Related papers: From Discrete Protein Kinetics to Continuous Brown…
We present a mesoscopic hydrodynamic description of the dynamics of colloidal suspensions. We consider the system as a gas of Brownian particles suspended in a Newtonian heat bath subjected to stationary non-equilibrium conditions imposed…
We briefly go through the problem of the quantum description of Brownian motion, concentrating on recent results about the connection between dynamics of the particle and dynamic structure factor of the medium.
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
The study of macro continuous flow has a long history. Simultaneously, the exploration of heat and mass transfer in small systems with a particle number of several hundred or less has gained significant interest in the fields of statistical…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
We consider mixtures of two species of spherical colloidal particles that differ in their hydrodynamic radii, but are otherwise identical, in the presence of an external field. Since the particle-particle and particle-field interactions are…
The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently,…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Starting from the many-particle Smoluchowski equation, we derive dynamical density functional theory for Brownian particles with an arbitrary shape. Both passive and active (self-propelled) particles are considered. The resulting theory…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of…
Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
While active matter physics has traditionally focused on particles with overdamped dynamics, recent years have seen an increase of experimental and theoretical work on active systems with inertia. This also leads to an increased need for…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Molecular dynamics in pure water and aqueous salt solutions remain incompletely understood, partly due to the apparent contradictions between results from different spectroscopic techniques. In this work, we demonstrate, by detailed…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…