Morphological variation in a collapsed single homopolymer chain

DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study

In eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin. During transcription, negative supercoils generated behind the polymerase during transcription may play a role in triggering nucleosome reassembly. To elucidate how supercoils influence the dynamics of wrapping of DNA around the histone cores, we developed a novel model to simulate the intricate interplay between DNA and histone. Our simulations reveal that both positively and negatively supercoiled DNAs are capable of wrapping around histone cores to adopt the nucleosome conformation. Notably, our findings confirm a strong preference for negative supercoiled DNA during nucleosome wrapping, and reveal that the both of the negative writhe and twist are beneficial to the formation of the DNA wrapping around histone. Additionally, the simulations of the multiple nucleosomes on the same DNA template indicate that the nucleosome tends to assemble in proximity to the original nucleosome. This advancement in understanding the spontaneous formation of nucleosomes may offer insights into the complex dynamics of chromatin assembly and the fundamental mechanisms governing the structure and function of chromatin.

Cutting-edge Bioinformatics strategies for synthesizing Cyclotriazadisulfonamide (CADA) analogs in next-Generation HIV therapies

Cyclotriazadisulfonamide (CADA) is a macrocyclic compound known for its unique mechanism in inhibiting HIV infection by downregulating the CD4 T-cell receptor, a crucial entry point for the virus. Unlike other antiretrovirals, CADA exhibits activity against a wide range of HIV strains, as all HIV variants require CD4 binding for infection. Furthermore, CADA has shown a synergistic effect with clinically approved anti-HIV drugs, offering potential for enhanced therapeutic strategies (Vermeire & Schols, [65]). One proposed mechanism for CADA's inhibition of the CD4 receptor involves blocking the gates of the Sec61 channel, thereby preventing its translocation. However, CADA suffers from poor solubility and bioavailability. To address this, the study aimed to design CADA analogs with improved binding to the Sec61 channel, enhanced bioavailability, and reduced toxicity. The analogs were designed using SeeSAR, with Avogadro and Meeko used for 3D configuration and pseudoatom placement, respectively. AutoDock Vina version 1.2.4 was employed to predict the binding energies of these analogs. Of the 113 analogs designed, 93 demonstrated a more negative binding energy to the Sec61 channel compared to CADA. Structure-binding energy analyses were done to the top-binding analogs to show favorable structural modifications. Enzyme-ligand interactions were analyzed to elucidate the forces contributing to these binding energies. Additionally, 33 of the 113 analogs were deemed bioavailable using a bioavailability criteria specific for macrocycles. Toxicity predictions using PASS Online and StopTox identified analogs JGL023, JGL024, JGL032, and JGL047 as potential drug candidates. Molecular dynamics simulations using Gromacs-2020.4 revealed that JGL023 and JGL032 exhibited the most favorable binding to the Sec61 channel, as determined by evaluating ligand and residue flexibility, compactness, contact frequency, motion pathways, free energy, and other relevant parameters. Synthetic routes for these four analogs were proposed for future studies. The results of this study offer a new perspective on developing drugs to inhibit HIV entry.

Computer Simulations of Responsive Nanogels at Lipid Membrane

The swelling and collapse of responsive nanogels on a planar lipid bilayer are studied by means of mesoscopic computer simulations. The effects of molecular weight, cross-linking density, and adhesion strength are examined. The conditions for collapse-mediated engulfing by the bilayer are found. In particular, the results show that at low hydrophobicity level the increase in the nanogel softness decreases the engulfing rate. On the contrary, for stronger hydrophobicity level the trend changes to the opposite one. At the same time, when the cross-linking density is too low or the adhesion strength is too high the nanogel deformation at the membrane suppresses the engulfing regardless of the network swelling ratio. Finally, for comparative reasons, the behavior of the nanogels is also studied at the solid surface. These results may be useful in the design of soft particles capable of tuning of their elasticity and porosity for successful intracellular drug delivery.

Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities

Disordered proteins are conformationally flexible proteins that are biologically important and have been implicated in devastating diseases such as Alzheimer's disease and cancer. Unlike stably folded structured proteins, disordered proteins sample a range of different conformations that needs to be accounted for. Here, we treat disordered proteins as polymer chains, and compute a dimensionless quantity called instantaneous shape ratio (Rs), as Rs = Ree2/Rg2, where Ree is end-to-end distance and Rg is radius of gyration. Extended protein conformations tend to have high Ree compared with Rg, and thus have high Rs values, whereas compact conformations have smaller Rs values. We use a scatter plot of Rs (representing shape) against Rg (representing size) as a simple map of conformational landscapes. We first examine the conformational landscape of simple polymer models such as Random Walk, Self-Avoiding Walk, and Gaussian Walk (GW), and we notice that all protein/polymer maps lie within the boundaries of the GW map. We thus use the GW map as a reference and, to assess conformational diversity, we compute the fraction of the GW conformations (fC) covered by each protein/polymer. Disordered proteins all have high fC scores, consistent with their disordered nature. Each disordered protein accesses a different region of the reference map, revealing differences in their conformational ensembles. We additionally examine the conformational maps of the nonviral gene delivery vector polyethyleneimine at various protonation states, and find that they resemble disordered proteins, with coverage of the reference map decreasing with increasing protonation state, indicating decreasing conformational diversity. We propose that our method of combining Rs and Rg in a scatter plot generates a simple, meaningful map of the conformational landscape of a disordered protein, which in turn can be used to assess conformational diversity of disordered proteins.

DNA Condensation by Peptide-Conjugated PAMAM Dendrimers. Influence of Peptide Charge

Nucleic acid delivery to cells is an important therapeutic strategy that requires the transport of nucleic acids to intracellular compartments and their protection from enzymatic degradation. This can be achieved through the complexation of the nucleic acids with polycations. Poly(amidoamine) (PAMAM) dendrimers and peptide-conjugated dendrimers have been investigated as delivery vectors. Inspired by these studies and the role of flexible peptide domains in protein-DNA interactions, we studied the impact of conjugating two peptides (tails) to generation 2 (G2) PAMAM dendrimers on DNA condensation and polyplex formation. Using gel electrophoresis, dye exclusion assays, atomic force microscopy, and Monte Carlo simulations, it is shown that the steric impact of neutral peptide tails is to hinder the formation of DNA-G2 polyplexes composed of multiple DNA chains. If the tails are negatively charged, which results in overall neutral G2 conjugates, then the interaction of G2 with DNA is hindered. Increasing the net positive charge of the tails resulted in the complexation capacity of G2 with the DNA being restored. While DNA complexation is obtained for a similar net charge balance for G2 and G2 conjugates with positive tails, fewer of the latter are required to achieve a comparable condensation degree. Furthermore, it is shown that about 40% of the DNA remains accessible to binding by small molecules. Overall, this shows that tuning the net charge of peptide tails conjugated to PAMAM dendrimers offers a handle to control the complexation capacity of DNA, which can be explored as a novel route for optimization as gene delivery vehicles.

Energetic preference and topological constraint effects on the formation of DNA twisted toroidal bundles

DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global conformations of DNA inside these bundles are still not well understood. In this study, we investigate this issue by solving different models for the toroidal bundles and performing replica-exchange molecular dynamics (REMD) simulations for self-attractive stiff polymers of various chain lengths. We find that a moderate degree of twisting is energetically favorable for toroidal bundles, yielding optimal configurations of lower energies than for other bundles corresponding to spool-like and constant radius of curvature arrangements. The REMD simulations show that the ground states of the stiff polymers are twisted toroidal bundles with the average twist degrees close to those predicted by the theoretical model. Constant-temperature simulations show that twisted toroidal bundles can be formed through successive processes of nucleation, growth, quick tightening, and slow tightening of the toroid, with the two last processes facilitating the polymer threading through the toroid's hole. A relatively long chain of 512 beads has an increased dynamical difficulty to access the twisted bundle states due to the polymer's topological constraint. Interestingly, we also observed significantly twisted toroidal bundles with a sharp U-shaped region in the polymer conformation. It is suggested that this U-shaped region makes the formation of twisted bundles easier by effectively reducing the polymer length. This effect can be equivalent to having multiple chains in the toroid.

Swelling and Collapse of Cylindrical Polyelectrolyte Microgels

In this study, we propose computer simulations of charged cylindrical microgels. The effects of cross-linking density, aspect ratio, and fraction of charged groups on the microgel swelling and collapse with a variation in the solvent quality were studied. The results were compared with those obtained for equivalent neutral cylindrical microgels. The study demonstrated that microgels' degree of swelling strongly depends on the fraction of charged groups. Polyelectrolyte microgels under adequate solvent conditions are characterized by a larger length and thickness than their neutral analogues: the higher the fraction of charged groups, the longer their length and greater their thickness. Microgels' collapse upon solvent quality decline is characterized by a decrease in length and non-monotonous behavior of its thickness. First, the thickness decreases due to the attraction of monomer units (beads) upon collapse. The further thickness increase is related to the surface tension, which tends to reduce the anisotropy of collapsed objects (the minimum surface energy is known to be achieved for the spherical objects). This reduction is opposed by the network elasticity. The microgels with a low cross-linking density and/or a low enough aspect ratio reveal a cylinder-to-sphere collapse. Otherwise, the cylindrical shape is preserved in the course of the collapse. Aspect ratio as a function of the solvent quality (interaction parameter) demonstrates the maximum, which is solely due to the electrostatics. Finally, we plotted radial concentration profiles for network segments, their charged groups, and counterions.

