Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity.

The ability to generate RNA aptamers for synthetic biology using in vitro selection depends on the informational complexity (IC) needed to specify functional structures that bind target ligands with desired affinities in physiological concentrations of magnesium. We investigate how selection for high-affinity aptamers is constrained by chemical properties of the ligand and the need to bind in low magnesium. We select two sets of RNA aptamers that bind planar ligands with dissociation constants (K(d)s) ranging from 65 nM to 100 microM in physiological buffer conditions. Aptamers selected to bind the non-proteinogenic amino acid, p-amino phenylalanine (pAF), are larger and more informationally complex (i.e., rarer in a pool of random sequences) than aptamers selected to bind a larger fluorescent dye, tetramethylrhodamine (TMR). Interestingly, tighter binding aptamers show less dependence on magnesium than weaker-binding aptamers. Thus, selection for high-affinity binding may automatically lead to structures that are functional in physiological conditions (1-2.5 mM Mg(2+)). We hypothesize that selection for high-affinity binding in physiological conditions is primarily constrained by ligand characteristics such as molecular weight (MW) and the number of rotatable bonds. We suggest that it may be possible to estimate aptamer-ligand affinities and predict whether a particular aptamer-based design goal is achievable before performing the selection

Design Index for Deep Neural Networks

AbstractIn this paper, we propose a Deep Neural Networks (DNN) Design Index which would aid a DNN designer during the designing phase of DNNs. We study the designing aspect of DNNs from model-specific and data-specific perspectives with focus on three performance metrics: training time, training error and, validation error. We use a simple example to illustrate the significance of the DNN design index. To validate it, we calculate the design indices for four benchmark problems. This is an elementary work aimed at setting a direction for creating design indices pertaining to deep learning

Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics

Many studies of RNA folding and catalysis have revealed conformational heterogeneity, metastable folding intermediates, and long-lived states with distinct catalytic activities. We have developed a single-molecule imaging approach for investigating the functional heterogeneity of in vitro-evolved RNA aptamers. Monitoring the association of fluorescently labeled ligands with individual RNA aptamer molecules has allowed us to record binding events over the course of multiple days, thus providing sufficient statistics to quantitatively define the kinetic properties at the single-molecule level. The ligand binding kinetics of the highly optimized RNA aptamer studied here displays a remarkable degree of uniformity and lack of memory. Such homogeneous behavior is quite different from the heterogeneity seen in previous single-molecule studies of naturally derived RNA and protein enzymes. The single-molecule methods we describe may be of use in analyzing the distribution of functional molecules in heterogeneous evolving populations or even in unselected samples of random sequences

Legislative strengthening meets party support in international assistance: a closer relationship?

Recent reports recommend that international efforts to help strengthen legislatures in emerging democracies should work more closely with support for building stronger political parties and competitive party systems. This article locates the recommendations within international assistance more generally and reviews the arguments. It explores problems that must be addressed if the recommendations are to be implemented effectively. The article argues that an alternative, issue-based approach to strengthening legislatures and closer links with civil society could gain more traction. However, that is directed more centrally at promoting good governance for the purpose of furthering development than at democratisation goals sought by party aid and legislative strengtheners in the democracy assistance industry

Numerical Solution of Differential Equations by the Parker-Sochacki Method

A tutorial is presented which demonstrates the theory and usage of the Parker-Sochacki method of numerically solving systems of differential equations. Solutions are demonstrated for the case of projectile motion in air, and for the classical Newtonian N-body problem with mutual gravitational attraction.Comment: Added in July 2010: This tutorial has been posted since 1998 on a university web site, but has now been cited and praised in one or more refereed journals. I am therefore submitting it to the Cornell arXiv so that it may be read in response to its citations. See "Spiking neural network simulation: numerical integration with the Parker-Sochacki method:" J. Comput Neurosci, Robert D. Stewart & Wyeth Bair and http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717378

Effects of crack tip geometry on dislocation emission and cleavage: A possible path to enhanced ductility

We present a systematic study of the effect of crack blunting on subsequent crack propagation and dislocation emission. We show that the stress intensity factor required to propagate the crack is increased as the crack is blunted by up to thirteen atomic layers, but only by a relatively modest amount for a crack with a sharp 60$^\circ$ corner. The effect of the blunting is far less than would be expected from a smoothly blunted crack; the sharp corners preserve the stress concentration, reducing the effect of the blunting. However, for some material parameters blunting changes the preferred deformation mode from brittle cleavage to dislocation emission. In such materials, the absorption of preexisting dislocations by the crack tip can cause the crack tip to be locally arrested, causing a significant increase in the microscopic toughness of the crack tip. Continuum plasticity models have shown that even a moderate increase in the microscopic toughness can lead to an increase in the macroscopic fracture toughness of the material by several orders of magnitude. We thus propose an atomic-scale mechanism at the crack tip, that ultimately may lead to a high fracture toughness in some materials where a sharp crack would seem to be able to propagate in a brittle manner. Results for blunt cracks loaded in mode II are also presented.Comment: 12 pages, REVTeX using epsfig.sty. 13 PostScript figures. Final version to appear in Phys. Rev. B. Main changes: Discussion slightly shortened, one figure remove

Load-sharing policies in parallel simulation of agent-based demographic models

Execution parallelism in agent-Based Simulation (ABS) allows to deal with complex/large-scale models. This raises the need for runtime environments able to fully exploit hardware parallelism, while jointly offering ABS-suited programming abstractions. In this paper, we target last-generation Parallel Discrete Event Simulation (PDES) platforms for multicore systems. We discuss a programming model to support both implicit (in-place access) and explicit (message passing) interactions across concurrent Logical Processes (LPs). We discuss different load-sharing policies combining event rate and implicit/explicit LPs’ interactions. We present a performance study conducted on a synthetic test case, representative of a class of agent-based models.Peer ReviewedPostprint (author's final draft