Unraveling the Microscopic Mechanism of Molecular Ion Interaction with Monoclonal Antibodies: Impact on Protein Aggregation.

Understanding and predicting protein aggregation represents one of the major challenges in accelerating the pharmaceutical development of protein therapeutics. In addition to maintaining the solution pH, buffers influence both monoclonal antibody (mAb) aggregation in solution and the aggregation mechanisms since the latter depend on the protein charge. Molecular-level insight is necessary to understand the relationship between the buffer-mAb interaction and mAb aggregation. Here, we use all-atom molecular dynamics simulations to investigate the interaction of phosphate (Phos) and citrate (Cit) buffer ions with the Fab and Fc domains of mAb COE3. We demonstrate that Phos and Cit ions feature binding mechanisms, with the protein that are very different from those reported previously for histidine (His). These differences are reflected in distinctive ion-protein binding modes and adsorption/desorption kinetics of the buffer molecules from the mAb surface and result in dissimilar effects of these buffer species on mAb aggregation. While His shows significant affinity toward hydrophobic amino acids on the protein surface, Phos and Cit ions preferentially bind to charged amino acids. We also show that Phos and Cit anions provide bridging contacts between basic amino acids in neighboring proteins. The implications of such contacts and their connection to mAb aggregation in therapeutic formulations are discussed.

Mechanistic Insights into the Adsorption of Monoclonal Antibodies at the Water/Vapor Interface.

Monoclonal antibodies (mAbs) are active components of therapeutic formulations that interact with the water-vapor interface during manufacturing, storage, and administration. Surface adsorption has been demonstrated to mediate antibody aggregation, which leads to a loss of therapeutic efficacy. Controlling mAb adsorption at interfaces requires a deep understanding of the microscopic processes that lead to adsorption and identification of the protein regions that drive mAb surface activity. Here, we report all-atom molecular dynamics (MD) simulations of the adsorption behavior of a full IgG1-type antibody at the water/vapor interface. We demonstrate that small local changes in the protein structure play a crucial role in promoting adsorption. Also, interfacial adsorption triggers structural changes in the antibody, potentially contributing to the further enhancement of surface activity. Moreover, we identify key amino acid sequences that determine the adsorption of antibodies at the water-air interface and outline strategies to control the surface activity of these important therapeutic proteins.

Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study.

The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure.

Mass dipole contribution to the isotopic Soret effect in molecular mixtures.

Temperature gradients induce mass separation in mixtures in a process called thermal diffusion and are quantified by the Soret coefficient ST. Thermal diffusion in fluid mixtures has been interpreted recently in terms of the so-called (pseudo-)isotopic Soret effect but only considering the mass and moment of inertia differences of the molecules. We demonstrate that the first moment of the molecular mass distribution, the mass dipole, contributes significantly to the isotopic Soret effect. To probe this physical effect, we investigate fluid mixtures consisting of rigid linear molecules that differ only by the first moment of their mass distributions. We demonstrate that such mixtures have non-zero Soret coefficients in contrast with ST = 0 predicted by current formulations. For the isotopic mixtures investigated in this work, the dependence of ST on the mass dipole arises mainly through the thermal diffusion coefficient DT. In turn, DT is correlated with the dependence of the molecular librational modes on the mass dipole. We examine the interplay of the mass dipole and the moment of inertia in defining the isotopic Soret effect and propose empirical equations that include the mass dipole contribution.

Theory and Simulations of Ionic Liquids in Nanoconfinement.

