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

Supraleitung, Magnetismus und Nicht-Fermi-Flüssigkeits-Verhalten in Schwere-Fermionen-Systemen

Diese Arbeit befasst sich mit dem Wechselspiel von magnetischer Ordnung und Supraleitung (SL), sowie der Beobachtung von sogenanntem Nicht-Fermi-Flüssigkeits (NFF)-Verhalten in einer speziellen Klasse intermetallischer Verbindungen, den Schwere-Fermionen (SF)-Systemen. Die elektronische spezifische Wärme sowie die Pauli-Suszeptibilität dieser Systeme sind im Vergleich zu einfachen Metallen um ein bis zwei Größenordnungen erhöht. Die physikalischen Eigenschaften lassen sich durch die Annahme wechselwirkungsfreier Quasiteilchen mit stark erhöhter effektiver Masse m* beschreiben. In SF-Supraleitern sind die schweren Quasiteilchen sowohl für das Auftreten magnetischer Ordnung als auch für die SL verantwortlich. Das Tieftemperaturverhalten von SF-Systemen lässt sich häufig nach dem von Landau vorgeschlagenen Fermi-Flüssigkeits (FF)-Modell beschreiben. In jüngster Zeit gelangen jedoch immer mehr Systeme in den Blickpunkt, die sich nicht mit dieser Theorie beschreiben lassen. Eine häufig diskutierte Erklärung für dieses sogenannte NFF-Verhalten ist die Nähe des untersuchten Systems zu einem „Quantenkritischen Punkt“ (QKP). Dies bezeichnet den Punkt im magnetischen Phasendiagramm, an dem die magnetische Ordnungstemperatur TM auf T = 0 abnimmt. Die vorliegende Arbeit enthält zunächst eine Beschreibung der grundlegenden experimentellen Techniken und Messmethoden. In einer Abhandlung der theoretischen Grundlagen werden wesentliche Eigenschaften von SF-Systemen sowie einige theoretische Modelle, welche sich mit dem Auftreten von NFF-Verhalten beschäftigen, vorgestellt. Im experimentellen Teil der Arbeit wird zunächst das SF-System CeNi2Ge2 behandelt, welches ausgeprägtes NFF-Verhalten bei Atmosphärendruck zeigt und das mit Abstand reinste System (r0 » 0.1mWcm) unter den Nicht-Fermi-Flüssigkeiten ist. Es wurde eine relativ starke Probenabhängigkeit im Tieftemperaturverhalten beobachtet, insbesondere wurde an einigen Proben SL im elektrischen Widerstand beobachtet. Um zu untersuchen, ob dies eine intrinsische Eigenschaft von CeNi2Ge2 ist, sowie zur Analyse von NFF-Effekten, wurde eine systematische Untersuchung an leicht von der exakten Stöchiometrie abweichenden Polykristallen durchgeführt. Die Ergebnisse zeigen einen systematischen Zusammenhang zwischen der Einwaage der Proben und deren physikalischen Eigenschaften. Für B ³ 6T kann in sehr sauberen Proben (RRR ³ 200) nahe der stöchiometrischen Zusammensetzung das Auftreten einer intrinsischen Hochfeldanomalie erfasst werden. Im Nullfeld bzw. für Felder B £ 2T können zwei weitere Anomalien an einer ganzen Reihe von Proben festgestellt werden, deren intrinsische Natur jedoch nicht belegt werden kann. Dabei zeigen Proben mit einem leichten Ni-Überschuss den Ansatz eines supraleitenden Phasenübergangs und Proben mit einem leichten Ni-Mangel eine als „A“-Phase bezeichnete Anomalie unbekannter Natur. Für alle in r(T) untersuchten Proben wird im Nullfeld ein NFF-Verhalten beobachtet, weshalb CeNi2Ge2 auf der paramagnetischen Seite sehr nahe an einem QKP angenommen werden kann. Allerdings wird in thermodynamischen Messungen hierzu widersprüchliches Verhalten beobachtet. Dies könnte auf ein Zusammenbrechen des Quasiteilchen-Konzepts am QKP hindeuten. Anschließend werden Untersuchungen am SF-Supraleiter CeCu2(Si0.9Ge0.1)2 vorgestellt. Die Dotierung von isoelektrischen Germanium-Atomen am Silizium-Platz führt zu einer Vergrößerung des Einheitszellenvolumens und damit zu einer Reduktion der Hybridisierungsstärke zwischen 4f- und Valenzelektronen. Dies führt zu einer Stabilisierung der schon für x = 0 beobachteten Spin-Dichte-Wellen-artigen, sogenannten „A“-Phase, wobei TA deutlich ansteigt. Die Untersuchungen an den Einkristallen zeigen neben der schon bekannten „A“-Phase das Auftreten einer weiteren Anomalie unterhalb von TA, deren genaue Natur zur Zeit noch untersucht wird. Eine charakteristische Eigenschaft der Dotierungsreihe U1-xThxBe13 ist der nicht-monotone Verlauf von Tc(x), der verbunden ist mit dem Auftreten eines zweiten Phasenüberganges Tc2 innerhalb der supraleitenden Phase im Dotierungsbereich xc1 » 1.9% £ x £ 4.55% » xc2. Die Untersuchungen der Wechselfeldsuszeptibilität und des Meissner-Effektes geben Aufschluss über die Entwicklung der SL in diesem System, wobei speziell der Konzentrationsbereich x > xc2 interessierte, da in thermodynamischen Untersuchungen die beobachtete Anomalie für x > 3% stark abnimmt und für x ® xc2 nicht mehr aufgelöst werden kann, so dass für x > xc2 keine Aussagen über das Auftreten von SL mehr möglich sind. Die Untersuchungen können nun auch für Th-Konzentrationen oberhalb von xc2 das Vorliegen von Volumensupraleitung nachweisen und somit das T-x-Phasendiagramm dieser Dotierungsreihe vervollständigen. An den hochwertigen SF-Systemen Yb2Ni2Al, YbCo2Ge2 und YbRh2Si2 bzw. YbRh2(Si0.95Ge0.05)2 wurde das Auftreten von NFF-Verhalten untersucht. Die Ergebnisse lokalisieren Yb2Ni2Al und YbCo2Ge2 auf der unmagnetischen Seite eines QKP, YbRh2Si2 (TN » 65mK) auf der magnetischen Seite eines QKP und YbRh2(Si0.95Ge0.05)2 in unmittelbarer Nähe eines QKP. Hier zeigt der elektrische Widerstand über drei Dekaden der Temperatur (10mK £ T £ 10K) ein lineares Verhalten. Dabei belegt der niedrige Restwiderstand (r0 = 5mWcm), dass das NFF-Verhalten nicht durch Unordnung sondern durch die Nähe zum QKP hervorgerufen wird. Es wird gezeigt, dass ein ähnliches Skalenverhalten wie bei CeCu5.9Au0.1 vorliegt, so dass das hierfür entwickelte Szenario eines lokalen QKP möglicherweise auch auf YbRh2(Si0.95Ge0.05)2 anwendbar ist

