@article{denmeersche2009xsample,
  abstract = {Functions that (1.) Find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(ai*xi) subject to equality constraints Ex=f and/or inequality constraints Gx>=h. (2.) Sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b. (3.) Solve a linear system Ax=B for the unknown x. Includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK},
  accepted = {2009-03-31},
  added-at = {2012-02-11T00:26:20.000+0100},
  author = {den Meersche, Karel Van and Soetaert, Karline and Oevelen, Dick Van},
  bibdate = {2009-03-31},
  biburl = {http://www.bibsonomy.org/bibtex/2d1696d45fe5d99782c48f3d37af0fe81/peter.ralph},
  coden = {JSSOBK},
  day = 27,
  interhash = {efd26310682037318fa16c88a6dd48fe},
  intrahash = {d1696d45fe5d99782c48f3d37af0fe81},
  issn = {1548-7660},
  journal = {Journal of Statistical Software, Code Snippets},
  keywords = {R ill-posed_problems inverse_problems mcmc statistics},
  month = {4},
  number = 1,
  pages = {1--15},
  submitted = {2008-05-26},
  timestamp = {2012-02-11T00:26:20.000+0100},
  title = {{\tt xsample()}: An {R} Function for Sampling Linear Inverse Problems},
  url = {http://www.jstatsoft.org/v30/c01},
  volume = 30,
  year = 2009
}

@article{doi:10.1021/cr2002239,
  abstract = {A review of the formalism and computational methods for determining molecular properties from ab initio wave function-based approaches.  Section headings are:  Many-Electron Hamiltonian;  Molecular Electronic Breit–Pauli Hamiltonian;  Second Quantization;  Perturbation-Dependent Basis Sets; Response Theory for Exact States --- Quasi-Energy Formulation;  Perturbation Expansion of the Wave Function;  Perturbation Expansion of the Quasi-Energy;  Response Functions; Response Functions As Derivatives of the Quasi-Energy Lagrangian; Elimination Rules;  Damped Response Theory;  Response Theory for Approximate States --- Hartree–Fock Theory;  Multiconfigurational Self-Consistent Field Theory; Coupled-Cluster Theory; Orbital-Relaxed Response Functions; Response Functions with Perturbation-Dependent Basis Sets;Overview of Developments and Implementations;Survey of Molecular Properties;},
  added-at = {2012-02-10T22:57:32.000+0100},
  author = {Helgaker, Trygve and Coriani, Sonia and Jorgensen, Poul and Kristensen, Kasper and Olsen, Jeppe and Ruud, Kenneth},
  biburl = {http://www.bibsonomy.org/bibtex/230fd1a254554574146b57467abf0c1aa/drmatusek},
  description = {Recent Advances in Wave Function-Based Methods of Molecular-Property Calculations - Chemical Reviews (ACS Publications)},
  doi = {10.1021/cr2002239},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/cr2002239},
  interhash = {d24101036fe6d28bf01cf40c1668ca9e},
  intrahash = {30fd1a254554574146b57467abf0c1aa},
  journal = {Chemical Reviews},
  keywords = {chemistry optical properties quantum review},
  month = {January},
  number = 1,
  pages = {543-631},
  timestamp = {2012-02-10T22:57:32.000+0100},
  title = {Recent Advances in Wave Function-Based Methods of Molecular-Property Calculations},
  url = {http://pubs.acs.org/doi/abs/10.1021/cr2002239},
  volume = 112,
  year = 2012
}

