Project description:Most computer simulations of molecular dynamics take place under equilibrium conditions-in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with detailed-balance-breaking Markov models, and we explicitly construct such a picture by coarse graining the microscopic dynamics of our simulations in order to extract rates. This work identifies inter-particle interactions that tune those rates to create a functional motor, thereby yielding a computational playground to investigate the interplay between directional bias, current generation, and coupling strength in molecular information ratchets.
Project description:We report here the development of a rotating molecular switch based on metal-catalyzed reversible (de)-hydrogenation. Under an argon atmosphere, acceptorless dehydrogenation induces a switch from an alcohol to a ketone, while reversing to a hydrogen pressure switches back the system to the alcohol. Based on a tolane scaffold, such reversible (de)-hydrogenation enables 180° rotation. The absence of waste accumulation in a switch relying on chemical stimuli is of great significance and could potentially be applied to the design of efficient complex molecular machines.
Project description:One of the grand challenges in contemporary systems chemistry research is to mimic life-like functions using simple synthetic molecular networks. This is particularly true for systems that are out of chemical equilibrium and show complex dynamic behaviour, such as multi-stability, oscillations and chaos. We report here on thiodepsipeptide-based non-enzymatic networks propelled by reversible replication processes out of equilibrium, displaying bistability. Accordingly, we present quantitative analyses of the bistable behaviour, featuring a phase transition from the simple equilibration processes taking place in reversible dynamic chemistry into the bistable region. This behaviour is observed only when the system is continuously fueled by a reducing agent that keeps it far from equilibrium, and only when operating within a specifically defined parameter space. We propose that the development of biomimetic bistable systems will pave the way towards the study of more elaborate functions, such as information transfer and signalling.
Project description:Electrophoresis of a mixture of NaCl and CaCl2 in a lysozyme crystal is investigated using nonequilibrium molecular dynamics (MD) simulations. Upon exposure to an electric field, the stability of lysozyme is found to decrease slightly. This finding is demonstrated by increases in the root mean-square deviations of the heavy atoms of lysozyme, in the solvent-accessible surface area of hydrophobic residues, and in the number of hydrogen bonds between lysozyme and water. The solvent-accessible surface area of hydrophilic residues changes marginally, and the number of hydrogen bonds between lysozyme molecules decreases. Water molecules tend to align preferentially parallel to the electric field, and the dipole moment along the pore axis increases linearly with increasing field strength. Two pronounced layered structures are observed for Na+ and Ca2+ in the vicinity of protein surface, but only one enriched layer is observed for Cl-. The number distributions of all ions are nearly independent of the electric field. The water coordination numbers of all ions are smaller in the crystal than in aqueous bulk solution; however, the reverse is found for the Cl- coordination numbers of cations. Both the water and the Cl- coordination numbers are insensitive to the electric field. Ion diffusivities in the crystal are approximately 2 orders of magnitude smaller than those in aqueous bulk solution. The drift velocities of ions increase proportionally to the electric field, particularly at high strengths, and depend on ionic charge and coordination with oppositely charged ions. Electrical current exhibits a linear relationship with the field strength. The zero-field electrical conductivity is estimated to be 0.56 S/m, which is very close to 0.61 S/m as predicted by the Nernst-Einstein equation.
Project description:Non-equilibrium, fuel-driven reaction cycles serve as model systems of the intricate reaction networks of life. Rich and dynamic behavior is observed when reaction cycles regulate assembly processes, such as phase separation. However, it remains unclear how the interplay between multiple reaction cycles affects the success of emergent assemblies. To tackle this question, we created a library of molecules that compete for a common fuel that transiently activates products. Often, the competition for fuel implies that a competitor decreases the lifetime of these products. However, in cases where the transient competitor product can phase-separate, such a competitor can increase the survival time of one product. Moreover, in the presence of oscillatory fueling, the same mechanism reduces variations in the product concentration while the concentration variations of the competitor product are enhanced. Like a parasite, the product benefits from the protection of the host against deactivation and increases its robustness against fuel variations at the expense of the robustness of the host. Such a parasitic behavior in multiple fuel-driven reaction cycles represents a lifelike trait, paving the way for the bottom-up design of synthetic life.
Project description:Microgels are soft colloids that show responsive behavior and are easy to functionalize for applications. They are considered key components for future smart colloidal material systems. However, so far microgel systems have almost exclusively been studied in classical responsive switching settings using external triggers, while internally organized, autonomous control mechanisms as found in supramolecular chemistry and DNA nanotechnology relying on fuel-driven out-of-equilibrium concepts have not been implemented into microgel systems. Here, we introduce chemically fueled transient volume phase transitions (VPTs) for poly(methacrylic acid) (PMAA) microgels, where the collapsed hydrophobic state can be programmed using the fuel concentration in a cyclic reaction network. We discuss details of the system behavior as a function of pH and fuel amount, unravel kinetically trapped regions and showcase transient encapsulation and time-programmed release as a first application.
Project description:Chemically fueled supramolecular materials offer unique properties that include spatial and temporal control and even the ability to self-heal. Indeed, a few studies have demonstrated the ability to self-heal, however, the underlying mechanisms remain unclear. Here, we designed a peptide that forms a fibrillar network upon chemical fueling. We were surprised that the hydrogel could self-heal despite the lack of dynamics in the fiber assembly and disassembly. We explain this behavior by a mechanism that involves the chemically fueled peptide molecules that cannot self-assemble due to the lack of nucleation sites. When the fibers are perturbed, new nucleation sites form that help the assembly resulting in the healing of the damaged network. Furthermore, we generalized the behavior for other peptides. We refer to this non-assembling, chemically-fueled peptide as a molecular glue. In future work, we aim to explore whether this self-healing mechanism applies to more complex structures, narrowing the gap between biological and synthetic self-assemblies.
Project description:Biology regulates the function and assembly of proteins through non-equilibrium reaction cycles. Reciprocally, the assembly of proteins can influence the reaction rates of these cycles. Such reciprocal coupling between assembly and reaction cycle is a prerequisite for behavior like dynamic instabilities, treadmilling, pattern formation, and oscillations between morphologies. While assemblies regulated by chemical reaction cycles gained traction, the concept of reciprocal coupling is under-explored. In this work, we provide two molecular design strategies to tweak the degree of reciprocal coupling between the assembly and reaction cycle. The strategies involve spacing the chemically active site away from the assembly or burying it into the assembly. We envision that design strategies facilitate the creation of reciprocally coupled and, by extension, dynamic supramolecular materials in the future.