An information-carrying and knowledge-producing molecular machine. A Monte-Carlo simulation

The concept called Knowledge is a measure of the quality of genetically transferred information. Its usefulness is demonstrated quantitatively in a Monte-Carlo simulation on critical steps in a origin of life model. The model describes the origin of a bio-like genetic apparatus by a long sequence of physical-chemical steps: it starts with the presence of a self-replicating oligomer and a specifically structured environment in time and space that allow for the formation of aggregates such as assembler-hairpins-devices and, at a later stage, an assembler-hairpins-enzyme device—a first translation machin

Survival Chances of Mutants Starting With One Individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given. First case: one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N individuals of the mutant $$W^{{\text{S}}}_{{\text{n}}} {\left( N \right)}$$ after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and $$W^{{\text{S}}}_{{\text{n}}} {\left( N \right)}$$ after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction $$W^{{\text{S}}}_{\infty } {\left( 0 \right)}$$ are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N p individuals of the primary mutant and N m individuals of the new form $$W^{{\text{M}}}_{{\text{n}}} {\left( {N_{{\text{p}}} ,\;N_{{\text{m}}} } \right)}$$ after the multiplication phase M of the n-th generation (probability ɛ of an error in the replication of the primary mutant giving the new form) and $$W^{{\text{S}}}_{{\text{n}}} {\left( {N_{{\text{p}}} ,\;N_{{\text{m}}} } \right)}$$ after the following selection phase S (probabilities β p and β m that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtaine

A Computer-Glimpse of the Origin of Life

Evolution is assumed to begin in a very particular compartmentalized location with periodic conditions. A highly diversified world is the driving force for the continuous increase in complexity by colonizing increasingly less favourable regions. Modeling the "origin-of-life” a Darwinian cyclic process is simulated (multiplication with sporadic errors followed by a construction and selection). Starting from a RNA-world (R-strands of R1 and R2 monomers building Hairpin-Assembler devices) and introducing another kind of monomers (A1 and A2 which interlink to the Hairpin-Assembler devices such that they become bound and form an A-oligomer) it is shown that a simple translation apparatus evolves producing enzymes (specific sequences of A1 and A2 monomers given by the sequences of R1 and R2 monomers on the assembler-strands). Later on D-strands are introduced, which are not capable of participating in the synthesis of A-oligomers. These D-strands become carriers of the genetic information and induce the formation of increasingly complex entities of functionally interplaying component

An information-carrying and knowledge-producing molecular machine. A Monte-Carlo simulation

The concept called Knowledge is a measure of the quality of genetically transferred information. Its usefulness is demonstrated quantitatively in a Monte-Carlo simulation on critical steps in a origin of life model. The model describes the origin of a bio-like genetic apparatus by a long sequence of physical-chemical steps: it starts with the presence of a self-replicating oligomer and a specifically structured environment in time and space that allow for the formation of aggregates such as assembler-hairpins-devices and, at a later stage, an assembler-hairpins-enzyme device—a first translation machine

Effects of Progesterone and Its Antagonist Mifepristone on Progesterone Receptor A Expression in Human Umbilical Vein Endothelial Cells

Effects of female steroid hormones on endothelial cells are gaining increased importance due to several studies on the effects of hormonal treatment on cardiovascular risk. Recent data argue for an improvement of endothelium-derived relaxation and impaired vascular contraction by estradiol, whereas progesterone and testosterone might entail contrary effects. So far, gestagenic influence on endothelial cell physiology is poorly understood. Human umbilical vein endothelial cells (HUVECs) exposed to the female sex hormones estradiol and progesterone show expression of estrogen receptor-beta (ER beta) and progesterone receptor A (PR-A), and are negative for ER alpha and PR-B. The aim of this study was to analyze the expression and stimulation of PR-A and -B in HUVECs after stimulation with progesterone and PR antagonists that are commercially available. PR-B expression or upregulation was abrogated after application of progesterone or antagonists to HUVECs. Expression of PR-A could be significantly upregulated with progesterone and mifepristone. Unexpectedly, stimulation with the progesterone antagonist RU486 (mifepristone) was accomplished by an upregulation of PR-A expression in our study. We conclude that gestagenic effects on HUVECs independent of modulators are mediated via the PR-A. Copyright (C) 2009 S. Karger AG, Base

Panini -- Anonymous Anycast and an Instantiation

Anycast messaging (i.e., sending a message to an unspecified receiver) has long been neglected by the anonymous communication community. An anonymous anycast prevents senders from learning who the receiver of their message is, allowing for greater privacy in areas such as political activism and whistleblowing. While there have been some protocol ideas proposed, formal treatment of the problem is absent. Formal definitions of what constitutes anonymous anycast and privacy in this context are however a requirement for constructing protocols with provable guarantees. In this work, we define the anycast functionality and use a game-based approach to formalize its privacy and security goals. We further propose Panini, the first anonymous anycast protocol that only requires readily available infrastructure. We show that Panini allows the actual receiver of the anycast message to remain anonymous, even in the presence of an honest but curious sender. In an empirical evaluation, we find that Panini adds only minimal overhead over regular unicast: Sending a message anonymously to one of eight possible receivers results in an end-to-end latency of 0.76s

A Phase Field Modeling Approach of Crack Growth in Materials with Anisotropic Fracture Toughness

Within this contribution, we present a diffuse interface approach for the simulation of crack nucleation and growth in materials, which incorporates an orientation dependency of the fracture toughness. After outlining the basic motivation for the model from an engineering standpoint, the phase field paradigm for fracture is introduced. Further, a specific phase field model for brittle fracture is reviewed, where we focus on the meaning of the auxiliary parameter differentiating between material phases and the coupling of such a parameter to continuum equations in order to obtain the characteristic self organizing model properties. This specific model, as will be explained, provides the phenomenological and methodical basis for the presented enhancement. The formulation of an appropriate evolution equation in terms of a Ginzburg-Landau type equation will be highlighted and several comments on sharp interface models will be made to present a brief comparison. Following up on the basics we then introduce the formulation of a modified version of the model, which additionally to the handling of cracks in linear elastic materials under quasi static loading is also capable of taking into account the effect of resistance variation with respect to the potential crack extension direction. The strong and also the weak forms of the respective governing equations corresponding to the developed anisotropic phase field model are presented. Utilizing the weak formulation as starting point for the discretization of the two fields (displacement field and the phase field), the computational framework in terms of finite elements is introduced. We finally explain several test cases investigated within simulations and discuss the corresponding numerical results. Besides examples, which are set up to illustrate the general model properties, a comparison with crack paths obtained by experimental investigations will be presented in order to show the potential of the developed phase field model