Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA

Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix site of DNA. The theoretical model explains the observed sequence specificity of Hin recombinase and leads to a number of testable predictions concerning altered sequence selectivity for various mutants of protein and DNA. Combining molecular dynamics simulations with constraints based on current knowledge of protein structure leads to a theoretical structure of the binding domain of Hin recombinase with the hix site of DNA. The model offers a mechanistic explanation of the presently known characteristics of Hin and predicts the effects of specific mutations of both protein and DNA. The predictions can be tested by currently feasible experiments that should lead to refinements in and improvements on the current theoretical model. Because current experimental and theoretical methods are all limited to providing only partial information about protein-DNA interactions, we believe that this approach of basing molecular simulations on experimental knowledge and using the results of these simulations to design new, more precise experimental tests will be of general utility. These results provide additional evidence for the generality of the helix-turn-helix motif in DNA recognition and stabilization of proteins on DNA

MLAPM - a C code for cosmological simulations

We present a computer code written in C that is designed to simulate structure formation from collisionless matter. The code is purely grid-based and uses a recursively refined Cartesian grid to solve Poisson's equation for the potential, rather than obtaining the potential from a Green's function. Refinements can have arbitrary shapes and in practice closely follow the complex morphology of the density field that evolves. The timestep shortens by a factor two with each successive refinement. It is argued that an appropriate choice of softening length is of great importance and that the softening should be at all points an appropriate multiple of the local inter-particle separation. Unlike tree and P3M codes, multigrid codes automatically satisfy this requirement. We show that at early times and low densities in cosmological simulations, the softening needs to be significantly smaller relative to the inter-particle separation than in virialized regions. Tests of the ability of the code's Poisson solver to recover the gravitational fields of both virialized halos and Zel'dovich waves are presented, as are tests of the code's ability to reproduce analytic solutions for plane-wave evolution. The times required to conduct a LCDM cosmological simulation for various configurations are compared with the times required to complete the same simulation with the ART, AP3M and GADGET codes. The power spectra, halo mass functions and halo-halo correlation functions of simulations conducted with different codes are compared.Comment: 20 pages, 20 figures, MNRAS in press, the code can be downloaded at http://www-thphys.physics.ox.ac.uk/users/MLAPM

Hydra: A Parallel Adaptive Grid Code

We describe the first parallel implementation of an adaptive particle-particle, particle-mesh code with smoothed particle hydrodynamics. Parallelisation of the serial code, ``Hydra'', is achieved by using CRAFT, a Cray proprietary language which allows rapid implementation of a serial code on a parallel machine by allowing global addressing of distributed memory. The collisionless variant of the code has already completed several 16.8 million particle cosmological simulations on a 128 processor Cray T3D whilst the full hydrodynamic code has completed several 4.2 million particle combined gas and dark matter runs. The efficiency of the code now allows parameter-space explorations to be performed routinely using $64^3$ particles of each species. A complete run including gas cooling, from high redshift to the present epoch requires approximately 10 hours on 64 processors. In this paper we present implementation details and results of the performance and scalability of the CRAFT version of Hydra under varying degrees of particle clustering.Comment: 23 pages, LaTex plus encapsulated figure

A theory of normed simulations

In existing simulation proof techniques, a single step in a lower-level specification may be simulated by an extended execution fragment in a higher-level one. As a result, it is cumbersome to mechanize these techniques using general purpose theorem provers. Moreover, it is undecidable whether a given relation is a simulation, even if tautology checking is decidable for the underlying specification logic. This paper introduces various types of normed simulations. In a normed simulation, each step in a lower-level specification can be simulated by at most one step in the higher-level one, for any related pair of states. In earlier work we demonstrated that normed simulations are quite useful as a vehicle for the formalization of refinement proofs via theorem provers. Here we show that normed simulations also have pleasant theoretical properties: (1) under some reasonable assumptions, it is decidable whether a given relation is a normed forward simulation, provided tautology checking is decidable for the underlying logic; (2) at the semantic level, normed forward and backward simulations together form a complete proof method for establishing behavior inclusion, provided that the higher-level specification has finite invisible nondeterminism.Comment: 31 pages, 10figure

The Grid Dependence of Well Inflow Performance in Reservoir Simulation

Imperial Users onl

A Parallel Adaptive P3M code with Hierarchical Particle Reordering

We discuss the design and implementation of HYDRA_OMP a parallel implementation of the Smoothed Particle Hydrodynamics-Adaptive P3M (SPH-AP3M) code HYDRA. The code is designed primarily for conducting cosmological hydrodynamic simulations and is written in Fortran77+OpenMP. A number of optimizations for RISC processors and SMP-NUMA architectures have been implemented, the most important optimization being hierarchical reordering of particles within chaining cells, which greatly improves data locality thereby removing the cache misses typically associated with linked lists. Parallel scaling is good, with a minimum parallel scaling of 73% achieved on 32 nodes for a variety of modern SMP architectures. We give performance data in terms of the number of particle updates per second, which is a more useful performance metric than raw MFlops. A basic version of the code will be made available to the community in the near future.Comment: 34 pages, 12 figures, accepted for publication in Computer Physics Communication

An adaptive grid refinement strategy for the simulation of negative streamers

The evolution of negative streamers during electric breakdown of a non-attaching gas can be described by a two-fluid model for electrons and positive ions. It consists of continuity equations for the charged particles including drift, diffusion and reaction in the local electric field, coupled to the Poisson equation for the electric potential. The model generates field enhancement and steep propagating ionization fronts at the tip of growing ionized filaments. An adaptive grid refinement method for the simulation of these structures is presented. It uses finite volume spatial discretizations and explicit time stepping, which allows the decoupling of the grids for the continuity equations from those for the Poisson equation. Standard refinement methods in which the refinement criterion is based on local error monitors fail due to the pulled character of the streamer front that propagates into a linearly unstable state. We present a refinement method which deals with all these features. Tests on one-dimensional streamer fronts as well as on three-dimensional streamers with cylindrical symmetry (hence effectively 2D for numerical purposes) are carried out successfully. Results on fine grids are presented, they show that such an adaptive grid method is needed to capture the streamer characteristics well. This refinement strategy enables us to adequately compute negative streamers in pure gases in the parameter regime where a physical instability appears: branching streamers.Comment: 46 pages, 19 figures, to appear in J. Comp. Phy