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Valentina Erastova

Publications and source records attributed to Valentina Erastova.

11 recordsLinked to original sources

What makes a useful molecular model of biochar? A community roadmap

Biochars are disordered carbonaceous materials produced by biomass pyrolysis, with applications spanning soil amendment, water remediation, carbon storage, and functional materials. Although they share structural features with other disordered carbons such as coal, kerogen, and activated carbons, the questions posed to biochar models are distinct, and no single model can answer all of them equally well. Model usefulness must be defined relative to a specific question and validated against independent experimental observables. This community roadmap, arising from a CECAM workshop, critically maps current molecular approaches: experimentally guided top-down reconstruction, mimetic bottom-up simulation, and hybrid methods. We argue that first-generation models have been more successful than is often acknowledged, provided they are built at sufficient length scale and with explicit control over microporosity and bulk chemistry. Structural and equilibrium interfacial properties are increasingly tractable with classical force fields, whereas dynamic and reactive behaviours require selective use of reactive methods within multiscale workflows. A parallel, largely unaddressed gap concerns the mineral and ash components of biochar, and the changes the material undergoes during ageing in soil. We identify seven open questions current models cannot yet answer reliably, and five community priorities: force field benchmarking, open model and data repositories, shared classification and metadata standards, ensemble validation, and training in reproducible practice. Across these, sustained interaction with experimentalists is essential to ground models in real observables and document where they fail. Progress will be accelerated by adapting transferable methods from coal, kerogen, and clay-organic matter frameworks rather than repeating trial-and-error development.

cond-mat.mtrl-sci

Decoupling Precipitation and Surface Complexation during Mn(II) Removal by Biochar via Experiments and Atomistic Simulations

Manganese(II) mobilised by mining activity poses a persistent water-quality challenge, yet the mechanisms by which low-cost sorbents, such as biochar, sequester Mn(II) remain poorly resolved. This study identifies the specific chemical drivers of Mn(II) sequestration by combining fixed-bed column and batch experiments with atomistic molecular dynamics simulations. Oilseed rape straw biochars, produced at 350\textdegree C, 550\textdegree C, and 700\textdegree C, removed 20-50% of dissolved Mn from acidic influent (pH 4, 5 ppm). High-temperature biochar achieved the greatest removal ($\sim$50%) and rapidly increased effluent pH to 9, triggering alkaline precipitation. Conversely, lower-temperature biochars removed 20-30% of Mn while maintaining a near-neutral pH (7-7.5). Enhanced \ce{K+} release in these systems indicates significant cation exchange and non-precipitative pathways. Molecular simulations confirmed that while neutral surfaces show weak Mn(II) association, deprotonated sites drive strong adsorption through inner-sphere complexation ($\sim$50% removal) and outer-sphere association ($\sim$10%). These results establish a mechanistic framework to distinguish between precipitation-led and surface-complexation-led removal. By providing specific chemical criteria for Mn-targeted sequestration, this work enables the rational design of engineered biochars for sustainable water remediation.

cond-mat.mtrl-sci

Unravelling 2,4-D -- biochar interactions by molecular dynamics: adsorption modes and surface functionalities

We report a molecular dynamics investigation of 2,4-dichlorophenoxyacetic acid (2,4-D) adsorption at the aqueous-biochar interface using experimentally constrained woody biochar models representative of softwood-derived biochars produced at 400, 600 and 800 $°$C. The models reproduce experimental descriptors (H/C, O/C, aromaticity, true density, and surface functionality) of their experimental counterparts, and simulations enable calculation of adsorption isotherms that align with available experimental measurements. Our results reveal that 2,4-D$^{-}$ uptake is governed by a synergy of three interaction classes: (i) $π$-$π$ and $π$-Cl contacts with graphitic domains with either parallel or perpendicular alignments, (ii) polar interactions including H-bonding to surface -OH and other oxygen-containing groups, and (iii) Na$^{+}$-mediated cation bridging that links 2,4-D$^{-}$ anion to surface oxygens, that would have an increasing relevance for biochars near or above the pH at point of zero charge. Notably, we found that low-temperature produced biochars, which retain higher densities of surface O functionalities, exhibit higher adsorption per unit surface area due to cooperative polar interactions alongside $π$-$π$ binding, whereas medium-to-high temperature biochars rely more on $π$-$π$ and cation-bridging mechanisms. The distinct adsorption distances measured emphasize surface heterogeneity and porosity. Taken together, these atomistic insights corroborate experimental observations and yield actionable guidance for the rational design of biochars for remediation of anionic herbicides, highlighting how surface functionality and solution chemistry can be tuned to optimize sorption. Our approach provides a general framework to interrogate pollutant-biochar interactions and to inform remediation strategies.

