Search results for "Statistical Mechanic"
showing 10 items of 707 documents
Statistics of reversible transitions in two-state trajectories in force-ramp spectroscopy
2014
A possible way to extract information about the reversible dissociation of a molecular adhesion bond from force fluctuations observed in force ramp experiments is discussed. For small loading rates the system undergoes a limited number of unbinding and rebinding transitions observable in the so-called force versus extension (FE) curves. The statistics of these transient fluctuations can be utilized to estimate the parameters for the rebinding rate. This is relevant in the experimentally important situation where the direct observation of the reversed FE-curves is hampered, e.g. due to the presence of soft linkers. I generalize the stochastic theory of the kinetics in two-state models to the…
Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force.
2009
The physics of nanoscopic systems is strongly governed by thermal fluctuations that produce significant deviations from the behaviour of large ensembles1,2. Stretching experiments of single molecules offer a unique way to study fundamental theories of statistical mechanics, as recently shown for the unzipping of RNA hairpins3. Here, we report a molecular design based on oligo calix[4]arene catenanes—calixarene dimers held together by 16 hydrogen bridges—in which loops within the molecules limit how far the calixarene nanocapsules can be separated. This mechanically locked structure tunes the energy landscape of dimers, thus permitting the reversible rupture and rejoining of the individual n…
Single-layer metal-on-metal islands driven by strong time-dependent forces
2012
Non-linear transport properties of single-layer metal-on-metal islands driven with strong static and time-dependent forces are studied. We apply a semi-empirical lattice model and use master equation and kinetic Monte Carlo simulation methods to compute observables such as the velocity and the diffusion coefficient. Two types of time-dependent driving are considered: a pulsed rotated field and an alternating field with a zero net force (electrophoretic ratchet). Small islands up to 12 atoms were studied in detail with the master equation method and larger ones with simulations. Results are presented mainly for a parametrization of Cu on Cu(001) surface, which has been the main system of int…
Liquid methane at extreme temperature and pressure: Implications for models of Uranus and Neptune
2012
We present large scale electronic structure based molecular dynamics simulations of liquid methane at planetary conditions. In particular, we address the controversy of whether or not the interior of Uranus and Neptune consists of diamond. In our simulations we find no evidence for the formation of diamond, but rather sp2-bonded polymeric carbon. Furthermore, we predict that at high tem- perature hydrogen may exist in its monoatomic and metallic state. The implications of our finding for the planetary models of Uranus and Neptune are in detail discussed.
Ion-ion correlation and charge reversal at titrating solid interfaces
2009
Confronting grand canonical titration Monte Carlo simulations (MC) with recently published titration and charge reversal (CR) experiments on silica surfaces by Dove et al. and van der Heyden it et al, we show that ion-ion correlations quantitatively explain why divalent counterions strongly promote surface charge which, in turn, eventually causes a charge reversal (CR). Titration and CR results from simulations and experiments are in excellent agreement without any fitting parameters. This is the first unambiguous evidence that ion-ion correlations are instrumental in the creation of highly charged surfaces and responsible for their CR. Finally, we show that charge correlations result in "a…
Multitasking associative networks.
2012
We introduce a bipartite, diluted and frustrated, network as a sparse restricted Boltzman machine and we show its thermodynamical equivalence to an associative working memory able to retrieve multiple patterns in parallel without falling into spurious states typical of classical neural networks. We focus on systems processing in parallel a finite (up to logarithmic growth in the volume) amount of patterns, mirroring the low-level storage of standard Amit-Gutfreund-Sompolinsky theory. Results obtained trough statistical mechanics, signal-to-noise technique and Monte Carlo simulations are overall in perfect agreement and carry interesting biological insights. Indeed, these associative network…
Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.
2014
Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both confo…
Role of noise in a market model with stochastic volatility
2006
We study a generalization of the Heston model, which consists of two coupled stochastic differential equations, one for the stock price and the other one for the volatility. We consider a cubic nonlinearity in the first equation and a correlation between the two Wiener processes, which model the two white noise sources. This model can be useful to describe the market dynamics characterized by different regimes corresponding to normal and extreme days. We analyze the effect of the noise on the statistical properties of the escape time with reference to the noise enhanced stability (NES) phenomenon, that is the noise induced enhancement of the lifetime of a metastable state. We observe NES ef…
Langevin Approach to Understand the Noise of Microwave Transistors
2004
A Langevin approach to understand the noise of microwave devices is presented. The device is represented by its equivalent circuit with the internal noise sources included as stochastic processes. From the circuit network analysis, a stochastic integral equation for the output voltage is derived and from its power spectrum the noise figure as a function of the operating frequency is obtained. The theoretical results have been compared with experimental data obtained by the characterization of an HEMT transistor series (NE20283A, by NEC) from 6 to 18 GHz at a low noise bias point. The reported procedure exhibits good accuracy, within the typical uncertainty range of any experimental determin…
Moment equations in a system of three interacting species subject to colored noise
2009
We study the effects of the colored noise on a Lotka-Volterra system of three interacting species, namely two preys and one predator, in a two-dimensional domain. The three species are affected by an external multiplicative time correlated noise, which accounts for environment fluctuations. Moreover, the interaction parameter between the two preys is a dichotomous stochastic process, which determines two dynamical regimes corresponding to different biological conditions. First, we study the noise effects on the three species dynamics in a single site. Afterwards, by a mean field approach we obtain, in Gaussian approximation, the moment equations for the species densities. Within this formal…