Quantitative computational models play an increasingly important role in modern biology. Such typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring vivo biochemical parameters difficult, collectively fitting them other experimental data yields large parameter uncertainties. Nevertheless, earlier work we showed growth-factor-signaling that collective could yield well-constrained predictions, even when it...

We study the topological order in resonating valence-bond state. The elementary excitations have reversed charge-statistics relations: There are neutral spin-1/2 fermions and charge \ifmmode\pm\else\textpm\fi{}e spinless bosons, analogous to solitons polyacetylene. charged very light, form a degenerate Bose gas even at high temperatures. discuss this model context of recently discovered oxide superconductors.

We use the zero-temperature random-field Ising model to study hysteretic behavior at first-order phase transitions. Sweeping external field through zero, exhibits hysteresis, return-point memory effect, and avalanche fluctuations. There is a critical value of disorder which jump in magnetization (corresponding an infinite avalanche) first occurs. universal this point using mean-field theory, also present results numerical simulations three dimensions.

Models of biochemical regulation in prokaryotes and eukaryotes, typically consisting a set first-order nonlinear ordinary differential equations, have become increasingly popular late. These systems large numbers poorly known parameters, simplified dynamics, uncertain connectivity: three key features class problems we call sloppy models, which are shared by many other high-dimensional multiparameter models. We use statistical ensemble method to study the behavior these order extract as much...

We present a theory of the cholesteric blue phase, assuming first-order cholesteric-isotropic transition. show, on basis Oseen-Frank elasticity equations, that planar helix structure, generally associated with becomes unstable at temperatures near transition point. It transforms into phase characterized by network disclination lines.

We report a similarity between the microscopic parameter dependance of emergent theories in physics and that multiparameter models common other areas science. In both cases, predictions are possible despite large uncertainties parameters because these details compressed into just few governing sufficient to describe relevant observables. make this commonality explicit by examining sensitivity hopping model diffusion generalized Ising ferromagnetism. trace emergence smaller effective...

Structural rearrangements control a wide range of behavior in amorphous materials, and visualizing these atomic-scale is critical for developing refining models how glasses bend, break, melt. It difficult, however, to directly image atomic motion disordered solids. We demonstrate that using aberration-corrected transmission electron microscopy, we can excite two-dimensional silica glass-revealing complex dance elastic plastic deformations, phase transitions, their interplay. identified the...

We explain Barkhausen noise in magnetic systems terms of avalanches domains near a plain old critical point the hysteretic zero-temperature random-field Ising model. The avalanche size distribution has universal scaling function, making nontrivial predictions shape up to 50% above point, where two decades are still observed. simulate with ${1000}^{3}$ domains, extract exponents 2, 3, 4, and 5 dimensions, compare our 2D $6\ensuremath{-}\ensuremath{\epsilon}$ predictions, variety experiments.

Defying the conventional wisdom regarding first--order transitions, {\it solid--solid displacive transformations} are often accompanied by pronounced pretransitional phenomena. Generally, these phenomena indicative of some mesoscopic lattice deformation that ``anticipates'' upcoming phase transition. Among precursive effects is observation so-called ``tweed'' pattern in transmission electron microscopy a wide variety materials. We have investigated tweed two dimensional model system, and...

It is becoming increasingly appreciated that the signal transduction systems used by eukaryotic cells to achieve a variety of essential responses represent highly complex networks rather than simple linear pathways. While significant effort being made experimentally measure rate constants for individual steps in these signaling networks, many parameters required describe behavior remain unknown, or at best, estimates. With goals and caveats mind, we use methods statistical mechanics extract...

An exact renormalization-group transformation is developed which describes how the transition to chaos may occur in a universal manner if frequency ratio quasi-periodic regime held fixed. The principal low-frequency peaks an experimental spectrum are universally determined at transition. Our approach natural extension of Kolmogorov-Arnold-Moser theory strong coupling.

Hysteresis loops are often seen in experiments at first-order phase transformations, when the system goes out of equilibrium. They may have a macroscopic jump (roughly as supercooling liquids) or they be smoothly varying (as most magnets). We studied nonequilibrium zero-temperature random-field Ising-model model for hysteretic behavior transformations. As disorder is added, one finds transition where magnetization (corresponding to an infinite avalanche) decreases zero. At this we find...

For $d$-dimensional short-range Ising spin-glasses with local spin-flip dynamics, the correlation function $〈{s}_{i}(0){s}_{i}(t)〉$ is argued to be bounded below by a of form $\mathrm{exp}[\ensuremath{-}c{(\mathrm{ln}t)}^{\frac{d}{(d\ensuremath{-}1)}}]$ in temperature range above spin-glass transition. The slow relaxation large isolated clusters unfrustrated spins responsible for this bound. We suggest that signature an intermediate Griffiths phase between and paramagnetic phases.

The response of single DNA molecules to externally applied forces and torques was directly measured using an angular optical trap. Upon overwinding, buckled abruptly as revealed by a sharp extension drop followed torque plateau. When the held at buckling transition, its hopped rapidly between two distinct states. Furthermore, initial plectonemic loop absorbed approximately twice much into plectoneme upon each additional turn. observed change after postbuckling support recent elasticity model.

We present numerical simulations of avalanches and critical phenomena associated with hysteresis loops, modeled using the zero-temperature random-field Ising model. study transition between smooth loops a sharp jump in magnetization, as disorder our model is decreased. In large region near point, we find scaling phenomena, which are well described by results an $\ensuremath{\epsilon}$ expansion about six dimensions. three, four, five dimensions, systems up to billion spins ${(1000}^{3}).$

We present a practical scheme for performing error estimates Density Functional Theory calculations. The approach which is based on ideas from Bayesian statistics involves creating an ensemble of exchange-correlation functionals by comparing with experimental database binding energies molecules and solids. Fluctuations within the can then be used to estimate errors relative experiment calculated quantities like energies, bond lengths, vibrational frequencies. It demonstrated that bars energy...

We measure electron tunneling in transistors made from C140, a molecule with mass−spring−mass geometry chosen as model system to study electron-vibration coupling. observe vibration-assisted at an energy corresponding the stretching mode of C140. Molecular modeling provides explanations for why this couples more strongly than other internal modes molecule. make comparisons between observed rates and those expected Franck−Condon model.