Emergent Properties of Antiagglomerant Films Control Methane Transport: Implications for Hydrate Management.

The relationship between collective properties and performance of antiagglomerants (AAs) used in hydrate management is handled using molecular dynamics simulations and enhanced sampling techniques. A thin film of AAs adsorbed at the interface between one flat sII methane hydrate substrate and a fluid hydrocarbon mixture containing methane and n-dodecane is studied. The AA considered is a surface-active compound with a complex hydrophilic head that contains both amide and tertiary ammonium cation groups and hydrophobic tails. At a sufficiently high AA density, the interplay between the surfactant layer and the liquid hydrocarbon excludes methane from the interfacial region. In this scenario, we combine metadynamics and umbrella sampling frameworks to study accurately the free-energy landscape and the equilibrium rates associated with the transport of one methane molecule across the AA film. We observe that the local configurational changes of the liquid hydrocarbon packed within the AA film are associated with high free-energy barriers for methane transport. The time scales estimated for the transport of methane across the AA film can be, in some cases, comparable to those reported in the literature for the growth of hydrates, suggesting that one possible mechanism by which AAs delay the formation of hydrate plugs could be providing a barrier to methane transport. Considering the interplay between the structural design and collective properties of AAs might be of relevance to improve their performance in flow assurance.

Numerical analysis of Pickering emulsion stability: insights from ABMD simulations.

The issue of the stability of Pickering emulsions is tackled at a mesoscopic level using dissipative particle dynamics simulations within the Adiabatic Biased Molecular Dynamics framework. We consider the early stage of the coalescence process between two spherical water droplets in a decane solvent. The droplets are stabilized by Janus nanoparticles of different shapes (spherical and ellipsoidal) with different three-phase contact angles. Given a sufficiently dense layer of particles on the droplets, we show that the stabilization mechanism strongly depends on the collision speed. This is consistent with a coalescence mechanism governed by the rheology of the interfacial region. When the system is forced to coalesce sufficiently slowly, we investigate at a mesoscopic level how the ability of the nanoparticles to stabilize Pickering emulsions is discriminated by nanoparticle mobility and the associated caging effect. These properties are both related to the interparticle interaction and the hydrodynamic resistance in the liquid film between the approaching interfaces.

DNA denaturation bubbles: free-energy landscape and nucleation/closure rates.

The issue of the nucleation and slow closure mechanisms of non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (respectively, closure) of an approximately 10 base-pair bubble, in agreement with experiments, are associated with the crossing of a free-energy barrier of 22 kBT (respectively, 13 kBT) at room temperature T. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, and thus to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the millisecond range. Contrary to small breathing bubbles, those more than 4 base-pair bubbles are of biological relevance, for example, when a pre-existing state of denaturation is required by specific DNA-binding proteins.

Scaling quasistationary states in long-range systems with dissipation.

Hamiltonian systems with long-range interactions give rise to long-lived out-of-equilibrium macroscopic states, so-called quasistationary states. We show here that, in a suitably generalized form, this result remains valid for many such systems in the presence of dissipation. Using an appropriate mean-field kinetic description, we show that models with dissipation due to a viscous damping or due to inelastic collisions admit "scaling quasistationary states," i.e., states that are quasistationary in rescaled variables. A numerical study of one-dimensional self-gravitating systems confirms the relevance of these solutions and gives indications of their regime of validity in line with theoretical predictions. We underline that the velocity distributions never show any tendency to evolve towards a Maxwell-Boltzmann form.

Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.

Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.

Biohybrid Membrane Formation by Directed Insertion of Aquaporin into a Solid-State Nanopore.

Biohybrid nanopores combine the durability of solid-state nanopores with the precise structure and function of biological nanopores. Particular care must be taken to control how biological nanopores adapt to their surroundings once they come into contact with the solid-state nanopores. Two major challenges are to precisely control this adaptability under dynamic conditions and provide predesigned functionalities that can be manipulated for engineering applications. In this work, we report on the computational design of a distinctive class of biohybrid active membrane layers, built from the directed-insertion of an aquaporin-incorporated lipid nanodisc into a model alkyl-functionalized silica pore. We show that in an aqueous environment when a pressure difference exists between the two sides of the solid-state nanopore, the preferential interactions between the hydrocarbon tail of the lipid molecules that surround the aquaporin protein and the alkyl group functionalizing the interior surface of the silica nanopore enable the insertion of the aquaporin-incorporated lipid shell into the nanopore by forcing out the water molecules. The same preferential interactions are responsible for the structural stability of the inserted aquaporin-incorporated lipid shell as well as the water sealing properties of the lipid-alkyl interface. We further show that the aquaporin protein stabilized in the alkyl-functionalized silica nanopore preserves its biological structure and function in both pure and saline water, and, remarkably, its water permeability is equal to the one measured in the biological environment. The designed biohybrid membrane could pave the way for the development of durable transformative devices for water filtration.

Armored Droplets as Soft Nanocarriers for Encapsulation and Release under Flow Conditions.

