Microscopic insights into the solvation of polyethylene glycol chains in water: A machine learning potential approach.

Polyethylene glycol (PEG) is a structurally simple, nontoxic, and water-soluble polymer widely utilized in medical and pharmaceutical applications. Notably, when a PEG chain is immersed in water, the surrounding water molecules play a key role in driving conformational changes of this macromolecule. In this study, we explore the solvation behavior of PEG under mechanical strain using molecular dynamics simulations, with an interatomic potential obtained from machine learning.

Rate theory of gas-liquid nucleation: Quest for the elusive quantitative accuracy.

The task of a first principles theoretical calculation of the rate of gas-liquid nucleation has remained largely incomplete despite the existence of reliable results from unbiased simulation studies at large supersaturation. Although the classical nucleation theory formulated by Becker-Doring-Zeldovich about a century ago provides an elegant, widely used picture of nucleation in a first-order phase transition, the theory finds difficulties in predicting the rate accurately, especially in the case of gas-to-liquid nucleation. Here, we use a multiple-order parameter description to construct the nucleation free energy surface needed to calculate the nucleation rate.

Exploration of Stokes hydrodynamic law at molecular length scales.

The celebrated generalized Stokes law predicts that the velocity of a particle pulled through a liquid by an external force, Fex, is directly proportional to the force and inversely proportional to the friction ζ acted by the medium on the particle. We investigate the range of validity of the generalized Stokes law at molecular length scales by employing computer simulations to calculate friction by pulling a tagged particle with a constant force. We thus calculate friction for two model interaction potentials, Lennard-Jones and soft sphere, for several particle sizes, ranging from radius (a) smaller than the solvent particles to three times larger.

Sensitivity of nonequilibrium relaxation to interaction potentials: Timescales of response from Boltzmann's H function.

We investigate, by simulations and analytic theory, the sensitivity of nonequilibrium relaxation to interaction potential and dimensionality by using Boltzmann's H function H(t). We evaluate H(t) for three different intermolecular potentials in all three dimensions and find that the well-known H theorem is valid and that the H function exhibits rather strong sensitivity to all these factors. The relaxation of H(t) is long in one dimension, but short in three dimensions, longer for the Lennard-Jones potential than for the hard spheres.

Ethanol exchange between two graphene surfaces in nanoconfined aqueous solution: Rate and mechanism.

We observe, by computer simulations, a remarkable long-distance, rare, but repetitive, exchange of ethanol molecules between two parallel graphene surfaces in nanoconfined, aqueous, ethanol solutions. We compute the rate of exchange as a function of the separation (d) between the two surfaces. We discover that the initiating (or, the launching) step in this exchange is the attainment of an instantaneous orientation of the carbon-oxygen bond vector relative to the graphene surface.

Non-Markovian rate theory on a multidimensional reaction surface: Complex interplay between enhanced configuration space and memory.

A theory of barrier crossing rate on a multidimensional reaction energy surface is presented. The theory is a generalization of the earlier theoretical schemes to higher dimensions, with the inclusion of non-Markovian friction along both the reactive and the nonreactive coordinates. The theory additionally includes the bilinear coupling between the reactive and the nonreactive modes at the Hamiltonian level.

Tug-of-War between Internal and External Frictions and Viscosity Dependence of Rate in Biological Reactions.

The role of water in biological processes is studied in three reactions, namely, the Fe-CO bond rupture in myoglobin, GB1 unfolding, and insulin dimer dissociation. We compute both internal and external components of friction on relevant reaction coordinates. In all of the three cases, the cross-correlation between forces from protein and water is found to be large and negative that serves to reduce the total friction significantly, increase the calculated reaction rate, and weaken solvent viscosity dependence.

Structural Stability of Insulin Oligomers and Protein Association-Dissociation Processes: Free Energy Landscape and Universal Role of Water.

Association and dissociation of proteins are important biochemical events. In this Feature Article, we analyze the available studies of these processes for insulin oligomers in aqueous solution. We focus on the solvation of the insulin monomer in water, stability and dissociation of its dimer, and structural integrity of the hexamer.

Rate of Insulin Dimer Dissociation: Interplay between Memory Effects and Higher Dimensionality.

We calculate the rate of dissociation of an insulin dimer into two monomers in water. The rate of this complex reaction is determined by multiple factors that are elucidated. By employing advanced sampling techniques, we first obtain the reaction free energy surface for the dimer dissociation as a function of two order parameters, namely, the distance between the center-of-mass of two monomers () and the number of cross-contacts () among the backbone C atoms of two monomers.

Unfolding of Dynamical Events in the Early Stage of Insulin Dimer Dissociation.

The dissociation of an insulin dimer is an important biochemical event that could also serve as a prototype of dissociations in similar biomolecular assemblies. We use a recently developed multidimensional free energy landscape for insulin dimer dissociation to unearth the microscopic and mechanistic aspects of the initial stages of the process that could hold the key to understanding the stability and the rate. The following sequence of events occurs in the initial stages: (i) The backbone hydrogen bonds break partially at the antiparallel β-sheet junction, (ii) the two α-helices (chain B) move away from each other while several residues (chain A) move closer, and (iii) a flow of adjacent water molecules occurs into the junction region.

Study of entropy-diffusion relation in deterministic Hamiltonian systems through microscopic analysis.

Although an intimate relation between entropy and diffusion has been advocated for many years and even seems to have been verified in theory and experiments, a quantitatively reliable study and any derivation of an algebraic relation between the two do not seem to exist. Here, we explore the nature of this entropy-diffusion relation in three deterministic systems where an accurate estimate of both can be carried out. We study three deterministic model systems: (a) the motion of a single point particle with constant energy in a two-dimensional periodic potential energy landscape, (b) the same in the regular Lorentz gas where a point particle with constant energy moves between collisions with hard disk scatterers, and (c) the motion of a point particle among the boxes with small apertures.

Rotation of small diatomics in water-ethanol mixture: Multiple breakdowns of hydrodynamic predictions.

We study the rotational and translational dynamics of three small important linear molecules, namely, carbon monoxide (CO), nitric oxide (NO), and cyanide ion (CN) in water-ethanol mixtures, at different compositions. Here, we report a detailed study of the dynamics of these diatomics in water-ethanol binary mixtures for the first time. We find multiple anomalous results, namely, (i) faster rotational motion of CO and NO than CN, (ii) larger translational diffusion of CO and NO in pure ethanol than in water but the reverse for CN, (iii) a pronounced anomaly in the composition dependence of translational-rotational dynamics at low ethanol composition, and (iv) a re-entrant type behavior in the viscosity dependence of orientational relaxation.

DNA Solvation Dynamics.

Experiments have revealed that DNA solvation dynamics is characterized by multiple time scales ranging from a few picoseconds to a few hundred nanoseconds and in some cases even up to several microseconds. The last part of decay is not only slow but can also be described by a power law (PL). The microscopic origin of this PL is yet to be clearly established.

Enhancement of reaction rate in small-sized droplets: A combined analytical and simulation study.

Several recent mass spectrometry experiments reveal a marked enhancement of the reaction rate of organic reactions in microdroplets. This enhancement has been tentatively attributed to the accumulation of excess charge on a surface, which in turn can give rise to a lowering of activation energy of the reaction. Here we model the reactions in droplets as a three-step process: (i) diffusion of a reactant from the core of the droplet to the surface, (ii) search by diffusion of the reactant on the surface to find a reactive partner, and finally (iii) the intrinsic reaction leading to bond breaking and product formation.