End-pulled polymer translocation through a many-body flexible pore

This paper studies the features of a homopolymer translocating through a flexible pore. The channel is modeled as a monolayer tube composed by monomers with two elastic parameters: spring-like two body interaction and bending three body recall interaction. In order to guarantee the stability of the system, the membrane is compounded by a lipid bilayer structure having hydrophobic body (internal), while the pore is hydrophilic in both edges. The polymer is end-pulled from the cis-side to the trans-side by a cantilever, to which is connected through a spring able to measure the force acting on the polymer during the translocation. All the structure reacts to the impacts of the monomers of the polymer with vibrations generated by the movement of its constituent bodies. In these conditions, the work done by the cantilever shows a nonmonotonic behavior with the elastic constant, revealing a resonant-like behavior in a parameter region. Moreover, the force spectroscopy registered as a function of time, is able to record the main kinetics of the polymer progression inside the pore

Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling.

Information from developmental signaling pathways must be accurately decoded to generate transcriptional outcomes. In the case of Notch, the intracellular domain (NICD) transduces the signal directly to the nucleus. How enhancers decipher NICD in the real time of developmental decisions is not known. Using the MS2-MCP system to visualize nascent transcripts in single cells in Drosophila embryos, we reveal how two target enhancers read Notch activity to produce synchronized and sustained profiles of transcription. By manipulating the levels of NICD and altering specific motifs within the enhancers, we uncover two key principles. First, increased NICD levels alter transcription by increasing duration rather than frequency of transcriptional bursts. Second, priming of enhancers by tissue-specific transcription factors is required for NICD to confer synchronized and sustained activity; in their absence, transcription is stochastic and bursty. The dynamic response of an individual enhancer to NICD thus differs depending on the cellular context.Wellcome Trus

Deterministic ratchets: route to diffusive transport

The rectification efficiency of an underdamped ratchet operated in the adiabatic regime increases according to a scaling current-amplitude curve as the damping constant approaches a critical threshold; below threshold the rectified signal becomes extremely irregular and eventually its time average drops to zero. Periodic (locked) and diffusive (fully chaotic) trajectories coexist on fine tuning the amplitude of the input signal. The transition from regular to chaotic transport in noiseless ratchets is studied numerically.Comment: 9 pages, 5 figures, to be published in Phys. Rev.

Spiral surface growth without desorption

Spiral surface growth is well understood in the limit where the step motion is controlled by the local supersaturation of adatoms near the spiral ridge. In epitaxial thin-film growth, however, spirals can form in a step-flow regime where desorption of adatoms is negligible and the ridge dynamics is governed by the non-local diffusion field of adatoms on the whole surface. We investigate this limit numerically using a phase-field formulation of the Burton-Cabrera-Frank model, as well as analytically. Quantitative predictions, which differ strikingly from those of the local limit, are made for the selected step spacing as a function of the deposition flux, as well as for the dependence of the relaxation time to steady-state growth on the screw dislocation density.Comment: 9 pages, 3 figures, RevTe

Domain Walls and Phase Transitions in the Frustrated Two-Dimensional XY Model

We study and compare the critical properties of the two-dimensional (2D) XY model in a transverse magnetic field with magnetic filling factors f=1/3 and f=2/5. In addition to the spin waves, the low energy excitations of the system consist of various domain walls between degenerate ground states. The lowest energy domain wall has a similar structure for both f=1/3 and f=2/5 and its properties dictate the nature of the phase transition. For f=2/5 these lowest energy walls have a negative energy for binding to each other, giving rise to a branching domain-wall structure and leading to a first order phase transition. For f=1/3 this binding energy is positive, resulting in a linear critical interface. In order to make a comparison to recent experiments, we investigate the effect of small quenched bond disorder for f=2/5. A finite-size scaling analysis of extensive Monte Carlo simulations strongly suggests that the critical exponents of the phase transition for f=1/3, and for f=2/5 with disorder, fall into the universality class of the two-dimensional Ising model.Comment: 5 pages, 3 eps figures, REVTEX, revised version with new figure

Domain Walls Motion and Resistivity in a Fully-Frustrated Josephson Array

It is identified numerically that the resistivity of a fully-frustrated Josephson-junction array is due to motion of domain walls in vortex lattice rather than to motion of single vortices

Soliton ratchets induced by ac forces with harmonic mixing

The ratchet dynamics of a kink (topological soliton) of a dissipative sine-Gordon equation in the presence of ac forces with harmonic mixing (at least bi-harmonic) of zero mean is studied. The dependence of the kink mean velocity on system parameters is investigated numerically and the results are compared with a perturbation analysis based on a point particle representation of the soliton. We find that first order perturbative calculations lead to incomplete descriptions, due to the important role played by the soliton-phonon interaction in establishing the phenomenon. The role played by the temporal symmetry of the system in establishing soliton ratchets is also emphasized. In particular, we show the existence of an asymmetric internal mode on the kink profile which couples to the kink translational mode through the damping in the system. Effective soliton transport is achieved when the internal mode and the external force get phase locked. We find that for kinks driven by bi-harmonic drivers consisting of the superposition of a fundamental driver with its first odd harmonic, the transport arises only due to this {\it internal mode} mechanism, while for bi-harmonic drivers with even harmonic superposition, also a point-particle contribution to the drift velocity is present. The phenomenon is robust enough to survive the presence of thermal noise in the system and can lead to several interesting physical applications.Comment: 9 pages, 13 figure

Anomalous resonance phenomena of solitary waves with internal modes

We investigate the non-parametric, pure ac driven dynamics of nonlinear Klein-Gordon solitary waves having an internal mode of frequency $\Omega_i$. We show that the strongest resonance arises when the driving frequency $\delta=\Omega_i/2$, whereas when $\delta=\Omega_i$ the resonance is weaker, disappearing for nonzero damping. At resonance, the dynamics of the kink center of mass becomes chaotic. As we identify the resonance mechanism as an {\em indirect} coupling to the internal mode due to its symmetry, we expect similar results for other systems.Comment: 4 pages, 4 figures, to appear in Phys Rev Let

The Exact Ground State of the Frenkel-Kontorova Model with Repeated Parabolic Potential: I. Basic Results

The problem of finding the exact energies and configurations for the Frenkel-Kontorova model consisting of particles in one dimension connected to their nearest-neighbors by springs and placed in a periodic potential consisting of segments from parabolas of identical (positive) curvature but arbitrary height and spacing, is reduced to that of minimizing a certain convex function defined on a finite simplex.Comment: 12 RevTeX pages, using AMS-Fonts (amssym.tex,amssym.def), 6 Postscript figures, accepted by Phys. Rev.

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press