A model that predicts the attachment behavior of Ulva linza zoospores on surface topography

A predictive model for the attachment of spores of the green alga Ulva on patterned topographical surfaces was developed using a constant refinement approach. This ‘attachment model’ incorporated two historical data sets and a modified version of the previously-described Engineered Roughness Index. Two sets of newly-designed surfaces were used to evaluate the effect of two components of the model on spore settlement. Spores attached in fewer numbers when the area fraction of feature tops increased or when the number of distinct features in the design increased, as predicted by the model. The model correctly predicted the spore attachment density on three previously-untested surfaces relative to a smooth surface. The two historical data sets and two new data sets showed high correlation (R ² = 0.88) with the model. This model may be useful for designing new antifouling topographies.     

Receptor aggregation by intermembrane interactions: a Monte Carlo study

The lateral organization of receptors on cell surfaces is critically important to their function; many receptors transmit transmembrane signals when redistributed into clusters, while the response of others is potentiated by their aggregation. Cell-cell contact can play a crucial role in receptor aggregation, even when the bonds between receptors on one cell and ligands on the other are monovalent. Monte Carlo simulations on a two-membrane model were carried out to determine whether weak enthalpic interactions among receptors in one membrane, and among ligands in another, can work synergistically to give large-scale clustering when the two membranes are brought into contact. The simulations give support to such a clustering mechanism. In addition, because clustering is a cooperative process akin to a phase separation, individual receptors and ligands may undergo repeated binding and unbinding while in a clustered "phase," and a single ligand could interact with multiple different receptor partners. The results suggest a resolution of the dichotomy between serial triggering and aggregation models of T cell activation.     

The role of surface energy and water wettability in aminoalkyl/fluorocarbon/hydrocarbon-modified xerogel surfaces in the control of marine biofouling

Xerogel films with uniform surface topogrophy, as determined by scanning electron microscopy, atomic force microscopy (AFM), and time-of-flight secondary ion mass spectrometry, were prepared from aminopropylsilyl-, fluorocarbonsilyl-, and hydrocarbonsilyl- containing precursors. Young's modulus was determined from AFM indentation measurements. The xerogel coatings gave reduced settlement of zoospores of the marine fouling alga Ulva compared to a poly(dimethylsiloxane) elastomer (PDMSE) standard. Increased settlement correlated with decreased water wettability as measured by the static water contact angle, θ_Ws, or with decreased polar contribution (γ_P) to the surface free energy (γ_S) as measured by comprehensive contact angle analysis. The strength of attachment of 7-day sporelings (young plants) of Ulva on several of the xerogels was similar to that on PDMSE although no overall correlation was observed with either θ_Ws or γ_S. For sporelings attached to the fluorocarbon/hydrocarbon-modified xerogels, the strength of attachment increased with increased water wettability. The aminopropyl-modified xerogels did not follow this trend.     

Prediction of protein conformation in water and on surfaces by Monte Carlo simulations using united-atom method

The united-atom method has been used to model an avian pancreatic polypeptide (APP) in water and the adsorption process of an albumin subdomain (AS) onto graphite surface to observe the capability of this lumped modelling approach to generate structures observed in protein data bank (PDB) and from atomistic modelling. The subdomain structure of a protein is simplified by the united-atom approximation where the side chains and peptide groups are represented by lumped spheres. The total potential energy of the adsorption process involves the interaction between these lumped spheres by means of virtual bond chain interaction and the interaction of the spheres with the graphite surface by means of Lennard-Jones potential. The protein/polypeptide structure has been perturbed by Monte Carlo with energy minimisation to obtain the global minimum. Results on the APP in water showed a near-to-experimental PDB conformation revealing the two α-helix structures of this small protein molecule with the root mean square deviation among carbon backbone atoms of 5.9 Å. Protein adsorption on biosurfaces has been made by modelling AS, which has 60 amino acids. The surface is graphite, which is characterised by its hydrophobicity. Graphite was chosen because of its widely used applications in certain implants that interact with blood. Our simulation results showed final conformation close to that obtained by atomistic modelling. It also proved that the whole pattern of intramolecular hydrogen bonds was distorted. The model also demonstrated the random conformation of the original α-helix secondary structures of AS consistent with experimental and atomistic results. While atomistic simulation works well for simulating individual small proteins, the united-atom model is more efficient when simulating macromolecular and multiple protein adsorption where time and limiting computer capacity are key factors.     