cond-mat.mtrl-sci

Molecular Insights into Caprock Integrity of Subsurface Hydrogen Storage: Perspective on Hydrogen-induced Swelling and Mechanical Response

The geological storage of hydrogen (H_2) requires reliable long-term caprock sealing, yet the nanoscale interactions between H_2 and clay minerals remain critically underexplored despite their importance for storage security. This lack of understanding has limited the ability to predict mechanical stability and leakage risks in H_2 storage formations. Using molecular simulations, this study investigates the swelling behavior and mechanical properties of sodium montmorillonite (Mt), a common smectite clay, under varying hydration states and interlayer H_2 contents. Results show that H_2 accelerates hydration-state transitions, narrows the stability window of crystalline swelling, and promotes asymmetric plume formation in confined interlayers. H_2 alters cation and water coordination, thereby weakening Na^+--Mt electrostatic interactions and modulating H-bond networks at the interface and in the bulk. Mechanical analysis reveals pronounced anisotropy in Mt. In-plane stiffness is mainly governed by basal spacing expansion, whereas out-of-plane stiffness is highly sensitive to the initial presence of water or H_2, which weaken interlayer cohesion. Tensile and compressive strengths in the in-plane directions follow in-plane stiffness trends, while the out-of-plane tensile strength is governed by Mt--water H-bonds. The presence of H_2 further promotes Mt sheets separation by disrupting nanoscale liquid bridges. Collectively, these results provide the first atomistic-scale evidence that intercalated H_2 reshapes swelling energetics, elastic anisotropy, and failure pathways in Mt, highlighting critical nanoscale mechanisms that may compromise caprock integrity during underground H_2 storage.

cond-mat.mtrl-sci

Modelling realistic clay systems with ClayCode

Clays are a broad class of ubiquitous layered materials. Their specific chemophysical properties are intimately connected to their molecular structure, featuring repeating patterns broken by substitutions. Molecular dynamics simulations can provide insight into the mechanisms leading to the emergent properties of these layered materials, however up to now idealised clay structures have been simulated to make the modelling process tractable. We present ClayCode, software facilitating the modelling of clay systems closely resembling experimentally determined structures. By comparing a realistic model to a commonly used montmorillonite clay model, we demonstrate that idealised models feature noticeably different ionic adsorption patterns. We then present an application of ClayCode to the study the competitive barium and sodium adsorption on Wyoming montmorillonite, Georgia kaolinite, and Montana illite, of interest in the context of nuclear waste disposal.

cond-mat.mtrl-sci

Revealing crucial effects of reservoir environment and hydrocarbon fractions on fluid behaviour in kaolinite pores

Interactions of hydrocarbons (HCs) and clay surfaces are responsible for fluid behaviour within shale reservoirs. These interactions are affected by the diversity of HC components and the variations in environmental conditions. This study examines the interactions between kaolinite clay, featuring two distinct basal surfaces, and an array of HCs. We assess the impact of various molecular structures, functional groups, and environmental conditions (focusing on the reservoir temperature and pressure ranges) on the adsorption selectivity, surface packing, molecular alignment and orientation, and diffusion of HCs. Analyses of molecular interaction energies provide a quantitative elucidation of the adsorption mechanisms of HCs on the different kaolinite surfaces. Our findings suggest that molecular configuration, functional groups, and spatial effects dictate the distribution patterns of HCs for the different kaolinite surfaces. The differences in the interaction energy between various HCs with kaolinite reveal the adsorption strength of different HCs in the order of asphaltenes>heteroatomic HCs>saturated HCs>aromatic HCs. Furthermore, we observe that the adsorptive characteristics are highly temperature-sensitive; with increased temperatures markedly reducing the adsorption amount. Beyond a certain threshold, the effect of pressure rise on the fluid behaviour of HCs is non-negligible and is related to molecular packing and reduced mobility. Simulation results based on actual geological characteristics demonstrate notable adsorption disparities among hydrocarbon components on different kaolinite surfaces, influenced by competitive adsorption and clay surface interactions. Polar surfaces are predominantly occupied by heteroatomic HCs, whereas on non-polar surfaces, asphaltenes and heavy saturated HCs develop multi-layer adsorption structures, with molecules aligned parallel to the surface.

