Impact of flexibility on the aggregation of polymeric macromolecules.

Dependence of the dimerization probability and the aggregation behavior of polymeric macromolecules on their flexibility is studied using Langevin dynamics simulations. It is found that the dimerization probability is a non-monotonic function of the polymers persistence length. For a given value of inter-polymer attraction strength, semiflexible polymers have lower dimerization probability relative to flexible and rigid polymers of the same length.

Controlled Differentiation of Human Neural Progenitor Cells on Molybdenum Disulfide/Graphene Oxide Heterojunction Scaffolds by Photostimulation.

Ultrathin MoS-MoO heterojunction nanosheets with unique features were introduced as biocompatible, non-cytotoxic, and visible light-sensitive stimulator layers for the controlled differentiation of human neural progenitor cells (hNPCs) into nervous lineages. hNPC differentiation was also investigated on reduced graphene oxide (rGO)-containing scaffolds, that is, rGO and rGO/MoS-MoO nanosheets. In darkness, hNPC differentiation into neurons increased on MoS-MoO by a factor of 2.

Dimerization of Aβ40 inside dipalmitoylphosphatidylcholine bilayer and its effect on bilayer integrity: Atomistic simulation at three temperatures.

Amyloid-beta (Aβ) protein is related to Alzheimer disease (AD), and various experiments have shown that oligomers as small as dimers are cytotoxic. Recent studies have concluded that interactions of Aβ with neuronal cell membranes lead to disruption of membrane integrity and toxicity and they play a key role in the development of AD. Molecular dynamics (MD) simulations have been used to investigate Aβ in aqueous solution and membranes.

Granular chain escape from a pore in a wall in the presence of particles on one side: a comparison to polymer translocation.

Escape of a granular chain from a pore in a wall in the presence of diffusing granular particles on one side of the wall is studied experimentally. The escape time shows power-law behavior as a function of the chain length (τ ∝ Nα). A Langevin dynamics simulation of a polymer chain in a similar geometry is also performed and similar results to those for a granular system are obtained.

The molecular behavior of a single β-amyloid inside a dipalmitoylphosphatidylcholine bilayer at three different temperatures: An atomistic simulation study: Aβ interaction with DPPC: Atomistic simulation.

The behavior of a single Aβ40 molecule within a dipalmitoylphosphatidylcholine (DPPC) bilayer was studied by all-atom molecular dynamics simulations. The effect of membrane structure was investigated on Aβ40 behavior, secondary structure, and insertion depth. Simulations were performed at three temperatures (323, 310, and 300 K) to probe three different bilayer fluidities.

Obstruction enhances the diffusivity of self-propelled rod-like particles.

Diffusion of self-propelled particles in the presence of randomly distributed obstacles is studied in three dimensions (3D) using Langevin dynamics simulations. It is found that depending on the magnitude of the propelling force and the particle aspect ratio, the diffusion coefficient can be a monotonically decreasing or a non-monotonic concave function of the obstructed volume fraction. Counterintuitive enhancement of the particle diffusivity with increasing the obstacle crowd is shown to be resulted from interplay of self-propulsion and anisotropy in the particle shape.

A flexible polymer confined inside a cone-shaped nano-channel.

The nano-scale confinement of polymers in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and by using molecular dynamics simulations. Distribution of the monomers inside the channel, configuration of the confined polymer, the entropic force acting on the polymer, and their dependence on the channel and the polymer parameters are investigated.

Mechanisms of the self-assembly of EAK16-family peptides into fibrillar and globular structures: molecular dynamics simulations from nano- to micro-seconds.

The self-assembly of EAK16-family peptides in a bulk solution was studied using a combination of all-atom and coarse-grained molecular dynamics simulations. In addition, specified concentrations of EAK16 peptides were induced to form fibrillary or globular assemblies in vitro. The results show that the combination of all-atom molecular dynamics simulations on the single- and double-chain levels and coarse-grained simulations on the many-chain level predicts the experimental observations reasonably well.

pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: coarse-grained molecular dynamics simulation.

Self-assembly behavior of the three types of ionic peptide, EAK16, is studied in the presence of a hydrophobic surface using coarse-grained molecular dynamics simulations at three pH ranges of the solution. It is found that the peptide chains of all the three types assemble on the hydrophobic surface. EAK16-I and EAK16-II peptides assemble into ribbon-like structures, regardless of the value of pH.

Association between Y-chromosome AZFc region micro-deletions with recurrent miscarriage.

Background: In human, about 25% of implanted embryos are losing 1-2 week following attachment to the uterus. A subset of this population will have three or more consecutive miscarriages which define as repeated pregnancy loss (RPL). Introducing the assisted reproductive technologies (ARTS) made a chance for infertile couples to solve their childless problem.

All-atom molecular dynamics study of EAK16 peptide: the effect of pH on single-chain conformation, dimerization and self-assembly behavior.

