Interpolation of intermolecular potentials using Gaussian processes

A procedure is proposed to produce intermolecular potential energy surfaces from limited data. The procedure involves generation of geometrical configurations using a Latin hypercube design, with a maximin criterion, based on inverse internuclear distances. Gaussian processes are used to interpolate the data, using over-specified inverse molecular distances as covariates, greatly improving the interpolation. Symmetric covariance functions are specified so that the interpolation surface obeys all relevant symmetries, reducing prediction errors. The interpolation scheme can be applied to many important molecular interactions with trivial modifications. Results are presented for three systems involving CO2, a system with a deep energy minimum (HF - HF) and a system with 48 symmetries (CH4 - N2). In each case the procedure accurately predicts an independent test set. Training this method with high-precision ab initio evaluations of the CO2 - CO interaction enables a parameter-free, first-principles prediction of the CO2 - CO cross virial coefficient that agree very well with experiments

Glycine Receptors Support Excitatory Neurotransmitter Release in Developing Mouse Visual Cortex.

Glycine receptors (GlyRs) are found in most areas of the brain, and their dysfunction can cause severe neurological disorders. While traditionally thought of as inhibitory receptors, presynaptic-acting GlyRs (preGlyRs) can also facilitate glutamate release under certain circumstances, although the underlying molecular mechanisms are unknown. In the current study, we sought to better understand the role of GlyRs in the facilitation of excitatory neurotransmitter release in mouse visual cortex. Using whole-cell recordings, we found that preGlyRs facilitate glutamate release in developing, but not adult, visual cortex. The glycinergic enhancement of neurotransmitter release in early development depends on the high intracellular to extracellular Cl(-) gradient maintained by the Na(+)-K(+)-2Cl(-) cotransporter and requires Ca(2+) entry through voltage-gated Ca(2+) channels. The glycine transporter 1, localized to glial cells, regulates extracellular glycine concentration and the activation of these preGlyRs. Our findings demonstrate a developmentally regulated mechanism for controlling excitatory neurotransmitter release in the neocortex

Maternal Loss of Ube3a Impairs Experience-Driven Dendritic Spine Maintenance in the Developing Visual Cortex

Dendritic spines are a morphological feature of the majority of excitatory synapses in the mammalian neocortex and are motile structures with shapes and lifetimes that change throughout development. Proper cortical development and function, including cortical contributions to learning and memory formation, require appropriate experience-dependent dendritic spine remodeling. Dendritic spine abnormalities have been reported for many neurodevelopmental disorders, including Angelman syndrome (AS), which is caused by the loss of the maternally inherited UBE3A allele (encoding ubiquitin protein ligase E3A). Prior studies revealed that UBE3A protein loss leads to reductions in dendritic spine density and diminished excitatory synaptic transmission. However, the decrease in spine density could come from either a reduction in spine formation or an increase in spine elimination. Here, we used acute and longitudinal in vivo two-photon microscopy to investigate developmental and experience-dependent changes in the numbers, dynamics, and morphology of layer 5 pyramidal neuron apical dendritic spines in the primary visual cortex of control and AS model mice (Ube3am−/p+ mice). We found that neurons in AS model mice undergo a greater elimination of dendritic spines than wild-type mice during the end of the first postnatal month. However, when raised in darkness, spine density and dynamics were indistinguishable between control and AS model mice, which indicates that decreased spine density in AS model mice reflects impaired experience-driven spine maintenance. Our data thus demonstrate an experience-dependent anatomical substrate by which the loss of UBE3A reduces dendritic spine density and disrupts cortical circuitry

Post-acute Brain Injury Urinary Signature: A New Resource for Molecular Diagnostics

Heterogeneity within brain injury presents a challenge to the development of informative molecular diagnostics. Recent studies show progress particularly in cerebrospinal fluid with biomarker assays targeting one or a few structural proteins. Protein-based assays in peripheral fluids, however, have been more challenging to develop in part due to restricted and intermittent barrier access. Further, a greater number of molecular variables may be required to inform on patient status given the multifactorial nature of brain injury. Presented is an alternative approach profiling peripheral fluid for a class of small metabolic by-products rendered by ongoing brain pathobiology. Urine specimens were collected for head trauma subjects upon admission to acute brain injury rehabilitation and nontraumatized matched controls. An innovative data-independent mass spectrometry approach was employed for reproducible molecular quantification across osmolarity-normalized samples. The postacute human traumatic brain injury urinary signature encompassed 2,476 discriminant variables reproducibly measured in specimens for subject classification. Multiple sub-profiles were then discerned in correlation with injury severity per Glasgow Comma Scale and behavioral and neurocognitive function per Patient Competency Rating Scale and Frontal Systems Behavioral Scale. Identified peptide constituents were enriched for outgrowth and guidance, extracellular matrix and post-synaptic density proteins, which were reflective of ongoing post-acute neuroplastic processes demonstrating pathobiological relevance. Taken together, these findings support further development of diagnostics based on brain injury urinary signatures using either combinatorial quantitative models or patternrecognition methods. Particularly, these findings espouse assay development to address unmet diagnostic and theragnostic needs in brain injury rehabilitative medicine

FDCCS16 molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS

Impurities from the CCS chain can greatly influence the physical properties of CO2. This has important design, safety and cost implications for the compression, transport and storage of CO2. There is an urgent need to understand and predict the properties of impure CO2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO2 phase behaviour over a wide range of temperature and pressure, and maintain that predictive power for CO2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to de- scribe the interactions between CO2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab-initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO2 binary mixtures with N2, O2, Ar and H2. A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab-initio evaluations of the interactions between CO2 and relevant impurities, taking N2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab-initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO2, without fitting to experimental data

