Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field

We examine the electrophoresis of spherical particles in microfluidic devices made of alternating wells and narrow channels, including a system previously used to separate DNA molecules. Our computer simulations predict that such systems can be used to separate spherical particles of different sizes that share the same free-solution mobility. Interestingly, the electrophoretic velocity shows an inversion as the field intensity is increased: while small particles have higher velocities at low field, the situation is reversed at high fields with the larger particles then moving faster. The resulting nonlinearity suggests that asymmetric pulsed electric fields could be used to build separation ratchets: particles then have a net size-dependent velocity in the presence of a zero-mean external field. Exploiting the inversion mentioned above, we show how to design pulsed field sequences that make particles move against the mean field (an example of negative mobility). Finally, we demonstrate that it is possible to use pulsed fields to make particles of different sizes move in opposite directions, even though their charge have the same sign.     

Size Effects in a Silica-Polystyrene Nanocomposite: Molecular Dynamics and Surface-enhanced Continuum Approaches

Size effects in a system composed of a polymer matrix with a single silica nanoparticle are studied using molecular dynamics and surface-enhanced continuum approaches. The dependence of the composite’s mechanical properties on the nanoparticle’s radius was examined. Mean values of the elastic moduli obtained using molecular dynamics were found to be lower than those of the polystyrene matrix alone. The surface-enhanced continuum theory produced a satisfactory fit of macroscopic stresses developing during relaxation due to the interface tension and uniaxial deformation. Neither analytical nor finite-element solutions correlated well with the size-effect in elastic moduli predicted by the molecular dynamics simulations.     

Structural Refolding and Thermal Stability of Myoglobin in the Presence of Mixture of Crowders: Importance of Various Interactions for Protein Stabilization in Crowded Conditions

The intracellular environment is overcrowded with a range of molecules (small and large), all of which influence protein conformation. As a result, understanding how proteins fold and stay functional in such crowded conditions is essential. Several in vitro experiments have looked into the effects of macromolecular crowding on different proteins. However, there are hardly any reports regarding small molecular crowders used alone and in mixtures to observe their effects on the structure and stability of the proteins, which mimics of the cellular conditions. Here we investigate the effect of different mixtures of crowders, ethylene glycol (EG) and its polymer polyethylene glycol (PEG 400 Da) on the structural and thermal stability of myoglobin (Mb). Our results show that monomer (EG) has no significant effect on the structure of Mb, while the polymer disrupts its structure and decreases its stability. Conversely, the additive effect of crowders showed structural refolding of the protein to some extent. Moreover, the calorimetric binding studies of the protein showed very weak interactions with the mixture of crowders. Usually, we can assume that soft interactions induce structural perturbations while exclusion volume effects stabilize the protein structure; therefore, we hypothesize that under in vivo crowded conditions, both phenomena occur and maintain the stability and function of proteins.     

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)₃ in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.     

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent

The influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all-atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A.     

Use of Cartesian Rotation Vectors in Brownian Dynamics Algorithms: Theory and Simulation Results

Summary: We have shown that the components of Cartesian rotation vectors can be used successfully as generalized coordinates describing angular orientation in Brownian dynamics simulations of non‐spherical nanoparticles. For this particular choice of generalized coordinates, we rigorously derived the conformation‐space diffusion equations from kinetic theory for both free nanoparticles and nanoparticles interconnected by springs or holonomic constraints into polymer chains. The equivalent stochastic differential equations were used as a foundation for the Brownian dynamics algorithms. These new algorithms contain singularities only for points in the conformation‐space where both the probability density and its first coordinate derivative equal zero (weak singularities). In addition, the coordinate values after a single Brownian dynamics time step are throughout the conformation‐space equal to the old coordinate values plus the respective increments. For some parts of the conformation‐space these features represent a major improvement compared to the situation when Eulerian angles describe rotational dynamics. The presented simulation results of the equilibrium probability density for free nanoparticles are in perfect agreement with the results from kinetic theory.

Simulation of p^(eq)(Φ) for free nanoparticles.     

In-silico structural analysis of E509K mutation in LARGE and T192M mutation in Alpha Dystroglycan in the inhibition of glycosylation of Alpha Dystroglycan by LARGE

Impaired glycosylation of cellular receptor Alpha Dystroglycan (α-DG) leads to dystroglycanopathy. Glycoprotein α-DG is the receptor protein in the Dystrophin Associated Protein Complex (DAPC), a macromolecular gathering on muscle cell membrane to form a bridge between extracellular matrix (ECM) and cellular actin cytoskeleton. Proper glycosylation of α-DG is mediated by the glycosylating enzyme LARGE. Mutations either in α-DG or in LARGE lead to improper glycosylations of α-DG thereby hampering the formation of final Laminin binding form α-DG resulting in dystroglycanopathy. In our current work, we explored the structural changes associated with the presence of mutations in α-DG as well as in the enzyme LARGE. We further extended our research to understand the effect of the mutations onto protein-enzyme interactions. Moreover, since LARGE transfers the sugar moiety (glucuronic acid; GlcA) onto α-DG, we tried to analyze what effect the mutation in LARGE confers on this enzyme ligand interaction. This work for the first time addressed the molecular changes occurring in the structures α-DG, LARGE and their interactions and shed lights on the as yet poorly understood mechanism behind the dystroglycanopathy onset.     

