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- Daniel J. Price
- J. Comput. Physics
- 2008

In this paper we discuss the treatment of discontinuities in Smoothed Particle Hydrodynamics (SPH) simulations. In particular we discuss the difference between integral and differential representations of the fluid equations in an SPH context and how this relates to the formulation of dissipative terms for the capture of shocks and other discontinuities.… (More)

- Daniel J. Price, Charles L. Brooks
- The Journal of chemical physics
- 2004

The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for molecular dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have… (More)

- Philippe Ferrara, Holger Gohlke, Daniel J. Price, Gerhard Klebe, Charles L. Brooks
- Journal of medicinal chemistry
- 2004

An assessment of nine scoring functions commonly applied in docking using a set of 189 protein-ligand complexes is presented. The scoring functions include the CHARMm potential, the scoring function DrugScore, the scoring function used in AutoDock, the three scoring functions implemented in DOCK, as well as three scoring functions implemented in the CScore… (More)

- Maneesh K. Yadav, Luke J Leman, Daniel J. Price, Charles L. Brooks, Charles David Stout, Mohammad Reza Ghadiri
- Biochemistry
- 2006

A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here, we describe the crystal structures of a single coiled-coil peptide in distinct parallel and… (More)

- Marty Shankland, Mark Q. Martindale, Denise Nardelli-Haefliger, Esther Baxter, Daniel J. Price
- Development (Cambridge, England). Supplement
- 1991

The leech embryo develops its segmental body plan by means of a stereotyped cell lineage. Each hemilateral segment arises from a small set of embryonic blast cells via a comparable sequence of formative cell divisions, and for the most part, lineally homologous cells manifest similar patterns of differentiation in the various hemisegments. Nonetheless, some… (More)

- Joseph D. Yesselman, Daniel J. Price, Jennifer L. Knight, Charles L. Brooks
- Journal of Computational Chemistry
- 2012

We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A… (More)

- Daniel J. Price
- J. Comput. Physics
- 2012

This paper presents an overview and introduction to Smoothed Particle Hydrodynamics and Magnetohydrodynamics in theory and in practice. Firstly, we give a basic grounding in the fundamentals of SPH, showing how the equations of motion and energy can be self-consistently derived from the density estimate. We then show how to interpret these equations using… (More)

- Ruth L. Cromie, Martha J Brown, Daniel J. Price, John L. Stanford
- Tubercle
- 1991

This study reports the findings of an epidemiological survey of death due to avian tuberculosis in the captive collection of wildfowl at The Wildfowl and Wetlands Trust Centre, Slimbridge, Gloucestershire. Both genetic and environmental factors have been shown to affect the incidence of, and the birds' susceptibility to, the disease. Seasonal body condition… (More)

In this paper we show how the Smoothed Particle Hydrodynamics (SPH) equations for ideal magnetohydrodynamics (MHD) can be written in conservation form with the positivity of the dissipation guaranteed. We call the resulting algorithm Smoothed Particle Magnetohydrodynamics (SPMHD). The equations appear to be accurate, robust and easy to apply and do not… (More)

We have developed a modified form of the equations of smoothed particle magnetohydrodynamics which are stable in the presence of very steep density gradients. Using this formalism, we have performed simulations of the collapse of magnetised molecular cloud cores to form protostars and drive outflows. Our stable formalism allows for smaller sink particles (<… (More)