COSMIC: a curated database of somatic variants and clinical data for cancer.

The Catalogue Of Somatic Mutations In Cancer (COSMIC), https://cancer.sanger.ac.uk/cosmic, is an expert-curated knowledgebase providing data on somatic variants in cancer, supported by a comprehensive suite of tools for interpreting genomic data, discerning the impact of somatic alterations on disease, and facilitating translational research. The catalogue is accessed and used by thousands of cancer researchers and clinicians daily, allowing them to quickly access information from an immense pool of data curated from over 29 thousand scientific publications and large studies. Within the last 4 years, COSMIC has substantially expanded its utility by adding new resources: the Mutational Signatures catalogue, the Cancer Mutation Census, and Actionability. To improve data accessibility and interoperability, somatic variants have received stable genomic identifiers that are associated with their genomic coordinates in GRCh37 and GRCh38, and new export files with reduced data redundancy have been made available for download.

Statistics and Dynamics of the Center-of-Mass Coordinate in a Quantum Liquid.

Motivated by recent experiments in ultracold gases, we focus on the properties of the center-of-mass coordinate of an interacting one-dimensional Fermi gas, displaying several distinct phases. While the variance of the center of mass vanishes in insulating phases such as phase-separated and charge density wave phases, it remains finite in the metallic phase, which realizes a Luttinger liquid. By combining numerics with bosonization, we demonstrate that the autocorrelation function of the center-of-mass coordinate is universal throughout the metallic phase. It exhibits persistent oscillations, and its short time dynamics reveal important features of the quantum liquid, such as the Luttinger liquid parameter and the renormalized velocity. The full counting statistics of the center of mass follows a normal distribution already for small systems. Our results apply to nonintegrable systems as well and are within experimental reach for, e.g., carbon nanotubes and cold atomic gases.

Theoretical evidence for a reentrant phase diagram in ortho-para mixtures of solid H2 at high pressure.

We develop a multiorder parameter mean-field formalism for systems of coupled quantum rotors. The scheme is developed to account for systems where ortho-para distinction is valid. We apply our formalism to solid H2 and D2. We find an anomalous reentrant orientational phase transition for both systems at thermal equilibrium. The correlation functions of the order parameter indicate short-range order at low temperatures. As the temperature is increased the correlation increases along the phase boundary. We also find that even extremely small odd-J concentrations (1%) can trigger short-range orientational ordering.

Quantum monte carlo algorithm based on two-body density functional theory for fermionic many-body systems: application to 3He.

We construct a quantum Monte Carlo algorithm for interacting fermions using the two-body density as the fundamental quantity. The central idea is mapping the interacting fermionic system onto an auxiliary system of interacting bosons. The correction term is approximated using correlated wave functions for the interacting system, resulting in an effective potential that represents the nodal surface. We calculate the properties of 3He and find good agreement with experiment and with other theoretical work. In particular, our results for the total energy agree well with other calculations where the same approximations were implemented but the standard quantum Monte Carlo algorithm was used.

Calculation of near-edge x-ray-absorption fine structure at finite temperatures: spectral signatures of hydrogen bond breaking in liquid water.

We calculate the near-edge x-ray-absorption fine structure of H(2)O in the gas, hexagonal ice, and liquid phases using heuristic density-functional based methods. We present a detailed comparison of our results with experiment. The differences between the ice and water spectra can be rationalized in terms of the breaking of hydrogen bonds around the absorbing molecule. In particular the increase in the pre-edge absorption feature from ice to water is shown to be due to the breaking of a donor hydrogen bond. We also find that in water approximately 19% of hydrogen bonds are broken.

Multiple "time step" Monte Carlo simulations: application to charged systems with Ewald summation.

Recently, we have proposed an efficient scheme for Monte Carlo simulations, the multiple "time step" Monte Carlo (MTS-MC) [J. Chem. Phys. 117, 8203 (2002)] based on the separation of the potential interactions into two additive parts. In this paper, the structural and thermodynamic properties of the simple point charge water model combined with the Ewald sum are compared for the MTS-MC real-/reciprocal-space split of the Ewald summation and the common Metropolis Monte Carlo method. We report a number of observables as a function of CPU time calculated using MC and MTS-MC. The correlation functions indicate that speedups on the order of 4.5-7.5 can be obtained for systems of 108-500 waters for n=10 splitting parameter.