Room-temperature ionic liquids (RTILs) have exciting properties such as nonvolatility, large electrochemical windows, and remarkable variety, drawing much interest in energy storage, gating, electrocatalysis, tunable lubrication, and other applications. Confined RTILs appear in various situations, for instance, in pores of nanostructured electrodes of supercapacitors and batteries, as such electrodes increase the contact area with RTILs and enhance the total capacitance and stored energy, between crossed cylinders in surface force balance experiments, between a tip and a sample in atomic force microscopy, and between sliding surfaces in tribology experiments, where RTILs act as lubricants. The properties and functioning of RTILs in confinement, especially nanoconfinement, result in fascinating structural and dynamic phenomena, including layering, overscreening and crowding, nanoscale capillary freezing, quantized and electrotunable friction, and superionic state. This review offers a comprehensive analysis of the fundamental physical phenomena controlling the properties of such systems and the current state-of-the-art theoretical and simulation approaches developed for their description. We discuss these approaches sequentially by increasing atomistic complexity, paying particular attention to new physical phenomena emerging in nanoscale confinement. This review covers theoretical models, most of which are based on mapping the problems on pertinent statistical mechanics models with exact analytical solutions, allowing systematic analysis and new physical insights to develop more easily. We also describe a classical density functional theory, which offers a reliable and computationally inexpensive tool to account for some microscopic details and correlations that simplified models often fail to consider. Molecular simulations play a vital role in studying confined ionic liquids, enabling deep microscopic insights otherwise unavailable to researchers. We describe the basics of various simulation approaches and discuss their challenges and applicability to specific problems, focusing on RTIL structure in cylindrical and slit confinement and how it relates to friction and capacitive and dynamic properties of confined ions.

Controlling local thermal gradients at molecular scales with Janus nanoheaters.

The generation and control of heat transport with nanoparticles is an essential objective of thermoplasmonics. Janus nanoparticles consisting of dissimilar materials with contrasting interfacial Kapitza conductance provide a route to control heat transport at the nanoscale. Here we use the recently introduced Atomistic Nodal Approach to map the surface temperature and Kapitza conductance of Janus nanoparticles to individual atoms. We show that the transition in the thermal transport properties between the hydrophobic and hydrophilic interfaces is exceptionally abrupt, occurring over length scales below 1 nm. We demonstrate the generality of this result using coarse-grained and all-atom models of gold nanoparticles. Further, we show how this behaviour provides a route to sustain significant temperature differences, on the order of tens of degrees for µW heat rates, between adjacent molecular layers attached to heated gold nanoparticles. Our work provides fundamental insight into nanoscale heat transport and a principle to design heterogeneous Janus nanoparticles for thermal transport applications.

On the microscopic origin of Soret coefficient minima in liquid mixtures.

Temperature gradients induce mass separation in mixtures in a process called thermodiffusion and quantified by the Soret coefficient. The existence of minima in the Soret coefficient of aqueous solutions at specific salt concentrations was controversial until fairly recently, where a combination of experiments and simulations provided evidence for the existence of this physical phenomenon. However, the physical origin of the minima and more importantly its generality, e.g. in non-aqueous liquid mixtures, is still an outstanding question. Here, we report the existence of a minimum in liquid mixtures of non-polar liquids modelled as Lennard-Jones mixtures, demonstrating the generality of minima in the Soret coefficient. The minimum originates from a coincident minimum in the thermodynamic factor, and hence denotes a maximization of non-ideality mixing conditions. We rationalize the microscopic origin of this effect in terms of the atomic coordination structure of the mixtures.

Limits to Crystallization Pressure.

Crystallization pressure drives deformation and damage in monuments, buildings, and the Earth's crust. Even though the phenomenon has been known for 170 years, there is no agreement between theoretical calculations of the maximum attainable pressure and experimentally measured pressures. We have therefore developed a novel experimental technique to image the nanoconfined crystallization process while controlling the pressure and applied it to calcite. The results show that displacement by crystallization pressure is arrested at pressures well below the thermodynamic limit. We use existing molecular dynamics simulations and atomic force microscopy data to construct a robust model of the disjoining pressure in this system and thereby calculate the absolute distance between the surfaces. On the basis of the high-resolution experiments and modeling, we formulate a novel mechanism for the transition between damage and adhesion by crystallization that may find application in Earth and materials sciences and in conservation of cultural heritage.

Understanding the Stabilizing Effect of Histidine on mAb Aggregation: A Molecular Dynamics Study.

