Surfactancy in a tadpole model of proteins.

We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexible molecules by polymers. We put particular focus on proteins with both globular and intrinsically disordered regions, which we represent with 'tadpole' constructed by grafting single polymers and colloids together. In Monte Carlo simulations, we find these tadpoles support phase separation via depletion flocculation, and demonstrate several surfactant behaviours, including being found preferentially at interfaces and forming micelles in single phase solution. Furthermore, the model parameters can be tuned to give a tadpole a preference for either bulk phase. However, we find entropy too weak to drive these behaviours by itself at likely biological concentrations.

Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis.

We apply a simulational proxy of the phi-value analysis and perform extensive mutagenesis experiments to identify the nucleating residues in the folding "reactions" of two small lattice Go polymers with different native geometries. Our findings show that for the more complex native fold (i.e., the one that is rich in nonlocal, long-range bonds), mutation of the residues that form the folding nucleus leads to a considerably larger increase in the folding time than the corresponding mutations in the geometry that is predominantly local. These results are compared to data obtained from an accurate analysis based on the reaction coordinate folding probability P(fold) and on structural clustering methods. Our study reveals a complex picture of the transition state ensemble. For both protein models, the transition state ensemble is rather heterogeneous and splits up into structurally different populations. For the more complex geometry the identified subpopulations are actually structurally disjoint. For the less complex native geometry we found a broad transition state with microscopic heterogeneity. These findings suggest that the existence of multiple transition state structures may be linked to the geometric complexity of the native fold. For both geometries, the identification of the folding nucleus via the P(fold) analysis agrees with the identification of the folding nucleus carried out with the phi-value analysis. For the most complex geometry, however, the applied methodologies give more consistent results than for the more local geometry. The study of the transition state structure reveals that the nucleus residues are not necessarily fully native in the transition state. Indeed, it is only for the more complex geometry that two of the five critical residues show a considerably high probability of having all its native bonds formed in the transition state. Therefore, one concludes that, in general, the phi-value correlates with the acceleration/deceleration of folding induced by mutation, rather than with the degree of nativeness of the transition state, and that the "traditional" interpretation of phi-values may provide a more realistic picture of the structure of the transition state only for more complex native geometries.

Fermions without fermion fields.

It is shown that an arbitrary fermion hopping Hamiltonian can be mapped into a system with no fermion fields, generalizing an earlier model of Levin and Wen. All operators in the Hamiltonian of the resulting description commute (rather than anticommute) when acting at different sites, despite the system having excitations obeying Fermi statistics. While extra conserved degrees of freedom are introduced, they are all locally identified in the representation obtained. The same methods apply to Majorana (half) fermions, which for Cartesian lattices mitigate the fermion doubling problem. The generality of these results suggests that the observation of Fermion excitations in nature does not demand that anticommuting Fermion fields be fundamental.

Theory of growth by differential sedimentation, with application to snowflake formation.

A simple model of irreversible aggregation under differential sedimentation of particles in a fluid is presented. The structure of the aggregates produced by this process is found to feed back on the dynamics in such a way as to stabilize both the exponents controlling the growth rate, and the fractal dimension of the clusters produced at readily predictable values. The aggregation of ice crystals to form snowflakes is considered as a potential application of the model.

Folding and form: insights from lattice simulations.

Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native structure's geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures of low contact order is driven by backbone distance and is characterized by a progressive accumulation of structure towards the native fold. By contrast, folding to high contact order targets is dominated by intermediate stage contacts not present in the native fold, yielding a more cooperative folding process.

From plasticity to a renormalization group.

The marginally rigid state is a candidate paradigm for what makes granular material a state of matter distinct from both liquid and solid. The coordination number is identified as a discriminating characteristic, and for rough-surfaced particles we show that the low values predicted are indeed approached in simple two-dimensional experiments. We show calculations of the stress transmission, suggesting that this is governed by local linear equations of constraint between the stress components. These constraints can in turn be related to the generalized forces conjugate to the motion of grains rolling over each other. The lack of a spatially coherent way of imposing a sign convention on these motions is a problem for scaling up the equations, which leads us to attempt a renormalization-group calculation. Finally, we discuss how perturbations propagate through such systems, suggesting a distinction between the behaviour of rough and smooth grains.

Diffusion-controlled growth: theory and closure approximations.

