Biological Matter Research Articles

Consistently inconsistent: The false promise of ‘sustainable’ plastics

Abstract This perspective explains why the lack of regulation around bioplastics remains a hurdle for the successful development and implementation of a legally binding agreement (the Global Plastics Treaty) by the United Nations Environment Assembly to curb plastic pollution by 2024. For example, bioplastics have been marketed to consumers as the panacea solution to our plastic waste crisis. Of the >400 million tonnes of plastics produced each year, <1% are bioplastics, but the market value of bioplastics is expected to grow. The rapid growth of the environmentally ‘sustainable’ plastic market has resulted in an overwhelming variety of products with different properties and labels, which has led to widespread public confusion, particularly about disposal guidelines. The umbrella term of ‘bioplastics’ describes plastics that can be fully or partially sourced from biological matter, unlike conventional petroleum-based plastics. Within this family of plastics, products can be ‘biodegradable’, ‘oxo-biodegradable’ and ‘compostable’ depending on their chemical composition and the external conditions required at disposal (end-of-life). However, cases of petroleum-based biodegradable plastics have been referred to as bioplastics, which is inaccurate. Overall, this lack of regulation remains a hurdle for the successful development and implementation of the Global Plastics Treaty.

Jamming on convex deformable surfaces.

Jamming is a fundamental transition that governs the behavior of particulate media, including sand, foams and dense suspensions. Upon compression, such media change from freely flowing to a disordered, marginally stable solid that exhibits non-Hookean elasticity. While the jamming process is well established for fixed geometries, the nature and dynamics of jamming for a diverse class of soft materials and deformable substrates, including emulsions and biological matter, remains unknown. Here we propose a new scenario, metric jamming, where rigidification occurs on a surface that has been deformed from its ground state. Unlike classical jamming processes that exhibit discrete mechanical transitions, surprisingly we find that metric jammed states possess mechanical properties continuously tunable between those of classically jammed and conventional elastic media. The compact and curved geometry significantly alters the vibrational spectra of the structures relative to jamming in flat Euclidean space, and metric jammed systems also possess new types of vibrational mode that couple particle and shape degrees of freedom. Our work provides a theoretical framework that unifies our understanding of solidification processes that take place on deformable media and lays the groundwork to exploit jamming for the control and stabilization of shape in self-assembly processes.

Meiofauna at a tropical sandy beach in the SW Atlantic: the influence of seasonality on diversity.

Sandy beaches are dynamic environments housing a large diversity of organisms and providing important environmental services. Meiofaunal metazoan are small organisms that play a key role in the sediment. Their diversity, distribution and composition are driven by sedimentary and oceanographic parameters. Understanding the diversity patterns of marine meiofauna is critical in a changing world. In this study, we investigate if there is seasonal difference in meiofaunal assemblage composition and diversity along 1 year and if the marine seascapes dynamics (water masses with particular biogeochemical features, characterized by temperature, salinity, absolute dynamic topography, chromophoric dissolved organic material, chlorophyll-a, and normalized fluorescent line height), rainfall, and sediment parameters (total organic matter, carbonate, carbohydrate, protein, lipids, protein-to-carbohydrate, carbohydrate-to-lipids, and biopolymeric carbon) affect significatively meiofaunal diversity at a tropical sandy beach. We tested two hypotheses here: (i) meiofaunal diversity is higher during warmer months and its composition changes significatively among seasons along a year at a tropical sandy beach, and (ii) meiofaunal diversity metrics are significantly explained by marine seascapes characteristics and sediment parameters. We used metabarcoding (V9 hypervariable region from 18S gene) from sediment samples to assess the meiofaunal assemblage composition and diversity (phylogenetic diversity and Shannon's diversity) over a period of 1 year. Meiofauna was dominated by Crustacea (46% of sequence reads), Annelida (28% of sequence reads) and Nematoda (12% of sequence reads) in periods of the year with high temperatures (>25 °C), high salinity (>31.5 ppt), and calm waters. Our data support our initial hypotheses revealing a higher meiofaunal diversity (phylogenetic and Shannon's Diversity) and different composition during warmer periods of the year. Meiofaunal diversity was driven by a set of multiple variables, including biological variables (biopolymeric carbon) and organic matter quality (protein content, lipid content, and carbohydrate-to-lipid ratio).