Membrane shape deformation induced by curvature-inducing proteins consisting of chiral crescent binding and intrinsically disordered domains

Curvature-inducing proteins containing a bin/amphiphysin/Rvs domain often have intrinsically disordered domains. Recent experiments have shown that these disordered chains enhance curvature sensing and generation. Here, we report on the modification of protein–membrane interactions by disordered chains using meshless membrane simulations. The protein and bound membrane are modeled together as a chiral crescent protein rod with two excluded-volume chains. As the chain length increases, the repulsion between them reduces the cluster size of the proteins. It induces spindle-shaped vesicles and a transition between arc-shaped and circular protein assemblies in a disk-shaped vesicle. For flat membranes, an intermediate chain length induces many tubules owing to the repulsion between the protein assemblies, whereas longer chains promote perpendicular elongation of tubules. Moreover, protein rods with zero rod curvature and sufficiently long chains stabilize the spherical buds. For proteins with a negative rod curvature, an intermediate chain length induces a rugged membrane with branched protein assemblies, whereas longer chains induce the formation of tubules with periodic concave-ring structures.

Temperature-Dependent Conformation Behavior of Isolated Poly(3-hexylthiopene) Chains

We use atomistic as well as coarse-grained molecular dynamics simulations to study the conformation of a single poly(3-hexylthiopene) chain as a function of temperature. We find that mainly bundle and toroid structures appear with bundles becoming more abundant for decreasing temperatures. We compare an atomistic and a Martini-based coarse-grained model which we find in very good agreement. We further illustrate how the temperature dependence of P3HT can be connected to that of simple Lennard–Jones model polymers in a vacuum. Upon adding solvent (THF) we observe the occurrence of a prominent swelling of the molecular size at a temperature of about 220 K. This swelling is in close agreement with the interpretation of recent spectroscopic experiments which allows us to explain the experimental observations by an increased frequency of bundle structures.

Modulation of flexo-rigid balance in photoresponsive thymine grafted copolymers towards designing smart healable coating

Efficacy and durability of the photovoltaic device mandates its protection against hot, humid weather condition, high energy of UV light and unwanted scratches. Such challenges can be mitigated by smart polymeric coating with inherent properties e.g. hydrophobicity to prevent moisture, optimal viscocity for better processibility and crack-healing. The hydrophobic polymers TP1-TP4 containing pendant photo-crosslinkable thymine moieties are designed that undergo [2 + 2] photocycloaddition upon UVB irradiation and can be dynamically reverted back upon irradiation with UVC light. A judicious control of solvent environment, chain length, functionality% and concentration of the polymers regulate the aspects of photodimerization thereby, rendering intra or inter-chain collapse to form diverse nanostructures. Photodimerization of the thymine moieties renders coil to globule transformation in dilute condition whereas irradiation performed at high macromolecular concentration regime exhibits higher order nanostructures. The photoresponsive chain collapse leads to the formation of rigid crosslinked domains within flexible polymer chains akin to the hard-soft phases of thermoplastic elastomers. Such rigidification of the crosslinked segments endows a tool to photomodulate the glass transition temperature (T g) that can dynamically revert back upon decrosslinking. Further, the structural modulation of the polymers is explored towards autonomic and nonautonomic self-healing behaviour at ambient conditions. Moreover, the self-healing efficacy can be tuned with the film thickness and it remains unaltered upon using solar simulator or direct sunlight. Overall, such hydrophobic low T g polymers display photo-regulated self-healing mechanism consisting of both autonomic and non-autonomic self-healing and may find applications in designing smart protective coatings for photovoltaic devices.

Effects of polymers on the cavitating flow around a cylinder: A large-scale molecular dynamics analysis

The cavitation flow of linear-polymer solutions around a cylinder is studied by performing a large-scale molecular dynamics simulation. The addition of polymer chains remarkably suppresses cavitation. The polymers are stretched into a linear shape near the cylinder and entrained in the vortex behind the cylinder. As the polymers stretch, the elongational viscosity increases, which suppresses the vortex formation. Furthermore, the polymers exhibit an entropic elasticity owing to stretching. This elastic energy increases the local temperature, which inhibits the cavitation inception. These effects of polymers result in the dramatic suppression of cavitation.

