Shape anisotropy of polymers in disordered environment

Unveiling the dynamic and thermodynamic interactions of hydrocortisone with β-cyclodextrin and its methylated derivatives through insights from molecular dynamics simulations

Cyclodextrins (CDs) can enhance the stability and bioavailability of pharmaceutical compounds by encapsulating them within their cavities. This study utilized molecular dynamics simulations to investigate the interaction mechanisms between hydrocortisone (HC) and various methylated CD derivatives. The results reveal that the loading of HC into CD cavities follows different mechanisms depending on the degree and position of methylation. Loading into βCD and 6-MeβCD was more complete, with the hydroxyl groups of HC facing the primary hydroxyl rim (PHR) and the ketone side facing the secondary hydroxyl rim (SHR). In contrast, 2,3-D-MeβCD and 2,6-D-MeβCD showed a different loading mechanism, with the ketone side facing the PHR and the hydroxyl groups facing the SHR. The root mean square fluctuation (RMSF) analysis demonstrated that methylation increases the flexibility of CD heavy atoms, with 3-MeβCD and 2,3-D-MeβCD exhibiting the highest flexibility. However, upon inclusion of HC, 3-MeβCD, 2,3-D-MeβCD, 2-MeβCD, and 6-MeβCD showed a significant reduction in flexibility, suggesting a more rigid structure that effectively retains HC within their cavities. The radial distribution function revealed a significant reduction in the number of water molecules within the innermost layer of the methylated CD cavities, particularly in TMeβCD, indicating a decrease in polarity. The presence of HC led to the release of high-energy water molecules, creating more favorable conditions for HC loading. Conformational analysis showed that methylation caused a partial decrease in the area of the PHR, a significant decrease in the area of the middle rim, and a notable decrease in the area of the SHR. The loading of HC increased the area of the PHR in most derivatives, with the most pronounced increase observed in 2,6-D-MeβCD and 6-MeβCD. The analysis of interaction energies and binding free energies demonstrated that the binding of HC to methylated CD derivatives is thermodynamically more favorable than to βCD, with the strongest association observed for 6-MeβCD, 2-MeβCD, and 2,3-D-MeβCD.

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics

This study presents a comprehensive analysis of the cholesterol binding mechanism and conformational changes in cyclodextrin (CD) carriers, namely βCD, 2HPβCD, and MβCD. The results revealed that the binding of cholesterol to CDs was spontaneous and thermodynamically favorable, with van der Waals interactions playing a dominant role, while Coulombic interactions have a negligible contribution. The solubility of cholesterol/βCD and cholesterol/MβCD complexes was lower compared to cholesterol/2HPβCD complex due to stronger vdW and Coulombic repulsion between water and CDs. Hydrogen bonding was found to have a minor role in the binding process. The investigation of mechanisms and kinetics of binding demonstrated that cholesterol permeates into the CD cavities completely. Replicas consideration indicated that while the binding to 2HPβCD occurred perpendicularly and solely through positioning cholesterol's oxygen toward the primary hydroxyl rim (PHR), the mechanism of cholesterol binding to βCD and MβCD could take place with the orientation of oxygen towards both rims. Functionalization resulted in decreased cavity polarity, increased constriction tendency, and altered solubility and configuration of the carrier. Upon cholesterol binding, the CDs expanded, increasing the cavity volume in cholesterol-containing systems. The effects of cholesterol on the relative shape anisotropy (κ2) and asphericity parameter (b) in cyclodextrins were investigated. βCD exhibited a spherical structure regardless of cholesterol presence, while 2HPβCD and MβCD displayed more pronounced non-sphericity in the absence of cholesterol. Loading cholesterol transformed 2HPβCD and MβCD into more spherical shapes, with increased probabilities of higher κ2. MβCD showed a higher maximum peak of κ2 compared to 2HPβCD after cholesterol loading, while 2HPβCD maintained a significant maximum peak at 0.2 for b.

Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study

This study delves into the interaction between benzodiazepine (BZD) drugs and 2-hydroxypropyl-β-cyclodextrin (2HPβCD), a cyclodextrin (CD) known to improve drug delivery and enhance therapeutic outcomes. We find that the 2HPβCD's atoms become more rigid in the presence of chlordiazepoxide (CDP), clonazepam (CLZ), and diazepam (DZM), whereas they become more flexible in the presence of nordazepam (NDM) and nitrazepam (NZP). We also investigated the structure of 2HPβCD and found that loading these drugs increases both the area and volume of the 2HPβCD cavity, making it more suitable for drug delivery. Moreover, this research found that all drugs exhibited negative values for the binding free energy, indicating thermodynamic favorability and improved solubility. The binding free energy order of the BZDs was consistent in both molecular dynamics and Monte Carlo methods, with CDP and DZM having the highest affinity for binding. We also analyzed the contribution of different interaction energies in binding between the carrier and the drugs and found that Van der Waals energy is the primary component. Our results indicate that the number of hydrogen bonds between 2HPβCD/water slightly decreases in the presence of BZDs, but the hydrogen bond's quality remains constant.

Coiling of semiflexible paramagnetic colloidal chains

Semiflexible filaments deform into a variety of configurations that dictate different phenomena manifesting at low Reynolds number. Harnessing the elasticity of these filaments to perform transport-related processes at the microfluidic scale requires structures that can be directly manipulated to attain controllable geometric features during their deformation. The configuration of semiflexible chains assembled from paramagnetic colloids can be readily controlled upon the application of external time-varying magnetic fields. In circularly rotating magnetic fields, these chains undergo coiling dynamics in which their ends close into loops that wrap inward, analogous to the curling of long nylon filaments under shear. The coiling is promising for the precise loading and targeted transport of small materials, however effective implementation requires an understanding of the role that field parameters and chain properties play on the coiling features. Here, we investigate the formation of coils in semiflexible paramagnetic chains using numerical simulations. We demonstrate that the size and shape of the initial coils are governed by the Mason and elastoviscous numbers, related to the field parameters and the chain bending stiffness. The size of the initial coil follows a nonmonotonic behavior with Mason number from which two regions are identified: (1) an elasticity-dependent nonlinear regime in which the coil size decreases with increasing field strength and for which loop shape tends to be circular, and (2) an elasticity-independent linear regime where the size increases with field strength and the shape become more elliptical. From the time scales associated to these regimes, we identify distinct coiling mechanisms for each case that relate the coiling dynamics to two other configurational dynamics of paramagnetic chains: wagging and folding behaviors.

Expansion of Single Chains Released from a Spherical Cavity

A two-stage model is developed to explain the phenomena of chain expansion, released from a confining cavity. In the first stage, the chain is assumed to expand as a sphere, while in the second stage it expands like a coil. The kinetic equations for the variation of chain size are derived in the two stages by balancing the rate of the free energy change with the rate of the energy dissipation. Langevin dynamics simulations are then performed to examine the theory. We find that the expansion process is dominated by the second stage and the evolution of chain size follows, mainly, the predicted curve for coil expansion, which depends on the chain length and is not sensitive to the confining volume fraction. It permits to define the expansion time for the process. Further study reveals that the chain does undergo a spherical expansion in the first stage with the characteristic time much shorter than the one for the second stage. As a consequence, the first-stage variation of chain size can be regarded as an add-on to the principal curve of expansion designated by the second stage. The scaling behaviors and the associated scaling exponents are analyzed in details. The simulation results well support the theory.

Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity

During in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (R _g) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize R _g) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger R _g). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower R _g values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.

Activity mediated globule to coil transition of a flexible polymer in a poor solvent

Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this work, we consider a flexible bead-spring model for active polymers with both attractive and repulsive interactions among the non-bonded monomers. The activity for each monomer works along its intrinsic direction of self-propulsion which changes diffusively with time. We study its kinetics in the overdamped limit, following quenching from good to poor solvent conditions. We observe that with low activities, though the kinetic pathways remain similar, the scaling exponent for the relaxation time of globule formation becomes smaller than that for the case with no activity. Interestingly, for higher activities when self-propulsion dominates over interaction energy, the polymer conformation becomes extended coil-like. There, in the steady state, the variation of the spatial extension of the polymer, measured via its gyration radius, shows two completely different scaling regimes: the corresponding Flory exponent ν changes from 1/3 to 3/5 similar to a transition of the polymer from a globular state to a self-avoiding walk. This can be explained by an interplay among the three energy scales present in the system, viz., the "ballistic", thermal, and interaction energy.