BioForms: 3-D printed mycelium wall panel systems

Abstract BioForms integrates sacrificial formworks, agent-based computational algorithms and biological growth in the generation of biodegradable internal wall panel systems. These wall panel systems are intended to minimize material waste, utilize local botany and generate a symbiosis between the artificially made and the naturally grown. This is achieved by utilizing local waste as a structural compressive core, mycelium as the binder, and recycled pellets as the architectural skin. Leveraging mycelium’s structural, acoustic and thermal properties, this exploration delves into unique methods of incorporating fungi and waste into architectural construction. The motivations for this research stem from the need to address the building industry’s contribution to climate change, by considering the lifecycle of our materials. BioForms aims to retrofit existing buildings by replacing foam insulation and MDF (medium-density fiberboard) wall panels with biodegradable and recyclable 3D-printed skins embedded with a mycelium core. Analysing mycelium’s reaction to BioForms I, the second iteration, BioForms II, evolves in design complexity and materiality. BioForms II explored robotically fabricated wood-based polylactic acid plastic (PLA) composite materials. Within the second iteration of this research stream, mycelia was both embedded within the compressed fabricated skins and on the external surface. Whilst BioForms explored the generation of biodegradable wall panel systems, the broader aims of this research is aimed at infiltrating biological matter into human-occupied spaces, completely omitting the use of synthetic building materials within the construction industry and advancing the architects relationship to nature in the generation of form.

Water is a radiation protection agent for ionised pyrrole.

Radiation-induced damage of biological matter is an ubiquitous problem in nature. The influence of the hydration environment is widely discussed, but its exact role remains elusive. Utilising well defined solvated-molecule aggregates, we experimentally observed a hydrogen-bonded water molecule acting as a radiation protection agent for ionised pyrrole, a prototypical aromatic biomolecule. Pure samples of pyrrole and pyrrole(H2O) were outer-valence ionised and the subsequent damage and relaxation processes were studied. Bare pyrrole ions fragmented through the breaking of C-C or N-C covalent bonds. However, for pyrrole(H2O)+, we observed a strong protection of the pyrrole ring through the dissociative release of neutral water or by transferring an electron or proton across the hydrogen bond. Overall, a single water molecule strongly reduces the fragmentation probability and thus the persistent radiation damage of singly-ionised pyrrole.

Analysis Of Bacterial Contamination By Total Plate Number (ALT) Method In Smoked Fish At One Of The Market Traders

Bacterial contamination can come from the environment as a result of food production processes in the form of biological, chemical and foreign matter contaminants that can interfere with, harm and endanger human health. One of the problems in the processed food sector is the high level of bacterial contamination in the food served on the market. The condition of open food is also the main factor causing food to be contaminated with bacteria. The Total Plate Count (ALT) or total plate count (TPC) is an examination used to determine the number of microorganisms both bacteria and fungi using solid media with the final result being colonies. The aim of the study was to determine bacterial contamination and to determine the total plate number (ALT) of bacterial colonies in smoked fish sold at Ngemplak Market, Tulungagung. This research used a Simple Random Design (RAS) method with four treatments and 3 repetitions. The results showed that for menot fish it was 16.2 x 105 cfu/g, for tuna it was 10.5 x 105 cfu/g, for tuna it was 9.4 x 105 cfu/g, for bader fish it was 16.4 x 105 cfu/g. g, and in whitefish 20.5 x 105 cfu/g. The conclusion is that the bacterial contamination of smoked fish sold at the Ngemplak Market using the ALT method exceeds the normal limit value set by SNI 2725:2013.

Landscapes of random diffusivity processes in harmonic potential

A huge number of experimental evidences support that Brownian yet non-Gaussian diffusion prevalently exists in biological and soft matter systems. To interpret the physical mechanism of the Brownian yet non-Gaussian diffusion, the superstatistical approach with random diffusivity and further general random diffusivity processes attract extensive attention. This paper focuses on the anomalous diffusion and nonergodic property of the random diffusivity processes confined in a harmonic potential. Based on the theoretical analyses in the framework of Langevin equation, we find the inherent disagreement between ensemble-averaged mean-squared displacement and time-averaged mean-squared displacement for any form of the random diffusivity D(t), which implies the ergodicity breaking of the confined dynamics. Further, the asymptotic distribution of the time-averaged mean-squared displacement is strictly derived and shows the explicit dependence on the time average of the diffusivity D(t), which means the randomness of the time-averaged mean-squared displacement is completely contributed by the random diffusivity D(t). These results hold true for a general diffusivity D(t), which has been verified through the simulations of three specific kinds of diffusivities D(t).

