Related papers: Quantitative evaluation of methods to analyze moti…
We examine the phenomenon of dynamical heterogeneity in computer simulations of an equilibrium, glass-forming liquid. We describe several approaches to quantify the spatial correlation of single-particle motion, and show that spatial…
Single-molecule junctions - nanoscale systems where a molecule is connected to metallic electrodes - offer a unique platform for studying charge, spin and energy transport in non-equilibrium many-body quantum systems, with few parallels in…
Single molecule fluorescence tracking provides information at nm-scale and ms-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Single Particle Tracking (SPT) can aid in understanding complex spatio-temporal processes. However, quantifying diffusivity and forces from individual live cell trajectories is complicated by inter- & intra-trajectory kinetic heterogeneity,…
The study of dynamics of single active particles plays an important role in the development of artificial or hybrid micro-systems for bio-medical and other applications at micro-scale. Here, we utilize the results of these studies to better…
We present a general theoretical model for the spatio-temporal dynamics of animal contests. Inspired by interactions between physical particles, the model is formulated in terms of effective interaction potentials, which map typical…
Complex systems in science and engineering sometimes exhibit behavior that changes across different regimes. Traditional global models struggle to capture the full range of this complex behavior, limiting their ability to accurately…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on…
In recent years Bayesian Inference has become an efficient tool to analyse single molecule trajectories. Recently, high density single molecule tagging, Langevin Equation modelling and Bayesian Inference [10] have been used to infer…
Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and…
A variety of experimental techniques have improved the 2D and 3D spatial resolution that can be extracted from \emph{in vivo} single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We develop a maximum likelihood method to infer relevant physical properties of elongated active particles. Using individual trajectories of advected swimmers as input, we are able to accurately determine their rotational diffusion…
Molecular motors do not work in isolation {\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like…
In a stochastic reaction network setting we consider the problem of tracking the fate of individual molecules. We show that using the classical large volume limit results, we may approximate the dynamics of a single tracked molecule in a…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…