Insights into characterizing and producing anisotropic food structures

Besides the flavor profile of food, texture plays a major role in terms of the acceptance and likeability of food products. In contrast to gel-like homogenous isotropic structures, where the characterization is established and structure-texture mechanisms are well understood, there is still a lack of knowledge in the field of anisotropic complex food matrices. Food systems that show anisotropic properties in terms of macroscopic mechanical anisotropy as in grown meat, or mixed complex systems where anisotropic shaped particles or fibers are embedded into an isotropic matrix are challenging to characterize, hence the structure-texture correlation is not trivial to understand. In this paper, we bring together the state of the art of different anisotropic structures as a source of food, their formation in terms of structured plant proteins, and consequently the structure-texture correlation of those. Characteristic terms and properties to differentiate between anisotropic systems are introduced with the purpose to facilitate characterization of those. Based on the here provided terms and characteristics, further studies toward understanding such systems and their perception can be conducted. Beyond that, a first opinion on crucial influencing factors on the perception of anisotropic systems and their mechanistic background is provided.

Phase equilibria and conformational behavior of dendrimers in porous media: Towards chromatographic analysis of dendrimers

HYPOTHESIS

The intricate entropy-enthalpy interplay of dendrimers confined in pores affects their conformation and retention in the porous stationary phase. This work aims at providing important insights into its impacts on partitioning and chromatographic separation in both size-exclusion chromatography (SEC) and interaction chromatography (IC) regimes.

SIMULATIONS

Using Monte Carlo (MC) simulations, we investigated the bulk-pore phase equilibria and the conformational behavior of flexible dendrimers differing in generation, in spacer length and in fraction of modified terminal groups interacting differently with pore walls than the majority building units.

FINDINGS

With increasing interaction strength, a distinct transition from a roughly spherical shape caused by simultaneous interactions with two walls to an ellipsoidal (or even disklike) conformation tenaciously adhering to only one wall was observed for moderately confined dendrimers. The strongly deformed dendrimers subjected to severe confinement gain high energy and the samples differing in the degree of modification become chromatographically discernable thanks to large energy differences. Consequently, our results suggest that the column fillings with fairly narrow pores which are ineffective in SEC, are highly efficient separation media for dendrimer studies by IC above the critical adsorption point (CAP). Overall, our simulations reveal useful information for advancing and optimizing experimental liquid chromatography studies of dendrimers.

Photophysical and Structural Characterization of Intrinsically Fluorescent Sterol Aggregates

Self-association of cholesterol into aggregates and crystals is a hallmark of developing atherosclerosis. Intrinsically fluorescent sterols, such as dehydroergosterol (DHE), can be used to study sterol aggregation by fluorescence spectroscopy and microscopy, but a thorough understanding of DHE's photophysical and structural properties in the aggregated state is missing. Here, we show that DHE forms submicron fluorescent aggregates when evaporated from an ethanol solution. Using atomic force microscopy, we find that DHE, like cholesterol, forms compact oblate-shape aggregates of <100 nm in diameter. DHE's fluorescence is lowered in the aggregate compared to the monomeric form, and characteristic spectral changes accompany the aggregation process. Electronic structure calculations of DHE dimers in water indicate that Frenkel-type exciton coupling contributes to the lowered DHE fluorescence in the aggregates. Using molecular dynamics (MD) simulations, we show that DHE forms compact aggregates on the nanosecond scale and with strong intermolecular attraction, in which a broad range of orientations, and therefore electronic couplings, will take place. Tight packing of DHE in aggregates also lowers the apparent absorption cross section, further reducing the molecular brightness of the aggregates. Our results pave the way for systematic solubility studies of intrinsically fluorescent analogues of biologically relevant sterols.

Nanoscale characterization of the biomolecular corona by cryo-electron microscopy, cryo-electron tomography, and image simulation

The biological identity of nanoparticles (NPs) is established by their interactions with a wide range of biomolecules around their surfaces after exposure to biological media. Understanding the true nature of the biomolecular corona (BC) in its native state is, therefore, essential for its safe and efficient application in clinical settings. The fundamental challenge is to visualize the biomolecules within the corona and their relationship/association to the surface of the NPs. Using a synergistic application of cryo-electron microscopy, cryo-electron tomography, and three-dimensional reconstruction, we revealed the unique morphological details of the biomolecules and their distribution/association with the surface of polystyrene NPs at a nanoscale resolution. The analysis of the BC at a single NP level and its variability among NPs in the same sample, and the discovery of the presence of nonspecific biomolecules in plasma residues, enable more precise characterization of NPs, improving predictions of their safety and efficacies.

