1,958 research outputs found
Inductive queries for a drug designing robot scientist
It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments
Astronomical spectrograph calibration with broad-spectrum frequency combs
Broadband femtosecond-laser frequency combs are filtered to
spectrographically resolvable frequency-mode spacing, and the limitations of
using cavities for spectral filtering are considered. Data and theory are used
to show implications to spectrographic calibration of high-resolution,
astronomical spectrometers
Tunneling Ionization Rates from Arbitrary Potential Wells
We present a practical numerical technique for calculating tunneling
ionization rates from arbitrary 1-D potential wells in the presence of a linear
external potential by determining the widths of the resonances in the spectral
density, rho(E), adiabatically connected to the field-free bound states. While
this technique applies to more general external potentials, we focus on the
ionization of electrons from atoms and molecules by DC electric fields, as this
has an important and immediate impact on the understanding of the multiphoton
ionization of molecules in strong laser fields.Comment: 13 pages, 7 figures, LaTe
Slow Light in Doppler Broadened Two level Systems
We show that the propagation of light in a Doppler broadened medium can be
slowed down considerably eventhough such medium exhibits very flat dispersion.
The slowing down is achieved by the application of a saturating counter
propagating beam that produces a hole in the inhomogeneous line shape. In
atomic vapors, we calculate group indices of the order of 10^3. The
calculations include all coherence effects.Comment: 6 pages, 5 figure
Predicting toxicity through computers: a changing world
The computational approaches used to predict toxicity are evolving rapidly, a process hastened on by the emergence of new ways of describing chemical information. Although this trend offers many opportunities, new regulations, such as the European Community's 'Registration, Evaluation, Authorisation and Restriction of Chemicals' (REACH), demand that models be ever more robust
Mechanisms of base selection by human single-stranded selective monofunctional uracil-DNA glycosylase
hSMUG1 (human single-stranded selective monofunctional uracil-DNA glyscosylase) is one of three glycosylases encoded within a small region of human chromosome 12. Those three glycosylases, UNG (uracil-DNA glycosylase), TDG (thymine-DNA glyscosylase), and hSMUG1, have in common the capacity to remove uracil from DNA. However, these glycosylases also repair other lesions and have distinct substrate preferences, indicating that they have potentially redundant but not overlapping physiological roles. The mechanisms by which these glycosylases locate and selectively remove target lesions are not well understood. In addition to uracil, hSMUG1 has been shown to remove some oxidized pyrimidines, suggesting a role in the repair of DNA oxidation damage. In this paper, we describe experiments in which a series of oligonucleotides containing purine and pyrimidine analogs have been used to probe mechanisms by which hSMUG1 distinguishes potential substrates. Our results indicate that the preference of hSMUG1 for mispaired uracil over uracil paired with adenine is best explained by the reduced stability of a duplex containing a mispair, consistent with previous reports with Escherichia coli mispaired uracil-DNA glycosylase. We have also extended the substrate range of hSMUG1 to include 5-carboxyuracil, the last in the series of damage products from thymine methyl group oxidation. The properties used by hSMUG1 to select damaged pyrimidines include the size and free energy of solvation of the 5-substituent but not electronic inductive properties. The observed distinct mechanisms of base selection demonstrated for members of the uracil glycosylase family help explain how considerable diversity in chemical lesion repair can be achieved
The inevitable QSAR renaissance
QSAR approaches, including recent advances in 3D-QSAR, are advantageous during the lead optimization phase of drug discovery and complementary with bioinformatics and growing data accessibility. Hints for future QSAR practitioners are also offered
Beyond Implications and Applications: the Story of ‘Safety by Design’
Using long-term anthropological observations at the Center for Biological and Environmental Nanotechnology in Houston, Texas, the article demonstrates in detail the creation of new objects, new venues and new modes of veridiction which have reoriented the disciplines of materials chemistry and nanotoxicology. Beginning with the confusion surrounding the meaning of ‘implications’ and ‘applications’ the article explores the creation of new venues (CBEN and its offshoot the International Council on Nanotechnology); it then demonstrates how the demands for a responsible, safe or ethical science were translated into new research and experiment in and through these venues. Finally it shows how ‘safety by design’ emerged as a way to go beyond implications and applications, even as it introduced a whole new array of controversies concerning its viability, validity and legitimacy
Resonant enhancements of high-order harmonic generation
Solving the one-dimensional time-dependent Schr\"odinger equation for simple
model potentials, we investigate resonance-enhanced high-order harmonic
generation, with emphasis on the physical mechanism of the enhancement. By
truncating a long-range potential, we investigate the significance of the
long-range tail, the Rydberg series, and the existence of highly excited states
for the enhancements in question. We conclude that the channel closings typical
of a short-range or zero-range potential are capable of generating essentially
the same effects.Comment: 7 pages revtex, 4 figures (ps files
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