A solvable model of the genesis of amino-acid sequences via coupled dynamics of folding and slow genetic variation

We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and long-range polarity-driven forces. Our solution is based on the diagonalization of replicated transfer matrices, and leads in the thermodynamic limit to explicit predictions regarding phase transitions and phase diagrams at genetic equilibrium. The predicted phenomenology allows for natural physical interpretations, and finds satisfactory support in numerical simulations.Comment: 51 pages, 13 figures, submitted to J. Phys.

Diagonalization of replicated transfer matrices for disordered Ising spin systems

We present an alternative procedure for solving the eigenvalue problem of replicated transfer matrices describing disordered spin systems with (random) 1D nearest neighbor bonds and/or random fields, possibly in combination with (random) long range bonds. Our method is based on transforming the original eigenvalue problem for a $2^n\times 2^n$ matrix (where $n\to 0$) into an eigenvalue problem for integral operators. We first develop our formalism for the Ising chain with random bonds and fields, where we recover known results. We then apply our methods to models of spins which interact simultaneously via a one-dimensional ring and via more complex long-range connectivity structures, e.g. $1+\infty$ dimensional neural networks and `small world' magnets. Numerical simulations confirm our predictions satisfactorily.Comment: 24 pages, LaTex, IOP macro

Slowly evolving geometry in recurrent neural networks I: extreme dilution regime

We study extremely diluted spin models of neural networks in which the connectivity evolves in time, although adiabatically slowly compared to the neurons, according to stochastic equations which on average aim to reduce frustration. The (fast) neurons and (slow) connectivity variables equilibrate separately, but at different temperatures. Our model is exactly solvable in equilibrium. We obtain phase diagrams upon making the condensed ansatz (i.e. recall of one pattern). These show that, as the connectivity temperature is lowered, the volume of the retrieval phase diverges and the fraction of mis-aligned spins is reduced. Still one always retains a region in the retrieval phase where recall states other than the one corresponding to the `condensed' pattern are locally stable, so the associative memory character of our model is preserved.Comment: 18 pages, 6 figure

Modelling topical photodynamic therapy treatment including the continuous production of Protoporphyrin IX

C L Campbell acknowledges financial support from an UK EPSRC PhD studentship (EP/K503162/1) and the Alfred Stewart Trust.Most existing theoretical models of photodynamic therapy (PDT) assume a uniform initial distribution of the photosensitive molecule, Protoporphyrin IX (PpIX). This is an adequate assumption when the prodrug is systematically administered; however for topical PDT this is no longer a valid assumption. Topical application and subsequent diffusion of the prodrug results in an inhomogeneous distribution of PpIX, especially after short incubation times, prior to light illumination. In this work a theoretical simulation of PDT where the PpIX distribution depends on the incubation time and the treatment modality is described. Three steps of the PpIX production are considered. The first is the distribution of the topically applied prodrug, the second in the conversion from the prodrug to PpIX and the third is the light distribution which affects the PpIX distribution through photobleaching. The light distribution is modelled using a Monte Carlo radiation transfer model and indicates treatment depths of around 2 mm during daylight PDT and approximately 3 mm during conventional PDT. The results suggest that treatment depths are not only limited by the light penetration but also by the PpIX distributionPostprintPeer reviewe

Comparison of three different application routes of butyrate to improve colonic anastomotic strength in rats

Despite extensive research, anastomotic leakage (AL) remains one of the most dreaded complications after colorectal surgery. Since butyrate enemas are known to enhance anastomotic healing, several administration routes have been explored in this study. Three intraluminal approaches involving butyrate were investigated: (1) butyrin-elucidating patch, (2) a single injection of hyaluronan-butyrate (HA-But) prior to construction of the proximal anastomosis and (3) rectal hyaluronan-butyrate (HA-But) enemas designed for distal anastomoses. The main outcome was AL and secondary outcomes were bursting pressure, histological analysis of the anastomosis, zymography to detect MMP activity and qPCR for gene expression of MMP2, MMP9, MUC2 and TFF3. RESULTS: Neither the patches nor the injections led to a reduction of AL in experiments 1 and 2. In experiment 3, a significant reduction of AL was accomplished with the (HA-But) enema compared to the control group together with a higher bursting pressure. Histological analysis detected only an increased inflammation in experiment 2 in the hyaluronan injection group compared to the control group. No other differences were found regarding wound healing. Zymography identified a decreased proenzyme of MMP9 when HA-But was administered as a rectal enema. qPCR did not show any significant differences between groups in any experiment. CONCLUSION: Butyrate enemas are effective in the enhancement of colonic anastomosis. Enhanced butyrate-based approaches designed to reduce AL in animal models for both proximal and distal anastomoses were not more effective than were butyrate enemas alone. Further research should focus on how exogenous butyrate can improve anastomotic healing after gastrointestinal surgery