We expand upon a new theoretical framework for diffusion-limited aggregation and associated dielectric breakdown models in two dimensions [R. C. Ball and E. Somfai, Phys. Rev. Lett. 89, 135503 (2002)]. Key steps are understanding how these models interrelate when the ultraviolet cut-off strategy is changed, the analogy with turbulence, and the use of logarithmic field variables. Within the simplest, Gaussian, truncation of mode-mode coupling, all properties can be calculated. The agreement with prior knowledge from simulations is encouraging, and a new superuniversality of the tip scaling exponent is discussed. We find angular resonances relatable to the cone angle theory, and we are led to predict a new screening transition in the DBM at large eta.

Theory of diffusion controlled growth.

We present a new theoretical framework for diffusion limited aggregation and associated dielectric breakdown models in two dimensions. Key steps are understanding how these models interrelate when the ultraviolet cutoff strategy is changed, the analogy with turbulence and the use of logarithmic field variables. Within the simplest, Gaussian, truncation of mode-mode coupling, all properties can be calculated. The agreement with prior knowledge from simulations is encouraging, and a new superuniversality of the tip scaling exponent is both predicted and confirmed.

How many conformations can a protein remember?

We show that a protein can be trained to recognize multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield network, the number of conformations which can be remembered by a protein sequence depends on the size of the amino acid alphabet as lnA, independent of protein length. This admits the possibility of certain proteins, such as prions, evolving to fold to independent stable conformations, as well as novel possibilities for protein and heteropolymer design.

Universal aging features in the restructuring of fractal colloidal gels.

We use multispeckle dynamic light scattering to measure the dynamic structure factor, f(q,tau), of gels formed by aggregation of colloids. Although the gel is an elastic solid, f(q,tau) nearly completely decays on long time scales, with an unusual form, f(q, tau) approximately exp{-(tau/tau(f))(mu)}, with mu approximately 1.5 and with tau(f) proportional variant q(-1). A model for restructuring of the gel with aging correctly accounts for this behavior. Aging leads to a dramatic increase in tau(f); however, all data can be scaled on a single master curve, with tau(f) asymptotically growing linearly with age. This behavior is strikingly similar to that predicted for aging in disordered glassy systems, offering convincing proof of the universality of these concepts.

Effects of grilling to 80 °C on the chemical composition of pork loin chops and some observations on the UK National Food Survey estimate of fat consumption.

The physical and chemical composition of pork loin chops was investigated, examining the changes that occurred in (i) the whole chop, (ii) the fat tissue and (iii) the lean tissue by grilling to 80 °C. Adjacent 25 mm thick chops, with backfat and rind attached, were cut from loins of 90 kg live weight pigs having a fat thickness (P(2)) of 11 mm, representative of current UK production. One chop was analysed fresh by dissection and standard analytical techniques and the other after grilling. Weights of chop (including rind) before and after cooking were 210 and 136 g, respectively. The average weight loss for the whole chop was 35%; the weight loss from fat, 44%, being greater than that from lean, 34%, or rind, 27%, the latter accounting for 14% of the whole raw chop. When expressed conventionally, on a percentage basis, the fat content of the whole rindless chop increased from 22 to 23%, and the fat content of the lean increased from 5.5 to 9%. In absolute terms, based on an initial 100 g, the fat content in the whole chop reduced from 22 to 15 g, with a slight increase in the fat content of the lean, from 5.5 to 6.0 g. It is argued that the National Food Survey (NFS) approach of estimating fat consumption on the basis of the fat content of the raw product is flawed. The terms 'meat consumption' and 'fat consumption' are misleading since they reflect amounts purchased rather than the amount of meat and fat actually consumed, making no allowance for fat lost during cooking or for subcutaneous fat removed by consumers before consumption. Actual fat consumption from cooked meat and meat products, after allowing for a 25% fat loss during cooking and trimming of visible fat, is estimated at 10.3 g per person per day compared with the NFS estimate of 18.1 g.

A survey to investigate potential dehydration in slaughtered broiler chickens.

A survey of 800 broilers arriving at two commercial slaughterhouses with a combined annual throughput of 40 million birds was carried out. Each plant was visited on four occasions throughout summer and winter and blood samples were collected from 100 broilers at exsanguination throughout the day of each visit. In all, the survey covered 16 lorry loads of broilers delivered to one plant and 20 loads delivered to the other. The blood collected was analysed for packed cell volume (PCV), plasma creatine kinase, total protein, sodium, glucose, osmolality and corticosterone. Based on the measures of PCV, plasma total protein, sodium and osmolality there was no evidence of dehydration amongst the lorry loads of birds delivered to the plants. There were differences between the two plants in the levels of all of the blood variables that were measured, except for those of plasma corticosterone.