Understanding the biomolecular corona is of key importance to nanomedicine. Here, the authors report on cryo-electron and tomographic imaging of the corona formed on model nanoparticles and the 3D reconstruction of the corona to study the distribution and association of the biomolecules with the nanoparticle.

Direct observation of nystatin binding to the plasma membrane of living cells

Nystatin is an antifungal polyene macrolide which is widely applied to treat yeast infections. Nystatin has also been used as a laboratory tool to inhibit endocytic processes in mammalian cells. The interaction of nystatin with model membranes has been studied thoroughly by various spectroscopic methods, making use of its weak fluorescence in the ultraviolet (UV). Studying its interaction with cells would require direct imaging, which, so far, required attachment of a fluorophore to nystatin. Using UV-sensitive microscopy, we show here how to visualize the interaction of nystatin with the plasma membrane (PM) directly. We find that nystatin forms micron-sized aggregates in buffer, and molecular dynamics simulations confirm that nystatin rapidly self-assembles into aggregates in aqueous solution. Using UV-sensitive microscopy, we find that large nystatin aggregates adhere to the surface of Chinese Hamster Ovarian (CHO) cells, causing slow spreading of nystatin fluorescence into the PM. Binding of nystatin to CHO cells does not interfere with cellular uptake or lateral membrane diffusion of the cholesterol analogue TopFluor-cholesterol (TF-Chol). Nystatin binds extensively to the PM of yeast cells as inferred from a strong UV signal in this membrane. Loading a yeast mutant unable to synthesize ergosterol with cholesterol gave much less nystatin membrane staining compared to loading such cells with ergosterol. These results explain the selective fungicidal effect of nystatin by differential interaction of nystatin with yeast membranes containing ergosterol compared to the mammalian cholesterol. Our combined experimental and computational approach provides a toolset for future design of new polyene macrolides.

Kinetically-arrested single-polymer nanostructures from amphiphilic mikto-grafted bottlebrushes in solution: a simulation study

Solution self-assembly of molecular bottlebrushes offers a rich platform to create complex functional organic nanostructures. Recently, it has become evident that kinetics, not just thermodynamics, plays an important role in defining the self-assembled structures that can be formed. In this work, we present results from extensive molecular dynamics simulations that explore the self-assembly behavior of mikto-grafted bottlebrushes when the solvent quality for one of the side blocks is changed by a rapid quench. We have performed a systematic study of the effect of different structural parameters and the degree of incompatibility between side chains on the final self-assembled nanostructures in the low concentration limit. We found that kinetically-trapped complex nanostructures are prevalent as the number of macromonomers increases. We performed a quantitative analysis of the self-assembled morphologies by computing the radius of gyration tensor and relative shape anisotropy as the different relevant parameters were varied. Our results are summarized in terms of non-equilibrium morphology diagrams.

Heterogeneous kinetics of the loop formation of a single polymer chain in crowded and disordered media

The cytoplasmic volume of cells is occupied and crowded by a variety of macromolecules, such as proteins and cytoskeleton structures. Such diverse macromolecules make the cell cytoplasm not only structurally heterogeneous but also dynamically heterogeneous: Some macromolecules may diffuse freely inside cell cytoplasm at certain timescales while others hardly diffuse. Studies on the effects of the dynamic heterogeneity on reaction kinetics have been limited even though the effects of the crowdedness and structural heterogeneity were investigated extensively. In this study, we employ a simple model of mixtures of mobile and immobile matrix particles, tune the degree of dynamic heterogeneity by changing the fraction of immobile matrix particles, and investigate reaction kinetics in such heterogeneous media. We employ the loop formation of a single polymer chain as a model reaction and perform Langevin dynamics simulations. We find that the free-energy barrier of the loop formation is decreased as the systems become more crowded with matrix particles. But the free-energy barrier is not sensitive to the dynamic heterogeneity. As dynamic heterogeneity increases with an increase in the fraction of immobile matrix particles, however, the diffusivity of the system decreases significantly. The decrease in the diffusion (due to the dynamic heterogeneity) and the decrease in the free-energy barrier (due to the crowdedness) lead together to a complicated trend of the loop formation kinetics. As the volume fraction of immobile matrix particles reaches a critical value at the percolation transition, the reaction kinetics becomes significantly heterogeneous and the survival probability distribution of the chain loop formation becomes stretched-exponential. We also illustrate that the heterogeneous reaction rate near the percolation transition relates closely to the structures of local pores in which the polymer is located.