Single-chain equilibrium conformation and dimerization of the three types of ionic EAK16 peptide are studied under three pH conditions using all-atom molecular dynamics simulations. It is found that both the single-chain conformation and the dimerization process of EAK16-IV are considerably different from those of the two other types, EAK16-I and EAK16-II. The value of pH is found to have a stronger effect on the single-chain conformation and dimerization of EAK16-IV.

Directed translocation of a flexible polymer through a cone-shaped nano-channel.

Translocation of a flexible polymer through a cone-shaped channel is studied, theoretically and using computer simulations. Our simulations show that the shape of the channel causes the polymer translocation to be a driven process. The effective driving force of entropic origin acting on the polymer is calculated as a function of the length and the apex-angle of the channel, theoretically.

Distribution of counterions and interaction between two similarly charged dielectric slabs: roles of charge discreteness and dielectric inhomogeneity.

The distribution of counterions and the electrostatic interaction between two similarly charged dielectric slabs is studied in the strong coupling limit. Dielectric inhomogeneities and discreteness of charge on the slabs have been taken into account. It is found that the amount of dielectric constant difference between the slabs and the environment, and the discreteness of charge on the slabs have opposing effects on the equilibrium distribution of the counterions.

Electric-field-driven polymer entry into asymmetric nanoscale channels.

The electric-field-driven entry process of flexible charged polymers such as single-stranded DNA (ssDNA) into asymmetric nanoscale channels such as the α-hemolysin protein channel is studied theoretically and using molecular dynamics simulations. Dependence of the height of the free-energy barrier on the polymer length, the strength of the applied electric field, and the channel entrance geometry is investigated. It is shown that the squeezing effect of the driving field on the polymer and the lateral confinement of the polymer before its entry to the channel crucially affect the barrier height and its dependence on the system parameters.

Free-energy barrier for electric-field-driven polymer entry into nanoscale channels.

Free-energy barrier for entry of a charged polymer into a nanoscale channel by a driving electric field is studied theoretically and using molecular dynamics simulations. Dependence of the barrier height on the polymer length, the driving field strength, and the channel entrance geometry is investigated. Squeezing effect of the electric field on the polymer before its entry to the channel is taken into account.

Three-dimensional Brownian diffusion of rod-like macromolecules in the presence of randomly distributed spherical obstacles: molecular dynamics simulation.

Brownian diffusion of rod-like polymers in the presence of randomly distributed spherical obstacles is studied using molecular dynamics simulations. It is observed that dependence of the reduced diffusion coefficient of these macromolecules on the available volume fraction can be described reasonably by a power law function. Despite the case of obstructed diffusion of flexible polymers in which reduced diffusion coefficient has a weak dependence on the polymer length, this dependence is noticeably strong in the case of rod-like polymers.

Brushes of flexible, semiflexible, and rodlike diblock polyampholytes: Molecular dynamics simulation and scaling analysis.

Planar brushes of flexible, semiflexible, and rodlike diblock polyampholytes are studied using molecular dynamics simulations in a wide range of the grafting density. Simulations show linear dependence of the average thickness on the grafting density in all cases regardless of different flexibility of anchored chains and the brushes' different equilibrium conformations. Slopes of fitted lines to the average thickness of the brushes of semiflexible and rodlike polyampholytes versus the grafting density are approximately the same and differ considerably from that of the brushes of flexible chains.

Salt-induced aggregation of stiff polyelectrolytes.

Molecular dynamics simulation techniques are used to study the process of aggregation of highly charged stiff polyelectrolytes due to the presence of multivalent salt. The dominant kinetic mode of aggregation is found to be the case of one end of one polyelectrolyte meeting others at right angles, and the kinetic pathway to bundle formation is found to be similar to that of flocculation dynamics of colloids as described by Smoluchowski. The aggregation process is found to favor the formation of finite bundles of 10-11 filaments at long times.

Aggregation kinetics of stiff polyelectrolytes in the presence of multivalent salt.

Using molecular dynamics simulations, the kinetics of bundle formation for stiff polyelectrolytes such as actin is studied in the solution of multivalent salt. The dominant kinetic mode of aggregation is found to be the case of one end of one rod meeting others at a right angle due to electrostatic interactions. The kinetic pathway to bundle formation involves a hierarchical structure of small clusters forming initially and then feeding into larger clusters, which is reminiscent of the flocculation dynamics of colloids.

Orientational ordering and dynamics of rodlike polyelectrolytes.

The interplay between electrostatic interactions and orientational correlations is studied for a model system of charged rods positioned on a chain, using Monte Carlo simulation techniques. It is shown that the coupling brings about the notion of electrostatic frustration, which in turn results in: (i) a rich variety of orientational orderings such as chiral phases, and (ii) an inherently slow dynamics characterized by stretched-exponential behavior in the relaxation functions of the system.