Localized States in Active Fluids.

Biological active matter is typically tightly coupled to chemical reaction networks affecting its assembly-disassembly dynamics and stress generation. We show that localized states can emerge spontaneously if assembly of active matter is regulated by chemical species that are advected with flows resulting from gradients in the active stress. The mechanochemical localized patterns form via a subcritical bifurcation and for parameter values for which patterns do not exist in absence of the advective coupling. Our work identifies a generic mechanism underlying localized cellular patterns.

Biological sources, paleoenvironment, and organic matter enrichment in source rocks of the Ordovician Majiagou Formation, Ordos Basin, China: Evidence from biomarkers, microfossils, and inorganic geochemical analyses

Carbonate deposits in the Ordovivian Majiagou Formation are significant source rocks for natural gas generation in the Ordos Basin, northwestern China. Previous studies mainly focused on the organic matter enrichment mechanism of shales rather than carbonate rocks. The biological sources and paleoenvironment of carbonate source rocks, and the main controlling factors of organic matter enrichment in the carbonate source rocks were studied in this paper in combination with evidence from biomarkers, microfossils and inorganic geochemistry analysis. The results show that four types of microfacies were identified in the Majiagou Formation, respectively as: mud flat microfacies, mud–dolomite flat microfacies, dolomite flat microfacies, and open marine microfacies. The biological sources of organic matter are chiefly planktonic algae, followed by bacteria. The mud flat and mud–dolomite flat contain a high abundance of terrigenous detrital inputs, as indicated by the high content of Al2O3, TiO2, Th, and Zr. The low Sr/Cu and high Rb/Sr values reveal warm and humid paleoclimate conditions in the mud flat and mud–dolomite flat, whereas the dolomite flat and open marine were likely formed in hot and arid paleoclimate conditions. The mud flat and mud–dolomite flat deposits were characterized by high paleoproductivity of the Majiagou Formation. Low Sr/Ba values were found in the mud flat samples, indicating fresh to brackish water condition, whereas samples of other facies have a relatively high degree of salinity. Based on Uauth, Moauth, Crauth, Coauth, δCe, and δEu values, the mud flat microfacies was formed in a suboxic and anoxic environment, whereas the mud–dolomite flat, dolomite flat and open marine microfacies were within dysoxic to oxic conditions. A model of organic matter enrichment in the Majiagou Formation is thus established. The level of terrigenous detrital inputs is the principal factor of organic matter enrichment in the Majiagou Formation, secondly are redox condition and then paleoproductivity. The mud flat and mud–dolomite flat microfacies show abundant terrestrial detrital inputs and nutrient elements, indicative of warm and humid climate that facilitated biotic productivity, including an abundance of planktonic algae (microfossils). The suboxic and anoxic environments promoted the preservation of organic matter, as evidenced by the relatively high TOC content. The mud flat as well as the mud–dolomite flat of the Majiagou Formation is prospecting for forming source rocks.

Using SRIM code for calculating Bragg curve, projected range, straggling of 12C ion in biological materials

‘The Stopping and Range of Ions in Matter’ SRIM program, utilizing the built-in compound directory has been used to compute Bragg curve, projected range, longitudinal, lateral straggle of 12C ion with energies of 1 − 150 MeV in biological matter: liquid water (benchmark) human blood, skin, thyroid, and spleen are assessed. Results show that in the studied biological media for higher energy beam i): noticeable modification are seen in Bragg peak, shift in peak-position; ii) maximum projected range: 595.2 μm suggests effective use of 12C ions for cancer tumor therapy, especially for superficial cancer tumors, without much damage to healthier cells; iii) longitudinal straggling ~ 22.6 μm, low lateral straggling ~ 4.7 μm suggests potential application of 12C ions in treating cancer tumor nearby critical organs, causing minimal damage in nearby normal tissues.

Acoustophoresis of monodisperse oil droplets in water: Effect of symmetry breaking and non-resonance operation on oil trapping behavior.

