A multidisciplinary survey of modeling techniques for biochemical networks

All processes of life are dominated by networks of interacting biochemical components. The purpose of modeling these networks is manifold. From a theoretical point of view it allows the exploration of network structures and dynamics, to find emergent properties or to explain the organization and evolution of networks. From a practical point of view, in silico experiments can be performed that would be very expensive or impossible to achieve in the laboratory, such as hypothesis-testing with regard to knockout experiments or overexpression, or checking the validity of a proposed molecular mechanism. The literature on modeling biochemical networks is growing rapidly and the motivations behind different modeling techniques are sometimes quite distant from each other. To clarify the current context, we present a systematic overview of the different philosophies to model biochemical networks. We put particular emphasis on three main domains which have been playing a major role in the past, namely: mathematics with ordinary and partial differential equations, statistics with stochastic simulation algorithms, Bayesian networks and Markov chains, and the field of computer science with process calculi, term rewriting systems and state based systems. For each school, we evaluate advantages and disadvantages such as the granularity of representation, scalability, accessibility or availability of analysis tools. Following this, we describe how one can combine some of those techniques and thus take advantages of several techniques through the use of bridging tools. Finally, we propose a next step for modeling biochemical networks by using artificial chemistries and evolutionary computation. This work was funded by ESIGNET (Evolving Cell Signaling Networks in Silico), an European Integrated Project in the EU FP6 NEST Initiative (contract no. 12789)

Determining Distributions of Security Means for WSNs based on the Model of a Neighbourhood Watch

Neighbourhood watch is a concept that allows a community to distribute a complex security task in between all members. Members of the community carry out individual security tasks to contribute to the overall security of it. It reduces the workload of a particular individual while securing all members and allowing them to carry out a multitude of security tasks. Wireless sensor networks (WSNs) are composed of resource-constraint independent battery driven computers as nodes communicating wirelessly. Security in WSNs is essential. Without sufficient security, an attacker is able to eavesdrop the communication, tamper monitoring results or deny critical nodes providing their service in a way to cut off larger network parts. The resource-constraint nature of sensor nodes prevents them from running full-fledged security protocols. Instead, it is necessary to assess the most significant security threats and implement specialised protocols. A neighbourhood-watch inspired distributed security scheme for WSNs has been introduced by Langend\"orfer. Its goal is to increase the variety of attacks a WSN can fend off. A framework of such complexity has to be designed in multiple steps. Here, we introduce an approach to determine distributions of security means on large-scale static homogeneous WSNs. Therefore, we model WSNs as undirected graphs in which two nodes connected iff they are in transmission range. The framework aims to partition the graph into $n$ distinct security means resulting in the targeted distribution. The underlying problems turn out to be NP hard and we attempt to solve them using linear programs (LPs). To evaluate the computability of the LPs, we generate large numbers of random {\lambda}-precision unit disk graphs (UDGs) as representation of WSNs. For this purpose, we introduce a novel {\lambda}-precision UDG generator to model WSNs with a minimal distance in between nodes

Underlying causal factors associated with construction worker fatalities involving stepladders

Stepladders are frequently utilized on construction projects as a means of access to elevation. Stepladder heights commonly range from 4 feet (1.2 m) to 14 feet (4.3 m). Since these heights are not extreme, there is a common misperception that stepladder use presents a low risk. On the contrary, extreme care must be exercised to ensure that work on stepladders is performed safely, as described in the conspicuously located recommendations and brightly-colored warnings that adorn virtually all newly-purchased equipment. Despite this, accidents involving stepladders occur on a regular basis.  This study was conducted to better understand the underlying causes of these accidents. The narrative descriptions of 180 stepladder-related fatalities were obtained from the U.S. Occupational Safety and Health Administration and were analyzed to identify the at-risk behaviors that preceded the fatality incidents. The results showed that most of the incidents should have been anticipated and could have been avoided. Unsafe practices such as improper lockout-tagout of electrical equipment, loss of balance, working on a folded stepladder, over-reaching, straddling the ladder, “walking” the ladder, poor footing, and unstable/shifting ladders, among others were identified. Virtually all of these fatalities could have been avoided by adhering to the guidelines posted on the stepladders and by complying with basic safe construction practices.