Histidine, a widely used buffer in monoclonal antibody (mAb) formulations, is known to reduce antibody aggregation. While experimental studies suggest a nonelectrostatic, nonstructural (relating to secondary structure preservation) origin of the phenomenon, the underlying microscopic mechanism behind the histidine action is still unknown. Understanding this mechanism will help evaluate and predict the stabilizing effect of this buffer under different experimental conditions and for different mAbs. We have used all-atom molecular dynamics simulations and contact-based free energy calculations to investigate molecular-level interactions between the histidine buffer and mAbs, which lead to the observed stability of therapeutic formulations in the presence of histidine. We reformulate the Spatial Aggregation Propensity index by including the buffer-protein interactions. The buffer adsorption on the protein surface leads to lower exposure of the hydrophobic regions to water. Our analysis indicates that the mechanism behind the stabilizing action of histidine is connected to the shielding of the solvent-exposed hydrophobic regions on the protein surface by the buffer molecules.

Janus-Nanojet as an efficient asymmetric photothermal source.

The combination of materials with radically different physical properties in the same nanostructure gives rise to the so-called Janus effects, allowing phenomena of a contrasting nature to occur in the same architecture. Interesting advantages can be taken from a thermal Janus effect for photoinduced hyperthermia cancer therapies. Such therapies have limitations associated to the heating control in terms of temperature stability and energy management. Single-material plasmonic nanoheaters have been widely used for cancer therapies, however, they are highly homogeneous sources that heat the surrounding biological medium isotropically, thus equally affecting cancerous and healthy cells. Here, we propose a prototype of a Janus-Nanojet heating unit based on toroidal shaped plasmonic nanoparticles able to efficiently generate and release local heat directionally under typical unpolarized illumination. Based on thermoplasmonic numerical calculations, we demonstrate that these Janus-based nanoheaters possess superior photothermal conversion features (up to [Formula: see text] K) and unique directional heating capacity, being able to channel up over 90% of the total thermal energy onto a target. We discuss the relevance of these innovative nanoheaters in thermoplasmonics, and hyperthermia cancer therapies, which motivate the development of fabrication techniques for nanomaterials.

Thermophoresis and thermal orientation of Janus nanoparticles in thermal fields.

Thermal fields provide a route to control the motion of nanoparticles and molecules and potentially modify the behaviour of soft matter systems. Janus nanoparticles have emerged as versatile building blocks for the self-assembly of materials with novel properties. Here we investigate using non-equilibrium molecular dynamics simulations the behaviour of coarse-grained models of Janus nanoparticles under thermal fields. We examine the role of the heterogeneous structure of the particle on the Soret coefficient and thermal orientation by studying particles with different internal structures, mass distribution, and particle-solvent interactions. We also examine the thermophoretic response with temperature, targeting liquid and supercritical states and near-critical conditions. We find evidence for a significant enhancement of the Soret coefficient near the critical point, leading to the complete alignment of a Janus particle in the thermal field. This behaviour can be modelled and rationalized using a theory that describes the thermal orientation with the nanoparticle Soret coefficient, the mass and interaction anisotropy of the Janus nanoparticle, and the thermal field's strength. Our simulations show that the mass anisotropy plays a crucial role in driving the thermal orientation of the Janus nanoparticles.

Thermal conductance of the water-gold interface: The impact of the treatment of surface polarization in non-equilibrium molecular simulations.

Interfacial thermal conductance (ITC) quantifies heat transport across material-fluid interfaces. It is a property of crucial importance to study heat transfer processes at both macro- and nanoscales. Therefore, it is essential to accurately model the specific interactions between solids and liquids. Here, we investigate the thermal conductance of gold-water interfaces using polarizable and non-polarizable models. Both models have been fitted to reproduce the interfacial tension of the gold-water interface, but they predict significantly different ITCs. We demonstrate that the treatment of polarization using Drude-like models, widely employed in molecular simulations, leads to a coupling of the solid and liquid vibrational modes that give rise to a significant overestimation of the ITCs. We analyze the dependence of the vibrational coupling with the mass of the Drude particle and propose a solution to the artificial enhancement of the ITC, preserving at the same time the polarization response of the solid. Based on our calculations, we estimate ITCs of 200 MW/(m2 K) for the water-gold interface. This magnitude is comparable to that reported recently for gold-water interfaces [279 ± 16 MW/(m2 K)] using atomic fluctuating charges to account for the polarization contribution.