Orbital order in the low-dimensional quantum spin system TiOCl probed by ESR

We present electron spin resonance data of Ti$^{3+}$ (3$d^1$) ions in single crystals of the novel layered quantum spin magnet TiOCl. The analysis of the g tensor yields direct evidence that the d_{xy} orbital from the t_{2g} set is predominantly occupied and owing to the occurrence of orbital order a linear spin chain forms along the crystallographic b axis. This result corroborates recent theoretical LDA+U calculations of the band structure. The temperature dependence of the parameters of the resonance signal suggests a strong coupling between spin and lattice degrees of freedom and gives evidence for a transition to a nonmagnetic ground state at 67 K.Comment: revised version, accepted for publication in Phys. Rev. B, Rapid Com

Optical study of orbital excitations in transition-metal oxides

The orbital excitations of a series of transition-metal compounds are studied by means of optical spectroscopy. Our aim was to identify signatures of collective orbital excitations by comparison with experimental and theoretical results for predominantly local crystal-field excitations. To this end, we have studied TiOCl, RTiO3 (R=La, Sm, Y), LaMnO3, Y2BaNiO5, CaCu2O3, and K4Cu4OCl10, ranging from early to late transition-metal ions, from t_2g to e_g systems, and including systems in which the exchange coupling is predominantly three-dimensional, one-dimensional or zero-dimensional. With the exception of LaMnO3, we find orbital excitations in all compounds. We discuss the competition between orbital fluctuations (for dominant exchange coupling) and crystal-field splitting (for dominant coupling to the lattice). Comparison of our experimental results with configuration-interaction cluster calculations in general yield good agreement, demonstrating that the coupling to the lattice is important for a quantitative description of the orbital excitations in these compounds. However, detailed theoretical predictions for the contribution of collective orbital modes to the optical conductivity (e.g., the line shape or the polarization dependence) are required to decide on a possible contribution of orbital fluctuations at low energies, in particular in case of the orbital excitations at about 0.25 eV in RTiO3. Further calculations are called for which take into account the exchange interactions between the orbitals and the coupling to the lattice on an equal footing.Comment: published version, discussion of TiOCl extended to low T, improved calculation of orbital excitation energies in TiOCl, figure 16 improved, references updated, 33 pages, 20 figure

Optical study of orbital excitations in transition-metal oxides

The orbital excitations of a series of transition-metal compounds are studied by means of optical spectroscopy. Our aim was to identify signatures of collective orbital excitations by comparison with experimental and theoretical results for predominantly local crystal-field excitations. To this end, we have studied TiOCl, RTiO3 (R = La, Sm and Y), LaMnO3, Y2BaNiO5, CaCu2O3 and K4Cu4OCl10, ranging from early to late transition-metal ions, from t2g to eg systems, and including systems in which the exchange coupling is predominantly three-dimensional, one-dimensional or zero-dimensional. With the exception of LaMnO3, we find orbital excitations in all compounds. We discuss the competition between orbital fluctuations (for dominant exchange coupling) and crystal-field splitting (for dominant coupling to the lattice). Comparison of our experimental results with configuration-interaction cluster calculations in general yields good agreement, demonstrating that the coupling to the lattice is important for a quantitative description of the orbital excitations in these compounds. However, detailed theoretical predictions for the contribution of collective orbital modes to the optical conductivity (e.g. the line shape or the polarization dependence) are required to decide on a possible contribution of orbital fluctuations at low energies, in particular, in case of the orbital excitations at ≈0.25 eV in RTiO3. Further calculations are called for which take into account the exchange interactions between the orbitals and the coupling to the lattice on an equal footing