Coherence-controlled transparency and far-from-degenerate parametric gain in a strongly-absorbing Doppler-broadened medium

An inversionless gain of anti-Stokes radiation above the oscillation threshold in an optically-dense far-from-degenerate double-Lambda Doppler-broadened medium accompanied by Stokes gain is predicted. The outcomes are illustrated with numerical simulations applied to sodium dimer vapor. Optical switching from absorption to gain via transparency controlled by a small variation of the medium and of the driving radiation parameters which are at a level less than one photon per molecule is shown. Related video/audio clips see in: A.K. Popov, S.A. Myslivets, and T.F. George, Optics Express Vol. 7, No 3, 148 (2000)(http://epubs.osa.org/oearchive/source/22947.htm) or download: http://kirensky.krasn.ru/popov/opa/opa.htmComment: 4 pages, 3 eps figures, to be published in Optics Letters, vol.25, No 18 (2000), minor style changes and reference correctio

Membrane computing with water

We introduce water tank systems as a new class of membrane systems inspired by a decentrally controlled circulation of water or other liquids throughout cells called tanks and capillaries called pipes. To our best knowledge, this is the first proposal addressing the behavioural principle of floating and stored water for modelling of information processing in terms of membrane computing. The volume of water within a tank stands for a non-negative rational value when acting in an analogue computation or it can be interpreted in a binary manner by distinction of “(nearly) full” or “(nearly) empty”. Water tanks might be interconnected by pipes for directed transport of water. Each pipe can be equipped with valves which in turn either fully open or fully close the hosting pipe according to permanent measurements whether the filling level in a dedicated water tank exceeds a certain threshold or not. We demonstrate dedicated water tank systems together with simulation case studies: a ring oscillator for generation of clock signals and for iteratively making available amounts of water in a cyclic scheme, analogue arithmetics by implementation of addition, non-negative subtraction, division, and multiplication complemented by systems in binary mode for implementation of selected logic gates

Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems

Exploration of chronobiological systems emerges as a growing research field within bioinformatics focusing on various applications in medicine, agriculture, and material sciences. From a systems biological perspective, the question arises whether biological control systems for regulation of oscillatory signals and their technical counterparts utilise similar mechanisms. If so, modelling approaches and parameterisation adopted from building blocks can help to identify general components for frequency control in circadian clocks along with gaining insight into mechanisms of clock synchronisation to external stimuli like the daily rhythm of sunlight and darkness. Phase-locked loops could be an interesting candidate in this context. Both, biology and engineering, can benefit from a unified view resulting from systems modularisation. In a first experimental study, we analyse a model of coupled repressilators. We demonstrate its ability to synchronise clock signals in a monofrequential manner. Several oscillators initially deviate in phase difference and frequency with respect to explicit reaction and diffusion rates. Accordingly, the duration of the synchronisation process depends on dedicated reaction and diffusion parameters whose settings still lack to be sufficiently captured analytically

A SF5 Derivative of Triphenylphosphine as an Electron-Poor Ligand Precursor for Rh and Ir Complexes

The synthesis of the triarylphosphine, P(p-C6H4SF5)3 containing a SF5 group, has been achieved. The experimental and theoretical studies showed that P(p-C6H4SF5)3 is a weaker σ-donor when compared with other substituted triarylphosphines, which is consistent with the electron-withdrawing effect of the SF5 moiety. The studies also revealed a moderate air stability of the phosphine. The σ-donor capabilities of P(p-C6H4SF5)3 were estimated from the phosphorus-selenium coupling constant in SeP(p-C6H4SF5)3 and by DFT calculations. The behavior of P(p-C6H4SF5)3 as ligand has been investigated by the synthesis of the iridium and rhodium complexes [MCl(COD){P(p-C6H4SF5)3}], [MCl(CO)2{P(p-C6H4SF5)3}2] (M = Ir, Rh), or [Rh(µ-Cl)(COE){P(p-C6H4SF5)3}]2, and the molecular structures of [IrCl(COD){P(p-C6H4SF5)3}] and [Rh(µ-Cl)(COE){P(p-C6H4SF5)3}]2 were determined by single X-ray diffraction. The structures revealed a slightly larger cone angle for P(p-C6H4SF5)3 when compared to other para-substituted triarylphosphines.Deutsche ForschungsgemeinschaftPeer Reviewe

Applying Membrane Systems in Food Engineering

Food engineering deals with manufacturing, packaging and distributing systems for drug and food products. In this work, we discuss about the applicability of membrane systems to model environmental conditions and their e ects on the produces during storage of fresh fruits and vegetables. In particular, we are interested in abstract molecular interactions that occur between produce, lm and surrounding atmosphere factors involved in fresh fruit and vegetable package designs. We present a basic implementation to simulate the dynamical behaviour of these systems, due to gas exchanges and temperature uctuations. Additionally, we reveal the bene ts of this modelling approach and suggest some extensions as future directions to be considered