Diffusion of hydrocarbons in confined media: Translational and rotational motion

Diffusion of monatomic guest species within confined media has been understood to a good degree due to investigations carried out during the past decade and a half. Most guest species that are of industrial relevance are actually polyatomics such as, for example, hydrocarbons in zeolites. We attempt to investigate the influence of non-spherical nature of guest species on diffusion. Recent molecular dynamics (MD) simulations of motion of methane in NaCaA and NaY, benzene in NaY and one-dimensional channels AlPO₄−5, VPI−5 and carbon nanotube indicate interesting insights into the influence of the host on rotational degrees of freedom and orientational properties. It is shown that benzene in one-dimensional channels where the levitation parameter is near unity exhibits translational motion opposite to what is expected on the basis of molecular anisotropy. Rotational motion of benzene also possesses rotational diffusivities aroundC ₆ and C₂axes opposite to what is expected on the basis of molecular geometry. Methane shows orientational preference for 2+ 2 or 1 + 3 depending on the magnitude of the levitation parameter.     

Size Distribution and Anisotropy of the MinorPhase Droplets in Polypropylene/Ethylene-OcteneCopolymer Blends: Effects of Shear andComponent Miscibility简

In this work, polypropylene （PP）/octene-ethylene copolymer （POE） blends were injection-molded using the so- called dynamic packing injection technique, which imposed oscillatory shear on the gradually cooling melt during the packing solidification stage. In this way, the effect of shear on the size distribution and anisotropy of the minor phase droplets could be investigated. Besides, by using two kinds of POE with different octene contents, the effect of component miscibility was also studied. The results show that the droplet size is mainly determined by composition and miscibility, and droplet anisotropy is mainly determined by droplet size and shear. Most importantly, under the same processing condition, droplet anisotropy increases with droplet size, and there seems a linear fit between them, disregarding the miscibility factor. These results may provide guidance for preparing polymer blends with desired properties by tailoring their phase morphologies.     

Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions,Structure, and Stability in Atomistic Simulations

We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π–π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π–π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π–π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.     

Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

The association of Mg²⁺ and H₂PO₄^? in water can give insights into Mg:phosphate interactions in general, which are very widespread, but for which experimental data is surprisingly sparse. It is studied through molecular dynamics simulations (>100 ns) by using the polarizable AMOEBA force field, and the association free energy is computed for the first time. Explicit consideration of outer‐sphere and two types of inner‐sphere association provides considerable insight into the dynamics and thermodynamics of ion pairing. After careful assessment of the computational approximations, the agreement with experimental values indicates that the methodology can be extended to other inorganic and biological Mg:phosphate interactions in solution.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Transport properties of a co-poly(amide-12-b-ethylene oxide) membrane: A comparative study between experimental and molecular modelling results

An experimental and theoretical study has been used to investigate gas diffusion and solubility in PEBAX^®2533 block copolymer membrane. Molecular simulations using COMPASS force field have been successful in predicting the gas-transport properties of a PEBAX^®2533 block copolymer and of a pure PTMO homopolymer. Gusev–Suter transition state theory (TST) and Monte Carlo methods are used for simulating the transport of five permanent gases (He, H₂, N₂, O₂, CO₂ and CH₄). Theoretical and experimental data have been compared.     

11-丁烯在MCM-2222分子筛中的吸附与扩散: Monte Carlo与动力学模拟研究

采用巨正则Monte Carlo方法和分子动力学方法研究了11-丁烯在MCM-2222分子筛中的吸附现象和扩散行为, 得到了11-丁烯吸附在该分子筛孔道中的相互作用能和在不同孔道中的扩散轨迹和扩散系数. 结果表明11-丁烯在MCM-2222分子筛中主要存在两个相互作用能区间, 11-丁烯优先吸附在十元环孔道中; 11-丁烯的扩散和移动主要发生在十二元环超笼的中部, 十元环孔道中的11-丁烯扩散速度明显小于十二元环超笼系统中的扩散速度.     

1-丁烯在MCM-22分子筛中的吸附与扩散：Monte Carlo与动力学模拟研究

采用巨正则Monte Carlo方法和分子动力学方法研究了1-丁烯在MCM-22分子筛中的吸附现象和扩散行为,得到了1-丁烯吸附在该分子筛孔道中的相互作用能和在不同孔道中的扩散轨迹和扩散系数.结果表明1-丁烯在MCM-22分子筛中主要存存两个相互作用能区间,1-丁烯优先吸附在十元环孔道中;1-丁烯的扩散和移动主要发生在十二元环超笼的中部,十元环孔道中的1-丁烯扩散速度明显小于十二元环超笼系统中的扩散速度.     

Formation of Long,Multicenter π‐[TCNE]22− Dimers in Solution: Solvation and Stability Assessed through Molecular Dynamics Simulations

Purely organic radical ions dimerize in solution at low temperature, forming long, multicenter bonds, despite the metastability of the isolated dimers. Here, we present the first computational study of these π‐dimers in solution, with explicit consideration of solvent molecules and finite temperature effects. By means of force‐field and ab initio molecular dynamics and free energy simulations, the structure and stability of π‐[TCNE]₂^2? (TCNE=tetracyanoethylene) dimers in dichloromethane have been evaluated. Although the dimers dissociate at room temperature, they are stable at 175 K and their structure is similar to the one in the solid state, with a cofacial arrangement of the radicals at an interplanar separation of approximately 3.0 Å. The π‐[TCNE]₂^2? dimers form dissociated ion pairs with the NBu₄⁺ counterions, and their first solvation shell comprises approximately 20 CH₂Cl₂ molecules. Among them, the eight molecules distributed along the equatorial plane of the dimer play a key role in stabilizing the dimer through bridging C?H???N contacts. The calculated free energy of dimerization of TCNE ^{. ?} in solution at 175 K is ?5.5 kcal mol^?1. These results provide the first quantitative model describing the pairing of radical ions in solution, and demonstrate the key role of solvation forces on the dimerization process.