Implications of relaxation dynamics of collapsed conjugated polymeric nanoparticles for light-harvesting applications

The mechanism of the formation of nanoparticles (collapsed state) from the extended state of polymers and their ultrafast excited state relaxation dynamics are illustrated.

Interplay between two radical species in the formation of periodic patterns during a polymerization reaction

Periodic patterns are ubiquitous in nature and spontaneously form on molecular to cosmic scales by the interplay between reaction and diffusion. Understanding how these patterns form is important to understand the construction rules of nature and apply them in the synthesis of functional artificial materials. This work clarifies how radical (R˙) species affect pattern formation in periodic precipitated and depleted zones during a polymerization process in an agarose gel. When a monomer (Mon) solution was poured on top of the gel doped with an initiator (In) in a test tube, periodic and continuous precipitation occurred near and far away from the solution/gel interface, respectively. In contrast, a system without In exhibited only a continuous band of precipitates beyond a depleted zone without precipitates at a certain distance from the interface. In the depleted region, an inhibitor (Q) added to the solution limited the polymerization triggered by R˙ formed thermally from Mon. With the addition of enough In to overcome the quenching effect of Q, periodic bands appeared near the solution/gel interface. These results suggest the involvement of two independent polymerization processes: (i) polymerization triggered by R˙ formed from In, which is the dominant process up to 100 h and yields periodic structures near the interface. After 100 h, the dominant process is the polymerization triggered by R˙ generated thermally from Mon, which yields a continuous precipitation zone. These two R˙ species compete and generate periodic bands near the interface (<100 h) and a continuous band far away from the interface (>100 h).

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.

Photoresponsive chain collapse in a flexo-rigid functional copolymer to modulate the self-healing behaviour

Synthetic systems mimicking the natural self-folding process are attractive to impart multiple structural control over polymer crosslinking and the subsequent alteration of their macroscopic self-healing properties. In that regard, polymers P1-P5 containing pendant photo-crosslinkable moieties were designed and underwent intra- or interchain collapse to form diverse nanostructures. The shape and dimension of the nanostructures could be efficiently controlled by the concentration, solvent compatibility and characteristics of the polymers. Photodimerization of the coumarin moieties transformed the extended coiled chain of the polymer to uniform sized nanoparticles in a dilute condition, while in the crowded macromolecular concentration regime, the polymer folded into nanostructures with polydisperse topologies that were far from a condensed globule or partially swollen globule conformation. Scaling law exponents for polymer chain compaction suggested an interchain collapse with rigid compact segments connected by flexible polymer chains that draws an analogy with elastomers. Such a hardening of the rigid segment as a consequence of photodimerization rendered a significant increase in the glass transition temperature (Tg), which could be reversibly controlled upon decrosslinking. Lastly, the structural variation of this class of polymers over self-healing was explored and the crosslinked polymers showed phototriggered non-autonomic and intrinsic self-healing behaviour under ambient conditions. This is an interesting approach to access a photomodulated self-healing system with low Tg polymers that shows the coexistence of autonomic and nonautonomic self-healing pathways and that may find application in designing smart coatings for photovoltaic devices.

Relaxation dynamics of semiflexible treelike small-world polymer networks

We study the relaxation dynamics of the polymer networks that are constructed based on a degree distribution specific to small-world networks. The employed building algorithm generates polymers with a large variety of architectures, thus allowing for a detailed study of the structural transition from a pure linear chain to dendritic polymer networks. This is done by varying a single parameter p, which measures the randomness in the degree of the network's nodes. The dynamics is investigated in the framework of the generalized Gaussian structures model by monitoring the influence of the parameter p and of the stiffness parameter q on the behavior of the relaxation quantities: averaged monomer displacement, storage modulus, and loss modulus. The structure properties of the constructed polymers are described by the mean-square radius of gyration. In the absence of stiffness, in the intermediate frequencies domain of the dynamical quantities we encounter different behaviours, such as a dendritic behavior followed by a linear one for very small values of p or a single well-marked dendritic behavior for higher values of p. The stiffness parameter q influences drastically the relaxation dynamics of these polymer networks and in general no evident scaling regions were encountered. However, for some values of the parameter set (p,q), such as (0.8,0.4), an extremely short constant slope region, less than one order of magnitude, was found.

