Force Modulating Dynamic Disorder: Physical Theory of Catch-slip bond Transitions in Receptor-Ligand Forced Dissociation Experiments

Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific chemical kinetic models have been developed to explain the intriguing transitions from the "catch-bonds" to the "slip-bonds". In this work we suggest that the counterintuitive forced dissociation of the complexes is a typical rate process with dynamic disorder. An uniform one-dimension force modulating Agmon-Hopfield model is used to quantitatively describe the transitions observed in the single bond P-selctin glycoprotein ligand 1(PSGL-1)$-$P-selectin forced dissociation experiments, which were respectively carried out on the constant force [Marshall, {\it et al.}, (2003) Nature {\bf 423}, 190-193] and the force steady- or jump-ramp [Evans {\it et al.}, (2004) Proc. Natl. Acad. Sci. USA {\bf 98}, 11281-11286] modes. Our calculation shows that the novel catch-slip bond transition arises from a competition of the two components of external applied force along the dissociation reaction coordinate and the complex conformational coordinate: the former accelerates the dissociation by lowering the height of the energy barrier between the bound and free states (slip), while the later stabilizes the complex by dragging the system to the higher barrier height (catch).Comment: 8 pages, 3 figures, submitte

Work probability distribution and tossing a biased coin

We show that the rare events present in dissipated work that enters Jarzynski equality, when mapped appropriately to the phenomenon of large deviations found in a biased coin toss, are enough to yield a quantitative work probability distribution for Jarzynski equality. This allows us to propose a recipe for constructing work probability distribution independent of the details of any relevant system. The underlying framework, developed herein, is expected to be of use in modelling other physical phenomena where rare events play an important role.Comment: 6 pages, 4 figures

Effect of Poisson ratio on cellular structure formation

Mechanically active cells in soft media act as force dipoles. The resulting elastic interactions are long-ranged and favor the formation of strings. We show analytically that due to screening, the effective interaction between strings decays exponentially, with a decay length determined only by geometry. Both for disordered and ordered arrangements of cells, we predict novel phase transitions from paraelastic to ferroelastic and anti-ferroelastic phases as a function of Poisson ratio.Comment: 4 pages, Revtex, 4 Postscript figures include

Spectral statistics for unitary transfer matrices of binary graphs

Quantum graphs have recently been introduced as model systems to study the spectral statistics of linear wave problems with chaotic classical limits. It is proposed here to generalise this approach by considering arbitrary, directed graphs with unitary transfer matrices. An exponentially increasing contribution to the form factor is identified when performing a diagonal summation over periodic orbit degeneracy classes. A special class of graphs, so-called binary graphs, is studied in more detail. For these, the conditions for periodic orbit pairs to be correlated (including correlations due to the unitarity of the transfer matrix) can be given explicitly. Using combinatorial techniques it is possible to perform the summation over correlated periodic orbit pair contributions to the form factor for some low--dimensional cases. Gradual convergence towards random matrix results is observed when increasing the number of vertices of the binary graphs.Comment: 18 pages, 8 figure

Relative Entropy: Free Energy Associated with Equilibrium Fluctuations and Nonequilibrium Deviations

Using a one-dimensional macromolecule in aqueous solution as an illustration, we demonstrate that the relative entropy from information theory, $\sum_k p_k\ln(p_k/p_k^*)$, has a natural role in the energetics of equilibrium and nonequilibrium conformational fluctuations of the single molecule. It is identified as the free energy difference associated with a fluctuating density in equilibrium, and is associated with the distribution deviate from the equilibrium in nonequilibrium relaxation. This result can be generalized to any other isothermal macromolecular systems using the mathematical theories of large deviations and Markov processes, and at the same time provides the well-known mathematical results with an interesting physical interpretations.Comment: 5 page

Asymptotics of the mean-field Heisenberg model

We consider the mean-field classical Heisenberg model and obtain detailed information about the total spin of the system by studying the model on a complete graph and sending the number of vertices to infinity. In particular, we obtain Cramer- and Sanov-type large deviations principles for the total spin and the empirical spin distribution and demonstrate a second-order phase transition in the Gibbs measures. We also study the asymptotics of the total spin throughout the phase transition using Stein's method, proving central limit theorems in the sub- and supercritical phases and a nonnormal limit theorem at the critical temperature.Comment: 44 page

Stochastic Budget Optimization in Internet Advertising

Internet advertising is a sophisticated game in which the many advertisers "play" to optimize their return on investment. There are many "targets" for the advertisements, and each "target" has a collection of games with a potentially different set of players involved. In this paper, we study the problem of how advertisers allocate their budget across these "targets". In particular, we focus on formulating their best response strategy as an optimization problem. Advertisers have a set of keywords ("targets") and some stochastic information about the future, namely a probability distribution over scenarios of cost vs click combinations. This summarizes the potential states of the world assuming that the strategies of other players are fixed. Then, the best response can be abstracted as stochastic budget optimization problems to figure out how to spread a given budget across these keywords to maximize the expected number of clicks. We present the first known non-trivial poly-logarithmic approximation for these problems as well as the first known hardness results of getting better than logarithmic approximation ratios in the various parameters involved. We also identify several special cases of these problems of practical interest, such as with fixed number of scenarios or with polynomial-sized parameters related to cost, which are solvable either in polynomial time or with improved approximation ratios. Stochastic budget optimization with scenarios has sophisticated technical structure. Our approximation and hardness results come from relating these problems to a special type of (0/1, bipartite) quadratic programs inherent in them. Our research answers some open problems raised by the authors in (Stochastic Models for Budget Optimization in Search-Based Advertising, Algorithmica, 58 (4), 1022-1044, 2010).Comment: FINAL versio

Dobrushin states in the \phi^4_1 model

We consider the van der Waals free energy functional in a bounded interval with inhomogeneous Dirichlet boundary conditions imposing the two stable phases at the endpoints. We compute the asymptotic free energy cost, as the length of the interval diverges, of shifting the interface from the midpoint. We then discuss the effect of thermal fluctuations by analyzing the \phi^4_1-measure with Dobrushin boundary conditions. In particular, we obtain a nontrivial limit in a suitable scaling in which the length of the interval diverges and the temperature vanishes. The limiting state is not translation invariant and describes a localized interface. This result can be seen as the probabilistic counterpart of the variational convergence of the associated excess free energy.Comment: 34 page

Discrete-time classical and quantum Markovian evolutions: Maximum entropy problems on path space

The theory of Schroedinger bridges for diffusion processes is extended to classical and quantum discrete-time Markovian evolutions. The solution of the path space maximum entropy problems is obtained from the a priori model in both cases via a suitable multiplicative functional transformation. In the quantum case, nonequilibrium time reversal of quantum channels is discussed and space-time harmonic processes are introduced.Comment: 34 page

The cavity method for large deviations

A method is introduced for studying large deviations in the context of statistical physics of disordered systems. The approach, based on an extension of the cavity method to atypical realizations of the quenched disorder, allows us to compute exponentially small probabilities (rate functions) over different classes of random graphs. It is illustrated with two combinatorial optimization problems, the vertex-cover and coloring problems, for which the presence of replica symmetry breaking phases is taken into account. Applications include the analysis of models on adaptive graph structures.Comment: 18 pages, 7 figure