Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance

Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by providing accurate 3D information about small organic molecules via their moments of inertia. Using these moments, Kraitchman analysis determines isotopic substitution coordinates, which are the unsigned $|x|,|y|,|z|$ coordinates of all atoms with natural isotopic abundance, including carbon, nitrogen, and oxygen. While unsigned substitution coordinates can verify guesses of structures, the missing $+/-$ signs make it challenging to determine the actual structure from the substitution coordinates alone. To tackle this inverse problem, we develop KREED (Kraitchman REflection-Equivariant Diffusion), a generative diffusion model that infers a molecule's complete 3D structure from its molecular formula, moments of inertia, and unsigned substitution coordinates of heavy atoms. KREED's top-1 predictions identify the correct 3D structure with >98% accuracy on the QM9 and GEOM datasets when provided with substitution coordinates of all heavy atoms with natural isotopic abundance. When substitution coordinates are restricted to only a subset of carbons, accuracy is retained at 91% on QM9 and 32% on GEOM. On a test set of experimentally measured substitution coordinates gathered from the literature, KREED predicts the correct all-atom 3D structure in 25 of 33 cases, demonstrating experimental applicability for context-free 3D structure determination with rotational spectroscopy.Comment: added software citation

A Pilot Survey for the H2_2O Southern Galactic Plane Survey (HOPS)

We describe observations with the Mopra radiotelescope designed to assess the feasibility of the H$_2$O maser southern Galactic plane survey (HOPS). We mapped two one-square-degree regions along the Galactic plane using the new 12 mm receiver and the UNSW Mopra spectrometer (MOPS). We covered the entire spectrum between 19.5 and 27.5 GHz using this setup with the main aims of finding out which spectral lines can be detected with a quick mapping survey. We report on detected emission from H$_2$O masers, NH$_3$ inversion transitions (1,1), (2,2) and (3,3), HC$_3$N (3-2), as well as several radio recombination lines.Comment: accepted by PAS

Models of organometallic complexes for optoelectronic applications

Organometallic complexes have potential applications as the optically active components of organic light emitting diodes (OLEDs) and organic photovoltaics (OPV). Development of more effective complexes may be aided by understanding their excited state properties. Here we discuss two key theoretical approaches to investigate these complexes: first principles atomistic models and effective Hamiltonian models. We review applications of these methods, such as, determining the nature of the emitting state, predicting the fraction of injected charges that form triplet excitations, and explaining the sensitivity of device performance to small changes in the molecular structure of the organometallic complexes.Comment: To appear in themed issue of J. Mat. Chem. on the modelling of material

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins

BACKGROUND: Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments. We investigated how the expansion of the Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family in Halobacterium salinarum NRC-1 has aided in niche-adaptation of this archaeon to a complex and dynamically changing hypersaline environment.RESULTS: We mapped genome-wide binding locations for all eight FFRPs, investigated their preference for binding different effector molecules, and identified the contexts in which they act by analyzing transcriptional responses across 35 growth conditions that mimic different environmental and nutritional conditions this organism is likely to encounter in the wild. Integrative analysis of these data constructed an FFRP regulatory network with conditionally active states that reveal how interrelated variations in DNA-binding domains, effector-molecule preferences, and binding sites in target gene promoters have tuned the functions of each FFRP to the environments in which they act. We demonstrate how conditional regulation of similar genes by two FFRPs, AsnC (an activator) and VNG1237C (a repressor), have striking environment-specific fitness consequences for oxidative stress management and growth, respectively.CONCLUSIONS: This study provides a systems perspective into the evolutionary process by which gene duplication within a transcription factor family contributes to environment-specific adaptation of an organism

3,3′-Di-tert-butyl-1,1′-[1,3-phenyl­enebis(methyl­ene)]diurea

The title compound, C18H30N4O2, contains two tert-butyl urea groups, each connected to a benzene ring though a methyl­ene group. One of the groups occupies a position almost normal to the aromatic plane with a C—N—C—C torsion angle of −94.4 (4)°, while the other is considerably twisted from the ring with a C—N—C—C torsion angle of −136.1 (4)°. In the crystal, pairs of mol­ecules are connected to each other, forming centrosymmetric dimers in which two NH groups of one mol­ecule act as hydrogen-bond donors to one carbonyl O atom of the other mol­ecule. The dimers are linked into sheets parallel to (100) by N—H⋯O hydrogen bonds involving the remaining N—H and C=O groups

True and apparent scaling: the proximity of the markov- switching multifractal model to long-range dependence

In this paper, we consider daily financial data of a collection of different stock market indices, exchange rates, and interest rates, and we analyze their multi-scaling properties by estimating a simple specification of the Markov-switching multifractal model (MSM). In order to see how well the estimated models capture the temporal dependence of the data, we estimate and compare the scaling exponents H(q) (for q = 1, 2) for both empirical data and simulated data of the estimated MSM models. In most cases the multifractal model appears to generate ‘apparent’ long memory in agreement with the empirical scaling laws

Secure Cooperation of Autonomous Mobile Sensors Using an Underwater Acoustic Network

Methodologies and algorithms are presented for the secure cooperation of a team of autonomous mobile underwater sensors, connected through an acoustic communication network, within surveillance and patrolling applications. In particular, the work proposes a cooperative algorithm in which the mobile underwater sensors (installed on Autonomous Underwater Vehicles—AUVs) respond to simple local rules based on the available information to perform the mission and maintain the communication link with the network (behavioral approach). The algorithm is intrinsically robust: with loss of communication among the vehicles the coverage performance (i.e., the mission goal) is degraded but not lost. The ensuing form of graceful degradation provides also a reactive measure against Denial of Service. The cooperative algorithm relies on the fact that the available information from the other sensors, though not necessarily complete, is trustworthy. To ensure trustworthiness, a security suite has been designed, specifically oriented to the underwater scenario, and in particular with the goal of reducing the communication overhead introduced by security in terms of number and size of messages. The paper gives implementation details on the integration between the security suite and the cooperative algorithm and provides statistics on the performance of the system as collected during the UAN project sea trial held in Trondheim, Norway, in May 2011

Declining Volatility, a General Property of Disparate Systems: From Fossils, to Stocks, to the Stars

There may be structural principles pertaining to the general behavior of systems that lead to similarities in a variety of different contexts. Classic examples include the descriptive power of fractals, the importance of surface area to volume constraints, the universality of entropy in systems, and mathematical rules of growth and form. Documenting such overarching principles may represent a rejoinder to the Neodarwinian synthesis that emphasizes adaptation and competition. Instead, these principles could indicate the importance of constraint and structure on form and evolution. Here we document a potential example of a phenomenon suggesting congruent behavior of very different systems. We focus on the notion that universally there has been a tendency for more volatile entities to disappear from systems such that the net volatility in these systems tends to decline. We specifically focus on origination and extinction rates in the marine animal fossil record, the performance of stocks in the stock market, and the characters of stars and stellar systems. We consider the evidence that each is experiencing declining volatility, and also consider the broader significance of this.Comment: Accepted for publication in Palaeontology. 13 pages, 3 figure

Comment on "Influence of HLA-C Expression Level on HIV Control"

Apps et al. found that high human HLA-C expression favors HIV-1 control. HLA-C was assessed with a monoclonal antibody that cross-reacts with HLA-E

Model Channel Ion Currents in NaCl - SPC/E Solution with Applied-Field Molecular Dynamics

Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125 Angstrom internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and SPC/E water. Channel and bath currents were computed from ten 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration-dependent and superlinear at high concentrations.Comment: Accepted for publication in Biophysical Journa