相关论文: The Relative Diffusivities of Bound and Unbound Pr…
Living cells are capable of interacting with their environments in a variety of ways, including cell signalling, adhesion, and directed motion. These behaviours are often mediated by receptor molecules embedded in the cell membrane, which…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to…
Biological systems like ciliated microorganisms are capable to respond to the external chemical gradients, a process known as chemotaxis which has been studied here using the chiral squirmer model. This theoretical model considers the…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Bacteria such as Escherichia coli (E. coli) exhibit biased motion if kept in a spatially non-uniform chemical environment. Here, we bring out unique time-dependent characteristics of bacterial chemotaxis, in response to a diffusing spatial…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
We theoretically study the transport properties of self-propelled particles on complex structures, such as motor proteins on filament networks. A general master equation formalism is developed to investigate the persistent motion of…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
We use colloidal suspensions encapsulated in emulsion droplets to model confined glass-forming liquids with tunable boundary mobility. We show dynamics in these idealized systems are governed by physical interactions with the boundary.…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
Curvatures in the most probable rupture force ($f^*$) versus log-loading rate ($\log{r_f}$) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple…
Aerotaxis is the particular form of chemotaxis in which oxygen plays the role of both the attractant and the repellent. Aerotaxis occurs without methylation adaptation, and it leads to fast and complete aggregation toward the most favorable…
The motion of molecules on solid surfaces is of interest for technological applications, but it is also a theoretical challenge. We study the deterministic and thermal diffusive dynamics of a dimer moving on a periodic substrate. The…
A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…
We study protein diffusion in multicomponent lipid membranes close to a rigid substrate separated by a layer of viscous fluid. The large-distance, long-time asymptotics for Brownian motion are calculated using a nonlinear stochastic…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Many of the cell membrane vital functions are achieved by the self-organization of the proteins and biopolymers embedded in it. The protein dynamics are in part determined by its drag. A large number of these proteins can polymerize to form…