Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Using Brownian dynamics simulation, we studied the effect of histone modifications On conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ＂cross-talking＂ interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

Brownian dynamics simulation of two confined colloidal particles

The dynamics of two confined colloidal particles is studied by means of Brownian dynamics simulation. The autocorrelation function and cross-correlation function of the two colloidal spheres are computed by utilizing the formulae of hydrodynamic diffusion matrix expanded to different orders, as well as the accurate tensor through numerical algorithm. Furthermore, the numerical results are compared with the experimental results and the theoretical approximation. It is found that the relatively simple theoretical approximation gives good predictions when two spheres are far away from each other, but fails when the two spheres are very close.

Statistics of Polymer Capture by a Nanopore:A Brownian Dynamics Simulation Study

We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0（N）-N^-0.8.

Brownian Dynamics Simulations of Rigid Polyelectrolyte Chains Grafting to Spherical Colloid

Brownian dynamics simulations are employed to explore the effects of chain stiffness and trivalent salt concentration on the conformational behavior of spherical polyelectrolyte brush. The rigid brush adopts bundle-like morphology at a wide range of trivalent salt concentration. The number variation of bundles pinned on the colloid surface shows a non-monotonic profile as a function of the chain stiffness. The radial distributions of monomers and ions and the charge ratio between condensed ions and monomers are calculated. The charge inversion is observed for the high salt concentration regardless of chain rigidity. Furthermore, the pair correlation functions of monomer-monomer and monomer-salt cation are used to elucidate the aggregated mechanism of the bundle-like structure.

Dynamical Properties of Potassium Ion Channels with a Hierarchical Model

It is well known that potassium ion channels have higher permeability than K ions, and the permeable rate of a single K ion channel is about 108 ions per second. We develop a hierarchical model of potassium ion channel permeation involving ab initio quantum calculations and Brownian dynamics simulations, which can consistently explain a range of channel dynamics. The results show that the average velocity of K ions, the mean permeable time of K ions and the permeable rate of single channel are about 0.92nm/ns, 4.35ns and 2.30 ×10^8 ions/s, respectively.

Stretching strongly confined semiflexible polymer chain

By the so-called wormlike chain （WLC） model in polymer physics envision- ing an isotropic rod that is continuously flexible, the force-extension relations of semi- flexible polymer chains strongly constrained by various confinements are theoretically investigated, including a slab-like confinement where the polymer chains are sandwiched between two parallel impenetrable walls, and a capped nanochannel confinement with a circular or rectangular cross-section where the chains are bounded in three directions. The Brownian dynamics （BD） simulations based on the generalized bead-rod （GBR） model are performed to verify the theoretical predictions.

Phoretic self-assembly of active colloidal molecules

We simulate the self-assembly of active colloidal molecules from binary mixtures of spherical particles using a Brownian dynamics algorithm.These particles interact via phoretic interactions,which are determined by two independently tunable parameters,surface activity and surface mobility.In systems composed of equal-size particles,we observe the formation of colloidal molecules with well-defined coordination numbers and spatial arrangement,which also display distinct dynamic functions,such as resting,translating,and rotating.By changing the size ratio to 2:1 between the two species,we further observe the formation of colloidal molecules with new structures arising from breaking the size symmetry.By tuning the mutual interactions between the smaller species via their surface mobility,we are able to control their spacing as well as the coordination number of the colloidal molecules.This study highlights the importance of tuning surface parameters and size asymmetry in controlling the structure and the active dynamics of colloidal molecules.

Conformation of an Amphiphilic Comb-like Copolymer in a Selective Solvent

We study the conformation of an amphiphilic comb-like copolymer in a selective solvent by using Brownian dynamics simulations.Our results demonstrate that,there is an optimal total degree of polymerization to form spherical micelles.Only when the total degree of polymerization is less than the optimal total degree of polymerization,a unimolecular spherical micelle can be formed,otherwise,the spherical micelle will be transformed into a cylindrical micelle.When the total degree of polymerization is less than the optimal total degree of polymerization,the radius of gyration and the stretching factor meet an exponential relationship,where the power exponent decreases with the increase of the length of hydrophilic side chains.The fundamental principles uncovered here afford insights for the optimization of molecular design of amphiphilic comb-like copolymers in various applications.

Self-assembled Conformations of a Core-shell Comb-like Chain with Adjustable Architectural Parameters

Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformations.When the ratio of hydrophilic and hydrophobic segments is N_(g,g)∶N_(g,r)=3∶1,no core-shell structure is observed,and unsegregated chains or clusters are substituted.When N_(g,g)∶N_(g,r)=3∶2or 3∶3,the core-shell comb-like chains can be assembled into single micelles or structures where several small micelles are strung together by the backbone,which is similar to the pearl-necklace structure formed by the polyelectrolytes in poor solvent.With the increase of backbone length or grafting density,the probability of forming single micelles becomes lower,but the structures of two,three or more small micelles strung together are more observed.Our results indicate how to obtain the desired self-assembled structures of core-shell comb-like chains by regulating the architectural parameters,which could provide insights for the optimization of molecular design in various applications.

Dynamical Demixing of a Binary Mixture Under Sedimentation

We investigate the sedimentation dynamics of a binary mixture,the species of which differ by their Stokes coefficients but are identical otherwise.We analyze the sedimentation dynamics and the morphology of the final deposits using Brownian dynamics simulations for mixtures with a range of sedimentation velocities of both species.In addition,we use the lattice Boltzmann method to study hydrodynamic effects.We found a threshold in the difference of the sedimentation velocities above which the species in the final deposit are segregated.The degree of segregation increases with the difference in the Stokes coefficients or the sedimentation velocities above the threshold.We propose a simple analytical model that captures the main features of the simulated deposits.

Effect of Hydrodynamic Interaction on Flow-induced Polymer Translocation Through a Nanotube

We investigated the effect of hydrodynamic interaction（HI） on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long po- lymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stret- ching, both of which play an important role in translocation process.

Structure of polyelectrolyte brushes studied by coarse grain simulations

As an example of a very low friction system,Monte Carlo Brownian dynamics simulations have been used to calculate equilibrium structures of a polyelectrolyte brush grafted onto planes.The polymers were calculated in a semi-flexible coarse-grain model that is appropriate to treat the charge density of the polyion.The effect of linear charge density on the polyionx,the surface negative charge,and added salts were studied.In salt-free solution,scaling theories predicted the structure well in the lowxregion.In the highxregion,additional shrinkage was found from the theories due to counterion condensation.The effect of surface charge showed not only the repulsion of the polyion from the surface but also the shrinkage in the highxregion due to the additional counterions required for electrical neutrality.The addition of salts led to the shrinkage of the brush heights,and in the highxregion,additional extension was found.The computational strategy for calculating the friction dynamics of the system is also discussed.