Acoustic manipulation of particles in microchannels has recently gained much attention. Ultrasonic standing wave (USW) separation of oil droplets or particles is an established technology for microscale applications. Acoustofluidic devices are normally operated at optimized conditions, namely, resonant frequency, to minimize power consumption. It has been recently shown that symmetry breaking is needed to obtain efficient conditions for acoustic particle trapping. In this work, we study the acoustophoretic behavior of monodisperse oil droplets (silicone oil and hexadecane) in water in the microfluidic chip operating at a non-resonant frequency and an off-center placement of the transducer. Finite element-based computer simulations are further performed to investigate the influence of these conditions on the acoustic pressure distribution and oil trapping behavior. Via investigating the Gor'kov potential, we obtained an overlap between the trapping patterns obtained in experiments and simulations. We demonstrate that an off-center placement of the transducer and driving the transducer at a non-resonant frequency can still lead to predictable behavior of particles in acoustofluidics. This is relevant to applications in which the theoretical resonant frequency cannot be achieved, e.g., manipulation of biological matter within living tissues.

The Hollywood Undead: Zombies Interpreted Scientifically

Modern media is fascinated by the undead. Zombie movies and shows comprise an entire genre by themselves, and there are many different renditions of the creatures in pop culture. This review was performed with the goal of analyzing the characteristics of zombies from The Walking Dead. This is organized around four major topics: organization of the biological hierarchy, energy and matter, interactions between systems, and evolution. These are the unifying principles of biology, and thus appropriate for assessing the biological principles behind zombie physiology. This review aims to show that some common features of zombies are simply exaggerations of preexisting human functions, and that they are not so removed from what we perceive as normal human behavior.

Not only biology matters: socioeconomic factors change land prioritization for restoration

Ecological restoration requires a holistic view of the interconnectedness between degraded areas, remaining ecosystems, and the repercussions of land use and other socioeconomic costs. In this study, we analyze how biological priorities for restoration change when ecological, social, and economic feasibility are considered. A multi‐criteria approach was used to prioritize restoration areas, using the Mexican side of the transboundary Grijalva‐Usumacinta basin (78,831 km2) as a study model, one of Mexico's most important regions, thanks to its hydrology, biology, and social conditions. Fourteen indicators of biological value and feasibility for restoration were identified. The results showed that when considering only biological factors (B scenario), 9.35% of the basin area had high or very high priority for restoration within or near natural protected areas (NPAs). When including feasibility (B + F scenario), the area with high to very high priority values for restoration increased to 34.3%. This means that many feasible areas had medium or low biological priority for restoration, and consequently, in many cases, there is a tradeoff between the possible biological recovery versus viability derived mainly from socioeconomic factors. Without discerning where restoration can offer the most pronounced ecological and socioeconomic benefits, efforts risk being misdirected or squandered. This approach provides a suitability assessment useful for decision‐makers and stakeholders because it generates a more complete picture of opportunities and threats to make a final selection of priority areas for intervention.

Airborne bacteria viability and air quality: a protocol to quantitatively investigate the possible correlation by an atmospheric simulation chamber

Abstract. Biological particulate matter or bioaerosol are a subset of atmospheric aerosol. They influence climate, air quality, and health via several mechanisms which often are poorly understood. In particular, the quantitative study of possible relationship between bioaerosol viability and air quality or meteorological conditions is an open and relevant issue. The difficulty of retrieving such possible correlations by analyses of data collected during in-field campaigns can benefit of targeted experiments conducted in well-controlled conditions inside atmospheric simulation chambers (ASCs). ChAMBRe (Chamber for Aerosol Modelling and Bio-aerosol Research) is an ASC in Genoa (Italy) designed and built to perform experimental research on bioaerosol. In this article, we focus on bacteria viability. A multi-step protocol was developed and thoroughly tested to cultivate a suitable bacteria population (E. coli), nebulize and inject in a chamber of viable cells, expose and monitor the viability variation inside ChAMBRe, hold at selected conditions, and finally incubate and count the concentration of viable bacteria. The whole procedure showed an estimated lifetime of total (T) and viable (V) E. coli of about 153 and 32 min, respectively and a V : T lifetime ratio of 40±5 min when ChAMBRe is held in a reference baseline condition. The coefficient of variation of 13 % shows how sensitive the protocol is also to changes in viability when the bacteria are exposed to other (e.g. polluted) conditions. First results showing a viability reduction observed exposing the E. coli strain to NOx concentrations and solar irradiation are presented and discussed. The present results pave the way for systematic studies aimed at the definition of dose–effect relationship for several bacteria strains under different conditions of atmospheric pollutants.

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

Lift at low Reynolds number.

