Wei-Ping Cao

Monte Carlo simulation on polymer translocation in crowded environment.

The effect of crowded environment with static obstacles on the translocation of a three-dimensional self-avoiding polymer through a small pore is studied using dynamic Monte Carlo simulation. The translocation time τ is dependent on polymer-obstacle interaction and obstacle concentration. The influence of obstacles on the polymer translocation is explained qualitatively by the free energy landscape. There exists a special polymer-obstacle interaction at which the translocation time is roughly independent of the obstacle concentration at low obstacle concentration, and the strength of the special interaction is roughly independent of chain length N. Scaling relation τ ~ N(1.25) is observed for strong driving translocations. The diffusion property of polymer chain is also influenced by obstacles. Normal diffusion is only observed in dilute solution without obstacles or in a crowded environment with weak polymer-obstacle attraction. Otherwise, subdiffusion behavior of polymer is observed.

Free energy landscape for the translocation of polymer through an interacting pore.

Free energy landscapes for polymer chain translocating through an interacting pore are calculated by using exact enumeration method. A potential barrier exists at weak attractive or repulsive polymer-pore interaction and it changes to a potential well with the increase in the attraction. The result reveals that there is a free translocation point where polymer is free of energy barrier. Using the free energy landscape, the translocation time tau for polymer worming through the pore and the migration time tau(m) for polymer migrating from cis side to trans side are calculated with the Fokker-Plank equation. It shows that a moderate attractive polymer-pore interaction accelerates the migration of polymer from cis side to trans side.

Translocation properties of copolymer (A(n)B(m))(l) through an interacting pore.

The translocation of a copolymer (A(n)B(m))(l) through an interacting pore was investigated by Monte Carlo simulation on a three-dimensional cubic lattice. Interactions between monomer A and pore ɛ(A) and between monomer B and pore ɛ(B) were considered. The difference between two translocation orientations, orientation A with monomer A entering the pore first and orientation B with monomer B first, was studied. Both the orientation probability and translocation time are dependent on monomer-pore interactions, block length, and fractions of monomers. The separation of different copolymers using translocation was also discussed. The results were explained qualitatively from the view of the free energy landscape of the copolymer translocation.

Numerical simulation on polymer translocation into crowded environment with nanoparticles

The effects of crowded environment with nano particles are studied for polymer translocation through a small pore. The translocation time τ is simulated by Fokker-Planck equation at different free energy landscapes F and diffusion coefficients of polymer D. The free energy is calculated using the Rosenbluth-Rosenbluth method, and the diffusion coefficient is followed the relation D∼1Ne−△F

DYNAMICAL MODES OF POLYMER TRANSLOCATING THROUGH INTERACTING PORE UNDER CHEMICAL POTENTIAL DIFFERENCE

D \sim \frac {1}{N} e^{-\triangle F}

Theoretical study on the polymer translocation into an attractive sphere

. We find that the free energy is dependent on polymer-nanoparticle interaction, size of the nanoparticle, and position of the nanoparticle. The attractive nanoparticles at the trans side can provide a driving force to polymer by lowering the free energy, but the exclusive effect of nanoparticle can raise the free energy of polymer. There exists an optimum interaction that τ is roughly independent on the size and position of nanoparticles. It is found that these effects are related to the conformational change of polymer chain in crowded environment.

Influence of polymer-pore interaction on the translocation of a polymer through a nanopore.

The translocation of polymer chain through an interacting pore under chemical potential difference Δμ is simulated using Monte Carlo technique. Three translocation modes, dependent on the polymer–pore interaction e and Δμ, are discovered. The translocation process is found to be an nonequilibrium process, which influences the dependence of translocation time τ on e and Δμ. It is found that τ decreases in a power law relation with the increase of Δμ, and the exponent is dependent on the interaction.

Translocation of polymers into crowded media with dynamic attractive nanoparticles.

We report a non-sampling model, combining the blob method with the standard lattice-based approximation, to calculate the free energy for the polymer translocation into an attractive sphere (i.e., spherical confined trans side) through a small pore. The translocation time is then calculated by the Fokker-Planck equation based on the free energy profile. There is a competition between the confinement effect of the sphere and the polymer-sphere attraction. The translocation time is increased due to the confinement effect of the sphere, whereas it is reduced by the polymer-sphere attraction. The two effects offset each other at a special polymer-sphere attraction which is dependent on the sphere size, the polymer length, and the driving force. Moreover, the entire translocation process can be divided into an uncrowded stage where the polymer does not experience the confinement effect of the sphere and a crowded stage where the polymer is confined by the sphere. At the critical sphere radius, the durations of the two (uncrowded and crowded) stages are the same. The critical sphere radius R* has a scaling relation with the polymer length N as R* ∼ Nβ. The calculation results show that the current model can effectively treat the translocation of a three-dimensional self-avoiding polymer into the spherical confined trans side.