Determination of the stretch tensor for structural transformations

The transformation stretch tensor plays an essential role in the evaluation of conditions of compatibility between phases and the use of the Cauchy-Born rule. This tensor is difficult to measure directly from experiment. We give an algorithm for the determination of the transformation stretch tensor from x-ray measurements of structure and lattice parameters. When evaluated on some traditional and emerging phase transformations the algorithm gives unexpected results.Comment: 3 figures, 1 tabl

Insights into GABA receptor signalling in TM3 Leydig cells

gamma-Aminobutyric acid (GABA) is an emerging signalling molecule in endocrine organs, since it is produced by endocrine cells and acts via GABA(A) receptors in a paracrine/autocrine fashion. Testicular Leydig cells are producers and targets for GABA. These cells express GABA(A) receptor subunits and in the murine Leydig cell line TM3 pharmacological activation leads to increased proliferation. The signalling pathway of GABA in these cells is not known in this study. We therefore attempted to elucidate details of GABA(A) signalling in TM3 and adult mouse Leydig cells using several experimental approaches. TM3 cells not only express GABA(A) receptor subunits, but also bind the GABA agonist {[}H-3] muscimol with a binding affinity in the range reported for other endocrine cells (K-d = 2.740 +/- 0.721 nM). However, they exhibit a low B-max value of 28.08 fmol/mg protein. Typical GABA(A) receptor-associated events, including Cl- currents, changes in resting membrane potential, intracellular Ca2+ or cAMP, were not measurable with the methods employed in TM3 cells, or, as studied in part, in primary mouse Leydig cells. GABA or GABA(A) agonist isoguvacine treatment resulted in increased or decreased levels of several mRNAs, including transcription factors (c-fos, hsf-1, egr-1) and cell cycle-associated genes (Cdk2, cyclin D1). In an attempt to verify the cDNA array results and because egr-1 was recently implied in Leydig cell development, we further studied this factor. RT-PCR and Western blotting confirmed a time-dependent regulation of egr-1 in TM3. In the postnatal testis egr-1 was seen in cytoplasmic and nuclear locations of developing Leydig cells, which bear GABA(A) receptors and correspond well to TM3 cells. Thus, GABA acts via an untypical novel signalling pathway in TM3 cells. Further details of this pathway remain to be elucidated. Copyright (c) 2005 S. Karger AG, Base

Constraints on Brane Inflation and Cosmic Strings

By considering simple, but representative, models of brane inflation from a single brane-antibrane pair in the slow roll regime, we provide constraints on the parameters of the theory imposed by measurements of the CMB anisotropies by WMAP including a cosmic string component. We find that inclusion of the string component is critical in constraining parameters. In the most general model studied, which includes an inflaton mass term, as well as the brane-antibrane attraction, values n_s < 1.02 are compatible with the data at 95 % confidence level. We are also able to constrain the volume of internal manifold (modulo factors dependent on the warp factor) and the value of the inflaton field to be less than 0.66M_P at horizon exit. We also investigate models with a mass term. These observational considerations suggest that such models have r < 2*10^-5, which can only be circumvented in the fast roll regime, or by increasing the number of antibranes. Such a value of r would not be detectable in CMB polarization experiment likely in the near future, but the B-mode signal from the cosmic strings could be detectable. We present forecasts of what a similar analysis using PLANCK data would yield and find that it should be possible to rule out G\mu > 6.5*10^-8 using just the TT, TE and EE power spectra.Comment: 11 pages, 3 figures, revtex4, typos corrected, references adde

Visual target tracking for rover-based planetary exploration

Abstract-To command a rover to go to a location of scientific interest on a remote planet, the rover must be capable of reliably tracking the target designated by a scientist from about ten rover lengths away. The rover must maintain lock on the target while traversing rough terrain and avoiding obstacles without the need for communication with Earth. Among the challenges of tracking targets from a rover are the large changes in the appearance and shape of the selected target as the rover approaches it, the limited frame rate at which images can be acquired and processed, and the sudden changes in camera pointing as the rover goes over rocky terrain. We have investigated various techniques for combining 2D and 3D information in order to increase the reliability of visually tracking targets under Mars like conditions. We will present the approaches that we have examined on simulated data and tested onboard the Rocky 8 rover in the JPL Mars Yard and the K9 rover in the ARC Marscape. These techniques include results for 2D trackers, ICP, visual odometry, and 2D/3D trackers

Non-Equilibrium Large N Yukawa Dynamics: marching through the Landau pole

The non-equilibrium dynamics of a Yukawa theory with N fermions coupled to a scalar field is studied in the large N limit with the goal of comparing the dynamics predicted from the renormalization group improved effective potential to that obtained including the fermionic backreaction. The effective potential is of the Coleman-Weinberg type. Its renormalization group improvement is unbounded from below and features a Landau pole. When viewed self-consistently, the initial time singularity does not arise. The different regimes of the dynamics of the fully renormalized theory are studied both analytically and numerically. Despite the existence of a Landau pole in the model, the dynamics of the mean field is smooth as it passes the location of the pole. This is a consequence of a remarkable cancellation between the effective potential and the dynamical chiral condensate. The asymptotic evolution is effectively described by a quartic upright effective potential. In all regimes, profuse particle production results in the formation of a dense fermionic plasma with occupation numbers nearly saturated up to a scale of the order of the mean field. This can be interpreted as a chemical potential. We discuss the implications of these results for cosmological preheating.Comment: 36 pages, 14 figures, LaTeX, submitted to Physical Review