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

A Health Check of Avondale\u27s Distance Education Program: Where Have we Been? Where are we Going Next?

Avondale College of Higher Education has been offering tertiary courses for over 120 years. In the past two decades, this institution has extended its programs to include distance courses for students who opt to study online or are not able to attend on-campus courses at Avondale’s Lake Macquarie and Sydney campuses. While all of the institutions courses are evaluated on a regular basis, no formal evaluation had ever been undertaken of the distance education program as a whole. During 2017, a mixed methods research project was conducted to gather evaluative data from recent and current distance students using questionnaires and focus groups. The results of the study provide insight into the extent to which the distance education program at the College provides a space in which learning relationships can develop in online communities. Also, suggestions for future improvement and further research recommendations are provided. Findings of this study may be of interest to educators and administrators who incorporate online components in their curricula

Rule-based spatial modeling with diffusing, geometrically constrained molecules

<p>Abstract</p> <p>Background</p> <p>We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined.</p> <p>For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided.</p> <p>Results</p> <p>Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa.</p> <p>Conclusions</p> <p>We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.</p

Role-Playing: A Smorgasbord of Learning Types

One tertiary institution sought to research the perceptions that tertiary students have of role-plays as a means of learning. Role-plays were used across a range of disciplines at that institution including: teacher training, business and chemistry. Each of these disciplines used a role-play in their classes and then collected opinions from the students on the usefulness of the activity. It was discovered that students value role-plays as a means to challenge preconceived ideas, encourage creative thinking, assist students in applying theory to practice, make lessons fun and provide active learning experiences that increase student learning and engagement

