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We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially des ...
The loop series provides a formal way to write down corrections to the Bethe entropy (and/or free energy) of graphical models. We provide methods to rigorously control such expansions for low-density parity-check codes used over a highly noisy binary symme ...
The free energies of activation for the aryl-aryl rotation of 17 biphenyl derivatives, bearing a heavy heteroatom (S, Se, Te, P, Si, Sn) as ortho substituent, have been measured by variable temperature NMR. These numbers, so called B values, represent a me ...
DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linke ...
Starting from a disordered aggregate, we have simulated the formation of ordered amyloid-like beta structures in a system formed by 18 polyvaline chains in explicit solvent, employing molecular dynamics accelerated by bias-exchange metadynamics. We exploit ...
We study, in the context of the full wave equation, an approximate cloaking scheme that was previously considered for the Helmholtz equation [R. V. Kohn, D. Onofrei, M. S. Vogelius, and M. I. Weinstein, Comm. Pure Appl. Math., 63 (2010), pp. 973--1016, H.- ...
Society for Industrial and Applied Mathematics2012
In this paperwe obtain a global characterization of the dynamics of even solutions to the one-dimensional nonlinear Klein–Gordon (NLKG) equation on the line with focusing nonlinearity |u|p−1u, p > 5, provided their energy exceeds that of the ground state o ...
Anionic, monolayer-protected gold nanoparticles (AuNPs) have been shown to nondisruptively penetrate cellular membranes. Here, we show that a critical first step in the penetration process is potentially the fusion of such AuNPs with lipid bilayers. Free e ...
In the current trend toward thicker aluminium plates, a major concern is the generation of high internal stresses during quenching, which can cause distortions during machining and pose serious safety concerns. Although the material is stretched after quen ...
Spherically collapsing cavitation bubbles produce a shock wave followed by a rebound bubble. Here we present a systematic investigation of the energy partition between the rebound and the shock. Highly spherical cavitation bubbles are produced in micrograv ...