78 research outputs found
A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation
Nanoparticles introduced in living cells are capable of strongly promoting
the aggregation of peptides and proteins. We use here molecular dynamics
simulations to characterise in detail the process by which nanoparticle
surfaces catalyse the self- assembly of peptides into fibrillar structures. The
simulation of a system of hundreds of peptides over the millisecond timescale
enables us to show that the mechanism of aggregation involves a first phase in
which small structurally disordered oligomers assemble onto the nanoparticle
and a second phase in which they evolve into highly ordered beta-sheets as
their size increases
Liquid-liquid critical point in supercooled silicon
A novel liquid-liquid phase transition has been proposed and investigated in
a wide variety of pure substances recently, including water, silica and
silicon. From computer simulations using the Stillinger-Weber classical
empirical potential, Sastry and Angell [1] demonstrated a first order
liquid-liquid transition in supercooled silicon, subsequently supported by
experimental and simulation studies. Here, we report evidence for a
liquid-liquid critical end point at negative pressures, from computer
simulations using the SW potential. Compressibilities exhibit a growing maximum
upon lowering temperature below 1500 K and isotherms exhibit density
discontinuities below 1120 K, at negative pressure. Below 1120 K, isotherms
obtained from constant volume-temperature simulations exhibit non-monotonic,
van der Waals-like behavior signaling a first order transition. We identify Tc
~ 1120 +/- 12 K, Pc -0.60 +/- 0.15 GPa as the critical temperature and pressure
for the liquid-liquid critical point. The structure of the liquid changes
dramatically upon decreasing the temperature and pressure. Diffusivities vary
over 4 orders of magnitude, and exhibit anomalous pressure dependence near the
critical point. A strong relationship between local geometry quantified by the
coordination number, and diffusivity, is seen, suggesting that atomic mobility
in both low and high density liquids can usefully be analyzed in terms of
defects in the tetrahedral network structure. We have constructed the phase
diagram of supercooled silicon. We identify the lines of compressibility,
density extrema (maxima and minima) and the spinodal which reveal the
interconnection between thermodynamic anomalies and the phase behaviour of the
system as suggested in previous works [2-9]Comment: (to be published in revised form); small corrections to previous
version; Nature Physics 201
Quantitative imaging of concentrated suspensions under flow
We review recent advances in imaging the flow of concentrated suspensions,
focussing on the use of confocal microscopy to obtain time-resolved information
on the single-particle level in these systems. After motivating the need for
quantitative (confocal) imaging in suspension rheology, we briefly describe the
particles, sample environments, microscopy tools and analysis algorithms needed
to perform this kind of experiments. The second part of the review focusses on
microscopic aspects of the flow of concentrated model hard-sphere-like
suspensions, and the relation to non-linear rheological phenomena such as
yielding, shear localization, wall slip and shear-induced ordering. Both
Brownian and non-Brownian systems will be described. We show how quantitative
imaging can improve our understanding of the connection between microscopic
dynamics and bulk flow.Comment: Review on imaging hard-sphere suspensions, incl summary of
methodology. Submitted for special volume 'High Solid Dispersions' ed. M.
Cloitre, Vol. xx of 'Advances and Polymer Science' (Springer, Berlin, 2009);
22 pages, 16 fig
Rasiowa–Sikorski deduction systems in computer science applications
AbstractA Rasiowa-Sikorski system is a sequence-type formalization of logics. The system uses invertible decomposition rules which decompose a formula into sequences of simpler formulae whose validity is equivalent to validity of the original formula. There may also be expansion rules which close indecomposable sequences under certain properties of relations appearing in the formulae, like symmetry or transitivity. Proofs are finite decomposition trees with leaves having “fundamental”, valid labels. The author describes a general method of applying the R-S formalism to develop complete deduction systems for various brands of C.S and A.I. logic, including a logic for reasoning about relative similarity, a three-valued software specification logic with McCarthy's connectives and Kleene quantifiers, a logic for nondeterministic specifications, many-sorted FOL with possibly empty carriers of some sorts, and a three-valued logic for reasoning about concurrency
Fundamental Limits to Cellular Sensing
In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what sets the fundamental limit to the precision of chemical sensing. Chemical concentration measurements start with the binding of ligand molecules to receptor proteins, which is an inherently noisy process, especially at low concentrations. The signaling networks that transmit the information on the ligand concentration from the receptors into the cell have to filter this receptor input noise as much as possible. These networks, however, are also intrinsically stochastic in nature, which means that they will also add noise to the transmitted signal. In this review, we will first discuss how the diffusive transport and binding of ligand to the receptor sets the receptor correlation time, which is the timescale over which fluctuations in the state of the receptor, arising from the stochastic receptor-ligand binding, decay. We then describe how downstream signaling pathways integrate these receptor-state fluctuations, and how the number of receptors, the receptor correlation time, and the effective integration time set by the downstream network, together impose a fundamental limit on the precision of sensing. We then discuss how cells can remove the receptor input noise while simultaneously suppressing the intrinsic noise in the signaling network. We describe why this mechanism of time integration requires three classes (groups) of resources—receptors and their integration time, readout molecules, energy—and how each resource class sets a fundamental sensing limit. We also briefly discuss the scheme of maximum-likelihood estimation, the role of receptor cooperativity, and how cellular copy protocols differ from canonical copy protocols typically considered in the computational literature, explaining why cellular sensing systems can never reach the Landauer limit on the optimal trade-off between accuracy and energetic cost
Fundamental Costs in the production and destruction of persistent polymer copies
Producing a polymer copy of a polymer template is central to biology, and effective copies must persist after template separation. We show that this separation has three fundamental thermodynamic effects. First, polymer-template interactions do not contribute to overall reaction thermodynamics and hence cannot drive the process. Second, the equilibrium state of the copied polymer is template independent and so additional work is required to provide specificity. Finally, the mixing of copies from distinct templates makes correlations between template and copy sequences unexploitable, combining with copying inaccuracy to reduce the free energy stored in a polymer ensemble. These basic principles set limits on the underlying costs and resource requirements, and suggest design principles, for autonomous copying and replication in biological and synthetic systems
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