chore(bib): Update bibliography

This includes some new citations

bibliography/bibliography.bib

@@ -587,7 +587,7 @@ @article{Barlow2003
 
 @article{Barrat1990,
   title = {Diffusion, Viscosity and Structural Slowing down in Soft Sphere Alloys near the Kinetic Glass Transition},
-  author = {Barrat, J. -L. and Roux, J. -N. and Hansen, J. -P.},
+  author = {Barrat, J. L. and Roux, J. N. and Hansen, J. P.},
   year = {1990},
   month = dec,
   volume = {149},
@@ -781,6 +781,18 @@ @chem.rug.nl).
   number = {1}
 }
 
+@article{bergerhoff1983inorganic,
+  title = {The Inorganic Crystal Structure Data Base},
+  author = {Bergerhoff, Guenter and Hundt, R and Sievers, R and Brown, ID},
+  year = {1983},
+  volume = {23},
+  pages = {66--69},
+  publisher = {{ACS Publications}},
+  journal = {J. Chem. Inf. Comput. Sci.},
+  keywords = {⛔ No DOI found},
+  number = {2}
+}
+
 @article{Bernades2019,
   title = {The {{Curious Case}} of {{Acetaldehyde Phenylhydrazone}}: {{Resolution}} of a 120 {{Year Old Puzzle}} Where {{Forms}} with {{Vastly Different Melting Points Have}} the {{Same Structure}}},
   shorttitle = {The {{Curious Case}} of {{Acetaldehyde Phenylhydrazone}}},
@@ -1650,6 +1662,22 @@ @article{Choudhury2013
   language = {en}
 }
 
+@article{Chubynsky2014,
+  title = {Diffusing {{Diffusivity}}: {{A Model}} for {{Anomalous}}, yet {{Brownian}}, {{Diffusion}}},
+  shorttitle = {Diffusing {{Diffusivity}}},
+  author = {Chubynsky, Mykyta V. and Slater, Gary W.},
+  year = {2014},
+  month = aug,
+  volume = {113},
+  pages = {098302},
+  publisher = {{American Physical Society}},
+  doi = {10.1103/PhysRevLett.113.098302},
+  abstract = {Wang et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 15160 (2009)] have found that in several systems the linear time dependence of the mean-square displacement (MSD) of diffusing colloidal particles, typical of normal diffusion, is accompanied by a non-Gaussian displacement distribution G(x,t), with roughly exponential tails at short times, a situation they termed ``anomalous yet Brownian'' diffusion. The diversity of systems in which this is observed calls for a generic model. We present such a model where there is diffusivity memory but no direction memory in the particle trajectory, and we show that it leads to both a linear MSD and a non-Gaussian G(x,t) at short times. In our model, the diffusivity is undergoing a (perhaps biased) random walk, hence the expression ``diffusing diffusivity''. G(x,t) is predicted to be exactly exponential at short times if the distribution of diffusivities is itself exponential, but an exponential remains a good fit for a variety of diffusivity distributions. Moreover, our generic model can be modified to produce subdiffusion.},
+  file = {/home/malcolm/Zotero/storage/V9B7QR53/Chubynsky_Slater_2014_Diffusing Diffusivity.pdf;/home/malcolm/Zotero/storage/M7JNCZYR/PhysRevLett.113.html},
+  journal = {Phys. Rev. Lett.},
+  number = {9}
+}
+
 @article{Ciccotti1986,
   title = {Molecular Dynamics Simulation of Rigid Molecules},
   author = {Ciccotti, G. and Ryckaert, J. P.},
@@ -2180,6 +2208,22 @@ @article{Doliwa2003
   number = {3}
 }
 
+@article{Doliwa2003a,
+  title = {Hopping in a Supercooled {{Lennard}}-{{Jones}} Liquid: {{Metabasins}}, Waiting Time Distribution, and Diffusion},
+  shorttitle = {Hopping in a Supercooled {{Lennard}}-{{Jones}} Liquid},
+  author = {Doliwa, B. and Heuer, A.},
+  year = {2003},
+  month = mar,
+  volume = {67},
+  pages = {030501},
+  publisher = {{American Physical Society}},
+  doi = {10.1103/PhysRevE.67.030501},
+  abstract = {We investigate the jump motion among potential energy minima of a Lennard-Jones model glass former by extensive computer simulation. From the time series of minima energies, it becomes clear that the energy landscape is organized in superstructures called metabasins. We show that diffusion can be pictured as a random walk among metabasins, and that the whole temperature dependence resides in the distribution of waiting times. The waiting time distribution exhibits algebraic decays: {$\tau-$}1/2 for very short times and {$\tau-\alpha$} for longer times, where {$\alpha\approx$}2 near Tc. We demonstrate that solely the waiting times in the very stable basins account for the temperature dependence of the diffusion constant.},
+  file = {/home/malcolm/Zotero/storage/LZ73HRV5/Doliwa_Heuer_2003_Hopping in a supercooled Lennard-Jones liquid.pdf;/home/malcolm/Zotero/storage/KIVKP9HR/PhysRevE.67.html},
+  journal = {Phys. Rev. E},
+  number = {3}
+}
+
 @article{Donati1999,
   title = {Spatial Correlations of Mobility and Immobility in a Glass-Forming {{Lennard}}-{{Jones}} Liquid.},
   author = {Donati, C and Glotzer, S C and Poole, P H and Kob, W and Plimpton, S J},
@@ -2304,6 +2348,22 @@ @article{Dries1988
   number = {4}
 }
 