cond-mat.mtrl-sci

Development of biochar molecular models with controlled porosity

Biochars are an exciting class of environmental materials with a wide range of applications, including carbon storage and sequestration, soil enhancement, and pollution remediation. However, the limited knowledge of their molecular structures and compositions and the lack of comprehensive understanding of the relationship between these structures and biochars' diverse functionality, is hindering advancements in their development. In this work, we further advance the approach, first introduced by Wood et al. (2023), to constructing biochar molecular models; and now include control of microporosity (pores < 2 nm size) within the developed models. We construct biochar models representative of woody biochars which are experimentally produced at 600 -- 650 oC highest heating temperatures. Our models reproduce experimental H/C and O/C atomic ratios, percentage aromatic carbon, true density, cumulative porosity, and pore size distribution. The development of microporous biochar molecular models allows us to identify the importance of chemical structures involved in the assembly of biochar materials, and describe the relationship between these structures and obtained micropores. To facilitate other researchers integrating our approach into their work, we detail the steps taken, including the tests and reasons for each decision, in the construction of the biochar models. Furthermore, we share our developed molecular models in a format that can be easily integrated into other group's work in the form of molecular dynamics simulations.

cond-mat.mtrl-sci

Biochars at the molecular level. Part 2 -- Development of realistic molecular models of biochars

Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level knowledge of the key interactions driving these applications. Molecular modelling techniques, such as molecular dynamics simulations, offer a systematic and reproducible alternative and yield atomistic insights into physicochemical processes, allowing the identification of adsorption mechanisms and, through this, informing and guiding experimental development. In this work, on the basis of the critical assessment of the analytical techniques for characterisation of biochars and collation of a large volume of experimental data, we develop molecular models of three woody biochar materials, representative of those produced under low-, medium-, and high-temperature treatments. We characterise these models, validating them against experimental data, and share them with the research community. Furthermore, we detail our iterative approach to the design of these biochar models, discuss what we have learned about the relationship between biochar composition and its morphology, and finally share all of the building blocks used to create these biochar models. With this work, we hope to speed up the uptake of molecular dynamics simulations for the study and development of biochar materials and, to this end, we distribute our easy-to-use surface-exposed biochar models ready for the adsorption studies.

cond-mat.mtrl-sci

Biochars at the molecular level. Part 1 -- Insights into the molecular structures within biochars

Biochars are black carbonaceous solids produced through biomass pyrolysis under conditions of little or no oxygen. Whilst their properties are well studied, and their applications numerous, the underlying molecular structures within biochars still need to be defined. This raises a substantial barrier to the molecular modelling of biochars and has limited computational study of these materials, despite the advantages of such techniques. In this work, we critically assess the analytical techniques used to characterise biochars and use this information to gain molecular-level insights into biochars' molecular compositions and nanostructures. We focus on properties present at the nanoscale and which provide atomic-resolution insights into the molecular structures within these materials. Our goal is to create a holistic understanding of biochars' chemical, physical and molecular properties and to lay the foundation for future work focused on developing realistic molecular models of these materials.

cond-mat.mtrl-sci

What it takes to solve the Origin(s) of Life: An integrated review of techniques

Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number of different scientific perspectives relevant to the problem has resulted in the coexistence of diverse tools, techniques, data, and software in OoL studies. This has made communication between the disciplines relevant to the OoL extremely difficult because the interpretation of data, analyses, or standards of evidence can vary dramatically. Here, we hope to bridge this wide field of study by providing common ground via the consolidation of tools and techniques rather than positing a unifying view on how life emerges. We review the common tools and techniques that have been used significantly in OoL studies in recent years. In particular, we aim to identify which information is most relevant for comparing and integrating the results of experimental analyses into mathematical and computational models. This review aims to provide a baseline expectation and understanding of technical aspects of origins research, rather than being a primer on any particular topic. As such, it spans broadly -- from analytical chemistry to mathematical models -- and highlights areas of future work that will benefit from a multidisciplinary approach to tackling the mystery of life's origin. Ultimately, we hope to empower a new generation of OoL scientists by reviewing how they can investigate life's origin, rather than dictating how to think about the problem.

q-bio.PE

Organic-mineral interactions under natural conditions -- a computational study of flavone adsorption on smectite clay

Interactions between organic species and natural minerals are fundamental to the processes around us. With the aid of molecular dynamics simulations, we identify key adsorption mechanisms of apigenin on smectite clay minerals. The mechanism is highly sensitive to the pH -- changing from co-crystallisation in acidic-to-neutral solutions to the ion-bridging in mild-alkaline. The ionic species play a significant role in alkaline environments: the deprotonated apigenin species chelate metals, which, in turn, leads to the formation of a stable organic-metal-mineral complex and stronger adsorption in the presence of divalent cations.Smectite clays buffer the solution to mildly alkaline; hence, the type of exchangeable cations in the clay will be critical in determining the adsorption mechanism and organic retention capacity. Overall, our study showcases a computational strategy that can be transferred to a wide variety of organic-mineral systems in the natural environment.

cond-mat.mtrl-sci