The shape of pinned forced polymer loops

Loop geometry is a frequent encounter in synthetic and biological polymers. Here we provide an analytical theory to characterize the shapes of polymer loops subjected to an external force field. We show how to calculate the polymer density, gyration radius and its distribution. Interestingly, the distribution of the gyration radius shows a non-monotonic behavior as a function of the external force. Furthermore, we analyzed the gyration tensor of the polymer loop characterizing its overall shape. Two parameters called asphericity and the nature of asphericity derived from the gyration tensor, along with the gyration radius, can be used to quantify the shape of polymer loops in theory and experiments.

Asphaltene Mesoscale Aggregation Behavior in Organic Solvents-A Brownian Dynamics Study

Significant advances have been achieved in understanding the main molecular mechanisms leading to asphaltene aggregation. However, the existing computational deficiency of molecular dynamics simulations did not allow full reproduction of the complex aggregation behavior of asphaltene in the past. In this work, we use the Brownian dynamics simulation to investigate asphaltene aggregation behavior on larger length and time scales that have not been previously accessed by molecular simulations. This enabled us to completely render the formation of clusters of asphaltene nanoaggregates and the resulting fractal or network of aggregates during the aggregation process. Asphaltene aggregation is studied at several volume fractions (ϕ = 1-7%) of asphaltene nanoaggregates in two solvents including heptane and heptol (i.e., a mixture of heptane and toluene). Our simulation results support the aggregation hierarchy proposed in the Yen-Mullins model (Mullins, Annu. Rev. Anal. Chem. 2011, 4, 393-418.) by demonstrating that asphaltene nanoaggregates form small clusters with an aggregation number of 7-8 and an average gyration radius of ∼4.0 nm capable of forming either fractal aggregates with a fractal dimension of 1.93-2.04 at low ϕ or percolating networks of aggregates at high ϕ. Percolating structures are observed at ϕ = 7% in both solvents. In heptol, the structures mainly percolate along two directions, whereas in heptane, they can percolate along three directions (i.e., x, y, and z). The self-diffusion coefficient ( D) significantly decreases as ϕ increases. Generally, D is larger in heptol than in heptane, but this difference diminishes as ϕ increases, approaching to almost the same value at ϕ = 7%.

Polymer adsorption on curved surfaces

The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data over a wide range of sphere radius and temperature, we have constructed entire phase diagrams both for nongrafted and end-grafted polymers. For the identification of the conformational phases, we have calculated several energetic and structural observables such as gyration tensor based shape parameters and their fluctuations by canonical statistical analysis. Despite the simplicity of our model, it qualitatively represents in the considered parameter range real systems that are studied in experiments. The work discussed here could have experimental implications from protein-ligand interactions to designing nanosmart materials.

Mesoscopic Adaptive Resolution Scheme toward Understanding of Interactions between Sickle Cell Fibers

Understanding of intracellular polymerization of sickle hemoglobin (HbS) and subsequent interaction with the membrane of a red blood cell (RBC) is important to predict the altered morphologies and mechanical properties of sickle RBCs in sickle cell anemia. However, modeling the integrated processes of HbS nucleation, polymerization, HbS fiber interaction, and subsequent distortion of RBCs is challenging as they occur at multispatial scales, ranging from nanometers to micrometers. To make progress toward simulating the integrated processes, we propose a hybrid HbS fiber model, which couples fine-grained and coarse-grained HbS fiber models through a mesoscopic adaptive resolution scheme (MARS). To this end, we apply a microscopic model to capture the dynamic process of polymerization of HbS fibers, while maintaining the mechanical properties of polymerized HbS fibers by the mesoscopic model, thus providing a means of bridging the subcellular and cellular phenomena in sickle cell disease. At the subcellular level, this model can simulate HbS polymerization with preexisting HbS nuclei. At the cellular level, if combined with RBC models, the generated HbS fibers could be applied to study the morphologies and membrane stiffening of sickle RBCs. One important feature of the MARS is that it can be easily employed in other particle-based multiscale simulations where a dynamic coarse-graining and force-blending method is required. As demonstrations, we first apply the hybrid HbS fiber model to simulate the interactions of two growing fibers and find that their final configurations depend on the orientation and interaction distance between two fibers, in good agreement with experimental observations. We also model the formation of fiber bundles and domains so that we explore the mechanism that causes fiber branching.