+@article{Dueby2019,
+  title = {Decoupling of {{Translational Diffusion}} from the {{Viscosity}} of {{Supercooled Water}}: {{Role}} of {{Translational Jump Diffusion}}},
+  shorttitle = {Decoupling of {{Translational Diffusion}} from the {{Viscosity}} of {{Supercooled Water}}},
+  author = {Dueby, Shivam and Dubey, Vikas and Daschakraborty, Snehasis},
+  year = {2019},
+  month = aug,
+  volume = {123},
+  pages = {7178--7189},
+  publisher = {{American Chemical Society}},
+  issn = {1520-6106},
+  doi = {10.1021/acs.jpcb.9b01719},
+  abstract = {Some experiments have witnessed gradual decoupling of viscosity from the translational self-diffusion of supercooled water with decreasing temperature. This indicates the breakdown of the Stokes\textendash Einstein equation in supercooled water. While some theoretical and computer simulation studies indicated the jump translation of the molecules as a probable origin of the above decoupling, direct quantitative evidence is still lacking. Through a molecular dynamics (MD) simulation study, along with careful consideration of translational jump motion, we have found the most definite proof of increasing relevance of translational jump diffusion in the above decoupling phenomena. By separating the jump-only diffusion contribution from the overall diffusion of the water, we obtain the residual diffusion coefficient, which remains strongly coupled to the viscosity of the medium at the supercooled regime. These new findings can help to elucidate many experimental studies featuring molecular transport properties, where strong diffusion\textendash viscosity decoupling is present.},
+  journal = {J. Phys. Chem. B},
+  number = {33}
+}
+
 @article{Dyre1996,
   title = {Local Elastic Expansion Model for Viscous-Flow Activation Energies of Glass-Forming Molecular Liquids},
   author = {Dyre, Jeppe C. and Olsen, Niels Boye and Christensen, Tage},
@@ -3503,6 +3563,19 @@ @article{Gruning2018
   number = {7}
 }
 
+@article{Gurland1971,
+  title = {A {{Simple Approximation}} for {{Unbiased Estimation}} of the {{Standard Deviation}}},
+  author = {Gurland, John and Tripathi, Ram C.},
+  year = {1971},
+  volume = {25},
+  pages = {30--32},
+  publisher = {{[American Statistical Association, Taylor \& Francis, Ltd.]}},
+  issn = {0003-1305},
+  doi = {10.2307/2682923},
+  journal = {Am. Stat.},
+  number = {4}
+}
+
 @misc{Haahr1998,
   title = {{{RANDOM}}.{{ORG}} - {{True Random Number Service}}},
   author = {Haahr, Mads},
@@ -5522,6 +5595,42 @@ @article{Maity2019
   number = {2}
 }
 