Shape Transformations of Vesicles Self-Assembled from Amphiphilic Hyperbranched Multiarm Copolymers via Simulation

The understanding of shape transformations of vesicles is of fundamental importance in biological and clinical sciences. Hyperbranched polymer vesicles (branched polymersomes) are newly emerging polymer vesicles with special structure and property. They have also been regarded as a good model for biomembranes. However, the shape transformations of hyperbranched polymer vesicles have not been studied from either an experimental or theoretical level. Herein, the shape transformations of vesicles self-assembled from amphiphilic hyperbranched multiarm copolymers (HMCs) in response to the interaction parameters between the hydrophobic core and hydrophilic arms and the polymer concentrations are investigated carefully through dissipative particle dynamics (DPD) simulations. In the morphological phase diagram, two types of vesicles are obtained: one type corresponds to vesicles without holes formed at low concentrations including unilamellar vesicles, double-lamellar vesicles, discocyte-shaped vesicles, and tubular vesicles, and the other type corresponds to vesicles with holes formed at high concentrations including stomatocyte-shaped vesicles, toroidal vesicles, genus-3 (G-3) toroidal vesicles with three holes, and genus-4 (G-4) toroidal vesicles with four holes. In addition, both the self-assembly mechanisms and the dynamics for the formation of these vesicles have been systematically studied. The current work will offer theoretical support for fabricating novel vesicles with various shapes from hyperbranched polymers.

H-Aggregation Effects between π-Conjugated Chromophores in Cofacial Dimers and Trimers: Comparison of Theory and Single-Molecule Experiment

Excited-state interchromophoric couplings in π-conjugated polymers present a daunting challenge to study as their spectroscopic signatures are difficult to separate from structure-dependent intrachromophoric spectral characteristics. Using custom-designed molecular model systems in combination with single-molecule spectroscopy, a controlled coupling of the excited states between cofacially arranged π-conjugated oligomers is shown to be possible. Multiscale molecular dynamics simulations allow us to generate a representative ensemble of molecular structures of the model molecule embedded in a polymer matrix and examine the connection between structural fluctuations of the molecule with theoretically predicted and measured spectral signatures. The single molecules in the embedding matrix polymer can be assigned to specific conformational features with the help of computer-based "virtual spectroscopy". By combining a quantum chemical approach with an analytical approach, we show that the coupling between the chromophores is well-described by transition dipole coupling above an interchromophoric separation of ∼4.5 Å. Even for aligned chromophores, however, twisting between repeat units of the π-system and bending of the individual π-systems can lead to a decoupling of the chromophores to a degree far beyond what their equilibrium structures would suggest: tiny displacements of the molecular constituents can dramatically impact excited-state interactions. This observation has profound implications for the design of future tunable organic optoelectronic materials.

The folding pathways and thermodynamics of semiflexible polymers

Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm. However, the population of the intermediates in the unfolding process is very low, insufficient to induce unfolding arm rollover. The total types of folding pathways from the coil state to the toroidal state for a semiflexible polymer chain remain unchanged by varying the solvent quality or temperature, whereas the kinetic partitioning into different folding events can be tuned significantly. In the process of knotting, three types of mechanisms, namely, plugging, slipknotting, and sliding, are discovered. Along the folding evolution, a semiflexible homopolymer chain can knot at any stage of folding upon leaving the extended coil state, and the probability to find a knot increases with chain compactness. In addition, we find rich types of knotted topologies during the folding of a semiflexible homopolymer chain. This study should be helpful in gaining insight into the general principles of biopolymer folding.

Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding

The megabase-sized length of chromatin is highly relevant to the state of chromatin in vivo, where it is subject to a highly crowded environment and is organized in topologically associating domains of similar dimension. We developed an in vitro experimental chromatin model system reconstituted from T4 DNA (approximately 166 kbp) and histone octamers and studied the monomolecular compaction of this megabase-sized chromatin fiber under the influence of macromolecular crowding. We used single-molecule fluorescence microscopy and observed compaction in aqueous solutions containing poly(ethylene glycol) in the presence of monovalent (Na+ and K+) and divalent (Mg2+) cations. Both DNA and chromatin demonstrated compaction under comparable conditions in the presence of poly(ethylene glycol) and Na+ or Mg2+ salt. However, the mechanism of the compaction changed from a first-order phase transition for DNA to a continuous folding for megabase-sized chromatin fibers. A more efficient and pronounced chromatin compaction was observed in the presence of Na+ compared to K+. A flow-stretching technique to unfold DNA and chromatin coils was used to gain further insight into the morphology of partially folded chromatin fibers. The results revealed a distribution of partially folded chromatin fibers. This variability is likely the result of the heterogeneous distribution of nucleosomes on the DNA chain. The packaging of DNA in the form of chromatin in the crowded nuclear environment appears essential to ensure gradual conformational changes of DNA.