The Influence of Human Support on the Effectiveness of an Online Mental Wellbeing Intervention

Purpose: To compare the influence of three modes of human support on the outcomes of an online, lifestyle-focused mental health promotion intervention. Background: There is a need for efficacious lifestyle interventions to promote the mental wellbeing of both healthy and clinical cohorts. Evidence regarding the usefulness of adding human support (i.e. guidance) to improve the outcomes of online interventions for clinical populations is mixed,1-3 however little is known about healthy cohorts. Methods: A total of 458 participants self-selected to participate in a 10-week online, multimodal lifestyle intervention that addressed mental wellbeing. The participants were randomized into three groups, differentiated by support mode: standard - automated emails only (S); standard plus personalised SMS messages (S+pSMS); standard plus videoconference support (S+VCS). At pre- and post-intervention, the participants completed the following measures: the ‘mental health’ and ‘vitality’ sub-scales from the Short Form Health Survey (SF-36); Depression Anxiety and Stress Scales (DASS-21); Satisfaction With Life (SWL) scale; and Flourishing scale. Results: A total of 320 participants (S, n=103; S+pSMS, n=114; S+VCS, n=103) completed the study. Significant within-group changes were recorded from pre- to post-intervention in all groups for every outcome measure (PP=0.77), vitality (P=0.65), depression (P=0.93), anxiety (P=0.25), stress (P=0.57), SWL (P=0.65) or flourishing (P=0.99). Attendance at the weekly videoconference support sessions was poor, but those who attended seven or more of the ten sessions experienced significantly better outcomes in mental health (P=.006, d=0.71), vitality (P=.005, d=0.73), depression (P=.04, d=0.54), and SWL (P=.046, d=0.50), than those who attended less than seven. Conclusions: A lifestyle-focused, online mental health promotion intervention enhanced measures of mental wellbeing among a healthy cohort, irrespective of the human support provided. Supplementing a psychological intervention with videoconference support might improve outcomes, when attendance is optimised

The Effect of an Online Multimodal Lifestyle Intervention on Mental Health and Emotional Wellness: A Randomised Control Trial

PURPOSE: This study examined the effect of an online multimodal lifestyle intervention, which incorporated evidence-based strategies from Lifestyle Medicine and Positive Psychology, on the mental health and emotional wellness of adults throughout Australia and New Zealand. BACKGROUND: Common mental health disorders have reached epidemic proportions worldwide (1). In the US, one in five adults have a common mental health disorder (2), and in Australia, a similar number have experienced an affective disorder in the past twelve months (3). Antidepressants are ranked in the top three most commonly used therapeutic drug classes in the US (4), and are the most commonly used psychotropic medications in Australia (5). A new paradigm is needed focusing on primary prevention to address this burgeoning mental health problem. METHODS: 508 individuals self-selected to participate in the study and were randomized to an intervention or delay-controlled group. Both groups completed an online survey using validated instruments which assessed the participantsʼ emotional wellness at three intervals: baseline, and at 3 months and 6 months post-intervention. 425 individuals completed the baseline assessment and entered the study (intervention n=217, control group n=208), and 359 (84%) completed the post intervention questionnaire. The intervention group participated in a 10-week online multimodal lifestyle intervention, called “The Live More Project” also known as The Lift Project”(6). RESULTS: Overall, the cohort was in the ‘normal’ range at baseline for the domains of emotional wellness measured. At 3 months, significant reductions were observed in symptoms of ‘depression’ (-31%, p\u3c0.001), ‘anxiety’ (-43%, p\u3c0.001) and ‘stress’ (-22%, p\u3c0.001) in the intervention compared to the control group. Significant improvements were observed in ‘mental health’ (8%, p\u3c0.001), ‘vitality’ (18%, p\u3c0.001) and overall ‘life 2 satisfaction’ (8%, p\u3c0.001). Improvements in the measures of mental health and emotional wellness were generally sustained in the 6-month follow-up. CONCLUSIONS: This study supports the use of an online multimodal lifestyle intervention combining strategies from Lifestyle Medicine and Positive Psychology for the promotion of mental health and emotional wellness among normal populations (i.e. primary prevention). Further analyses will examine the impact of the intervention on subnormal populations to assess its potential role in secondary and tertiary prevention