+@misc{MalcolmRamsay2020,
+  title = {Malramsay64/Statdyn-Analysis: {{Release}} v0.11.6},
+  shorttitle = {Malramsay64/Statdyn-Analysis},
+  author = {Malcolm Ramsay},
+  year = {2020},
+  month = jul,
+  doi = {10.5281/zenodo.3966880},
+  abstract = {Collection of tools for the statistical dynamics analysis of Molecular Dynamics trajectories.},
+  file = {/home/malcolm/Zotero/storage/IHP35NIL/3966880.html},
+  howpublished = {Zenodo}
+}
+
+@misc{MalcolmRamsay2020a,
+  title = {Malramsay64/Statdyn-Simulation: {{Release}} v0.8.1},
+  shorttitle = {Malramsay64/Statdyn-Simulation},
+  author = {Malcolm Ramsay},
+  year = {2020},
+  month = jul,
+  doi = {10.5281/zenodo.3967979},
+  abstract = {Command line interface for running simulations for small molecules with hoomd-blue.},
+  file = {/home/malcolm/Zotero/storage/JUB3FE8I/3967979.html},
+  howpublished = {Zenodo}
+}
+
+@misc{MalcolmRamsay2020b,
+  title = {Malramsay64/Experi: {{Release}} v0.3.6},
+  shorttitle = {Malramsay64/Experi},
+  author = {Malcolm Ramsay and Tom Nicholas},
+  year = {2020},
+  month = jul,
+  doi = {10.5281/zenodo.3967989},
+  abstract = {Create a release with a proper title for Zenodo},
+  file = {/home/malcolm/Zotero/storage/B7FB3XLB/3967989.html},
+  howpublished = {Zenodo}
+}
+
 @article{Mallamace2014,
   title = {On the Ergodicity of Supercooled Molecular Glass-Forming Liquids at the Dynamical Arrest: The o-Terphenyl Case},
   shorttitle = {On the Ergodicity of Supercooled Molecular Glass-Forming Liquids at the Dynamical Arrest},
@@ -7196,6 +7305,18 @@ @phdthesis{Ramsay2015
   school = {The University of Sydney}
 }
 
+@misc{Ramsay2018,
+  ids = {MalcolmRamasy2018},
+  title = {Melting of {{2D}} Molecular Crystals},
+  author = {Ramsay, Malcolm},
+  year = {2018},
+  month = nov,
+  publisher = {{Zenodo}},
+  doi = {10.5281/zenodo.3958341},
+  abstract = {Melting data},
+  file = {/home/malcolm/Zotero/storage/BYV9YNEQ/3958341.html;/home/malcolm/Zotero/storage/G2F9NKYV/3958341.html}
+}
+
 @article{Rapaport1985,
   title = {Molecular Dynamics Simulation Using Quaternions},
   author = {Rapaport, D. C},
@@ -8328,6 +8449,27 @@ @article{Somers2018
   journal = {The Atlantic}
 }
 
+@article{Song2019,
+  title = {Transport Dynamics of Complex Fluids},
+  author = {Song, Sanggeun and Park, Seong Jun and Kim, Minjung and Kim, Jun Soo and Sung, Bong June and Lee, Sangyoub and Kim, Ji-Hyun and Sung, Jaeyoung},
+  year = {2019},
+  month = jun,
+  volume = {116},
+  pages = {12733--12742},
+  publisher = {{National Academy of Sciences}},
+  issn = {0027-8424, 1091-6490},
+  doi = {10.1073/pnas.1900239116},
+  abstract = {Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate subdiffusive, and long-time diffusive motion, unless interrupted. Despite its relevance to numerous dynamical processes of interest in modern science, a unified, quantitative understanding of thermal motion in complex fluids remains a challenging problem. Here, we present a transport equation and its solutions, which yield a unified quantitative explanation of the mean-square displacement (MSD), the non-Gaussian parameter (NGP), and the displacement distribution of complex fluids. In our approach, the environment-coupled diffusion kernel and its time correlation function (TCF) are the essential quantities that determine transport dynamics and characterize mobility fluctuation of complex fluids; their time profiles are directly extractable from a model-free analysis of the MSD and NGP or, with greater computational expense, from the two-point and four-point velocity autocorrelation functions. We construct a general, explicit model of the diffusion kernel, comprising one unbound-mode and multiple bound-mode components, which provides an excellent approximate description of transport dynamics of various complex fluidic systems such as supercooled water, colloidal beads diffusing on lipid tubes, and dense hard disk fluid. We also introduce the concepts of intrinsic disorder and extrinsic disorder that have distinct effects on transport dynamics and different dependencies on temperature and density. This work presents an unexplored direction for quantitative understanding of transport and transport-coupled processes in complex disordered media.},
+  chapter = {PNAS Plus},
+  copyright = {Copyright \textcopyright{} 2019 the Author(s). Published by PNAS.. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).},
+  file = {/home/malcolm/Zotero/storage/XWZDAGHZ/Song et al_2019_Transport dynamics of complex fluids.pdf;/home/malcolm/Zotero/storage/4GIQZ2YA/12733.html},
+  journal = {PNAS},
+  keywords = {colloidal particles on lipid tube,complex fluids,diffusion kernel correlation,supercooled water,thermal motion},
+  language = {en},
+  number = {26},
+  pmid = {31175151}
+}
+
 @article{Spaepen1979,
   title = {Kinetics of Motion of Crystal-melt Interfaces},
   author = {Spaepen, F. and Turnbull, D.},
@@ -8431,6 +8573,21 @@ @article{Srnec2017
   number = {6}
 }
 