Lift forces are widespread in hydrodynamics. These are typically observed for big and fast objects and are often associated with a combination of fluid inertia (i.e. large Reynolds numbers) and specific symmetry-breaking mechanisms. In contrast, the properties of viscosity-dominated (i.e. low Reynolds numbers) flows make it more difficult for such lift forces to emerge. However, the inclusion of boundary effects qualitatively changes this picture. Indeed, in the context of soft and biological matter, recent studies have revealed the emergence of novel lift forces generated by boundary softness, flow gradients and/or surface charges. The aim of the present review is to gather and analyse this corpus of literature, in order to identify and unify the questioning within the associated communities, and pave the way towards future research.

Transient pattern formation in an active matter contact poisoning model

One of the most notable features in repulsive particle based active matter systems is motility-induced-phase separation (MIPS) where a dense, often crystalline phase and low density fluid coexist. Most active matter studies involve time-dependent activity; however, there are many active systems where individual particles transition from living or moving to dead or nonmotile due to lack of fuel, infection, or poisoning. Here we consider an active matter particle system at densities where MIPS does not occur. When we add a small number of infected particles that can poison other particles, rendering them nonmotile, we find a rich variety of time dependent pattern formation, including MIPS, a wetting phase, and a fragmented state formed when mobile particles plow through a nonmotile packing. We map the patterns as a function of time scaled by epidemic duration, and show that the pattern formation is robust for a wide range of poisoning rates and activity levels. We also show that pattern formation does not occur in a random death model, but requires the promotion of nucleation by contact poisoning. Our results should be relevant to biological and active matter systems where there is some form of poisoning, death, or transition to nonmotility.

Overcrowding induces fast colloidal solitons in a slowly rotating potential landscape

Collective particle transport across periodic energy landscapes is ubiquitously present in many condensed matter systems spanning from vortices in high-temperature superconductors, frictional atomic sliding, driven skyrmions to biological and active matter. Here we report the emergence of fast solitons propagating against a rotating optical landscape. These experimentally observed solitons are stable cluster waves that originate from a coordinated particle exchange process which occurs when the number of trapped microparticles exceeds the number of potential wells. The size and speed of individual solitons rapidly increase with the particle diameter as predicted by theory and confirmed by numerical simulations. We show that when several solitons coexist, an effective repulsive interaction can stabilize their propagation along the periodic potential. Our experiments demonstrate a generic mechanism for cluster-mediated transport with potential applications to condensed matter systems on different length scales.

Heating-Induced Switching to Hierarchical Liquid Crystallinity Combining Colloidal and Molecular Order in Zwitterionic Molecules.

Hierarchical self-assemblies of soft matter involving triggerable or switchable structures at different length scales have been pursued toward multifunctional behaviors and complexity inspired by biological matter. They require several and balanced competing attractive and repulsive interactions, which provide a grand challenge in particular in the "bulk" state, i.e., in the absence of plasticizing solvents. Here, we disclose that zwitterionic bis-n-tetradecylphosphobetaine, as a model compound, shows a complex thermally switchable hierarchical self-assembly in the solvent-free state. It shows polymorphism and heating-induced reversible switching from low-temperature molecular-level assemblies to high-temperature hierarchical self-assemblies, unexpectedly combining colloidal and molecular self-assemblies, as inferred by synchrotron small-angle X-ray scattering (SAXS). The high-temperature phase sustains birefringent flow, indicating a new type of hierarchical thermotropic liquid crystallinity. The high-temperature colloidal-level SAXS reflections suggest indexation as a 2D oblique pattern and their well-defined layer separation in the perpendicular direction. We suggest that the colloidal self-assembled motifs are 2D nanoplatelets formed by the lateral packing of the molecules, where the molecular packing frustration between the tightly packed zwitterionic moieties and the coiled alkyl chains demanding more space limits the lateral platelet growth controlled by the alkyl stretching entropy. An indirect proof is provided by the addition of plasticizing ionic liquids, which relieve the ionic dense packings of zwitterions, thus allowing purely smectic liquid crystallinity without the colloidal level order. Thus, molecules with a simple chemical structure can lead to structural hierarchy and tunable complexity in the solvent-free state by balancing the competing long-range electrostatics and short-range nanosegregations.

Mixtures of self-propelled particles interacting with asymmetric obstacles.

In the presence of an obstacle, active particles condensate into a surface "wetting" layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of "fast" and "slow" active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion "diversity," defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter.