Related papers: Fluctuation Assisted Ejection of DNA From Bacterio…
The experimental search for the QCD critical point by means of relativistic heavy-ion collisions necessitates the development of dynamical models of fluctuations. In this work we study the fluctuations of the net-baryon density near the…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
Because of the broken time-translation symmetry, in periodically driven vibrational systems fluctuations of different vibration components have different intensities. Fluctuations of one of the components are often squeezed, whereas…
We consider the dynamic escape of a small packet of ultracold atoms launched from within an optical dipole trap. Based on a theoretical analysis of the underlying nonlinear dynamics, we predict that fractal behavior can be seen in the…
We investigate the role played by subcritical bubbles at the onset of the electroweak phase transition. Treating the configuration modelling the thermal fluctuations around the homogeneous zero configuration of the Higgs field as a…
We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
Thermal shape fluctuations of grafted microtubules were studied using high resolution particle tracking of attached fluorescent beads. First mode relaxation times were extracted from the mean square displacement in the transverse…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
Molecular dynamics approaches use wave packets as nucleon wave functions to simulate the time evolution of nuclear reactions. It is crucial to activate the momentum fluctuation inherent in each wave packet so that it properly affects the…
Elastic confinements are an important component of many biological systems and dictate the transport properties of suspended particles under flow. In this chapter, we review the Brownian motion of a particle moving in the vicinity of a…
We consider the fluctuations in atom number that occur within finite-sized measurement cells in a trapped Bose-Einstein condensate (BEC). This approximates the fluctuation measurements made in current experiments with finite resolution in…
We discuss an extension of the fluctuation theorem to stochastic models that, in the limit of zero external drive, are not able to equilibrate with their environment, extending results presented by Sellitto (cond-mat/9809186). We show that…
Particle momentum distributions originating from a quark-gluon plasma as produced in high-energy nuclear collisions can be influenced by thermal fluctuations in fluid dynamic fields. We study this effect by generalizing the commonly used…
A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it…
We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E.…
The adhesion bonds connecting a lipid bilayer to an underlying surface may undergo a condensation transition resulting from an interplay between a short range attractive potential between them, and a long range fluctuation-induced potential…