We study the finite-size corrections of the critical dense polymer (CDP) and the dimer models on $\infty \times N$ rectangular lattice. We find that the finite-size corrections in the CDP and dimer models depend in a crucial way on the parity of $N$, and a change of the parity of $N$ is equivalent to the change of boundary conditions. We present a set of universal amplitude ratios for amplitudes in finite-size correction terms of critical systems in the universality class with central charge $c=-2$. The results are in perfect agreement with a perturbated conformal field theory under the assumption that all analytical corrections coming from the operators which belongs to the tower of the identity. Our results inspire many interesting problems for further studies.

We address the issue of minimizing the heat generated when erasing the information stored in an array of quantum dots in finite time. We identify the fundamental limitations and trade-offs involved in this process and analyze how a feedback operation can help improve it.

We present a combined x-ray and neutron reflectivity study characterizing the interface between polystyrene (PS) and silanized surfaces. Motivated by the large difference in slip velocity of PS on top of dodecyl-trichlorosilane (DTS) and octadecyl-trichlorosilane (OTS) found in previous studies, these two systems were chosen for the present investigation. The results reveal the molecular conformation of PS on silanized silicon. Differences in the molecular tilt of OTS and DTS are replicated by the adjacent phenyl rings of the PS. We discuss our findings in terms of a potential link between the microscopic interfacial structure and dynamic properties of polymeric liquids at interfaces.

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.

Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open problem in structural biology, pursued with increasing vigor as more and more protein sequences continue to fill the data banks. Within this task lies a statistical inference problem, rooted in the following: correlation between two sites in a protein sequence can arise from firsthand interaction but can also be network-propagated via intermediate sites; observed correlation is not enough to guarantee proximity. To separate direct from indirect interactions is an instance of the general problem of inverse statistical mechanics, where the task is to learn model parameters (fields, couplings) from observables (magnetizations, correlations, samples) in large systems. In the context of protein sequences, the approach has been referred to as direct-coupling analysis. Here we show that the pseudolikelihood method, applied to 21-state Potts models describing the statistical properties of families of evolutionarily related proteins, significantly outperforms existing approaches to the direct-coupling analysis, the latter being based on standard mean-field techniques. This improved performance also relies on a modified score for the coupling strength. The results are verified using known crystal structures of specific sequence instances of various protein families. Code implementing the new method can be found at http://plmdca.csc.kth.se/.

To uncover an underlying mechanism of collective human dynamics, we survey more than 1.8 billion blog entries and observe the statistical properties of word appearances. We focus on words that show dynamic growth and decay with a tendency to diverge on a certain day. After careful pretreatment and the use of a fitting method, we found power laws generally approximate the functional forms of growth and decay with various exponents values between $-$0.1 and $-$2.5. We also observe news words whose frequencies increase suddenly and decay following power laws. In order to explain these dynamics, we propose a simple model of posting blogs involving a keyword, and its validity is checked directly from the data. The model suggests that bloggers are not only responding to the latest number of blogs but also suffering deadline pressure from the divergence day. Our empirical results can be used for predicting the number of blogs in advance and for estimating the period to return to the normal fluctuation level.

We present a method for modeling immiscible fluid flow in narrow fractures. The method combines a parallel-plate flow model with a recoloration approach adapted from multiple-component lattice-Boltzmann methods. The resulting numerical method is straightforward to implement and accurately reproduces the relevant fluid behavior. To demonstrate the method, single-droplet simulations are compared to analytical solutions that isolate the contributions from the in-plane and normal curvature. Simulations reproducing capillary forces inside a widening aperture are also presented. Excellent agreement is found in all cases considered. Finally, the method's ability to model fracture flow is demonstrated by deriving relative permeability curves for flow through a heterogeneous aperture created between two fractal surfaces.

The 84-residue homotetrameric BBAT1 is one of the smallest stable protein complexes and therefore is a good test system to study the self-assembly of multimeric proteins. We have researched for this protein the interplay between the folding of monomers and their assembly into tetramers. Replica exchange molecular dynamics simulations relying on a Go model are compared with earlier simulations that use the physics-based coarse-grained UNRES model.

In $d$-dimensional lattices of coupled quantum harmonic oscillators, we analyze the heat current caused by two thermal baths of different temperatures, which are coupled to opposite ends of the lattice, with a focus on the validity of Fourier's law of heat conduction. We provide analytical solutions of the heat current through the quantum system in the nonequilibrium steady state using the rotating-wave approximation and bath interactions described by a master equation of Lindblad form. The influence of local dephasing in the transition of ballistic to diffusive transport is investigated.

