An algorithm for coarse particle sedimentation simulation by Stokesian dynamics

Coarse Particle sedimentation is studied by using an algorithm with no adjustable parameters based on stokesian dynamics. Only inter-particle interactions of hydrodynamic force and gravity are considered. The sedimentation of a simple cubic array of spheres is used to verify the computational results. The scaling and parallelism with OpenMP of the method are presented. Random suspension sedimentation is investigated with Mont Carlo simulation. The computational results are shown in good agreement with experimental fitting at the lower computational cost of O(N In N).

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Micro-systems for Optical Protein-Chip

Protein-Chip as micro-assays for the determination of protein interaction, the analysis, the identification and the purification of proteins has large potential applications. The Optical Protein-Chip is able to detect the multi-interaction of proteins and multi-bio-activities of molecules directly and simultaneously with no labeling. The chip is a small matrix on solid substrate containing multi-micro-area prepared by microfabrication with photolithography or soft lithography for surface patterning, and processed with surface modification which includes the physical, chemical, and bio-chemical modifications, etc. The ligand immobilization, such as protein immobilization, especially the oriented immobilization with low steric hindrance and high bio-specific binding activity between ligand and receptor is used to form a sensing surface. Each area of the pattern is corresponding to only one bioactivity. The interval between the areas is non-bioactive and optically extinctive. The affinity between proteins is used to realize non-labeling microassays for the determination of protein identification and protein interaction. The sampling of the chip is non-disturbing, performed with imaging ellipsometry and image processing on a database of proteins.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

THE RESPONSES OF Microcystis TO SEDIMENT ENVIRONMENTS AND THE ASSESSMENT FOR ITS OVERWINTERING - A SIMULATION STUDY IN A NOVEL DEVICE

A novel multi-cell device made of organic glass was designed to study morphological and physiological characteristics of Microcystis population trapped in simulated sediment conditions. Changes of colonial morphology and antioxidant activities of the population were observed and measured over the range of 31-day incubation. During the incubation, the antioxidant enzyme activities fluctuated significantly in sediment environments. The activities of catalase (CAT), glutathione peroxidase (GPx) and malondialdehyde (NIDA) reached the highest on the 11(th) day, 6(th) day and 6(th) day. respectively, and then dropped down remarkably in the following days. The ratios of Fv/Fm and the maximal electron transfer rate (ETRm) declined during the initial days (1 similar to 11(th) day), but rebounded on the 16(th) day, which were consistent with the variations of total protein. In the end of incubation. gas vacuoles were hard]), observed and the gelatinous sheath was partly disappeared in the population of Microcystis. Nevertheless, the remaining populations. upon transferred to culture medium, were able to grow though experiencing a longer lag phase of nine days. The results indicated that the sediment environments were able to cause negative effects on M. aeruginosa cells. The cells, however, responded to against the possible damage afterwards. It is thus proposed the acute responses in the population during the early stage of sedimentation could be of importance in aiding the long-term survivor of Microcystis and recruitment in lake sediments. The present study also demonstrated the utility of the device in simulating the sediment environments for further investigation.

Analysis of steric mass-action model for protein adsorption equilibrium onto porous anion-exchange adsorbent

The ion-exchange equilibrium of bovine serum albumin (BSA) to an anion exchanger, DEAE Spherodex M, has been studied by batch adsorption experiments at pH values ranging from 5.26 to 7.6 and ionic strengths from 10 to 117.1 mmol/l. Using the unadjustable adsorption equilibrium parameters obtained from batch experiments, the applicability of the steric mass-action (SMA) model was analyzed for describing protein ion-exchange equilibrium in different buffer systems. The parametric sensitivity analysis was performed by perturbing each of the model parameters, while holding the rest constant. The simulation results showed that, at high salt concentrations or low pHs close to the isoelectric point of the protein, the precision of the model prediction decreased. Parametric sensitivity analysis showed that the characteristic charge and protein steric factor had the largest effects on ion-exchange equilibrium, while the effect of equilibrium constant was about 70%-95% smaller than those of characteristic charge and steric factor under all conditions investigated. The SMA model with the relationship between the adjusted characteristic charge and the salt concentration can well predict the protein adsorption isotherms in a wide pH range from 5.84 to 7.6. It is considered that the SMA model could be further improved by taking into account the effect of salt concentration on the intermolecular interactions of proteins. (c) 2006 Elsevier Ltd. All rights reserved.

