Biomedical subjects

G J Ackland

Publications and source records attributed to G J Ackland.

10 recordsLinked to original sources

PubMed2006

Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia.

We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.

Journal Article↗

PubMed2006

Magnetically induced immiscibility in the Ising model of FeCr stainless steel.

The iron-chromium alloy system has an unexplained anomaly: although there is a broad miscibility gap it appears to be favorable for chromium to dissolve in iron. This is consistent with ab initio calculation, but no simpler physically intuitive picture has been presented. Here it is shown that the Ising model, based on the bcc lattice with antiferromagnetic and ferromagnetic species, has the potential to exhibit similar behavior, with a skew miscibility gap arising from the solubility of antiferromagnetic species on nonadjacent sites. Essential characteristics of stainless steel (high Cr solubility and surface segregation) are correctly reproduced. Under some conditions, magnetization increases with temperature. The equilibrium miscibility gap due to mixed magnetism and segregation-driven positive dM/dT are fundamental features of the bcc Ising model itself, not just FeCr.

Journal Article↗

PubMed2006

Mutation of albedo and growth response produces oscillations in a spatial Daisyworld.

We extended a two-dimensional cellular automaton (CA) Daisyworld to include mutation of optimal growth temperature as well as mutation of albedo. Thus, the organisms (daisies) can adapt to prevailing environmental conditions or evolve to alter their environment. We find the resulting system oscillates with a period of hundreds of daisy generations. Weaker and less regular oscillations exist in previous daisyworld models, but they become much stronger and more regular here with mutation in the growth response. Despite the existence of a particular combination of mean albedo and optimum individual growth temperature which maximises growth, we find that this global state is unstable with respect to mutations which lower absolute growth rate, but increase marginal growth rate. The resulting system oscillates with a period that is found to decrease with increasing death rate, and to increase with increasing heat diffusion and heat capacity. We speculate that the origin of this oscillation is a Hopf bifurcation, previously predicted in a zero-dimensional system.

Climate↗

PubMed2006

Microscopic model of diffusion limited aggregation and electrodeposition in the presence of leveling molecules.

We present a cellular automata approach for microscopic modeling of the effect of unbinding in diffusion limited aggregation. The automata represent active particles, which are able to change their internal state and affect their neighbors. The geometry resembles electrochemical deposition-"ions" diffuse at random from the top of a container until encountering an aggregate in contact with the bottom, to which they stick. This model exhibits dendritic (fractal) growth in the diffusion limited case. The addition of a field eliminates the fractal nature but the density remains low. The addition of molecules that unbind atoms from the aggregate transforms the deposit to a 100% dense one (in three dimensions). The molecules are remarkably adept at avoiding being trapped. This mimics the effect of so-called leveler molecules which are used in electrochemical deposition.

Journal Article↗

PubMed2004

Stabilization of large generalized Lotka-Volterra foodwebs by evolutionary feedback.

Conventional ecological models show that complexity destabilizes foodwebs, suggesting that foodwebs should have neither large numbers of species nor a large number of interactions. However, in nature the opposite appears to be the case. Here we show that if the interactions between species are allowed to evolve within a generalized Lotka-Volterra model such stabilizing feedbacks and weak interactions emerge automatically. Moreover, we show that trophic levels also emerge spontaneously from the evolutionary approach, and the efficiency of the unperturbed ecosystem increases with time. The key to stability in large foodwebs appears to arise not from complexity per se but from evolution at the level of the ecosystem which favors stabilizing (negative) feedbacks.

Animals↗

PubMed2004

Maximization principles and daisyworld.

We investigate whether the equilibrium time-averaged state of a self-organizing system with many internal degrees of freedom, 2D-daisyworld, can be described by optimizing a single quantity. Unlike physical systems where a principle of maximum energy production has been observed, daisyworld follows evolutionary dynamics rather than Hamiltonian dynamics. We find that this is sufficient to invalidate the maximum entropy production principle, finding instead a different principle, that the system self-organizes to a state which maximizes the amount of life.

Biological Evolution↗

PubMed2002

Devil's staircase in kinetically limited growth.

The devil's staircase is a term used to describe surface or an equilibrium phase diagram in which various ordered facets or phases are infinitely closely packed as a function of some model parameter. A classic example is a one-dimensional Ising model [P. Bak and R. Bruinsma, Phys. Rev. Lett. 49, 249 (1982)] wherein long-range and short-range forces compete, and the periodicity of the gaps between minority species covers all rational values. In many physical cases, crystal growth proceeds by adding surface layers that have the lowest energy, but are then frozen in place. The emerging layered structure is not the thermodynamic ground state, but is uniquely defined by the growth kinetics. It is shown that for such a system, the grown structure tends to the equilibrium ground state via a devil's staircase traversing an infinity of intermediate phases. It would be extremely difficult to deduce the simple growth law based on measurement made on such a grown structure.

Journal Article↗

PubMed2002

Lattice-switch Monte Carlo method: application to soft potentials.

The lattice-switch Monte Carlo method, recently introduced and applied in the context of hard spheres, is extended to particles interacting through a soft potential. The method utilizes a transformation that switches between configurations of two different crystalline structures, allowing the phase space of both structures to be explored in a single simulation and the difference between their free energies to be determined directly. We apply the method to determine the fcc-hcp crystalline phase behavior of the classical Lennard-Jones solid.

Journal Article↗

PubMed2001

Pack formation in cycling and orienteering.

In cycling and orienteering competitions, competitors can become bunched into packs, which may mask an individual's true ability. Here we model this process with a view to determining when competitors' times are determined more by others than by their own ability. Our results may prove useful in helping to stage events so that pack formation can be avoided.

Bicycling↗

PubMed2001

Two disordered phases of the beta-tin structure in binary semiconductors.

The Ising model on a beta-tin structure has a phase diagram containing three distinct phases involving order, disorder, and a frustrated ordering. The x-ray crystallographic observation that no ordered beta-tin phases exist at room temperature in compound semiconductors may indicate either "paramagnetic" (dynamic) or frustrated (static) disorder. Density functional pseudopotential calculations determine which regimes real materials fall into and predict that in materials such as GaSb, there may be two temperature-driven transitions between beta-tin structures: from ordered, to frustrated order, to disordered.

Journal Article↗