Single-molecule compaction of megabase-long chromatin molecules by multivalent cations

To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.

Reporting pH-sensitive drug releaseviaunpaired spin fluorescence silencing

We pioneer an approach for the visualization of a self-reporting pH-controlled molecular release of a fluorescent drug from a nitroxide polymer scaffold.

Toroidal Condensates by Semiflexible Polymer Chains: Insights into Nucleation, Growth and Packing Defects

Deciphering the principles of DNA condensation is important to understand problems such as genome packing and DNA compaction for delivery in gene therapy. DNA molecules condense into toroids and spindles upon the addition of multivalent ions. Nucleation of a loop in the semiflexible DNA chain is critical for both the toroid and spindle formation. To understand the structural differences in the nucleated loop, which cause bifurcation in the condensation pathways leading to toroid or spindle formation, we performed molecular dynamics simulations using a coarse-grained bead-spring polymer model. We find that the formation of a toroid or a spindle is correlated with the orientation of the chain segments close to the loop closure in the nucleated loop. Simulations show that toroids grow in size when spindles in solution interact with a pre-existing toroid and merge into it by spooling around the circumference of the toroid, forming multimolecular toroidal condensates. The merging of spindles with toroids is facile, indicating that this should be the dominant pathway through which the toroids grow in size. The Steinhardt bond order parameter analysis of the toroid cross section shows that the chains pack in a hexagonal fashion. In agreement with the experiments there are regions in the toroid with good hexagonal packing and also with considerable disorder. The disorder in packing is due to the defects, which are propagated during the growth of toroids. In addition to the well-known crossover defect, we have identified three other forms of defects, which perturb hexagonal packing. The new defects identified in the simulations are amenable to experimental verification.

Lagrangian Modeling of Turbulent Dispersion from Instantaneous Point Sources at the Center of a Turbulent Flow Channel

The paper is focused on the simulation and modeling of the dispersion from an instantaneous source of heat or mass located at the center of a turbulent flow channel. The flow is modeled with a direct numerical simulation, and the dispersion is modeled with Lagrangian methods based on Lagrangian scalar tracking (LST). The LST technique allows the simulation of scalar sources that span a range of Prandtl or Schmidt numbers that cover orders of magnitude. The trajectories of individual heat or mass markers are tracked, generating a probability distribution function that describes the behavior of instantaneous point sources of a scalar in the turbulent field. The effect of the Prandtl or Schmidt number on turbulent dispersion is examined, with emphasis on the dispersion pattern. Results for Prandtl or Schmidt numbers between 0.1 and 15,000 are presented. For an instantaneous source at the channel center, it is found that there are two zones of cloud development: one where molecular diffusion plays a role at very small times (early stage of the dispersion), and one where turbulent convection dominates. The asphericity of the scalar marker cloud is found to increase monotonically, in contrast to published results for isotropic, homogenous turbulence, where the asphericity goes through a maximum.

On the Pseudo Phase Diagram of Single Semi-Flexible Polymer Chains: A Flat-Histogram Monte Carlo Study

Local stiffness of polymer chains is instrumental in all structure formation processes of polymers, from crystallization of synthetic polymers to protein folding and DNA compactification. We present Stochastic Approximation Monte Carlo simulations-a type of flat-histogram Monte Carlo method-determining the density of states of a model class of single semi-flexible polymer chains, and, from this, their complete thermodynamic behavior. The chains possess a rich pseudo phase diagram as a function of stiffness and temperature, displaying non-trivial ground-state morphologies. This pseudo phase diagram also depends on chain length. Differences to existing pseudo phase diagrams of semi-flexible chains in the literature emphasize the fact that the mechanism of stiffness creation matters.

Dilute Semiflexible Polymers with Attraction: Collapse, Folding and Aggregation

We review the current state on the thermodynamic behavior and structural phases of self- and mutually-attractive dilute semiflexible polymers that undergo temperature-driven transitions. In extreme dilution, polymers may be considered isolated, and this single polymer undergoes a collapse or folding transition depending on the internal structure. This may go as far as to stable knot phases. Adding polymers results in aggregation, where structural motifs again depend on the internal structure. We discuss in detail the effect of semiflexibility on the collapse and aggregation transition and provide perspectives for interesting future investigations.

Diagram of states and morphologies of flexible-semiflexible copolymer chains: A Monte Carlo simulation

A single copolymer chain consisting of multiple flexible (F) and semiflexible (S) blocks has been studied using a continuum bead-spring model by Stochastic Approximation Monte Carlo simulations, which determine the density of states of the model. The only difference between F and S blocks is the intramolecular bending potential, all non-bonded interactions are equal. The state diagrams for this class of models display multiple nematic phases in the collapsed state, characterized through a demixing of the blocks of different stiffness and orientational ordering of the stiff blocks. We observe dumbbell-like morphologies, lamellar phases, and for the larger block lengths also Saturn-like structures with a core of flexible segments and the stiff segments forming a ring around the core.

