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Driven by physical questions pertaining to quantifying particle dynamics, microscopy can now resolve complex systems at the single particle level, from cellular organisms to individual ions. Yet, available analysis techniques face…
This paper discusses temporally continuous and discrete forms of the speed-limited particle-in-cell (SLPIC) method first treated by Werner et al. [Phys. Plasmas 25, 123512 (2018)]. The dispersion relation for a 1D1V electrostatic plasma…
Single-molecule experiments provide insight into the motion (conformational dynamics) of individual protein molecules. Usually, a well-defined but coarse-grained intramolecular coordinate is measured and subsequently analysed with the help…
We investigate single-cell directional sensing from diffusing chemoattractant signals released by a localized source. We focus on the low-concentration regime in which receptor activity is discrete and cellular decisions are made on…
We detail and extend the results of [Milman {\it et al.}, Phys. Rev. Lett. {\bf 99}, 130405 (2007)] on Bell-type inequalities based on correlations between measurements of continuous observables performed on trapped molecular systems. We…
Single cell responses are shaped by the geometry of signaling kinetic trajectories carved in a multidimensional space spanned by signaling protein abundances. It is however challenging to assay large number (>3) of signaling species in…
An engineering technique using continuous quantum measurement together with a change detection algorithm is proposed to improve the probability of single photon emission for a quantum-dot based single-photon source. The technique involves…
The behavior of a single molecule driven simultaneously by a laser and by an electric radio frequency field is investigated using a non-Hermitian Hamiltonian approach. Employing the renormalization group method for differential equations we…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
The precise tracking of micron sized colloidal particles - held in the vicinity of each other using optical tweezers - is an elegant way to gain information about the particle-particle pair interaction potential. The accuracy of the method,…
The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…
Molecular dynamics is often considered as a numerical experiment. The error bars on the results are therefore mandatory, but sometimes difficult to determine and computationally demanding. As a low-cost approach, we describe the application…
Temporal data, obtained in the setting where it is only possible to observe one time point per experiment, is widely used in different research fields, yet remains insufficiently addressed from the statistical point of view. Such data often…
We introduce a class of distributed nonlinear control systems, termed as the flow-tracker dynamics, which capture phenomena where the average state is controlled by the average control input, with no individual agent has direct access to…
We explore theoretically the electroluminescence of single molecules. We adopt a local-electrode framework that is appropriate for scanning tunneling microscopy (STM) experiments where electroluminescence originates from individual…
Several experiments on tagged molecules or particles in living systems suggest that they move anomalously slow - their mean squared displacement (MSD) increase slower than linearly with time. Leading models aimed at understanding these…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to…
Experiments on particles' motion in living cells show that it is often subdiffusive. This subdiffusion may be due to trapping, percolation-like structures, or viscoelatic behavior of the medium. While the models based on trapping (leading…
The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiment showed that the waiting time distribution and other properties of single enzyme…