Maximum entropy models for antibody diversity

Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM sequences in zebrafish. These models are based solely on pairwise correlations between residue positions, but correctly capture the higher order statistical properties of the repertoire. Exploiting the interpretation of these models as statistical physics problems, we make several predictions for the collective properties of the sequence ensemble: the distribution of sequences obeys Zipf's law, the repertoire decomposes into several clusters, and there is a massive restriction of diversity due to the correlations. These predictions are completely inconsistent with models in which amino acid substitutions are made independently at each site, and are in good agreement with the data. Our results suggest that antibody diversity is not limited by the sequences encoded in the genome, and may reflect rapid adaptation to antigenic challenges. This approach should be applicable to the study of the global properties of other protein families

Dynamics of magnetization coupled to a thermal bath of elastic modes

We study the dynamics of magnetization coupled to a thermal bath of elastic modes using a system plus reservoir approach with realistic magnetoelastic coupling. After integrating out the elastic modes we obtain a self-contained equation for the dynamics of the magnetization. We find explicit expressions for the memory friction kernel and hence, {\em via} the Fluctuation-Dissipation Theorem, for the spectral density of the magnetization thermal fluctuations. For magnetic samples in which the single domain approximation is valid, we derive an equation for the dynamics of the uniform mode. Finally we apply this equation to study the dynamics of the uniform magnetization mode in insulating ferromagnetic thin films. As experimental consequences we find that the fluctuation correlation time is of the order of the ratio between the film thickness, $h$, and the speed of sound in the magnet and that the line-width of the ferromagnetic resonance peak should scale as $B_1^2h$ where $B_1$ is the magnetoelastic coupling constant.Comment: Revised version as appeared in print. 12 pages 9 figure

Time evolution towards q-Gaussian stationary states through unified Ito-Stratonovich stochastic equation

We consider a class of single-particle one-dimensional stochastic equations which include external field, additive and multiplicative noises. We use a parameter $\theta \in [0,1]$ which enables the unification of the traditional It\^o and Stratonovich approaches, now recovered respectively as the $\theta=0$ and $\theta=1/2$ particular cases to derive the associated Fokker-Planck equation (FPE). These FPE is a {\it linear} one, and its stationary state is given by a $q$-Gaussian distribution with $q = \frac{\tau + 2M (2 - \theta)}{\tau + 2M (1 - \theta)}<3$, where $\tau \ge 0$ characterizes the strength of the confining external field, and $M \ge 0$ is the (normalized) amplitude of the multiplicative noise. We also calculate the standard kurtosis $\kappa_1$ and the $q$-generalized kurtosis $\kappa_q$ (i.e., the standard kurtosis but using the escort distribution instead of the direct one). Through these two quantities we numerically follow the time evolution of the distributions. Finally, we exhibit how these quantities can be used as convenient calibrations for determining the index $q$ from numerical data obtained through experiments, observations or numerical computations.Comment: 9 pages, 2 figure

Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

Thermal conductivity of one-dimensional lattices with self-consistent heat baths: a heuristic derivation

We derive the thermal conductivities of one-dimensional harmonic and anharmonic lattices with self-consistent heat baths (BRV lattice) from the Single-Mode Relaxation Time (SMRT) approximation. For harmonic lattice, we obtain the same result as previous works. However, our approach is heuristic and reveals phonon picture explicitly within the heat transport process. The results for harmonic and anharmonic lattices are compared with numerical calculations from Green-Kubo formula. The consistency between derivation and simulation strongly supports that effective (renormalized) phonons are energy carriers in anharmonic lattices although there exist some other excitations such as solitons and breathers.Comment: 4 pages, 3 figures. accepted for publication in JPS

Dynamics of barrier penetration in thermal medium: exact result for inverted harmonic oscillator

Time evolution of quantum tunneling is studied when the tunneling system is immersed in thermal medium. We analyze in detail the behavior of the system after integrating out the environment. Exact result for the inverted harmonic oscillator of the tunneling potential is derived and the barrier penetration factor is explicitly worked out as a function of time. Quantum mechanical formula without environment is modifed both by the potential renormalization effect and by a dynamical factor which may appreciably differ from the previously obtained one in the time range of 1/(curvature at the top of potential barrier).Comment: 30 pages, LATEX file with 11 PS figure

Connected Network of Minima as a Model Glass: Long Time Dynamics

A simple model to investigate the long time dynamics of glass-formers is presented and applied to study a Lennard-Jones system in supercooled and glassy phases. According to our model, the point representing the system in the configurational phase space performs harmonic vibrations around (and activated jumps between) minima pertaining to a connected network. Exploiting the model, in agreement with the experimental results, we find evidence for: i) stretched relaxational dynamics; ii) a strong T-dependence of the stretching parameter; iii) breakdown of the Stokes-Einstein law.Comment: 4 pages (Latex), 4 eps figure

Polarons as Nucleation Droplets in Non-Degenerate Polymers

We present a study of the nucleation mechanism that allows the decay of the metastable phase (trans-cisoid) to the stable phase (cis-transoid) in quasi one-dimensional non-degenerate polymers within the continuum electron-phonon model. The electron-phonon configurations that lead to the decay, i.e. the critical droplets (or transition state), are identified as polarons of the metastable phase. We obtain an estimate for the decay rate via thermal activation within a range of parameters consistent with experimental values for the gap of the cis-configuration. It is pointed out that, upon doping, the activation barriers of the excited states are quite smaller and the decay rate is greatly enhanced. Typical activation energies for electron or hole polarons are $\approx 0.1$ eV and the typical size for a critical droplet (polaron) is about $20 \AA$. Decay via quantum nucleation is also studied and it is found that the crossover temperature between quantum nucleation and thermal activation is of order $T_c \leq 40 ^oK$. Metastable configurations of non-degenerate polymers may provide examples for mesoscopic quantum tunneling.Comment: REVTEX 3.0, 28 PAGES, 3 FIGURES AVAILABLE UPON REQUEST, PITT 94-0

Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism

Two-state models provide phenomenological descriptions of many different systems, ranging from physics to chemistry and biology. We investigate work fluctuations in an ensemble of two-state systems driven out of equilibrium under the action of an external perturbation. We calculate the probability density P(W) that a work equal to W is exerted upon the system along a given non-equilibrium trajectory and introduce a trajectory thermodynamics formalism to quantify work fluctuations in the large-size limit. We then define a trajectory entropy S(W) that counts the number of non-equilibrium trajectories P(W)=exp(S(W)/kT) with work equal to W. A trajectory free-energy F(W) can also be defined, which has a minimum at a value of the work that has to be efficiently sampled to quantitatively test the Jarzynski equality. Within this formalism a Lagrange multiplier is also introduced, the inverse of which plays the role of a trajectory temperature. Our solution for P(W) exactly satisfies the fluctuation theorem by Crooks and allows us to investigate heat-fluctuations for a protocol that is invariant under time reversal. The heat distribution is then characterized by a Gaussian component (describing small and frequent heat exchange events) and exponential tails (describing the statistics of large deviations and rare events). For the latter, the width of the exponential tails is related to the aforementioned trajectory temperature. Finite-size effects to the large-N theory and the recovery of work distributions for finite N are also discussed. Finally, we pay particular attention to the case of magnetic nanoparticle systems under the action of a magnetic field H where work and heat fluctuations are predicted to be observable in ramping experiments in micro-SQUIDs.Comment: 28 pages, 14 figures (Latex