Quenched central limit theorem for the stochastic heat equation in weak disorder

We continue with the study of the mollified stochastic heat equation in $d\geq 3$ given by $d u_{\epsilon,t}=\frac 12\Delta u_{\epsilon,t}+ \beta \epsilon^{(d-2)/2} \,u_{\epsilon,t} \,d B_{\epsilon,t}$ with spatially smoothened cylindrical Wiener process $B$, whose (renormalized) Feynman-Kac solution describes the partition function of the continuous directed polymer. In an earlier work (\cite{MSZ16}), a phase transition was obtained, depending on the value of $\beta>0$ in the limiting object of the smoothened solution $u_\epsilon$ as the smoothing parameter $\epsilon\to 0$ This partition function naturally defines a quenched polymer path measure and we prove that as long as $\beta>0$ stays small enough while $u_\epsilon$ converges to a strictly positive non-degenerate random variable, the distribution of the diffusively rescaled Brownian path converges under the aforementioned polymer path measure to standard Gaussian distribution.Comment: Minor revisio

Dimer diffusion in a washboard potential

The transport of a dimer, consisting of two Brownian particles bounded by a harmonic potential, moving on a periodic substrate is investigated both numerically and analytically. The mobility and diffusion of the dimer center of mass present distinct properties when compared with those of a monomer under the same transport conditions. Both the average current and the diffusion coefficient are found to be complicated non-monotonic functions of the driving force. The influence of dimer equilibrium length, coupling strength and damping constant on the dimer transport properties are also examined in detail.Comment: Final revised version. 7 pages, 6 figure

Probing molecular free energy landscapes by periodic loading

Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a challenge, in particular for the unstable barrier regions. We propose a new method for obtaining the full profile by introducing a periodic ramp and using Jarzynski's identity for obtaining equilibrium quantities from non-equilibrium data. Our simulated experiments show that this method delivers significant more accurate data than previous methods, under the constraint of equal experimental effort.Comment: 4 pages, 3 figure

The Continuum Directed Random Polymer

Motivated by discrete directed polymers in one space and one time dimension, we construct a continuum directed random polymer that is modeled by a continuous path interacting with a space-time white noise. The strength of the interaction is determined by an inverse temperature parameter beta, and for a given beta and realization of the noise the path evolves in a Markovian way. The transition probabilities are determined by solutions to the one-dimensional stochastic heat equation. We show that for all beta > 0 and for almost all realizations of the white noise the path measure has the same Holder continuity and quadratic variation properties as Brownian motion, but that it is actually singular with respect to the standard Wiener measure on C([0,1]).Comment: 21 page

Automation and robotics considerations for a lunar base

An envisioned lunar outpost shares with other NASA missions many of the same criteria that have prompted the development of intelligent automation techniques with NASA. Because of increased radiation hazards, crew surface activities will probably be even more restricted than current extravehicular activity in low Earth orbit. Crew availability for routine and repetitive tasks will be at least as limited as that envisioned for the space station, particularly in the early phases of lunar development. Certain tasks are better suited to the untiring watchfulness of computers, such as the monitoring and diagnosis of multiple complex systems, and the perception and analysis of slowly developing faults in such systems. In addition, mounting costs and constrained budgets require that human resource requirements for ground control be minimized. This paper provides a glimpse of certain lunar base tasks as seen through the lens of automation and robotic (A&R) considerations. This can allow a more efficient focusing of research and development not only in A&R, but also in those technologies that will depend on A&R in the lunar environment

Undulation Instability of Epithelial Tissues

Treating the epithelium as an incompressible fluid adjacent to a viscoelastic stroma, we find a novel hydrodynamic instability that leads to the formation of protrusions of the epithelium into the stroma. This instability is a candidate for epithelial fingering observed in vivo. It occurs for sufficiently large viscosity, cell-division rate and thickness of the dividing region in the epithelium. Our work provides physical insight into a potential mechanism by which interfaces between epithelia and stromas undulate, and potentially by which tissue dysplasia leads to cancerous invasion.Comment: 4 pages, 3 figure

Sequence-dependent thermodynamics of a coarse-grained DNA model

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands and (e) the structure of a kissing-loop complex. Where possible we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as free software.Comment: 15 page

Diffusion-controlled generation of a proton-motive force across a biomembrane

Respiration in bacteria involves a sequence of energetically-coupled electron and proton transfers creating an electrochemical gradient of protons (a proton-motive force) across the inner bacterial membrane. With a simple kinetic model we analyze a redox loop mechanism of proton-motive force generation mediated by a molecular shuttle diffusing inside the membrane. This model, which includes six electron-binding and two proton-binding sites, reflects the main features of nitrate respiration in E. coli bacteria. We describe the time evolution of the proton translocation process. We find that the electron-proton electrostatic coupling on the shuttle plays a significant role in the process of energy conversion between electron and proton components. We determine the conditions where the redox loop mechanism is able to translocate protons against the transmembrane voltage gradient above 200 mV with a thermodynamic efficiency of about 37%, in the physiologically important range of temperatures from 250 to 350 K.Comment: 26 pages, 4 figures. A similar model is used in arXiv:0806.3233 for a different biological system. Minor changes in the Acknowledgements sectio

Fluctuation-Induced Interactions between Rods on Membranes and Interfaces

We consider the interaction between two rods embedded in a fluctuating surface which is governed by either surface tension or rigidity. The modification of fluctuations by the rods leads to an attractive long-range interaction that falls off as $1/R^4$ with their separation. The orientational dependence of the resulting interaction is non-trivial and may lead to interesting patterns of rod-like objects on such surfaces.Comment: Revtex, 10 pages, one figur