相关论文: Sensitivity of peptide conformational dynamics in …
How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
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…
Extensive molecular dynamics simulations of water permeation and ion selectivity of the single-walled carbon nanotubes with the radial deformation are presented . The simulated results indicate that there is a close relationship between the…
The effect of curvature and how it induces and enhances the transport of colloidal particles driven through narrow channels represent an unexplored research avenue. Here we combine experiments and simulations to investigate the dynamics of…
The presence of membrane tubules in living cells is essential to many biological processes. In cells, one mechanism to form nanosized lipid tubules is via molecular motor induced bilayer extraction. In this paper, we describe a simple…
When particles suspended in a fluid are driven through a regular lattice of cylindrical obstacles, the particle motion is usually not simply in the direction of the force, and in the high Peclet number limit particle trajectories tend to…
The objective of the present paper is to investigate the mechanical properties of carbon nanotubes. We use classical molecular dynamics simulation in order to study the effect of external compression, bending and torsion to nanotubes. We…
The friction between concentric carbon nanotubes sliding one inside the other has been widely studied and simulated, but not so far using external force as the driving variable. Our molecular dynamics (MD) simulations show that as the…
We report a study of the rotational dynamics in double-walled nanotubes using molecular dynamics simulations and a simple analytical model reproducing very well the observations. We show that the dynamic friction is linear in the angular…
Interfacial friction plays a crucial role in the mechanical properties of carbon nanotube based fibers, composites, and devices. Here we use molecular dynamics simulation to investigate the pressure effect on the friction within carbon…
When transported in confined geometries rigid fibers show interesting transport dynamics induced by friction with the top and bottom walls. Fiber flexibility causes an additional coupling between fiber deformation and transport and is…
The frictional properties of individual carbon nanotubes (CNTs) are studied by sliding an atomic force microscopy tip across and along its principle axis. This direction-dependent frictional behavior is found to correlate strongly with the…
We theoretically study the interplay between electrical and mechanical properties of suspended, doubly clamped carbon nanotubes in which charging effects dominate. In this geometry, the capacitance between the nanotube and the gate(s)…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
Transport of nanoscale objects in complex, structured environments plays a key role in a wide range of processes, from biomolecular dynamics in extracellular spaces to transport in porous materials such as filters and catalysts. While…
We study, numerically and analytically, the forced transport of deformable containers through a narrow constriction. Our central aim is to quantify the competition between the constriction geometry and the active forcing, regulating whether…
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…