We present here a detailed granular flow characterization together with force measurements for the quasi-bidimensional situation of a horizontal cylinder penetrating vertically at a constant velocity in dry granular matter between two parallel glass walls. In the velocity range studied here, the drag force on the cylinder does not depend on the velocity $V_0$ and is mainly proportional to the cylinder diameter $d$. While the force on the cylinder increases with its penetration depth, the granular velocity profile around the cylinder is found to be stationary with fluctuations around a mean value leading to the granular temperature profile. Both mean velocity profile and temperature profile exhibit strong localization near the cylinder. The mean flow perturbation induced by the cylinder decreases exponentially away from the cylinder on a characteristic length $\lambda$ that is mainly governed by the cylinder diameter for a large enough cylinder/grain size ratio $d/d_g$: $\lambda \sim d/4+2d_g$. The granular temperature exhibits a constant plateau value $T_0$ in a thin layer close to the cylinder of extension ${\delta }_{T_0}\sim \lambda /2$ and decays exponentially far away with a characteristic length ${\lambda }_T$ of a few grain diameters (${\lambda }_T\sim 3d_g$). The granular temperature plateau $T_0$ that scales as $V_0^2{d}_g/d$ is created by the flow itself from the balance between the “granular heat” production by the shear rate $V_0/\lambda$ over ${\delta }_{T_0}$ close to the cylinder and the granular dissipation far away.

In a previous paper [Hidalgo et al., Phys. Rev. Lett. 103, 118001 (2009)] it was shown that square particles deposited in a silo tend to align with a diagonal parallel to the gravity, giving rise to a deposit with very particular properties. Here we explore, both experimentally and numerically, the effect on these properties of the filling mechanism. In particular, we modify the volume fraction of the initial configuration from which the grains are deposited. Starting from a very dilute case, increasing the volume fraction results in an enhancement of the disorder in the final deposit characterized by a decrease of the final packing fraction and a reduction of the number of particles oriented with their diagonal in the direction of gravity. However, for very high initial volume fractions, the final packing fraction increases again. This result implies that two deposits with the same final packing fraction can be obtained from very different initial conditions. The structural properties of such deposits are analyzed, revealing that, although the final volume fraction is the same, their micromechanical properties notably differ.

The crystallization transition of an undercooled monodisperse Lennard-Jones fluid in the presence of small prestructured seeds is studied with transition path sampling combined with molecular dynamics simulations. Compared to the homogeneous crystallization, clusters of a few particles arranged into a face- and body-centered cubic structure enhance the crystallization, while icosahedrally ordered seeds do not change the reaction rate. We identify two distinct nucleation regimes—close to the seed and in the bulk. Crystallites form close to the face- and body-centered structures and tend to stay away from the icosahedrally ordered seeds.

We study random graphs with arbitrary distributions of expected degree and derive expressions for the spectra of their adjacency and modularity matrices. We give a complete prescription for calculating the spectra that is exact in the limit of large network size and large vertex degrees. We also study the effect on the spectra of hubs in the network, vertices of unusually high degree, and show that these produce isolated eigenvalues outside the main spectral band, akin to impurity states in condensed matter systems, with accompanying eigenvectors that are strongly localized around the hubs. We give numerical results that confirm our analytic expressions.

We propose and document the evidence for an analogy between the dynamics of granular counterflows in the presence of bottlenecks or restrictions and financial price formation processes. Using extensive simulations, we find that the counterflows of simulated pedestrians through a door display eight stylized facts observed in financial markets when the density around the door is compared with the logarithm of the price. Finding so many stylized facts is very rare indeed among all agent-based models of financial markets. The stylized properties are present when the agents in the pedestrian model are assumed to display a zero-intelligent behavior. If agents are given decision-making capacity and adapt to partially follow the majority, periods of herding behavior may additionally occur. This generates the very slow decay of the autocorrelation of absolute return due to an intermittent dynamics. Our findings suggest that the stylized facts in the fluctuations of the financial prices result from a competition of two groups with opposite interests in the presence of a constraint funneling the flow of transactions to a narrow band of prices with limited liquidity.

