16,985 research outputs found
Synthetic biologyâputting engineering into biology
Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesisâsynthetic biologyâs system fabrication processâsupplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.
BlenX-based compositional modeling of complex reaction mechanisms
Molecular interactions are wired in a fascinating way resulting in complex
behavior of biological systems. Theoretical modeling provides a useful
framework for understanding the dynamics and the function of such networks. The
complexity of the biological networks calls for conceptual tools that manage
the combinatorial explosion of the set of possible interactions. A suitable
conceptual tool to attack complexity is compositionality, already successfully
used in the process algebra field to model computer systems. We rely on the
BlenX programming language, originated by the beta-binders process calculus, to
specify and simulate high-level descriptions of biological circuits. The
Gillespie's stochastic framework of BlenX requires the decomposition of
phenomenological functions into basic elementary reactions. Systematic
unpacking of complex reaction mechanisms into BlenX templates is shown in this
study. The estimation/derivation of missing parameters and the challenges
emerging from compositional model building in stochastic process algebras are
discussed. A biological example on circadian clock is presented as a case study
of BlenX compositionality
Trend-based analysis of a population model of the AKAP scaffold protein
We formalise a continuous-time Markov chain with multi-dimensional discrete state space model of the AKAP scaffold protein as a crosstalk mediator between two biochemical signalling pathways. The analysis by temporal properties of the AKAP model requires reasoning about whether the counts of individuals of the same type (species) are increasing or decreasing. For this purpose we propose the concept of stochastic trends based on formulating the probabilities of transitions that increase (resp. decrease) the counts of individuals of the same type, and express these probabilities as formulae such that the state space of the model is not altered. We define a number of stochastic trend formulae (e.g. weakly increasing, strictly increasing, weakly decreasing, etc.) and use them to extend the set of state formulae of Continuous Stochastic Logic. We show how stochastic trends can be implemented in a guarded-command style specification language for transition systems. We illustrate the application of stochastic trends with numerous small examples and then we analyse the AKAP model in order to characterise and show causality and pulsating behaviours in this biochemical system
Modeling biological systems with delays in Bio-PEPA
Delays in biological systems may be used to model events for which the
underlying dynamics cannot be precisely observed, or to provide abstraction of
some behavior of the system resulting more compact models. In this paper we
enrich the stochastic process algebra Bio-PEPA, with the possibility of
assigning delays to actions, yielding a new non-Markovian process algebra:
Bio-PEPAd. This is a conservative extension meaning that the original syntax of
Bio-PEPA is retained and the delay specification which can now be associated
with actions may be added to existing Bio-PEPA models. The semantics of the
firing of the actions with delays is the delay-as-duration approach, earlier
presented in papers on the stochastic simulation of biological systems with
delays. These semantics of the algebra are given in the Starting-Terminating
style, meaning that the state and the completion of an action are observed as
two separate events, as required by delays. Furthermore we outline how to
perform stochastic simulation of Bio-PEPAd systems and how to automatically
translate a Bio-PEPAd system into a set of Delay Differential Equations, the
deterministic framework for modeling of biological systems with delays. We end
the paper with two example models of biological systems with delays to
illustrate the approach.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Grain Surface Models and Data for Astrochemistry
AbstractThe cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of âŒ25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions
Formal methods for modeling and analysis of hybrid systems
A technique based on the use of a quantifier elimination decision procedure for real closed fields and simple theorem proving to construct a series of successively finer qualitative abstractions of hybrid automata is taught. The resulting abstractions are always discrete transition systems which can then be used by any traditional analysis tool. The constructed abstractions are conservative and can be used to establish safety properties of the original system. The technique works on linear and non-linear polynomial hybrid systems: the guards on discrete transitions and the continuous flows in all modes can be specified using arbitrary polynomial expressions over the continuous variables. An exemplar tool in the SAL environment built over the theorem prover PVS is detailed. The technique scales well to large and complex hybrid systems
Quantum Transition State Theory for proton transfer reactions in enzymes
We consider the role of quantum effects in the transfer of hyrogen-like
species in enzyme-catalysed reactions. This study is stimulated by claims that
the observed magnitude and temperature dependence of kinetic isotope effects
imply that quantum tunneling below the energy barrier associated with the
transition state significantly enhances the reaction rate in many enzymes. We
use a path integral approach which provides a general framework to understand
tunneling in a quantum system which interacts with an environment at non-zero
temperature. Here the quantum system is the active site of the enzyme and the
environment is the surrounding protein and water. Tunneling well below the
barrier only occurs for temperatures less than a temperature which is
determined by the curvature of potential energy surface near the top of the
barrier. We argue that for most enzymes this temperature is less than room
temperature. For physically reasonable parameters quantum transition state
theory gives a quantitative description of the temperature dependence and
magnitude of kinetic isotope effects for two classes of enzymes which have been
claimed to exhibit signatures of quantum tunneling. The only quantum effects
are those associated with the transition state, both reflection at the barrier
top and tunneling just below the barrier. We establish that the friction due to
the environment is weak and only slightly modifies the reaction rate.
Furthermore, at room temperature and for typical energy barriers environmental
degrees of freedom with frequencies much less than 1000 cm do not have a
significant effect on quantum corrections to the reaction rate.Comment: Aspects of the article are discussed at
condensedconcepts.blogspot.co
The impact of high density receptor clusters on VEGF signaling
Vascular endothelial growth factor (VEGF) signaling is involved in the
process of blood vessel development and maintenance. Signaling is initiated by
binding of the bivalent VEGF ligand to the membrane-bound receptors (VEGFR),
which in turn stimulates receptor dimerization. Herein, we discuss experimental
evidence that VEGF receptors localize in caveloae and other regions of the
plasma membrane, and for other receptors, it has been shown that receptor
clustering has an impact on dimerization and thus also on signaling. Overall,
receptor clustering is part of a complex ecosystem of interactions and how
receptor clustering impacts dimerization is not well understood. To address
these questions, we have formulated the simplest possible model. We have
postulated the existence of a single high affinity region in the cell membrane,
which acts as a transient trap for receptors. We have defined an ODE model by
introducing high- and low-density receptor variables and introduce the
corresponding reactions from a realistic model of VEGF signal initiation.
Finally, we use the model to investigate the relation between the degree of
VEGFR concentration, ligand availability, and signaling. In conclusion, our
simulation results provide a deeper understanding of the role of receptor
clustering in cell signaling.Comment: In Proceedings HSB 2013, arXiv:1308.572
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