Structural organization of sterol molecules in DPPC bilayers: a coarse-grained molecular dynamics investigation

We investigate the structural organization of cholesterol (CHOL) analogues in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers using coarse-grained molecular dynamics simulations and the MARTINI forcefield. Different sterol molecules are modelled by increasing (CHOLL) or decreasing (CHOLS) the diameter of the sterol beads employed in the MARTINI model of CHOL. At high sterol concentrations, (xsterol = 0.5), typical of liquid ordered phases, we find that the sterol arrangement and sterol-DPPC interactions strongly depend on the sterol size. Smaller sterols (CHOLS and CHOL) form linear clusters, while the larger sterols (CHOLL) arrange themselves into disc shaped clusters. By combining structural and dynamical properties we also investigate the So→ Ld transition for the CHOLL and CHOLS sterols. We show that small changes in the sterol size significantly affect the stability of the gel phase with the gel phase stabilized by the small sterols, but destabilized by large sterols. The general dependence of the phase behaviour of the membrane with sterol content is reminiscent of the one observed in naturally occurring membranes. The relevance of our results to understand current cholesterol-bilayer structural models is discussed.

Ring polymers in crowded environment: conformational properties

We analyze the universal size characteristics of flexible ring polymers in solutions in presence of structural obstacles (impurities) in d dimensions. One encounters such situations when considering polymers in gels, colloidal solutions, intra- and extracellular environments. A special case of extended impurities correlated on large distances r according to a power law ~r(-a) is considered. Applying the direct polymer renormalization scheme, we evaluate the estimates for averaged gyration radius ⟨R(g ring)⟩ and spanning radius ⟨R(1/2 ring)⟩ of typical ring polymer conformation up to the first order of double ɛ = 4 - d, δ = 4 - a expansion. Our results quantitatively reveal an extent of the effective size and anisotropy of closed ring macromolecules in disordered environment. In particular, the size ratio of ring and open (linear) polymers of the same molecular weight grows when increasing the strength of disorder according to ⟨R(g ring)(2)⟩/⟨R(g chain)(2)⟩=½(1+(13/48)δ).

Scalable replica-exchange framework for Wang-Landau sampling

We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

Ground-state properties of a polymer chain in an attractive sphere

We analyze the structural formation of a polymer chain inside of an attractive sphere depending on the attraction strength. Our model is composed of a coarse-grained polymer and an attractive sphere potential. Within this frame, multicanonical Monte Carlo simulations are employed to identify the global minimum energies for a polymer chain interacting with the attractive inner wall of the sphere. Different compact structures are found with varying attraction strengths, among which are spherical, three/two, or monolayer. The conformational properties of these structures are presented.

Hydrophobic moments, shape, and packing in disordered proteins

Disordered proteins play a significant role in many biological processes and provide an attractive target for biophysical studies under physiological conditions. Disordered proteins may be classified as (a) proteins with overall well-defined secondary structures, interspersed with regions of missing residues, or (b) natively unstructured proteins which lack definite secondary structure. The spatial profile of second order hydrophobic moment for disordered proteins depicts the distribution of hydrophobic residues from the interior to the surface of the protein and indicates the lack of a well-formed hydrophobic core unlike that of the globular proteins. This trend is independent of the size or position of the disordered region in the sequence. The hydrophobicity profile of the ordered regions of the disordered proteins differ considerably from that of globular proteins implying the role of disordered parts and the significance of hydrophobic interactions in the folding of proteins. The shape asymmetry of the two classes of disordered proteins is determined by calculating the asphercity and shape parameters, derived from the cartesian components of radius of gyration tensor. Disordered proteins of group a are more spherical as compared to the natively unstructured proteins (group b), which are more prolate. Both groups of proteins exhibit similar types of side-chain backbone contacts, as that of the globular proteins. While disordered proteins contains few hydrophobic residues natively unstructured proteins are characterized by a residues of low mean hydrophobicity and high mean net charge.