Restructuring dynamics of du 145 and LNCaP prostate cancer spheroids

Summary Neoplastic cells acquire multidrug resistance as they assemble into multicellular spheroids. Image analysis and Monte Carlo simulation provided an insight into the adhesion and motility events during spheroid restructuring in liquid-overlay culture of DU 145 and LNCaP human prostate cancer cells. Irregularly shaped, two-dimensional aggregates restructured through incremental cell movements into three-dimensional spheroids. Of the two cultures examined, restructuring was more pronounced for DU 145 aggregates. Motile DU 145 cells formed spheroids with a minimum cell overlay of 30% for 25-mers as estimated by simulation versus 5% for adhesive LNCaP cells in aggregates of the same size. Over 72 h, the texture ratio increased from 0.55±0.05 for DU 145 aggregates with projected areas exceeding 2000 μm² to a value approaching 0.75±0.02 (P<0.05). For LNCaP aggregates of comparable size, the increase in texture ratio was more modest, less than 15% during the same time period (P<0.05). Combined, these data suggest that motility events govern the overall rate of spheroid restructuring. This information has application to the chemosensitization of solid tumors and kinetic modeling of spheroid production.     

Bias in Markov models of disease

We examine bias in Markov models of diseases, including both chronic and infectious diseases. We consider two common types of Markov disease models: ones where disease progression changes by severity of disease, and ones where progression of disease changes in time or by age. We find sufficient conditions for bias to exist in models with aggregated transition probabilities when compared to models with state/time dependent transition probabilities. We also find that when aggregating data to compute transition probabilities, bias increases with the degree of data aggregation. We illustrate by examining bias in Markov models of Hepatitis C, Alzheimer’s disease, and lung cancer using medical data and find that the bias is significant depending on the method used to aggregate the data. A key implication is that by not incorporating state/time dependent transition probabilities, studies that use Markov models of diseases may be significantly overestimating or underestimating disease progression. This could potentially result in incorrect recommendations from cost-effectiveness studies and incorrect disease burden forecasts.     

Effect of rate of chemical or thermal renaturation on refolding and aggregation of a simple lattice protein

We used dynamic Monte Carlo simulation to investigate how changing the rate of chemical or thermal renaturation affects the folding and aggregation behavior of a system of simple, two-dimensional lattice protein molecules. Four renaturation methods were simulated: infinitely slow cooling; slow but finite cooling; quenching; and pulse renaturation. The infinitely slow cooling method, which is equivalent to dialysis or diafiltration, provides refolding yields that are relatively high and aggregates that are relatively small (mostly dimers or trimers). The slow but finite cooling method, which is equivalent to multiple-step dilution, provides refolding yields that are almost as high as those observed in the infinitely slow cooling case, but in a relatively short period of time. Quenching, which is equivalent to one-step dilution or quick quenching, is extremely slow and has low re- folding yields. A maximum appears in the refolding yield as a function of denaturant concentration in the simulation but disappears after a very long duration. Finally, the pulse renaturation method provides refolding yields that are substantially higher than those observed in the other three methods, even at high packing fractions. As in the early stages of quenching, there is a maximum in the refolding yield as a function of denaturant concentration when relatively large numbers of denatured chains are added to the refolding solution at each step.     

Structure and stability of a model three-helix-bundle protein on tailored surfaces

The interaction of protein molecules with surfaces is important in numerous applications. Theoretical work on protein adsorption has been limited. In particular, it is difficult to obtain quantitative predictions about the structure and stability of proteins on surfaces. In this study, density-of-states-based simulations were performed on a Gō-like model of a three-helix-bundle fragment from protein A (PDB ID: 1bdd). Both mechanical and thermal stability were investigated on neutral and attractive surfaces and compared to that in the absence of a surface. It was found that attaching the peptide to any type of surface decreases its melting temperature by as much as 9 K, depending upon orientation. Calorimetric cooperativity, as measured by van't Hoff to calorimetric enthalpy ratios, similarly decreased. It was also found that the mechanical strength of the peptide attached to surfaces is degraded to varying extents, depending upon the surface type and protein orientation. A comparison of mechanical and thermal stability showed that the two are not synonymous, but occur through different pathways, and that system configurations that are more thermally stable are not always so mechanically.     

A Monte Carlo method for the simulation of kinetie models

The purpose of this note is to illustrate the feasibility of simulating kinetic systems, such as commonly encountered in photosynthesis research, using the Monte Carlo (MC) method. In this approach, chemical events are considered at the molecular level where they occur randomly and the macroscopic kinetic evolution results from averaging a large number of such events. Their repeated simulation is easily accomplished using digital computing. It is shown that the MC approach is well suited to the capabilities and resources of modern microcomputers. A software package is briefly described and discussed, allowing a simple programming of any kinetic model system and its resolution. The execution is reasonably fast and accurate; it is not subject to such instabilities as found with the conventional analytical approach.Abbreviations MC Monte Carlo - RN random number - PSU photosynthetic unit Dedicated to Prof. L.N.M. Duysens on the occasion of his retirement.     

加性-显性-母体效应及GE互作效应遗传模型的模拟比较

运用蒙特卡罗方法比较了8个亲本正反应的加性－显性－母体效应的全模型及缩减模型,当σ^2M和σ^2ME存在时,检测各项遗传方差分量的功效高达97％以上,如何存在σ^2M和σ^2ME而缩减模型未包括这两项效应时,除显性效应以外的各项方差分量都被高估。对于加性－显性模型,如果忽略了基因型与环境互作,σ^2ε和σ^2A将被高估。当母体效应和基因型与环境互作被忽略时,将显著地增加遗传效应预测值的方差。     

A theoretical model for the association of amphiphilic transmembrane peptides in lipid bilayers

A theoretical model is proposed for the association of trans-bilayer peptides in lipid bilayers. The model is based on a lattice model for the pure lipid bilayer, which accounts accurately for the most important conformational states of the lipids and their mutual interactions and statistics. Within the lattice formulation the bilayer is formed by two independent monolayers, each represented by a triangular lattice, on which sites the lipid chains are arrayed. The peptides are represented by regular objects, with no internal flexibility, and with a projected area on the bilayer plane corresponding to a hexagon with seven lattice sites. In addition, it is assumed that each peptide surface at the interface with the lipid chains is partially hydrophilic, and therefore interacts with the surrounding lipid matrix via selective anisotropic forces. The peptides would therefore assemble in order to shield their hydrophilic residues from the hydrophobic surroundings. The model describes the self-association of peptides in lipid bilayers via lateral and rotational diffusion, anisotropic lipid-peptide interactions, and peptide-peptide interactions involving the peptide hydrophilic regions. The intent of this model study is to analyse the conditions under which the association of trans-bilayer and partially hydrophilic peptides (or their dispersion in the lipid matrix) is lipid-mediated, and to what extent it is induced by direct interactions between the hydrophilic regions of the peptides. The model properties are calculated by a Monte Carlo computer simulation technique within the canonical ensemble. The results from the model study indicate that direct interactions between the hydrophilic regions of the peptides are necessary to induce peptide association in the lipid bilayer in the fluid phase. Furthermore, peptides within each aggregate are oriented in such a way as to shield their hydrophilic regions from the hydrophobic environment. The average number of peptides present in the aggregates formed depends on the degree of mismatch between the peptide hydrophobic length and the lipid bilayer hydrophobic thickness: The lower the degree of mismatch is the higher this number is. Received: 30 December 1996 / Accepted: 9 May 1997     

Reproductive skew can provide a net advantage in both conditional and unconditional social interactions

We revisit a model for the evolution of costly social behaviour in the presence of reproductive skew. The model population is structured into groups, and reproductive skew is captured by assuming individuals adopt one of two social roles (dominant/subordinate). Unlike previous work, we adopt an ultimate perspective by tracking a mutant allele over the entire course of an invasion. Our main analysis applies the theory of branching processes, but a parallel analysis using the inclusive-fitness approach is also provided. Our first two results are modifications of known inequalities describing selective advantages for behaviours expressed conditional upon social status. We find that altruistic subordinate individuals are favoured more readily than previously thought; spiteful dominant individuals, however, are favoured less readily. Secondly, we identify the condition under which unconditional altruism (performed by both dominant and subordinate) will be adaptive. Our third main result shows that increasing the strength of selection can also change the range of parameters over which costly social behaviours are favoured. We find that stronger selection makes it relatively easier for subordinate altruism to emerge, but more difficult for dominant spite and unconditional altruism to occur. We discuss the possible implications of our results for human social evolution.     

Effect of short- and long-range interactions on protein folding

The relative importance of short- and long-range interactions is examined using a Monte Carlo simulation of protein folding on bovine pancreatic trypsin inhibitor. The model of the protein and the interaction energies were parametrized using X-ray structures of 30 native proteins. A nearest neighbor Ising model is used to determine the conformational state at each stage of the Monte Carlo procedure. Long-range interactions are simulated by contact free energies which become effective as two residues, separated by four or more residues along the chain, approach each other, and by disulfide-bond energies. Short-range interactions for residues separated by one, two, or three residues along the chain are also modeled by contact free energies and by -helical hydrogen bonds. A hard-sphere model is used to represent repulsive interactions. The ratios of short- to long-range interactions studied are 1:1, 2:1, 1:2, 0:1, and 1:0; e.g., for the 2:1 ratio, short-range interactions are weighted twice as much as long-range interactions, and for the 1:0 ratio, long-range interactions are omitted. For each ratio of short- to long-range interactions, a native conformation is found by a Monte Carlo procedure, a segment of 11 residues (residue numbers 1–11) is then rotated away from the rest of the molecule [breaking the 5–55 native disulfide bond, and moving this segment so that the distance between the sulfur atoms of the 5 and 55 cystine side chains (averaged for all native conformations) increases from 3.9 to 7.3 Å], and the Monte Carlo simulation is carried out (allowing the conformation of the whole molecule to change) until equilibrium is attained. For each ratio, the refolded conformation is compared to the native one using triangular distance maps and differential geometry distance criteria. With ratios of short- to long-range interaction energies of 1:1 and 0:1, the native disulfide bond could be re-formed; with ratios of 2:1 and 1:2 it did not; and with the 1:0 ratio, even a stable native conformation was not achieved. Therefore, long-range interactions (in addition to short-range ones) are required to bring remote parts of the protein together and to stabilize its native conformation.NIH Postdoctoral Fellow, 1977–1978.     

Test of the Inverse Monte Carlo Method for the Calculation of Interatomic Potential Energies in Atomic Liquids

Abstract

The principle purpose of this paper is to demonstrate the use of the Inverse Monte Carlo technique for calculating pair interaction energies in monoatomic liquids from a given equilibrium property. This method is based on the mathematical relation between transition probability and pair potential given by the fundamental equation of the “importance sampling” Monte Carlo method. In order to have well defined conditions for the test of the Inverse Monte Carlo method a Metropolis Monte Carlo simulation of a Lennard Jones liquid is carried out to give the equilibrium pair correlation function determined by the assumed potential. Because an equilibrium configuration is prerequisite for an Inverse Monte Carlo simulation a model system is generated reproducing the pair correlation function, which has been calculated by the Metropolis Monte Carlo simulation and therefore representing the system in thermal equilibrium. This configuration is used to simulate virtual atom displacements. The resulting changes in atom distribution for each single simulation step are inserted in a set of non-linear equations defining the transition probability for the virtual change of configuration. The solution of the set of equations for pair interaction energies yields the Lennard Jones potential by which the equilibrium configuration has been determined.     

Influence of substrate pattern on the adsorption of HP lattice proteins

With the highly simplified hydrophobic-polar model representation of a protein, we can study essential qualitative physics without an unnecessarily large computational overhead. Using Wang-Landau sampling in conjunction with a set of efficient Monte Carlo trial moves, we studied the adsorption of short HP lattice proteins on various simple patterned substrates and in particular for checkered patterned surfaces. A set of single-site mutated HP proteins is used to investigate the role of hydrophobicity of a protein chain and surface pattern for substrates with various pattern cell sizes relative to the protein’s native configuration. For most cases, we found that the adsorption transition occurs at a lower temperature, while the hydrophobic core formation is less affected. The flattening procedure after the HP protein is adsorbed is more sensitive to the change in surface patterns and single-site mutations. These observations stay valid for both strongly and weakly attractive surfaces.     

Non-native interactions play an effective role in protein folding dynamics

Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well‐defined order. The detailed study of the folding dynamics of protein‐like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non‐native interactions in the folding process), reveals significant differences in the corresponding locking scenarios—the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non‐native contacts. Furthermore, strong evidence for a positive role played by non‐native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non‐native contacts is observed also toward the end of the folding process, suggesting that non‐native contacts may indeed affect the overall folding process. For target models exhibiting clear two‐state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.     

Effects of excluded volume and polydispersity on solution properties of lentinan in 0.1 M NaOH solution

Seven lentinan fractions of various weight-average molecular weights (M(w)), ranging from 1.45 x 10(5) to 1.13 x 10(6) g mol(-1) were investigated by static light scattering and viscometry in 0.1M NaOH solution at 25 degrees C. The intrinsic viscosity [eta] - M(w) and radius of gyration s(2)(z) (1/2) - M(w) relationships for lentinan in 0.1M NaOH solution were found to be represented by [eta] = 5.1 x 10(-3)M(w) (0.81) cm(3) g(-1) and s(2)(z) (1/2) = 2.3 x 10(-1)M(w) (0.58) nm, respectively. Focusing on the effects of the M(w) polydispersity with the Schulz-Zimm distribution function, the data of M(w), s(2)(z) (1/2), and [eta] was analyzed on the basis of the Yoshizaki-Nitta-Yamakawa theory for the unperturbed helical wormlike chain combined with the quasi-two-parameter (QTP) theory for excluded-volume effects. The persistence length, molecular weight per unit contour length, and the excluded-volume strength were determined roughly to be 6.2 nm, 980 nm(-1), and 0.1, respectively. Compared with the theoretical value calculated by the Monte Carlo model, the persistence length is longer than that of the single (1 --> 3)-beta-(D)-glucan chain. The results revealed that lentinan exists as single-stranded flexible chains in 0.1M NaOH solution with a certain degree of expansion due to the electrostatic repulsion from the interaction between the OH(-) anions and lentinan molecules.     

The activity coefficient of high density systems with hard-sphere interactions: the application of the IGCMC method

The inverse grand-canonical Monte Carlo (IGCMC) technique is used to calculate the activity coefficients of the following hard-sphere systems: one-component fluid, binary mixture and solvent primitive model (SPM) electrolyte. The calculations for a one-component fluid are performed at different densities. The components of a binary mixture differ in diameters (300 and 500 pm) with the results being presented for different density and composition of a mixture. For the SPM model, simulations are performed for a 1:1 electrolyte at different electrolyte concentrations at the packing fraction equal to 0.3. Ions and solvent molecules of the same or different sizes are considered. The results are compared with those reported by Adams (one-component fluid), with those calculated using the Ebeling and Scherwinski equation (one-component fluid and binary mixture) and with the predictions from the symmetric Poisson–Boltzmann theory and the mean spherical approximation (SPM electrolyte).     

Effects of surface texture and interrelated properties on marine biofouling: a systematic review

This systematic review examines effects of surface texture on marine biofouling and characterizes key research methodologies. Seventy-five published articles met selection criteria for qualitative analysis; experimental data from 36 underwent quantitative meta-analysis. Most studies investigated fouling mechanisms and antifouling performance only in laboratory assays with one to several test species. Textures were almost exclusively a single layer of regularly arranged geometric features rather than complex hierarchical or irregular designs. Textures in general had no effect or an inconclusive effect on fouling in 46% of cases. However, effective textures more often decreased (35%) rather than increased (19%) fouling. Complex designs were more effective against fouling (51%) than were regular geometric features (32%). Ratios of feature height, width, or pitch to organism body length were significant influences. The authors recommend further research on promising complex and hierarchical texture designs with more test species, as well as field studies to ground-truth laboratory results.     

Evaluation of three scatter correction methods based on estimation of photopeak scatter spectrum in SPECT imaging: A simulation study

Three practical methods for scatter correction of Tc-99m SPECT images are evaluated. Among these, two methods, three-energy window (TEW) methods using the trapezoidal and triangular approximations, have been described previously by investigators, and a new approximation is offered in this work. The SIMIND (SIMulation of Imaging Nuclear Detectors) Monte Carlo program is used to simulate a line source placed at on-axis and 5 cm off-axis locations, a cold-sphere/hot-background phantom, a hot-sphere/cold-background phantom, and a more clinically realistic NCAT (Nonuniform Rational B-spline-based CArdiac-Torso) phantom. For evaluation of these methods, the scatter line-spread functions and scatter fractions for the on- and off-axis line source, image contrast, signal-to-noise ratio and relative noise for the cold spheres, and recovery coefficient for the hot spheres of different diameters are compared. For the NCAT phantom, a line profile through a slice of the reconstructed image is considered before and after scatter correction, and also image contrast defined by this profile is used to compare the correction methods. The results of this study indicate that for the line source simulation the scatter fractions obtained from the proposed method are a better estimation of true scatter fractions. Also, for both the sphere simulation and NCAT simulation, the proposed method improves the image contrast as compared to the two other methods.