14 research outputs found
Lead clusters: different potentials, different structures
The lowest-energy structures of lead clusters interacting via a Gupta
potential are obtained for N<151. Structures based on Marks decahedra dominate
at the larger sizes. These results are very different from those obtained
previously using a lead glue potential, and the origins of the differences are
related back to differences in the potential.Comment: 6 pages, 4 figures, TAMC4 proceeding
Exploring the origins of the power-law properties of energy landscapes: An egg-box model
Multidimensional potential energy landscapes (PELs) have a Gaussian
distribution for the energies of the minima, but at the same time the
distribution of the hyperareas for the basins of attraction surrounding the
minima follows a power-law. To explore how both these features can
simultaneously be true, we introduce an ``egg-box'' model. In these model
landscapes, the Gaussian energy distribution is used as a starting point and we
examine whether a power-law basin area distribution can arise as a natural
consequence through the swallowing up of higher-energy minima by larger
low-energy basins when the variance of this Gaussian is increased sufficiently.
Although the basin area distribution is substantially broadened by this
process,it is insufficient to generate power-laws, highlighting the role played
by the inhomogeneous distribution of basins in configuration space for actual
PELs.Comment: 7 pages, 8 figure
A self-consistent approach to measure preferential attachment in networks and its application to an inherent structure network
Preferential attachment is one possible way to obtain a scale-free network.
We develop a self-consistent method to determine whether preferential
attachment occurs during the growth of a network, and to extract the
preferential attachment rule using time-dependent data. Model networks are
grown with known preferential attachment rules to test the method, which is
seen to be robust. The method is then applied to a scale-free inherent
structure network, which represents the connections between minima via
transition states on a potential energy landscape. Even though this network is
static, we can examine the growth of the network as a function of a threshold
energy (rather than time), where only those transition states with energies
lower than the threshold energy contribute to the network.For these networks we
are able to detect the presence of preferential attachment, and this helps to
explain the ubiquity of funnels on energy landscapes. However, the scale-free
degree distribution shows some differences from that of a model network grown
using the obtained preferential attachment rules, implying that other factors
are also important in the growth process.Comment: 8 pages, 8 figure
DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization
The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ∼100 and ∼2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of similar to 100 and similar to 2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands
The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks
We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the
interplay between evolvability and robustness of model gene regulatory networks
with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006)
we find that networks with SFin topologies, that is SF topology for incoming
nodes and ER topology for outgoing nodes, are significantly more evolvable
towards specific oscillatory targets than networks with ER topology for both
incoming and outgoing nodes. Similar results are found for networks with SFboth
and SFout topologies. The functionality of the SFout topology, which most
closely resembles the structure of biological gene networks (Babu et al.,
2004), is compared to the ER topology in further detail through an extension to
multiple target outputs, with either an oscillatory or a non-oscillatory
nature. For multiple oscillatory targets of the same length, the differences
between SFout and ER networks are enhanced, but for non-oscillatory targets
both types of networks show fairly similar evolvability. We find that SF
networks generate oscillations much more easily than ER networks do, and this
may explain why SF networks are more evolvable than ER networks are for
oscillatory phenotypes. In spite of their greater evolvability, we find that
networks with SFout topologies are also more robust to mutations than ER
networks. Furthermore, the SFout topologies are more robust to changes in
initial conditions (environmental robustness). For both topologies, we find
that once a population of networks has reached the target state, further
neutral evolution can lead to an increase in both the mutational robustness and
the environmental robustness to changes in initial conditions.Comment: 16 pages, 15 figure
Note: Heterogeneous ice nucleation on silver-iodide-like surfaces
We attempt to simulate the heterogeneous nucleation of ice at model silver-iodide surfaces and find relatively facile ice nucleation and growth at the Ag(+) terminated basal face, but never see nucleation at the I(-) terminated basal face or the prism and normal faces. Water molecules strongly adsorb onto the Ag(+) terminated face to give a well-ordered hexagonal ice-like bilayer that then acts as a template for further ice growth
Note: Heterogeneous ice nucleation on silver-iodide-like surfaces
We attempt to simulate the heterogeneous nucleation of ice at model silver-iodide surfaces and find relatively facile ice nucleation and growth at the Ag(+) terminated basal face, but never see nucleation at the I(-) terminated basal face or the prism and normal faces. Water molecules strongly adsorb onto the Ag(+) terminated face to give a well-ordered hexagonal ice-like bilayer that then acts as a template for further ice growth
Apicultura ecològica vs. tradicional
Treball presentat a l'assignatura de Deontologia i Veterinària Legal (21223
Plectoneme tip bubbles : coupled denaturation and writhing in supercoiled DNA
We predict a novel conformational regime for DNA, where denaturation bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. For negative supercoiling, this regime lies between bubble-dominated and plectoneme-dominated phases, and explains the broad transition between the two observed in experiment. Tip bubbles cause localisation of plectonemes within thermodynamically weaker AT-rich sequences, and can greatly suppress plectoneme diffusion by a pinning mechanism. They occur for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes