Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Luminogenic materials with aggregation-induced emission (AIE) attributes have attracted much interest since the debut of the AIE concept in 2001. In this critical review, recent progress in the area of AIE research is summarized. Typical examples of AIE systems are discussed, from which their structure–property relationships are derived. Through mechanistic decipherment of the photophysical processes, structural design strategies for generating new AIE luminogens are developed. Technological, especially optoelectronic and biological, applications of the AIE systems are exemplified to illustrate how the novel AIE effect can be utilized for high-tech innovations (183 references).

Aggregation-induced emission

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

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Cellulose nanomaterials review: structure, properties and nanocomposites

Cellulose constitutes the most abundant renewable polymer resource available today. As a chemical raw material, it is generally well-known that it has been used in the form of fibers or derivatives for nearly 150 years for a wide spectrum of products and materials in daily life. What has not been known until relatively recently is that when cellulose fibers are subjected to acid hydrolysis, the fibers yield defect-free, rod-like crystalline residues. Cellulose nanocrystals (CNs) have garnered in the materials community a tremendous level of attention that does not appear to be relenting. These biopolymeric assemblies warrant such attention not only because of their unsurpassed quintessential physical and chemical properties (as will become evident in the review) but also because of their inherent renewability and sustainability in addition to their abundance. They have been the subject of a wide array of research efforts as reinforcing agents in nanocomposites due to their low cost, availability, renewability, light weight, nanoscale dimension, and unique morphology. Indeed, CNs are the fundamental constitutive polymeric motifs of macroscopic cellulosic-based fibers whose sheer volume dwarfs any known natural or synthetic biomaterial. Biopolymers such as cellulose and lignin and † North Carolina State University. ‡ Helsinki University of Technology. Dr. Youssef Habibi is a research assistant professor at the Department of Forest Biomaterials at North Carolina State University. He received his Ph.D. in 2004 in organic chemistry from Joseph Fourier University (Grenoble, France) jointly with CERMAV (Centre de Recherche sur les Macromolecules Vegetales) and Cadi Ayyad University (Marrakesh, Morocco). During his Ph.D., he worked on the structural characterization of cell wall polysaccharides and also performed surface chemical modification, mainly TEMPO-mediated oxidation, of crystalline polysaccharides, as well as their nanocrystals. Prior to joining NCSU, he worked as assistant professor at the French Engineering School of Paper, Printing and Biomaterials (PAGORA, Grenoble Institute of Technology, France) on the development of biodegradable nanocomposites based on nanocrystalline polysaccharides. He also spent two years as postdoctoral fellow at the French Institute for Agricultural Research, INRA, where he developed new nanostructured thin films based on cellulose nanowiskers. Dr. Habibi’s research interests include the sustainable production of materials from biomass, development of high performance nanocomposites from lignocellulosic materials, biomass conversion technologies, and the application of novel analytical tools in biomass research. Chem. Rev. 2010, 110, 3479–3500 3479

Cellulose nanocrystals: chemistry, self-assembly, and applications.

Detection of chemical and biological agents plays a fundamental role in biomedical, forensic and environmental sciences1–4 as well as in anti bioterrorism applications.5–7 The development of highly sensitive, cost effective, miniature sensors is therefore in high demand which requires advanced technology coupled with fundamental knowledge in chemistry, biology and material sciences.8–13

In general, sensors feature two functional components: a recognition element to provide selective/specific binding with the target analytes and a transducer component for signaling the binding event. An efficient sensor relies heavily on these two essential components for the recognition process in terms of response time, signal to noise (S/N) ratio, selectivity and limits of detection (LOD).14,15 Therefore, designing sensors with higher efficacy depends on the development of novel materials to improve both the recognition and transduction processes. Nanomaterials feature unique physicochemical properties that can be of great utility in creating new recognition and transduction processes for chemical and biological sensors15–27 as well as improving the S/N ratio by miniaturization of the sensor elements.28

Gold nanoparticles (AuNPs) possess distinct physical and chemical attributes that make them excellent scaffolds for the fabrication of novel chemical and biological sensors (Figure 1).29–36 First, AuNPs can be synthesized in a straightforward manner and can be made highly stable. Second, they possess unique optoelectronic properties. Third, they provide high surface-to-volume ratio with excellent biocompatibility using appropriate ligands.30 Fourth, these properties of AuNPs can be readily tuned varying their size, shape and the surrounding chemical environment. For example, the binding event between recognition element and the analyte can alter physicochemical properties of transducer AuNPs, such as plasmon resonance absorption, conductivity, redox behavior, etc. that in turn can generate a detectable response signal. Finally, AuNPs offer a suitable platform for multi-functionalization with a wide range of organic or biological ligands for the selective binding and detection of small molecules and biological targets.30–32,36 Each of these attributes of AuNPs has allowed researchers to develop novel sensing strategies with improved sensitivity, stability and selectivity. In the last decade of research, the advent of AuNP as a sensory element provided us a broad spectrum of innovative approaches for the detection of metal ions, small molecules, proteins, nucleic acids, malignant cells, etc. in a rapid and efficient manner.37



Figure 1

Physical properties of AuNPs and schematic illustration of an AuNP-based detection system.



In this current review, we have highlighted the several synthetic routes and properties of AuNPs that make them excellent probes for different sensing strategies. Furthermore, we will discuss various sensing strategies and major advances in the last two decades of research utilizing AuNPs in the detection of variety of target analytes including metal ions, organic molecules, proteins, nucleic acids, and microorganisms.

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Gold nanoparticles in chemical and biological sensing.

Liquid condensates are membraneless organelles that form via phase separation in living cells. These condensates provide unique heterogeneous environments that have much potential in regulating a range of biochemical processes from gene expression to ﬁlamentous protein aggregation—a process linked to Alzheimer’s and Parkinson’s diseases. Here we theoretically study the physical interplay between protein aggregation, its inhibition, and liquid-liquid phase separation. Our key ﬁnding is that the action of protein aggregation inhibitors can be strongly enhanced by liquid condensates. The physical mechanism of this enhancement relies on the partitioning and colocalization of inhibitors with their targets inside the liquid condensate. Our theory uncovers how the physicochemical properties of condensates can be used to modulate inhibitor potency, and we provide experimentally testable conditions under which drug potency is maximal. Our ﬁndings suggest design principles for protein aggregation inhibitors with respect to their phase-separation properties. DOI

/pdf/enhanced-potency-of-aggregation-inhibitors-mediated-by-1vntohkg.pdf

Enhanced potency of aggregation inhibitors mediated by liquid condensates

Recent experimental studies suggest that wet-dry cycles and coexisting phases can each strongly alter chemical processes. The mechanisms of why and to which degree chemical processes are altered when subject to evaporation and condensation are unclear. To close this gap, we developed a theoretical framework for non-dilute chemical reactions subject to non-equilibrium conditions of evaporation or condensation. We find that evaporation and condensation can each accelerate the initial rate of chemical processes by more than an order of magnitude, depending on the substrate-solvent interaction. When maintaining the system out of equilibrium by wet-dry cycles, the cycle frequency controls the chemical turnover. Strikingly, there is resonance behavior in the cycle frequency where the turnover is maximal. This resonance behavior enables wet-dry cycles to select specific chemical reactions suggesting a potential mechanism for chemical evolution in prebiotic soups at early Earth.

Wet-dry cycles away from equilibrium catalyse chemical reactions

Formation of biomolecular condensates via phase separation enables compartmentation of many cellular processes. However, how cells can control condensation at specific locations to create complex cellular structures remains poorly understood. Here, we investigated the mechanism of tight junction formation, which involves condensation of scaffold proteins at cell-cell contacts and elongation of the condensates into a belt around the cellular perimeter. Using cell biology, reconstitution, and thermodynamic theory, we discovered that cells use surface phase transitions to control local condensation at the membrane far below bulk saturation. Surface condensation of junctional ZO-scaffold proteins is mediated by receptor binding and regulated by the receptor’s oligomerization state. Functionally, ZO surface condensation is directly coupled to actin polymerization and bundling, which drives elongation of receptor-ZO-actin condensates similar to tight junction belt formation in cells. We conclude that surface phase transitions provide a robust mechanism to control the position and shape of protein condensates. One-Sentence Summary Local surface binding of cytosolic scaffold proteins provides spatial control of protein condensation to assemble adhesion junctions.

https://www.biorxiv.org/content/biorxiv/early/2023/06/26/2023.06.24.546380.full.pdf

Assembly of tight junction belts by surface condensation and actin elongation

Supramolecular polymers (SPs) are assemblies of monomers that bind to another through non-covalent interactions. The reversible nature of these interactions permits one to temporarily disassemble SPs “on command” by applying an appropriate stimulus, which is advantageous for processing and recycling and allows creating stimuli-responsive materials. Here we report on the dielectric properties of an SP network assembled from monomers based on polypropylene oxide (PPO) cores, functionalized with UPy groups. In this work, we measured the DC breakdown strength, dielectric relaxation and electrical conductivity and show that the dielectric properties are similar to those of silicones or silicon-based adhesives. However, the material is reprocessable, thus has a potential for medium voltage applications, within the context of a circular economy.

Dielectric Properties of a Semicrystalline Supramolecular Polymer

Stimuli-responsive polymers are of great interest due to their ability to translate changing environmental conditions into responses in defined materials. One possibility to impart such behavior is the incorporation of optically active molecules into a polymer host. Here, we describe how sensor molecules that consist of a π-extended benzothiadiazole emitter and a naphthalene diimide quencher can be exploited in this context. The two optically active entities were connected via different spacers and, thanks to attractive intramolecular interactions between them, the new sensor molecules assembled into cyclic structures in which the fluorescence was quenched by up to 43% when compared to solutions of the individual dyes. Detailed spectroscopic investigations of the sensor molecules in solution show that the extent of donor/acceptor interactions is influenced by various factors, including solvent polarity and ion concentration. The new sensor molecule was covalently incorporated into a polyurethane; the investigation of the optical characteristics in both the solid and solvent-swollen states indicates that a stimulus-induced formation of associated dye pairs is possible in polymeric materials. Indeed, a solvatochromic quenching effect similar to the behavior in solution was observed for solvent-swollen polymer samples, leading to an effective change of the green emission color of the dye to a yellow color.

/pdf/supramolecular-rings-as-building-blocks-for-stimuli-2zck91ly.pdf

Christoph Weder

Papers

Enhanced potency of aggregation inhibitors mediated by liquid condensates

Wet-dry cycles away from equilibrium catalyse chemical reactions

Assembly of tight junction belts by surface condensation and actin elongation

Dielectric Properties of a Semicrystalline Supramolecular Polymer

Supramolecular Rings as Building Blocks for Stimuli-Responsive Materials