Technical challenges in precision medicine and environmental remediation create an increasing demand for smart materials that can select and deliver a probe load to targets with high precision. In this context, soft nanomaterials have attracted considerable attention due to their ability to simultaneously adapt their morphology and functionality to complex ambients. Two major challenges are to precisely control this adaptability under dynamic conditions and provide predesigned functionalities that can be manipulated by external stimuli. Here, we report on the computational design of a distinctive class of soft nanocarriers, built from armored nanodroplets, able to selectively encapsulate or release a probe load under specific flow conditions. First, we describe in detail the mechanisms at play in the formation of pocket-like structures in armored nanodroplets and their stability under external flow. Then we use that knowledge to test the capacity of these pockets to yield flow-assisted encapsulation or expulsion of a probe load. Finally, the rheological properties of these nanocarriers are put into perspective with those of delivery systems employed in pharmaceutical and cosmetic technology.

Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis.

A variety of enhanced statistical and numerical methods are now routinely used to extract important thermodynamic and kinetic information from the vast amount of complex, high-dimensional data obtained from molecular simulations. For the characterization of kinetic properties, Markov state models, in which the long-time statistical dynamics of a system is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. However, obtaining kinetic properties for molecular systems with high energy barriers remains challenging as often enhanced sampling techniques are required with biased simulations to observe the relevant rare events. Particularly, the calculation of diffusion coefficients remains elusive from biased molecular simulation data. Here, we propose a novel method that can calculate multidimensional position-dependent diffusion coefficients equally from either biased or unbiased simulations using the same formalism. Our method builds on Markov state model analysis and the Kramers-Moyal expansion. We demonstrate the validity of our formalism using one- and two-dimensional analytic potentials and also apply it to data from explicit solvent molecular dynamics simulations, including the water-mediated conformations of alanine dipeptide and umbrella sampling simulations of drug transport across a lipid bilayer. Importantly, the developed algorithm presents significant improvement compared to standard methods when the transport of solute across three-dimensional heterogeneous porous media is studied, for example, the prediction of membrane permeation of drug molecules.

Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles.

We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein.

Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2 fixation. How the protein shell directs influx and efflux of molecules in an effective manner has remained elusive. Here we use molecular dynamics and umbrella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarbonate, CO2 and ribulose bisphosphate and the product 3-phosphoglycerate associated with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating molecular transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated experimentally by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates molecular transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biology.

Nanoparticles Actively Fragment Armored Droplets.

Understanding the complexity of fragmentation processes is essential for regulating intercellular communication in mechanistic biology and developing bottom-up approaches in a large range of multiphase flow processes. In this context, self-fragmentation proceeds without any external mechanical energy input, allowing one to create efficiently micro- and nanodroplets. Here we examine self-fragmentation in emulsion nanodroplets stabilized by solid particles with different surface features. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations and offer detailed insight into the interplay between the evolution of the droplet shape and the particle finite-size effects at the interface. We show that finite-size nanoparticles play an active role in the necking breakup, behaving like nanoscale razors, and affect strongly the thermodynamic properties of the system. The role played by the particles during self-fragmentation might be of relevance to multifunctional biomaterial design and tuning of signaling pathways in mechanistic biology.

Antiagglomerants Affect Gas Hydrate Growth.

In gas clathrate hydrates, inclusion gas molecules stabilize crystalline water structures. In addition to being fundamentally interesting, gas hydrates attract significant practical attention because of their possible application in various high-tech technologies. However, gas hydrates pose health, safety, and environmental risks when they form within oil and gas pipelines, as well as within hydrocarbon-producing and treatment facilities. Among available strategies to control and sometimes prevent hydrate plug formation is the use of surface-active low-molecular-weight compounds, known as antiagglomerants (AAs). AAs prevent the agglomeration of small hydrate particles into large plugs. It is not clear whether AAs promote or frustrate hydrate growth. We present two molecular mechanisms by which AAs promote and frustrate, respectively, hydrate growth. Our results could lead to innovative methodologies for managing hydrates in high-tech applications, as well as for securing the safety of oil and gas operations.

Buckling in armored droplets.

The buckling mechanism in droplets stabilized by solid particles (armored droplets) is tackled at a mesoscopic level using dissipative particle dynamics simulations. We consider one spherical water droplet in a decane solvent coated with nanoparticle monolayers of two different types: Janus (particles whose surface shows two regions with different wetting properties) and homogeneous. The chosen particles yield comparable initial three-phase contact angles, selected to maximize the adsorption energy at the interface. We study the interplay between the evolution of droplet shape, layering of the particles, and their distribution at the interface when the volume of the droplets is reduced. We show that Janus particles affect strongly the shape of the droplet with the formation of a crater-like depression. This evolution is actively controlled by a close-packed particle monolayer at the curved interface. In contrast, homogeneous particles follow passively the volume reduction of the droplet, whose shape does not deviate too much from spherical, even when a nanoparticle monolayer/bilayer transition is detected at the interface. We discuss how these buckled armored droplets might be of relevance in various applications including potential drug delivery systems and biomimetic design of functional surfaces.