Enzymes and other biomolecules are often anchored onto solid materials so they can be reused, purified more easily, and made more stable, a strategy biotechnology has relied on since industrial-scale immobilized enzymes first appeared in chemical manufacturing in the mid-twentieth century. Immobilized enzymes today drive processes from food and pharmaceutical production to biosensors and medical diagnostics. Fixing a biomolecule in place, however, is not as simple as gluing it down. The exact spot where it attaches, the direction it faces, and how much freedom it retains to move can all change how well it works. Testing every possible arrangement in the laboratory is slow and costly, which is why computer simulation has become such a valuable complement to experiments.

The Martini force field

One of the main tools for this kind of study is molecular dynamics simulation, which calculates how atoms move over time by applying the basic laws of physics. Simulating every single atom of a protein, its surrounding water, and a supporting material gives rich detail, but is extremely demanding on computing power, especially when many attachment geometries need comparing. A widely used shortcut is coarse-grained modeling, in which small clusters of atoms are grouped into single, simplified particles. This keeps the essential physical behavior of the system while making the calculations far cheaper. The most established coarse-grained approach for biological molecules is the Martini force field, first developed in 2004 to describe fatty, membrane-forming molecules and later extended to proteins and, more recently, to a more accurate third generation of the model. Martini has since become a standard tool for simulating large biological assemblies that would otherwise be out of reach.

Introducing MartiniSurf

A team of researchers now introduces MartiniSurf ¹, an open-source software package that automates the preparation of these coarse-grained simulations for biomolecules attached to surfaces. Building such a system by hand normally involves several separate programs and many manual steps, which makes it hard to reproduce results or compare different setups fairly. MartiniSurf instead combines the whole process into a single, streamlined workflow. Starting from the structure of a protein or a DNA strand, it converts the molecule into its coarse-grained form, builds a model of the supporting surface, positions the molecule in a chosen orientation, adds water and dissolved ions, and produces all the files needed to run the simulation with GROMACS, a molecular dynamics program that has been developed and refined for decades. Because every step is controlled by explicit settings rather than manual adjustments, two researchers using the same settings should obtain the same starting system, making comparisons across studies far more reliable.

Restraining forces or linkers

A central feature of the software is its flexibility in representing how a biomolecule is attached. In one mode, selected regions of the molecule are held near the surface through simple restraining forces, without modeling the physical connector itself. In another mode, an explicit molecular linker is placed between the biomolecule and the surface, so that the linker’s own length and flexibility can influence the simulation. Because the properties of such linkers are known to affect how active and stable an attached enzyme remains, this second option offers a more realistic picture whenever the necessary coarse-grained description of the linker is available.

Variety of supporting surfaces

The supporting surfaces themselves can also be varied widely. The software can generate simple flat reference surfaces or draw on previously developed coarse-grained models of real materials such as graphene, graphite, carbon nanotubes, and agarose-like gels, the type of porous material commonly used to immobilize enzymes in the laboratory. Properties such as surface chemistry, electric charge, particle spacing, and added chemical groups can all be adjusted. Recent studies have shown that surfaces built without care can cause water molecules near the interface to line up in unrealistic, almost frozen patterns, an artifact rather than genuine physical behavior. The software includes options that let users introduce controlled irregularity into the surface to reduce this problem, while staying consistent with the wider Martini modeling framework.

In practice

To demonstrate how the approach works in practice, the study presents examples involving both proteins and DNA. For an enzyme attached to an agarose-like surface, the software reproduces several different attachment arrangements, including a complete system containing the enzyme together with its natural helper molecule and reaction substrate. These examples show how changing the attachment point or adding chemical groups to the surface can be explored systematically, without needing to reconstruct every model from scratch by hand.

The approach is also extended to DNA tethered to a graphene-like surface, comparing an electrically neutral surface with a positively charged one. The coarse-grained simulations reproduce the same general behavior previously reported in much more computationally demanding all-atom studies: the DNA strand remains mostly upright above the neutral surface but bends progressively toward the surface when it carries a positive charge, drawn in by electrostatic attraction. This comparison is not meant to reproduce exact experimental values, but rather to confirm that the automated setup captures the right physical trends, providing a check on the reliability of the workflow.

Reproducibility

Every simulation generated by the software automatically records the settings, software versions, and modeling choices used to build it, so that another researcher can repeat or directly compare a given calculation later. Importantly, the software does not introduce new physical models or new force-field parameters of its own. Instead, it draws on already validated Martini tools and organizes them into a consistent, automated pipeline.

