Computational design of dynamic receptor-peptide signaling complexes applied to chemotaxis.

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well-defined molecules. In contrast, approaches that couple the sensing of flexible compounds to intended cellular responses would greatly expand potential biosensor applications. Here, to address these challenges, we develop a computational strategy for designing signaling complexes between conformationally dynamic proteins and peptides. To demonstrate the power of the approach, we create ultrasensitive chemotactic receptor-peptide pairs capable of eliciting potent signaling responses and strong chemotaxis in primary human T cells. Unlike traditional approaches that engineer static binding complexes, our dynamic structure design strategy optimizes contacts with multiple binding and allosteric sites accessible through dynamic conformational ensembles to achieve strongly enhanced signaling efficacy and potency. Our study suggests that a conformationally adaptable binding interface coupled to a robust allosteric transmission region is a key evolutionary determinant of peptidergic GPCR signaling systems. The approach lays a foundation for designing peptide-sensing receptors and signaling peptide ligands for basic and therapeutic applications

Rotational and vibrational spectra of quantum rings

One can confine the two-dimensional electron gas in semiconductor heterostructures electrostatically or by etching techniques such that a small electron island is formed. These man-made ``artificial atoms'' provide the experimental realization of a text-book example of many-particle physics: a finite number of quantum particles in a trap. Much effort was spent on making such "quantum dots" smaller and going from the mesoscopic to the quantum regime. Far-reaching analogies to the physics of atoms, nuclei or metal clusters were obvious from the very beginning: The concepts of shell structure and Hund's rules were found to apply -- just as in real atoms! In this Letter, we report the discovery that electrons confined in ring-shaped quantum dots form rather rigid molecules with antiferromagnetic order in the ground state. This can be seen best from an analysis of the rotational and vibrational excitations

Recoil Polarization for Delta Excitation in Pion Electroproduction

We measured angular distributions of recoil-polarization response functions for neutral pion electroproduction for W=1.23 GeV at Q^2=1.0 (GeV/c)^2, obtaining 14 separated response functions plus 2 Rosenbluth combinations; of these, 12 have been observed for the first time. Dynamical models do not describe quantities governed by imaginary parts of interference products well, indicating the need for adjusting magnitudes and phases for nonresonant amplitudes. We performed a nearly model-independent multipole analysis and obtained values for Re(S1+/M1+)=-(6.84+/-0.15)% and Re(E1+/M1+)=-(2.91+/-0.19)% that are distinctly different from those from the traditional Legendre analysis based upon M1+ dominance and sp truncation.Comment: 5 pages, 2 figures, for PR

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

A coupled chemo-mechanical damage-healing model for cementitious materials

A model is described for representing simultaneous damage and healing behaviour in cementitious structural elements that contain embedded autonomic healing systems. The model uses a crack-healing cohesive zone formulation in which damaged and healed proportions of the cohesive zone can both grow and diminish, with no restrictions placed on the number or timing of these damage-healing events. The cohesive zone sub-model is implemented in a finite element with strong discontinuity and is coupled to both capillary flow and chemical curing model components. The flow model simulates the transport of healing agents within discrete cracks as well as through micro-cracked regions within the fracture process zone. An important aspect of the damage-healing component of the model is the way that permanent strains are computed so as to satisfy the second law of thermodynamics. This is accomplished with the assumption that the stress in a component of healing agent is zero at the moment of solidification, which applies to both null and non-zero displacement fields. The new coupled model is assessed using some recent data obtained from a number of experiments undertaken at Cardiff University. These tests were conducted on both reinforced and unreinforced specimens, and encompass a range of cracking scenarios. The paper shows that the model accurately predicts the flow of healing agents within discrete cracks and that it is able to represent the mechanical behaviour associated with multiple and simultaneous damage-healing events with good accuracy