistic greater-than-additive effects: nonlinearities of the thermostatistical transcriptional machinery and three-body interactions between RNA polymerase and two activators. In particular, our model-based analysis suggests that at low transcription factor concentrations cooperative activation cannot yield synergistic greater-than-additive effects, i.e., DNA transcription can only exhibit less-than-additive effects. Accordingly, transcriptional activity turns from synergistic greater-than-additive responses at relatively high transcription factor concentrations into less-than-additive responses at relatively low concentrations. In addition, two types of re-entrant phenomena are predicted. First, our analysis predicts that under particular circumstances transcriptional activity will feature a sequence of less-than-additive, greater-than-additive, and eventually less-than-additive effects when for fixed activator concentrations the regulatory impact of activators on the binding of RNA polymerase to the promoter increases from weak, to moderate, to strong. Second, for appropriate promoter conditions when activator concentrations are increased then the aforementioned re-entrant sequence of less-than-additive, greater-than-additive, and less-than-additive effects is predicted as well. Finally, our model-based analysis suggests that even for weak activators that individually induce only negligible increases in promoter activity, promoter activity can exhibit greater-than-additive responses when transcription factors and RNA polymerase interact by means of three-body interactions. Overall, we show that versatility of transcriptional activation is brought about by nonlinearities of transcriptional response functions and interactions between transcription factors, RNA polymerase and DNA. 264Scopus© Citations 10
- PublicationThree-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data(Oxford University Press, 2016-04-14)
; ; ;Signal integration determines cell fate on the cellular level, affects cognitive processes and affective responses on the behavioural level, and is likely to be involved in psychoneurobiological processes underlying mood disorders. Interactions between stimuli may subjected to time effects. Time-dependencies of interactions between stimuli typically lead to complex cell responses and complex responses on the behavioural level. We show that both three-factor models and time series models can be used to uncover such time-dependencies. However, we argue that for short longitudinal data the three factor modelling approach is more suitable. In order to illustrate both approaches, we re-analysed previously published short longitudinal data sets. We found that in human embryonic kidney 293 cells cells the interaction effect in the regulation of extracellular signal-regulated kinase (ERK) 1 signalling activation by insulin and epidermal growth factor is subjected to a time effect and dramatically decays at peak values of ERK activation. In contrast, we found that the interaction effect induced by hypoxia and tumour necrosis factoralpha for the transcriptional activity of the human cyclo-oxygenase-2 promoter in HEK293 cells is time invariant at least in the first 12-h time window after stimulation. Furthermore, we applied the three-factor model to previously reported animal studies. In these studies, memory storage was found to be subjected to an interaction effect of the beta-adrenoceptor agonist clenbuterol and certain antagonists acting on the alpha-1-adrenoceptor / glucocorticoid-receptor system. Our model-based analysis suggests that only if the antagonist drug is administer in a critical time window, then the interaction effect is relevant. 318
- PublicationNFκB and HIF display synergistic behaviour during hypoxic inflammation(Springer-Verlag, 2011-11-09)
; ; ;The oxygen-sensitive transcription factor hypoxia inducible factor (HIF) is a key regulator of gene expression during adaptation to hypoxia. Crucially, inflamed tissue often displays regions of prominent hypoxia. Recent studies have shown HIF signalling is intricately linked to that of the pro-inflammatory transcription factor nuclear factor kappa B (NFκB) during hypoxic inflammation. We describe the relative temporal contributions of each to hypoxia-induced inflammatory gene expression and investigate the level of crosstalk between the two pathways using a novel Gaussia princeps luciferase (Gluc) reporter system. Under the control of an active promoter, Gluc is expressed and secreted into the cell culture media, where it can be sampled and measured over time. Thus, Gluc constructs under the control of either HIF or NFκB were used to resolve their temporal transcriptional dynamics in response to hypoxia and to cytokine stimuli, respectively. We also investigated the interactions between HIF and NFκB activities using a construct containing the sequence from the promoter of the inflammatory gene cyclooxygenase 2 (COX-2), which includes functionally active binding sites for both HIF and NFκB. Finally, based on our experimental data, we constructed a mathematical model of the binding affinities of HIF and NFκB to their respective response elements to analyse transcriptional crosstalk. Taken together, these data reveal distinct temporal HIF and NFκB transcriptional activities in response to hypoxic inflammation. Furthermore, we demonstrate synergistic activity between these two transcription factors on the regulation of the COX-2 promoter, implicating a co-ordinated role for both HIF and NFκB in the expression of COX-2 in hypoxic inflammation. 521Scopus© Citations 59
- PublicationNegative hysteresis in the behavioral dynamics of the affordance graspable(Springer - Psychonomic Society, 2013-03-08)
; ;One commonly perceives whether a visible object will afford grasping with one hand or with both hands. In experiments in which differently sized objects of a fixed type are presented, the transition from using one of these manual modes to the other depends on the ratio of object size to hand span and on the presentation sequence, with size increasing versus decreasing. Conventional positive hysteresis (i.e., a larger transition ratio for the increasing sequence) can be accommodated by the order parameter dynamics that typify self-organizing systems (Lopresti-Goodman, Turvey, and Frank, Attention, Perception, & Psychophysics 73:1948–1965, 2011). Here we identified and addressed conditions of unconventional negative hysteresis (i.e., a larger transition ratio for the decreasing sequence). They suggest a second control parameter in the self-organization of affordance perception, one that is seemingly regulated by inhibitory dynamics occurring in the agent–task–environment system. Our experimental results and modeling extend the investigation of affordance perception within dynamical systems theory. 350Scopus© Citations 27
- PublicationCatching transcriptional regulation by thermostatistical modeling(IOP Publishing, 2012-08-07)
; ; ;Gene expression is frequently regulated by multiple transcription factors (TFs). Thermostatistical methods allow for a quantitative description of interactions between TFs, RNA polymerase and DNA, and their impact on the transcription rates. We illustrate three different scales of the thermostatistical approach: the microscale of TF molecules, the mesoscale of promoter energy levels and the macroscale of transcriptionally active and inactive cells in a cell population. We demonstrate versatility of combinatorial transcriptional activation by exemplifying logic functions, such as AND and OR gates. We discuss a metric for cell-to-cell transcriptional activation variability known as Fermi entropy. Suitability of thermostatistical modeling is illustrated by describing the experimental data on transcriptional induction of NFκB and the c-Fos protein. 295Scopus© Citations 8