+@article{Steffen1994,
+  title = {Depolarized-Light-Scattering Study of Orthoterphenyl and Comparison with the Mode-Coupling Model},
+  author = {Steffen, W. and Patkowski, A. and Gl{\"a}ser, H. and Meier, G. and Fischer, E. W.},
+  year = {1994},
+  month = apr,
+  volume = {49},
+  pages = {2992--3002},
+  publisher = {{American Physical Society}},
+  doi = {10.1103/PhysRevE.49.2992},
+  abstract = {The dynamics of the molecular glass-forming liquid orthoterphenyl above the glass-transition temperature was studied combining several experimental techniques: depolarized Raman, depolarized Rayleigh-Brillouin light scattering, and photon correlation spectroscopy in the temperature range from 250 to 440 K. The combined spectra covering a frequency range from 10-2 to 1013 Hz were analyzed using the mode-coupling theory. The coordinates of the susceptibility minimum, {$\omega$}min and {$\chi$}min, as well as the position of the maximum, {$\omega$}max ({$\alpha$} peak), scale with temperature according to the mode-coupling theory, resulting in Tc=290 K. The construction of the predicted master curve in the vicinity of the minimum of the rescaled susceptibility was possible in a narrow frequency range only if the values of {$\omega$}min resulting from the mode-coupling-theory force fit were used. The width of the {$\alpha$} peak appears to increase with increasing temperatures for temperatures above Tc, although when the effects of fast processes on the high-frequency wing are included, the corrected width appears to decrease instead approaching a Debye relaxation shape at high temperatures. Below Tc it was not possible to fit objectively the data using the mode-coupling theory; thus it was impossible to corroborate the divergence of the scaling time of the mode-coupling {$\beta$} relaxation on both sides of Tc. Assuming a priori that the mode-coupling model is correct, it is possible to make the data compatible with the mode-coupling theory.},
+  file = {/home/malcolm/Zotero/storage/M396KND9/Steffen et al_1994_Depolarized-light-scattering study of orthoterphenyl and comparison with the.pdf;/home/malcolm/Zotero/storage/9FJBPR49/PhysRevE.49.html},
+  journal = {Phys. Rev. E},
+  number = {4}
+}
+
 @article{Steinhardt1983,
   title = {Bond-Orientational Order in Liquids and Glasses},
   author = {Steinhardt, Paul J. and Nelson, David R. and Ronchetti, Marco},
@@ -9985,6 +10142,22 @@ @article{Yang2019
   primaryClass = {cs}
 }
 
+@article{Yeh2004,
+  title = {System-{{Size Dependence}} of {{Diffusion Coefficients}} and {{Viscosities}} from {{Molecular Dynamics Simulations}} with {{Periodic Boundary Conditions}}},
+  author = {Yeh, In-Chul and Hummer, Gerhard},
+  year = {2004},
+  month = oct,
+  volume = {108},
+  pages = {15873--15879},
+  publisher = {{American Chemical Society}},
+  issn = {1520-6106},
+  doi = {10.1021/jp0477147},
+  abstract = {We study the system-size dependence of translational diffusion coefficients and viscosities in molecular dynamics simulations under periodic boundary conditions. Simulations of water under ambient conditions and a Lennard-Jones (LJ) fluid show that the diffusion coefficients increase strongly as the system size increases. We test a simple analytic correction for the system-size effects that is based on hydrodynamic arguments. This correction scales as N-1/3, where N is the number of particles. For a cubic simulation box of length L, the diffusion coefficient corrected for system-size effects is D0 = DPBC + 2.837297kBT/(6{$\pi\eta$}L), where DPBC is the diffusion coefficient calculated in the simulation, kB the Boltzmann constant, T the absolute temperature, and {$\eta$} the shear viscosity of the solvent. For water, LJ fluids, and hard-sphere fluids, this correction quantitatively accounts for the system-size dependence of the calculated self-diffusion coefficients. In contrast to diffusion coefficients, the shear viscosities of water and the LJ fluid show no significant system-size dependences.},
+  file = {/home/malcolm/Zotero/storage/TG8I5YX2/Yeh_Hummer_2004_System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular.pdf;/home/malcolm/Zotero/storage/KKTLJZLU/jp0477147.html},
+  journal = {J. Phys. Chem. B},
+  number = {40}
+}
+
 @misc{Yon2019,
   title = {{{slurmR}}: {{A}} Lightweight Wrapper for {{HPC}} with {{Slurm}}},
   shorttitle = {{{slurmR}}},