Nanovoid formation and mechanics: a comparison of poly(dicyclopentadiene) and epoxy networks from molecular dynamics simulations

Protective equipment in civilian and military applications requires the use of polymer materials that are both stiff and tough over a wide range of strain rates. However, typical structural materials, like tightly cross-linked epoxies, are very brittle. Recent experiments demonstrated that cross-linked poly(dicyclopentadiene) (pDCPD) networks can circumvent this trade-off by providing structural properties such as a high glass transition temperature and glassy modulus, while simultaneously exhibiting excellent toughness and high-rate impact resistance. The greater performance of pDCPD was attributed to more facile plastic deformation and nano-scale void formation, but the chemical and structural mechanisms underlying this response were not clear. Here, we use atomistic molecular dynamics to compare the molecular- and chain-level properties of pDCPD and epoxy networks undergoing high strain rate deformation. We quantify the tensile modulus and yield strength of the networks as well as the prevalence and characteristics of nanovoids that form during deformation. Networks of similar molecular weight between cross-links are compared. Two key molecular-level properties are identified - monomer flexibility and polar chemistry - that influence the behavior of the networks. Increasing monomer flexibility reduces the modulus and yield strength, while strong non-covalent interactions (e.g., hydrogen bonds) that accompany polar moieties provide higher modulus and yield strength. The lack of strong non-covalent interactions in pDCPD was found to account for its lower modulus and yield strength compared to the epoxies. We examine the molecular-level properties of nanovoids, such as shape, alignment, and local stress distribution, as well as the local chemical environment, finding that nanovoid formation and growth are increased by the monomer rigidity but decreased by polar chemistry. As a result, the pDCPD network, which has a stiff chain backbone with nonpolar alkane chemistry, exhibits more and larger nanovoids that grow more readily during deformation, which could account for the higher toughness and more ductile behavior observed in pDCPD.

Equilibrium self-assembly of small RNA viruses

We propose a description for the quasiequilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordered tails that associate with the negatively charged RNA genome molecules. We describe the assembly of such viruses as the interplay between two coupled phase-transition-like events: the formation of the protein shell (the capsid) by CPs and the condensation of a large ss viral RNA molecule. Electrostatic repulsion between the CPs competes with attractive hydrophobic interactions and attractive interaction between neutralized RNA segments mediated by the tail groups. An assembly diagram is derived in terms of the strength of attractive interactions between CPs and between CPs and the RNA molecules. It is compared with the results of recent studies of viral assembly. We demonstrate that the conventional theory of self-assembly, which does describe the assembly of empty capsids, is in general not applicable to the self-assembly of RNA-encapsidating virions.

Conformations of Low-Molecular-Weight Lignin Polymers in Water

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.

Thermodynamics and structure of macromolecules from flat-histogram Monte Carlo simulations

Over the last decade flat-histogram Monte Carlo simulations, especially multi-canonical and Wang-Landau simulations, have emerged as a strong tool to study the statistical mechanics of polymer chains. These investigations have focused on coarse-grained models of polymers on the lattice and in the continuum. Phase diagrams of chains in bulk as well as chains attached to surfaces were studied, for homopolymers as well as for protein-like models. Also, aggregation behavior in solution of these models has been investigated. We will present here the theoretical background for these simulations, explain the algorithms used and discuss their performance and give an overview over the systems studied with these methods in the literature, where we will limit ourselves to studies of coarse-grained model systems. Implementations of these algorithms on parallel computers will be also briefly described. In parallel to the development of these simulation methods, the power of a micro-canonical analysis of such simulations has been recognized, and we present the current state of the art in applying the micro-canonical analysis to phase transitions in nanoscopic polymer systems.

Coil-globule transition of a single semiflexible chain in slitlike confinement

Single polymer chains undergo a phase transition from coiled conformations to globular conformations as the effective attraction between monomers becomes strong enough. In this work, we investigated the coil-globule transition of a semiflexible chain confined between two parallel plates, i.e. a slit, using the lattice model and Pruned-enriched Rosenbluth method (PERM) algorithm. We find that as the slit height decreases, the critical attraction for the coil-globule transition changes non-monotonically due to the competition of the confinement free energies of the coiled and globular states. In wide (narrow) slits, the coiled state experiences more (less) confinement free energy, and hence the transition becomes easier (more difficult). In addition, we find that the transition becomes less sharp with the decreasing slit height. Here, the sharpness refers to the sensitivity of thermodynamic quantities when varying the attraction around the critical value. The relevant experiments can be performed for DNA condensation in microfluidic devices.