Optimization of evanescent wave imaging for the visualization of protein adsorption layers

We have optimized the settings of evanescent wave imaging for the visualization of a protein adsorption layer. The enhancement of the evanescent wave at the interface brought by the incident angle, the polarized state of light beam as well as a gold layer is considered. In order to improve the image contrast of a protein monolayer in experiments, we have optimized three factors-the incident angle, the polarization of light beam, and the thickness of an introduced thin gold layer with a theoretical simulation.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

Effects of chain flexibility on polymer conformation in dilute solution studied by lattice Monte Carlo simulation

Effects of chain flexibility on the conformation of homopolymers in good solvents have been investigated by Monte Carlo simulation. Bond angle constraint coupled with persistence length of polymer chains has been introduced in the modified eight-site bond fluctuation simulation model. The study about the effects of chain flexibility on polymer sizes reveals that the orientation of polymer chains under confinement is driven by the loss of conformation entropy. The conformation of polymer chains undergoing a gradual change from spherical iso-diametric ellipsoid to rodlike iso-diametric ellipsoid with the decrease of polymer chain flexibility in a wide region has been clearly illustrated from several aspects. Furthermore, a comparison of the freely jointed chain (FJC) model and the wormlike chain (WLC) model has also been made to describe the polymer sizes in terms of chain flexibility and quasi-quantitative boundary toward the suitability of the models.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Computer simulation of miscibility and self-assembly structure for polymer-containing systems with special interactions

The miscibility and structure of A-B copolymer/C homopolymer blends with special interactions were studied by a Monte Carlo simulation in two dimensions. The interaction between segment A and segment C was repulsive, whereas it was attractive between segment B and segment C. In order to study the effect of copolymer chain structure on the morphology and structure of A-B copolymer/C homopolymer blends, the alternating, random and block A-B copolymers were introduced into the blends, respectively. The simulation results indicated that the miscibility of A-B block copolymer/C homopolymer blends depended on the chain structure of the A-B copolymer. Compared with alternating or random copolymer, the block copolymer, especially the diblock copolymer, could lead to a poor miscibility of A-B copolymer/C homopolymer blends. Moreover, for diblock A-B copolymer/C homopolymer blends, obvious self-organized core-shell structure was observed in the segment B composition region from 20% to 60%. However, if diblock copolymer composition in the blends is less than 40%, obvious self-organized core-shell structure could be formed in the B-segment component region from 10 to 90%. Furthermore, computer statistical analysis for the simulation results showed that the core sizes tended to increase continuously and their distribution became wider with decreasing B-segment component.

Monte Carlo simulation of phase behavior of polymer blends with special interactions

Full Paper: The phase, behavior of A-B-random copolymer/C-homopolymer, blends with special interaction was studied by a. Monte, Carlo simulation in two dimensions. The interaction between I segment A and segment C was repulsive, whereas it was attractive between segment B and segment C. The simulation results showed that the blend became two large co-continuous phase domains at lower segment-B component compositions, indicating that the blend showed spinodal decomposition. With an increase of the segment-B component, the miscibility between the copolymer,and the polymer was gradually improved up to being miscible. In addition, it was found that segment B tended to move to the surface of the copolymer phase in the case of a lower component of segment B. On the other hand, if was observed that the average, end-to-end distances ((h) over bar) for both copolymer and polymer changed slowly with increasing segment-B component of the copolymer up to 40%, thereafter they increased considerably with increasing segment B component. Moreover, it was found that the (h) over bar of the copolymer was obviously shorter than that of the homopolymer for the segment-B composition, region from 0% to 80%. Finally, a, phase diagram showing I phase and - II phase regions under the condition of constant-temperature is presented.