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At least 649 records · Page 36

Synthesis and spectroscopic characterization of actinyl(VI) tetrahalide coordination compounds containing 2, 2'-bipyridine

A series of three new actinide tetrahalide coordination compounds containing 2,2'-bipyridinium (H 2 bpy) have been synthesized by room temperature evaporation and characterized via single crystal X-ray diffraction, Raman spectroscopy, and infrared spectroscopy. The solid-state compounds (Np1, U1, and U2) contain the AnO 2 2+ cation coordinated to four halide (chloride or bromide) atoms to form the anionic tetrahalide molecular unit [AnO 2 X 4 ] 2– (X = Cl, Br) and are charge balanced by the 2,2'-bipyridinium cations that engage in electrostatic interactions with the actinyl complex. Np1 (N 2 C 10 H 10 )[NpO 2 Cl 4 ] contains 2,2'-bipyridine in the cis conformation where both the nitrogen atoms are directed towards the [NpO 2 Cl 4 ] 2– monomer. Within U1 (N 2 C 10 H 9 )[UO 2 Cl 4 ], the 2,2'-bipyridine is in a trans conformation, and found in the same orientation in the isomorphous structure U2 (N 2 C 10 H 9 )[UO 2 Br 4 ]. The compounds were further characterized by vibrational spectroscopy with specific interest in the actinyl cation. Raman spectroscopy provided information on the actinyl symmetric stretch (ν 1 ) whereas IR spectroscopy is used to determine the location of the asymmetric stretch (ν 3 ). Here, spectral similarities are observed between the two isomorphous structures, but slight variations across the series of structures are found to be associated with bipyridine bands in the various conformations. Additional analysis of these vibrational features in U1 and U2 provided information on the actinyl force constants, allowing insight into the relative uranyl bond strength that was compared to similar tetrahalide compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-Assembled Thermoresponsive Molecular Brushes as Nanoreactors for Asymmetric Aldol Addition in Water

The manipulation and tunability of self-assembled block copolymers through external stimuli presents an attractive strategy to develop smart polymer-based nanoreactors as supports for non-orthogonal tandem catalysis. We report on thermoresponsive core-shell micelles based on poly[norbornene-poly(2-methyl-2-oxazoline-block-2-propyl-2-oxazoline)]-graft-poly[norbornene L-proline] (P[NB-P(MeOx-b-PropOx)]-graft-P[NB-L-proline]) as catalyst supports for L-proline. These molecular brushes exhibit large differences in lower critical solution temperature behavior and nanostructure size in water depending on the chain-lengths and proline connectivity. L-Proline-mediated aldol reactions expose the efficiency by which the molecular brushes self-assemble into micelles. Molecular brushes with an extended backbone show higher activity and selectivity, suggesting better core-shell segregation of the micelles and exclusion of water from the catalytic site. Catalytic efficiencies are not improved above the cloud point temperature, the catalytic be-havior is rather sensitive to conformational changes of the polymer chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-Based Design of Dual Bactericidal and Bacteria-Releasing Nanosurfaces

Here, we report synergistic nanostructured surfaces combining bactericidal and bacteria-releasing properties. A polystyrene-block-poly(methyl methacrylate) (PS-block-PMMA) diblock copolymer is used to fabricate vertically oriented cylindrical PS structures (“PS nanopillars”) on silicon substrates. The results demonstrate that the PS nanopillars (with a height of about 10 nm, size of about 50 nm, and spacing of about 70 nm) exhibit highly effective bactericidal and bacteria-releasing properties (“dual properties”) against Escherichia coli for at least 36 h of immersion in an E. coli solution. Interestingly, the PS nanopillars coated with a thin layer (≈3 nm thick) of titanium oxide (TiO 2 ) (“TiO 2 nanopillars”) show much improved dual properties against E. coli (a Gram-negative bacterium) compared to the PS nanopillars. Moreover, the dual properties emerge against Listeria monocytogenes (a Gram-positive bacterium). To understand the mechanisms underlying the multifaceted property of the nanopillars, coarse-grained molecular dynamics (MD) simulations of a lipid bilayer (as a simplified model for E. coli) in contact with a substrate containing hexagonally packed hydrophilic nanopillars were performed. The MD results demonstrate that when the bacterium–substrate interaction is strong, the lipid heads adsorb onto the nanopillar surfaces, conforming the shape of a lipid bilayer to the structure/curvature of nanopillars and generating high stress concentrations within the membrane (i.e., the driving force for rupture) at the edge of the nanopillars. Membrane rupture begins with the formation of pores between nanopillars (i.e., bactericidal activity) and ultimately leads to the membrane withdrawal from the nanopillar surface (i.e., bacteria-releasing activity). In the case of Gram-positive bacteria, the adhesion area to the pillar surface is limited due to the inherent stiffness of the bacteria, creating higher stress concentrations within a bacterial cell wall. In conclusion, the present study provides insight into the mechanism underlying the “adhesion-mediated” multifaceted property of nanosurfaces, which is crucial for the development of next-generation antibacterial surface coatings for relevant medical applications.