Theory and simulations of toroidal and rod-like structures in single-molecule DNA condensation

DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical condensation forces have been used to estimate the amplitude of the attractive DNA-DNA interactions. Here, to describe these experiments, we developed an analytical model and a rigid body Langevin dynamics assay to investigate the behavior of a polymer with self-interactions, in the presence of a traction force applied at its extremities. We model self-interactions using a pairwise attractive potential, thereby treating the counterions implicitly. The analytical model allows to accurately predict the equilibrium structures of toroidal and rod-like condensed structures, and the dependence of the critical condensation force on the DNA length. We find that the critical condensation force depends strongly on the length of the DNA, and finite-size effects are important for molecules of length up to 10(5)μm. Our Langevin dynamics simulations show that the force-extension behavior of the rod-like structures is very different from the toroidal ones, so that their presence in experiments should be easily detectable. In double-stranded DNA condensation experiments, the signature of the presence of rod-like structures was not unambiguously detected, suggesting that the polyamines used to condense DNA may protect it from bending sharply as needed in the rod-like structures.

Dissipative particle dynamics simulation study on self-assembly of amphiphilic hyperbranched multiarm copolymers with different degrees of branching

Hyperbranched multiarm copolymers (HMCs) have shown great potential to be excellent precursors in self-assembly to form various supramolecular structures in all scales and dimensions in solution. However, theoretical studies on the self-assembly of HMCs, especially the self-assembly dynamics and mechanisms, have been greatly lagging behind the experimental progress. Herein, we investigate the effect of degree of branching (DB) on the self-assembly structures of HMCs by dissipative particle dynamics (DPD) simulation. Our simulation results demonstrate that the self-assembly morphologies of HMCs can be changed from spherical micelles, wormlike micelles, to vesicles with the increase of DBs, which are qualitatively consistent with the experimental observations. In addition, both the self-assembly mechanisms and the dynamic processes for the formation of these three aggregates have been systematically disclosed through the simulations. These self-assembly details are difficult to be shown by experiments and are very useful to fully understand the self-assembly behaviors of HMCs.

Novel imaging technologies for characterization of microbial extracellular polysaccharides

Understanding of biology is underpinned by the ability to observe structures at various length scales. This is so in a historical context and is also valid today. Evolution of novel insight often emerges from technological advancement. Recent developments in imaging technologies that is relevant for characterization of extraceullar microbiological polysaccharides are summarized. Emphasis is on scanning probe and optical based techniques since these tools offers imaging capabilities under aqueous conditions more closely resembling the physiological state than other ultramicroscopy imaging techniques. Following the demonstration of the scanning probe microscopy principle, novel operation modes to increase data capture speed toward video rate, exploitation of several cantilever frequencies, and advancement of utilization of specimen mechanical properties as contrast, also including their mode of operation in liquid, have been developed on this platform. Combined with steps in advancing light microscopy with resolution beyond the far field diffraction limit, non-linear methods, and combinations of the various imaging modalities, the potential ultramicroscopy toolbox available for characterization of exopolysaccharides (EPS) are richer than ever. Examples of application of such ultramicroscopy strategies range from imaging of isolated microbial polysaccharides, structures being observed when they are involved in polyelectrolyte complexes, aspects of their enzymatic degradation, and cell surface localization of secreted polysaccharides. These, and other examples, illustrate that the advancement in imaging technologies relevant for EPS characterization supports characterization of structural aspects.

Chitosans for delivery of nucleic acids

Alternatives to efficient viral vectors in gene therapy are desired because of their poor safety profiles. Chitosan is a promising non-viral nucleotide delivery vector because of its biocompatibility, biodegradability, low immunogenicity and ease of manufacturing. Since the transfection efficiency of chitosan polyplexes is relatively low compared to viral counterparts, there is an impetus to gain a better understanding of the structure-performance relationship. Recent progress in preparation and characterisation has enabled coupling analysis of chitosans structural parameters that has led to increased TE by tailoring of chitosan's structure. In this review, we summarize the recent advances that have lead to a more rational design of chitosan polyplexes. We present an integrated review of all major areas of chitosan-based transfection, including preparation, chitosan and polyplexes physicochemical characterisation, in vitro and in vivo assessment. In each, we present the obstacles to efficient transfection and the strategies adopted over time to surmount these impediments.