Related papers: Expanding the Temporal Analysis in Single-Molecule…
The general scheme for the treatment of relaxation processes and temporal autocorrelations of dynamical variables for many particle systems is presented in framework of the recurrence relations approach. The time autocorrelation functions…
We study the autocorrelation function of different types of eigenfunctions in quantum mechanical systems with either chaotic or mixed classical limits. We obtain an expansion of the autocorrelation function in terms of the correlation…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Complex systems are often characterized by the interplay of multiple interconnected dynamical processes operating across a range of temporal scales. This phenomenon is widespread in both biological and artificial scenarios, making it…
A simple ansatz for the study of velocity autocorrelation functions in fluids at different timescales is proposed. The ansatz is based on an effective summation of the infinite continued fraction at a reasonable assumption about convergence…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
Recovering properties of correlation functions is typically challenging. On one hand, experimentally, it requires measurements with a temporal resolution finer than the system's dynamics. On the other hand, analytical or numerical analysis…
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…
Here, we discuss a collection of cutting-edge techniques and applications in use today by some of the leading experts in the field of correlative approaches in single-molecule biophysics. A key difference in emphasis, compared with…
The concept of time correlation functions is a very convenient theoretical tool in describing relaxation processes in multiparticle systems because, on one hand, correlation functions are directly related to experimentally measured…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of trajectories has remained difficult to assess. Such assessment is critical not only for establishing the…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule F\"orster Resonance Energy Transfer (smFRET) is a powerful approach to inform on the structure and the dynamics of labeled molecules.…
Time series data provided by single-molecule Forster resonance energy transfer (sm-FRET) experiments offer the opportunity to infer not only model parameters describing molecular complexes, e.g. rate constants, but also information about…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…