36 MATERIALS SCIENCE↗

Brominated lipid probes expose structural asymmetries in constricted membranes

Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.

59 BASIC BIOLOGICAL SCIENCES↗

On the use of NMR distance measurements for assessing surface site homogeneity

The past few decades have seen tremendous growth in the area of single-site heterogeneous catalysis, which aims to combine the best aspects of homogeneous and heterogeneous catalysis, namely molecular-level site control and ease of separation/recycling. Despite this, we still do not have a means of assessing site homogeneity and whether the produced catalyst is indeed a “single-site”. Recent developments have enabled the use of NMR-based distance measurements to determine the conformations and configurations of surface sites, leading to the question whether such measurements can be used to distinguish materials containing either single or multiple surface sites with otherwise indistinguishable NMR properties. Here, we describe a Monte Carlo-based multi-structure search algorithm and its application to the determination of multi-site structures from supported metal complexes. The sensitivity of REDOR data to the existence of multiple sites is assessed using synthetic data and prior literature examples are revisited to determine whether the single-site approximation was indeed appropriate. We lastly apply this new methodology to differentiate the configurations of zirconocene complexes grafted onto alumina supports that were thermally treated at different temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding the Impacts of Support–Polymer Interactions on the Dynamics of Poly(ethyleneimine) Confined in Mesoporous SBA-15

Supported amines are a promising class of CO 2 sorbents offering large uptake capacities and fast uptake rates. Additionally, among supported amines, poly(ethyleneimine) (PEI) physically impregnated in the mesopores of SBA-15 silica is widely used. Within these composite materials, the chain dynamics and morphologies of PEI strongly influence the CO 2 capture performance, yet little is known about chain and macromolecule mobility in confined pores. Here, we probe the impact of the support–PEI interactions on the dynamics and structures of PEI at the support interface and the corresponding impact on CO 2 uptake performance, which yields critical structure–property relationships. The pore walls of the support are grafted with organosilanes with different chemical end groups to differentiate interaction modes (spanning from strong attraction to repulsion) between the pore surface and PEI. Combinations of techniques, such as quasi-elastic neutron scattering (QENS), 1 H T 1 –T 2 relaxation correlation solid-state NMR, and molecular dynamics (MD) simulations, are used to comprehensively assess the physical properties of confined PEI. We hypothesized that PEI would have faster dynamics when subjected to less attractive or repulsive interactions. However, we discover that complex interfacial interactions resulted in complex structure–property relationships. Indeed, both the chain conformation of the surface-grafted chains and of the PEI around the surface influenced the chain mobility and CO 2 uptake performance. By coupling knowledge of the dynamics and distributions of PEI with CO 2 sorption performance and other characteristics, we determine that the macroscopic structures of the hybrid materials dictate the first rapid CO 2 uptake, and the rate of CO 2 sorption during the subsequent gradual uptake stage is determined by PEI chain motions that promote diffusive jumps of CO 2 through PEI-packed domains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic/molecular layer deposition for energy storage and conversion

Energy storage and conversion systems, including batteries, supercapacitors, fuel cells, solar cells, and photoelectrochemical water splitting, have played vital roles in the reduction of fossil fuel usage, addressing environmental issues and the development of electric vehicles. The fabrication and surface/interface engineering of electrode materials with refined structures are indispensable for achieving optimal performances for the different energy-related devices. Atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques, the gas-phase thin film deposition processes with self-limiting and saturated surface reactions, have emerged as powerful techniques for surface and interface engineering in energy-related devices due to their exceptional capability of precise thickness control, excellent uniformity and conformity, tunable composition and relatively low deposition temperature. In the past few decades, ALD and MLD have been intensively studied for energy storage and conversion applications with remarkable progress. In this work, we give a comprehensive summary of the development and achievements of ALD and MLD and their applications for energy storage and conversion, including batteries, supercapacitors, fuel cells, solar cells, and photoelectrochemical water splitting. Moreover, the fundamental understanding of the mechanisms involved in different devices will be deeply reviewed. Furthermore, the large-scale potential of ALD and MLD techniques is discussed and predicted. Finally, we will provide insightful perspectives on future directions for new material design by ALD and MLD and untapped opportunities in energy storage and conversion.