Overall, MartiniSurf addresses a practical bottleneck in computational chemistry rather than proposing a new simulation method. By automating the construction of surface-bound protein and DNA systems, it makes coarse-grained molecular dynamics studies faster to set up, easier to reproduce, and simpler to scale across many attachment geometries. This kind of tool should make it easier to systematically study how surface properties, attachment geometry, and molecular flexibility shape the behavior of immobilized biomolecules, supporting the design of better catalysts, biosensors, and other biotechnology applications.

Author: César Tomé López is a science writer and the editor of Mapping Ignorance

Disclaimer: Parts of this article may have been copied verbatim or almost verbatim from the referenced research paper/s.

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Author: Tamara Cruz Tena, strategy consultant, CIC  energiGUNE

 

When energy storage is discussed in the context of the energy transition, the conversation almost invariably turns to electricity. Solar and wind power have made the temporal mismatch between energy production and energy demand one of the defining challenges of low-carbon energy systems, and technologies capable of storing electrical energy have consequently become central to discussions about decarbonization.

Yet this emphasis on electricity raises an interesting question. If a substantial fraction of the energy ultimately consumed by modern societies is required not as electricity but as thermal energy, should future energy systems necessarily store energy in electrical form?

The question may appear deceptively simple. Electricity plays a visible role in modern economies, powering everything from communications and transportation to industrial equipment and domestic appliances. Thermal energy, by contrast, often remains hidden within industrial processes, heating systems and manufacturing operations. Nevertheless, many of the activities that sustain modern societies depend primarily on heat rather than electricity.

Steelmaking, cement production, chemical manufacturing, food processing, paper production and numerous other industrial activities require thermal energy delivered under specific conditions of temperature, power and duration. In many cases, fossil fuels have historically fulfilled this role not because alternative energy sources were unavailable, but because combustion offers a relatively direct means of producing high-temperature thermal energy where and when it is required.

As renewable electricity becomes increasingly available, this situation may encourage a different way of thinking about energy storage. Rather than focusing exclusively on how electricity can be stored and later returned to the grid, it may also be worth considering whether part of that energy could instead be stored in forms intended for later thermal use.

Such an approach would not eliminate the need for batteries, nor would it necessarily be appropriate for every application. It does, however, suggest that thermal energy storage may represent a distinct scientific and engineering problem whose requirements differ from those associated with conventional electrical storage technologies.

Storing energy for later thermal use

At the heart of the discussion lies a relatively straightforward physical observation. Electrical energy can be converted into thermal energy with high efficiency through a variety of heating technologies. Once this conversion has taken place, the resulting energy may be stored within a material or chemical system and later recovered when thermal energy is required.

Importantly, what is stored is not temperature itself. Temperature is an intensive thermodynamic property and therefore cannot be accumulated in the same way as energy. Instead, thermal energy storage systems retain energy through changes in the state of a material, whether by increasing its temperature, inducing a phase transition or driving a reversible chemical reaction.

The simplest of these approaches is generally known as sensible heat storage. In such systems, energy is stored through an increase in the temperature of a material. Water provides the most familiar example, although industrial applications may employ molten salts, rocks, ceramics, graphite or other materials capable of operating under more demanding thermal conditions. The amount of energy stored depends on the mass of the storage medium, its heat capacity and the temperature interval over which it operates.

A second possibility involves latent heat storage, where energy is absorbed or released during a phase transition. Because phase transitions may involve substantial enthalpy changes while temperature remains relatively constant, these systems can store significant amounts of energy within comparatively narrow temperature ranges. This characteristic has made phase change materials attractive for applications in which thermal energy must be supplied near a particular operating temperature.

Even more ambitious concepts involve thermochemical storage. In these systems, thermal energy drives reversible chemical reactions, allowing energy to be stored in chemical form and later recovered when the reverse reaction occurs. Under certain conditions, such approaches could potentially enable storage over much longer timescales than conventional thermal systems, although their practical implementation remains associated with significant scientific and engineering challenges.

At first sight, these approaches may appear to offer relatively straightforward solutions. However, as is often the case in energy research, the situation becomes considerably more complicated once practical constraints are taken into account.

Materials operating at elevated temperatures may experience degradation through corrosion, thermal fatigue, creep, phase instability or other mechanisms whose importance depends on the operating conditions and storage medium. Repeated thermal cycling can gradually alter material properties, while large-scale systems introduce additional challenges related to heat transfer, containment and long-term reliability. In thermochemical systems, reaction kinetics, cycling stability and reactor design may become equally important considerations.

As a result, the central question is not whether thermal energy can be stored. It clearly can. The more difficult question is whether such storage can remain technically reliable, economically viable and operationally robust under the conditions required by industrial applications.