Enhanced Thermo-optical Response by Means of Anapole Excitation.

High refractive index (HRI) dielectric nanostructures offer a versatile platform to control the light-matter interaction at the nanoscale as they can easily support electric and magnetic modes with low losses. An additional property that makes them extraordinary is that they can support low radiative modes, so-called anapole modes. In this work, we propose a spectrally tunable anapole nanoheater based on the use of a dielectric anapole resonator. We show that a gold ring nanostructure, a priori nonresonant, can be turned into a resonant unit by just filling its hole with an HRI material supporting anapole modes, resulting in a more efficient nanoheater able to amplify the photothermal response of the bare nanoring. As proof of concept, we perform a detailed study of the thermoplasmonic response of a gold nanoring used as heating source and a silicon disk, designed to support anapole modes, located in its center acting as an anapolar resonator. Furthermore, we utilize the anapole excitation to easily shift the thermal response of these structures from the shortwave infrared range to the near-infrared range.

Polarisation of water under thermal fields: the effect of the molecular dipole and quadrupole moments.

The investigation of the behaviour of water under thermal fields is important to understand thermoelectricity of solutions, aqueous suspensions, bioelectric effects or the properties of wet materials under spatially inhomogeneous temperature conditions. Here we discuss the response of bulk water to external thermal fields using non-equilibrium molecular dynamics simulations, and five widely used forcefields: TIP4P/2005, TIP4P/2005f, OPC, SPC/E and TIP3P. These models all show the thermal polarisation (TP) effect in bulk water, namely the build-up of an electrostatic field induced by the temperature gradient. The strength of this effect is ∼0.1-1 mV K-1 at near-standard conditions for all forcefields, supporting the generality of TP. Moreover, all the models predict a temperature inversion of the polarisation field, although the inversion temperatures vary significantly across different models. We rationalise this result by deriving theoretical equations that describe the temperature inversion as a balance of the isobaric thermal expansion, dipole orientation in the thermal field and the ratio of the molecular dipole/quadrupole moments. Lower ratios lead to higher inversion temperatures. Based on our results, we conclude that the accuracy of the forcefields describing the TP effect decreases as, TIP4P/2005 ∼ TIP4P/2005f ∼ OPC > SPC/E > TIP3P. At coexistence conditions, the inversion temperature is expected to be around 400 K. Furthermore, we establish a correlation between the TP inversion temperature and the temperature corresponding to the minimum of the liquid-vapour surface potential of water.

Electrotunable friction with ionic liquid lubricants.

Room-temperature ionic liquids and their mixtures with organic solvents as lubricants open a route to control lubricity at the nanoscale via electrical polarization of the sliding surfaces. Electronanotribology is an emerging field that has a potential to realize in situ control of friction-that is, turning the friction on and off on demand. However, fulfilling its promise needs more research. Here we provide an overview of this emerging research area, from its birth to the current state, reviewing the main achievements in non-equilibrium molecular dynamics simulations and experiments using atomic force microscopes and surface force apparatus. We also present a discussion of the challenges that need to be solved for future applications of electrotunable friction.

Bending Modulus of Lipid Membranes from Density Correlation Functions.

The bending modulus κ quantifies the elasticity of biological membranes in terms of the free energy cost of increasing the membrane corrugation. Molecular dynamics (MD) simulations provide a powerful approach to quantify κ by analyzing the thermal fluctuations of the lipid bilayer. However, existing methods require the identification and filtering of non-mesoscopic fluctuation modes. State of the art methods rely on identifying a smooth surface to describe the membrane shape. These methods introduce uncertainties in calculating κ since they rely on different criteria to select the relevant fluctuation modes. Here, we present a method to compute κ using molecular simulations. Our approach circumvents the need to define a mesoscopic surface or an orientation field for the lipid tails explicitly. The bending and tilt moduli can be extracted from the analysis of the density correlation function (DCF). The method introduced here builds on the Bedeaux and Weeks (BW) theory for the DCF of fluctuating interfaces and on the coupled undulatory (CU) mode introduced by us in previous work. We test the BW-DCF method by computing the elastic properties of lipid membranes with different system sizes (from 500 to 6000 lipid molecules) and using coarse-grained (for POPC and DPPC lipids) and fully atomistic models (for DPPC). Further, we quantify the impact of cholesterol on the bending modulus of DPPC bilayers. We compare our results with bending moduli obtained with X-ray diffraction data and different computer simulation methods.