25 ENERGY STORAGE↗

Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

60 APPLIED LIFE SCIENCES↗

Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements

Residing in the 5' untranslated region of the mRNA, the 2'-deoxyguanosine (2'-dG) riboswitch mRNA element adopts an alternative structure upon binding of the 2'-dG molecule, which terminates transcription. RNA conformations are generally strongly affected by positively charged metal ions (especially Mg 2+ ). We have quantitatively explored the combined effect of ligand (2'-dG) and Mg 2+ binding on the energy landscape of the aptamer domain of the 2'-dG riboswitch with both explicit solvent all-atom molecular dynamics simulations (99 μsec aggregate sampling for the study) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments. We show that both ligand and Mg 2+ are required for the stabilization of the aptamer domain; however, the two factors act with different modalities. The addition of Mg 2+ remodels the energy landscape and reduces its frustration by the formation of additional contacts. In contrast, the binding of 2'-dG eliminates the metastable states by nucleating a compact core for the aptamer domain. Mg 2+ ions and ligand binding are required to stabilize the least stable helix, P1 (which needs to unfold to activate the transcription platform), and the riboswitch core formed by the backbone of the P2 and P3 helices. Mg 2+ and ligand also facilitate a more compact structure in the three-way junction region.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of the Impact of Lipid Acyl Chain Saturation on Fusion Peptide Interactions with Lipid Bilayers

The interaction of many peptides with lipid bilayer membranes strongly depends on the lipid composition. Here, a study of the impact of unsaturated lipid acyl chains on the interaction of a derivative of the HIV-1 fusion peptide with lipid bilayer vesicles is presented. Lipid bilayer vesicles composed of mixtures of lipids with two saturated acyl chains and lipids and one saturated and one unsaturated acyl chain, but identical head groups, were studied. The dependence of the peptide conformation on the unsaturated lipid content was probed by circular dichroism spectroscopy, while the impact of the peptide on the bilayer structure was determined by small-angle neutron scattering. The impact of the peptide on the lipid bilayer vesicle dynamics was investigated using neutron spin echo spectroscopy. Molecular dynamics simulations were used to characterize the behavior of the systems studied to determine if there were clear differences in their physical properties. The results reveal that the peptide–bilayer interaction is not a simple function of the unsaturated lipid acyl chain content of the bilayer. Instead, the peptide behavior is more consistent with that seen for the bilayer containing only unsaturated lipids, which is supported by lipid-specific interactions revealed by the simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Mobile barrier mechanisms for Na + -coupled symport in an MFS sugar transporter

While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na + -bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.

59 BASIC BIOLOGICAL SCIENCES↗

Recent evidence for evolution of the genetic code

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

Review↗

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular Dynamics of a Water-Lipid Bilayer Interface

We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

Wilson, Michael A.↗

Comparison of Oxygen Gauche Effects in Poly(Oxyethylene) and Poly(ethylene terephtylene) Based on Quantum Chemistry Calculations

The so-called oxygen gauche effect in poly(oxyethylene) (POE) and its model molecules such as 1,2-dimethoxyethane (DME) and diglyme (CH3OC2H4OC2H4OCH3) is manifested in the preference for gauche C-C bond conformations over trans. This has also been observed for poly(ethylene terephthalate) (PET). Our previous quantum chemistry calculations demonstrated that the large C-C gauche population in DME is due, in part, to a low-lying tg +/- g+ conformer that exhibits a substantial 1,5 CH ... O attraction. New calculations will be described that demonstrate the accuracy of the original quantum chemistry calculations. In addition, an extension of this work to model molecules for PET will be presented. It is seen that the C-C gauche preference is much stronger in 1,2 diacetoxyethane than in DME. In addition, there exist low-lying tg +/- g+/- and g+/-g+/-g+/- conformers that exhibit 1,5 CH ... O attractions involving the carbonyl oxygens. It is expected that the -O-C-C-O- torsional properties will be quite different in these two polymers. The quantum chemistry results are used to parameterize rotational isomeric states models (RIS) and force fields for molecular dynamics simulations of these polymers.

Jaffe, Richard↗