Related papers: Translational Mobilities of Proteins in Nanochanne…
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the…
Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. Design of diverse applications of bacterial cellulose films also relies on understanding…
We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of propagating front of…
Transport of rodlike particles in confinement environments of macromolecular networks plays crucial roles in many important biological processes and technological applications. The relevant understanding has been limited to thin rods with…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Force-driven translocation of a macromolecule through a nanopore is investigated by taking into account the monomer-pore friction as well as the "crowding" of monomers on the {\it trans} - side of the membrane which counterbalance the…
Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a non-uniform force F(y). We considered linear-gradient, parabolic and delta-like driving-force profiles.…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
We study colloidal particles in a nematic-liquid-crystal-filled microfluidic channel and show how elastic interactions between the particle and the channel wall lead to different particle dynamics compared with conventional microfluidics.…
We study the dynamics of neutral and charged rods embedded in varying-section channels. By means of systematic approximations, we derive the dependence of the local diffusion coefficient on both the geometry and charge of the rods. This…
In the last decades a large effort has been devoted to the study of water confined in hydrophobic geometries at the nanoscale (tubes, slit pores), because of the multiple technological applications of such systems, ranging from drugs…
One of the most promising applications in nanoscience is the design of new materials to improve water permeability and selectivity of nanoporous membranes. Understanding the molecular architecture behind these fascinating structures and how…
We analyze the diffusive transport of Brownian particles in narrow channels with periodically varying cross-section. The geometrical confinements lead to entropic barriers, the particle has to overcome in order to proceed in transport…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
A closed set of coupled equations of motion for the description of time-dependent electron transport is derived. It provides the time evolution of energy-resolved quantities constructed from non-equilibrium Green functions. By means of an…