@article{JCC:JCC21989,
  abstract = {The weighted histogram analysis method (WHAM) has become the standard technique for the analysis of umbrella sampling simulations. In this article, we address the challenges (1) of obtaining fast and accurate solutions of the coupled nonlinear WHAM equations, (2) of quantifying the statistical errors of the resulting free energies, (3) of diagnosing possible systematic errors, and (4) of optimally allocating of the computational resources. Traditionally, the WHAM equations are solved by a fixed-point direct iteration method, despite poor convergence and possible numerical inaccuracies in the solutions. Here, we instead solve the mathematically equivalent problem of maximizing a target likelihood function, by using superlinear numerical optimization algorithms with a significantly faster convergence rate. To estimate the statistical errors in one-dimensional free energy profiles obtained from WHAM, we note that for densely spaced umbrella windows with harmonic biasing potentials, the WHAM free energy profile can be approximated by a coarse-grained free energy obtained by integrating the mean restraining forces. The statistical errors of the coarse-grained free energies can be estimated straightforwardly and then used for the WHAM results. A generalization to multidimensional WHAM is described. We also propose two simple statistical criteria to test the consistency between the histograms of adjacent umbrella windows, which help identify inadequate sampling and hysteresis in the degrees of freedom orthogonal to the reaction coordinate. Together, the estimates of the statistical errors and the diagnostics of inconsistencies in the potentials of mean force provide a basis for the efficient allocation of computational resources in free energy simulations. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012},
  added-at = {2012-02-10T22:43:12.000+0100},
  author = {Zhu, Fangqiang and Hummer, Gerhard},
  biburl = {http://www.bibsonomy.org/bibtex/284c193747106f6b312314cc3a9ad83c3/drmatusek},
  description = {Convergence and error estimation in free energy calculations using the weighted histogram analysis method - Zhu - 2011 - Journal of Computational Chemistry - Wiley Online Library},
  doi = {10.1002/jcc.21989},
  interhash = {87ef3d6dff10563cac31b10e182bd2ca},
  intrahash = {84c193747106f6b312314cc3a9ad83c3},
  issn = {1096-987X},
  journal = {Journal of Computational Chemistry},
  keywords = {convergence energy error estimation free molecular simulation},
  month = {February},
  number = 4,
  pages = {453--465},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2012-02-10T22:43:12.000+0100},
  title = {Convergence and error estimation in free energy calculations using the weighted histogram analysis method},
  url = {http://dx.doi.org/10.1002/jcc.21989},
  volume = 33,
  year = 2012
}

@mastersthesis{deBuitléir-msc-thesis-2011,
  added-at = {2012-02-10T22:07:00.000+0100},
  author = {de Buitléir, Amy},
  biburl = {http://www.bibsonomy.org/bibtex/24d40f31bc95328fadbe69a201e4603f0/mhwombat},
  interhash = {1929c523a40b1e35c31db46c4863ccec},
  intrahash = {4d40f31bc95328fadbe69a201e4603f0},
  keywords = {MSc myown},
  timestamp = {2012-02-10T22:07:00.000+0100},
  title = {Evolving Pattern-seeking Artificial Life with Créatúr
},
  year = 2011
}

@misc{Braun2012,
  abstract = {  Galaxy disks are shown to contain a significant population of atomic clouds
of 100pc linear size which are self-opaque in the 21cm transition. These
objects have HI column densities as high as 10^23 and contribute to a global
opacity correction factor of 1.34+/-0.05 that applies to the integrated 21cm
emission to obtain a total HI mass estimate. Opacity-corrected images of the
nearest external galaxies have been used to form a robust z=0 distribution
function of HI, f(N_HI,X,z=0), the probability of encountering a specific HI
column density per unit comoving distance. This is contrasted with previously
published determinations of f(N_HI,X) at z=1 and 3. A systematic decline of
moderate column density (18<log(N_HI)<21) HI is observed that corresponds to a
decline in surface area of such gas by a factor of five since z=3. The number
of equivalent DLA absorbers (log(N_HI)>20.3) has also declined systematically
over this redshift interval by a similar amount, while the cosmological mass
density in such systems has declined by only a factor of two to its current,
opacity corrected value of Omega_HI^DLA(z=0) = 5.4 +/- 0.9x10^-4.
  We utilize the tight, but strongly non-linear dependence of 21cm absorption
opacity on column density at z=0 to transform our HI images into ones of 21cm
absorption opacity. These images are used to calculate distribution and
pathlength functions of integrated 21cm opacity. The incidence of deep 21cm
absorption systems is predicted to show very little evolution with redshift,
while that of faint absorbers should decline by a factor of five between z=3
and the present. We explicitly consider the effects of HI absorption against
background sources that are extended relative to the 100pc intervening absorber
size scale. Future surveys of 21cm absorption will require very high angular
resolution, of about 15mas, for their unambiguous interpretation. (Abridged.)
},
  added-at = {2012-02-10T21:15:08.000+0100},
  author = {Braun, Robert},
  biburl = {http://www.bibsonomy.org/bibtex/241a51ea6f4e9be7ed2f7c20acd1fe1c1/miki},
  description = {[1202.1840] Cosmological evolution of atomic gas and implications for 21 cm HI absorption},
  interhash = {6f45e5213ac178370681aa8e02cb310f},
  intrahash = {41a51ea6f4e9be7ed2f7c20acd1fe1c1},
  keywords = {atomic evolution fnx gas},
  note = {cite arxiv:1202.1840
Comment: 32 pages, 11 figures, accepted for publication in ApJ},
  timestamp = {2012-02-10T21:15:08.000+0100},
  title = {Cosmological evolution of atomic gas and implications for 21 cm HI
  absorption},
  url = {http://arxiv.org/abs/1202.1840},
  year = 2012
}