Related papers: Colloidal particle motion as a diagnostic of DNA c…
Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…
Colloidal particles with DNA `legs' that can bind reversibly to receptors on a surface can be made to `walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how…
In the absence of directional motion it is often hard to recognize athermal fluctuations. Probability currents provide such a measure in terms of the rate at which they enclose area in the reduced phase space. We measure this area enclosing…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
We track particle motions in a granular material subjected to compaction using a laser scattering based imaging method where compaction is achieved through thermal cycling. Particle displacements in this jammed fluid correlate strongly with…
The motion of topological defects is an important feature of the dynamics of all liquid crystals, and is especially conspicuous in active liquid crystals. Understanding defect motion is a challenging theoretical problem, because the…
This work deals with the overdamped motion of a particle in a fluctuating one-dimensional periodic potential. If the potential has no inversion symmetry and its fluctuations are asymmetric and correlated in time, a net flow can be generated…
We report experimental measurements of particle dynamics on slowly sheared granular matter in a three-dimensional (3D) Couette cell. A closely-packed ensemble of transparent spherical beads is confined by an external pressure and filled…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereo-isomers, even at very low temperatures. In this paper we discuss the different approaches for the manipulation of the motion of…
We propose a feedback scheme to control the vibrational motion of a single trapped particle based on indirect measurements of its position. It results the possibility of a motional phase space uncertainty contraction, correponding to cool…
Microelectromechanical systems (MEMS) that require contact of moving parts to implement complex functions exhibit limits to their performance and reliability. Here, we advance our particle tracking method to measure MEMS motion in operando…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
Precise quantum control and measurement of several harmonic oscillators, such as the modes of the electromagnetic field in a cavity or of mechanical motion, are key for their use as quantum platforms. The motional modes of trapped ions can…
In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics…
The nuclear time-dependent density functional theory (TDDFT) is a tool of choice for describing various dynamical phenomena in atomic nuclei. In a recent study, we reported an extension of the framework - the multiconfigurational TDDFT…
In a system of many similar self-propelled entities such as flocks of birds, fish school, cells and molecules, the interactions with neighbors can lead to a "coherent state", meaning the formation of visually compelling aggregation patterns…
Self-powered motion in catalytic colloidal particles provides a compelling example of active matter, i.e. systems that engage in single-particle and collective behavior far from equilibrium. The long-time, long-distance behavior of such…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…