Gold nanodoughnut as an outstanding nanoheater for photothermal applications.

Photoinduced hyperthermia is a cancer therapy technique that induces death to cancerous cells via heat generated by plasmonic nanoparticles. While previous studies have shown that some nanoparticles can be effective at killing cancer cells under certain conditions, there is still a necessity (or the need) to improve its heating efficiency. In this work, we perform a detailed theoretical study comparing the thermoplasmonic response of the most effective nanoparticle geometries up to now with a doughnut-shaped nanoparticle. We numerically demonstrate that the latter exhibits a superior tunable photothermal response in practical illumination conditions (unpolarized light). Furthermore, we show that nanoparticle heating in fluidic environments, i.e., nanoparticles undergoing Brownian rotations, strongly depends on the particle orientation with respect to the illumination source. We conclude that nanodoughnuts are the best nanoheaters in our set of structures, with an average temperature increment 40% higher than the second best nanoheater (nanodisk). Furthermore, nanodoughnuts feature a weak dependence on orientation, being therefore ideal candidates for photothermal therapy applications. Finally, we present a designing guide, covering a wide range of toroid designs, which can help on its experimental implementation.

Heterogeneous thermal conductance of nanoparticle-fluid interfaces: An atomistic nodal approach.

The Interfacial Thermal Conductance (ITC) is a fundamental property of materials and has particular relevance at the nanoscale. The ITC quantifies the thermal resistance between materials of different compositions or between fluids in contact with materials. Furthermore, the ITC determines the rate of cooling/heating of the materials and the temperature drop across the interface. Here, we propose a method to compute local ITCs and temperature drops of nanoparticle-fluid interfaces. Our approach resolves the ITC at the atomic level using the atomic coordinates of the nanomaterial as nodes to compute local thermal transport properties. We obtain high-resolution descriptions of the interfacial thermal transport by combining the atomistic nodal approach, computational geometry techniques, and "computational farming" using non-equilibrium molecular dynamics simulations. We use our method to investigate the ITC of nanoparticle-fluid interfaces as a function of the nanoparticle size and geometry, targeting experimentally relevant structures of gold nanoparticles: capped octagonal rods, cuboctahedrons, decahedrons, rhombic dodecahedrons, cubes, icosahedrons, truncated octahedrons, octahedrons, and spheres. We show that the ITC of these very different geometries varies significantly in different regions of the nanoparticle, increasing generally in the order face < edge < vertex. We show that the ITC of these complex geometries can be accurately described in terms of the local coordination number of the atoms in the nanoparticle surface. Nanoparticle geometries with lower surface coordination numbers feature higher ITCs, and the ITC generally increases with the decreasing particle size.

Spatial Control of Heat Flow at the Nanoscale Using Janus Particles.

Janus nanoparticles (JNPs) feature heterogeneous compositions, bringing opportunities in technological and medical applications. We introduce a theoretical approach based on nonequilibrium molecular dynamics simulations and heat transfer continuum theory to investigate the temperature fields generated around heated spherical JNPs covering a wide range of particle sizes, from a few nm to 100 nm. We assess the performance of these nanoparticles to generate anisotropic heating at the nanoscale. We demonstrate that the contrasting interfacial thermal conductances of the fluid-material interfaces arising from the heterogeneous composition of the JNPs can be exploited to control the thermal fields around the nanoparticle, leading to a temperature difference between both sides of the nanoparticle (temperature contrast) that is significant for particles comprising regions with disparate hydrophilicity. We illustrate this idea using coarse-grained and atomistic models of gold nanoparticles with hydrophobic and hydrophilic coatings, in water. Furthermore, we introduce a continuum model to predict the temperature contrast as a function of the interfacial thermal conductance and nanoparticle size. We further show that, unlike homogeneous nanoparticles, the interfacial fluid temperature depends on the interfacial thermal conductance of Janus nanoparticles.