A phase-field-based hybrid model that combines the lattice Boltzmann method with the finite difference method is proposed for simulating immiscible thermocapillary flows with variable fluid-property ratios. Using a phase field methodology, an interfacial force formula is analytically derived to model the interfacial tension force and the Marangoni stress. We present an improved lattice Boltzmann equation (LBE) method to capture the interface between different phases and solve the pressure and velocity fields, which can recover the correct Cahn-Hilliard equation (CHE) and Navier-Stokes equations. The LBE method allows not only use of variable mobility in the CHE, but also simulation of multiphase flows with high density ratio because a stable discretization scheme is used for calculating the derivative terms in forcing terms. An additional convection-diffusion equation is solved by the finite difference method for spatial discretization and the Runge-Kutta method for time marching to obtain the temperature field, which is coupled to the interfacial tension through an equation of state. The model is first validated against analytical solutions for the thermocapillary driven convection in two superimposed fluids at negligibly small Reynolds and Marangoni numbers. It is then used to simulate thermocapillary migration of a three-dimensional deformable droplet and bubble at various Marangoni numbers and density ratios, and satisfactory agreement is obtained between numerical results and theoretical predictions.

We present predictions of transport through micro-CT images of porous media that include the analysis of correlation structure, velocity, and the dynamics of the evolving plume. We simulate solute transport through millimeter-sized three-dimensional images of a beadpack, a sandstone, and a carbonate, representing porous media with an increasing degree of pore-scale complexity. The Navier-Stokes equations are solved to compute the flow field and a streamline simulation approach is used to move particles by advection, while the random walk method is employed to represent diffusion. We show how the computed propagators (concentration as a function of displacement) for the beadpack, sandstone, and carbonate depend on the width of the velocity distribution. A narrow velocity distribution in the beadpack leads to the least anomalous behavior, where the propagators rapidly become Gaussian in shape; the wider velocity distribution in the sandstone gives rise to a small immobile concentration peak, and a large secondary mobile peak moving at approximately the average flow speed; in the carbonate with the widest velocity distribution, the stagnant concentration peak is persistent, with a slower emergence of a smaller secondary mobile peak, characteristic of highly anomalous behavior. This defines different types of transport in the three media and quantifies the effect of pore structure on transport. The propagators obtained by the model are in excellent agreement with those measured on similar cores in nuclear magnetic resonance experiments by Scheven, Verganelakis, Harris, Johns, and Gladden, Phys. Fluids 17, 117107 (2005).

The results of a numerical implementation of the recent average atom model including ion-ion correlations of Starrett and Saumon [Phys. Rev. E 85, 026403 (2012)] are presented. The solution is obtained by coupling an average atom model to a two-component plasma model of electrons and ions. The two models are solved self-consistently and results are given in the form of pair distribution functions. Ion-ion pair distribution functions for hydrogen, carbon, aluminum, and iron are compared to quantum and Thomas-Fermi molecular dynamics simulations as well as path-integral Monte Carlo calculations and good agreement is found for a wide variety of plasma conditions in the warm and hot dense matter regime.

We solve the equations of motion of a one-dimensional planar Heisenberg (or Vaks-Larkin) model consisting of a system of interacting macrospins aligned along a ring. Each spin has unit length and is described by its angle with respect to the rotational axis. The orientation of the spins can vary in time due to spin-spin interaction and random forcing. We statistically describe the behavior of the sum of all spins for different parameters. The term “domino model” in the title refers to the interaction among the spins. We compare the model results with geomagnetic field reversals and dynamo simulations and find strikingly similar behavior. The aggregate of all spins keeps the same direction for a long time and, once in a while, begins flipping to change the orientation by almost 180 degrees (mimicking a geomagnetic reversal) or to move back to the original direction (mimicking an excursion). Most of the time the spins are aligned or antialigned and deviate only slightly with respect to the rotational axis (mimicking the secular variation of the geomagnetic pole with respect to the geographic pole). Reversals are fast compared to the times in between and they occur at random times, both in the model and in the case of the Earth's magnetic field.

Many transport processes in nature take place on substrates, often considered as unidimensional lanes. These unidimensional substrates are typically nonstatic: Affected by a fluctuating environment, they can undergo conformational changes. This is particularly true in biological cells, where the state of the substrate is often coupled to the active motion of macromolecular complexes, such as motor proteins on microtubules or ribosomes on mRNAs, causing new interesting phenomena. Inspired by biological processes such as protein synthesis by ribosomes and motor protein transport, we introduce the concept of localized dynamical sites coupled to a driven lattice gas dynamics. We investigate the phenomenology of transport in the presence of dynamical defects and find a regime characterized by an intermittent current and subject to severe finite-size effects. Our results demonstrate the impact of the regulatory role of the dynamical defects in transport not only in biology but also in more general contexts.