A maturity paradox

Interestingly, many of the technologies that could contribute to this objective are no longer at an early stage of development. Electric heat pumps, electric boilers, electric resistance heaters and several forms of sensible and latent thermal energy storage have reached relatively high levels of technological maturity. From a purely technological perspective, the challenge is therefore not always one of invention. In many cases, the relevant technologies already exist.

Yet this observation introduces a different question. If a number of these technologies are already mature, why does their future role remain difficult to assess?

Part of the answer may lie in the complexity of modern energy systems themselves. The behaviour of a heat pump, an electric boiler or a thermal storage unit can often be described in considerable detail. However, energy systems contain thousands of interacting components operating across multiple spatial and temporal scales. Incorporating detailed representations of thermal technologies into large-scale energy models may therefore become computationally challenging, particularly when such models are intended to optimize entire electricity, heating and industrial sectors simultaneously.

This creates an interesting tension. The physical behaviour of thermal technologies is often governed by complex thermodynamic processes, yet large-scale energy planning frequently requires simplified mathematical representations that remain computationally tractable. Determining how much detail can be removed without losing essential information remains an active area of research and may influence how the future role of thermal energy storage is assessed.

This distinction may help explain why thermal energy storage has attracted increasing scientific interest in recent years. A significant fraction of industrial energy demand is thermal rather than electrical, and many industrial processes require heat directly. Under such circumstances, converting electrical energy into thermal energy, storing it, and subsequently using it as heat may sometimes prove more practical than repeatedly converting energy between different forms.

Beyond storage

The implications extend beyond individual storage technologies. Some researchers have suggested that thermal energy storage could also contribute to system flexibility by partially decoupling heat demand from the instantaneous availability of renewable electricity. During periods of abundant renewable generation, electrical energy could be converted into thermal energy and stored for later use. If such approaches prove technically and economically viable at scale, they could potentially help reduce some of the temporal mismatches that arise in renewable-dominated energy systems.

Whether this possibility ultimately becomes significant remains uncertain. Industrial sectors differ substantially in their temperature requirements, operating schedules and process constraints. Storage technologies that appear promising in one context may prove less suitable in another. Likewise, systems that perform well under laboratory conditions may encounter unexpected limitations when deployed at industrial scales.

For this reason, thermal energy storage may be best understood not as a single technology but as a broad collection of approaches aimed at addressing a common problem. The details differ from one system to another, but the underlying question remains remarkably simple: if much of the energy consumed by modern societies is ultimately required in thermal form, what is the most effective way of ensuring that such energy remains available when it is needed?

Viewed from this perspective, the challenge is not simply one of storage. The objective of an energy system is not merely to retain energy for later use, but to ensure that energy remains available in a form compatible with the process that ultimately consumes it. In some cases that form may be electrical. In others, it may be thermal. Determining when each option is preferable remains an active area of research.

Whether any particular thermal energy storage technology ultimately becomes a major component of future energy systems remains unclear. What already appears increasingly difficult to ignore, however, is the observation from which the entire discussion emerges. A substantial fraction of the energy consumed by modern societies is required in thermal form. This fact alone may justify a closer examination of how such energy can be stored, transported and recovered efficiently. As researchers continue to investigate the materials, mechanisms and constraints involved, thermal energy storage may offer a useful reminder that decarbonization involves more than replacing one source of electricity with another. It may also require a deeper understanding of how energy itself is used.

The BRTA is a consortium that remains a step ahead of future socio-economic challenges worldwide and in the Basque Autonomous Community; it addresses them through research and technological development, thus projecting itself internationally. The BRTA centres collaborate to generate knowledge and transfer it to Basque society and industry so as to make them more innovative and competitive. The BRTA is an alliance of 17 R&D centres and cooperative research centres with the support of the Basque Government, the SPRI and the Chartered Provincial Councils of Araba, Bizkaia and Gipuzkoa.

 

References

1. Maruf, M. N. I., Morales-Espana, G., Sijm, J., Helistö, N., and Kiviluoma, J. (2021) Classification, potential role, and modeling of power-to-heat and thermal energy storage in energy systems: A review. arXiv. Available at: https://arxiv.org/abs/2107.03960
2. CIC energiGUNE (2022) Thermal energy storage: a key factor in energy transition. Available at: https://cicenergigune.com/en/blog/thermal-energy-storage-key-energy-transition
3. International Energy Agency (2024) Energy Efficiency 2024. International Energy Agency. Available at: https://www.iea.org/reports/energy-efficiency-2024

 

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A newly engineered catalyst overcomes key obstacles that have long limited ammonia as a clean fuel for heavy industry. A newly developed single-atom platinum catalyst can ignite ammonia at about 200°C (392°F) and sustain stable combustion at 1,100°C (2,012°F) while producing very little NOx. The breakthrough could provide carbon-free, high-grade heat for industries such as [...]