Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable

Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.

Effect of Confinement and Coulomb Interactions on the Electronic Structure of the (111) LaAlO3/SrTiO3 Interface

A tight binding supercell approach is used for the calculation of the electronic structure of the (111) LaAlO3/SrTiO3 interface. The confinement potential at the interface is evaluated solving a discrete Poisson equation by means of an iterative method. In addition to the effect of the confinement, local Hubbard electron-electron terms are included at the mean-field level within a fully self-consistent procedure. The calculation carefully describes how the two-dimensional electron gas arises from the quantum confinement of electrons near the interface due to the band bending potential. The resulting electronic sub-bands and Fermi surfaces show full agreement with the electronic structure determined by angle-resolved photoelectron spectroscopy experiments. In particular, we analyse how the effect of local Hubbard interactions change the density distribution over the layers from the interface to the bulk. Interestingly, the two-dimensional electron gas at the interface is not depleted by local Hubbard interactions which indeed induce an enhancement of the electron density between the first layers and the bulk.

Discovery of Type II Interlayer Trions

In terms of interlayer trions, electronic excitations in van der Waals heterostructures (vdWHs) can be classified into Type I (i.e., two identical charges in the same layer) and Type II (i.e., two identical charges in the different layers). Type I interlayer trions are investigated theoretically and experimentally. By contrast, Type II interlayer trions remain elusive in vdWHs, due to inadequate free charges, unsuitable band alignment, reduced Coulomb interactions, poor interface quality, etc. Here, the first observation of Type II interlayer trions is reported by exploring band alignments and choosing an atomically thin organic-inorganic system-monolayer WSe₂ /bilayer pentacene heterostructure (1L + 2L HS). Both positive and negative Type II interlayer trions are electrically tuned and observed via PL spectroscopy. In particular, Type II interlayer trions exhibit in-plane anisotropic emission, possibly caused by their unique spatial structure and anisotropic charge interactions, which is highly correlated with the transition dipole moment of pentacene. The results pave the way to develop excitonic devices and all-optical circuits using atomically thin organic-inorganic bilayers.

Sub-gap Fano resonances in a topological superconducting wire with on-site Coulomb interactions

We consider theoretically a 1D-semiconducting wire with strong Rashba interaction in proximity withs-wave superconductor, driven into topological phase by external magnetic field. Additionally, we take into account on-site Coulomb interactions inside the wire. The system is modelled by a tight binding Hamiltonian with Rashba hopping term and induceds-wave superconductivity. Calculations are performed utilizing recursive Green's function method, and Coulomb interactions are treated selfconsistently within Hubbard I approximation. For the Hubbard levels residing withinp-wave superconducting gap, particle-hole symmetric four-resonance structure develops in the density of states, apart from Majorana resonance. One pair of particle-hole symmetric resonances is created by the discrete II-Hubbard levels of the particular site, and the second pair of Hubbard sub-bands originates from recursive summation over the sites of the wire. Quantum interference between both types of pairs of states creates in-gap charge-conjugated Fano resonances with opposite asymmetry factors. We demonstrate that when quantum interference is dominated by two-particle tunneling, the Majorana resonance is strongly diminished, while it is not altered when single-particle tunneling dominates in interference process. We also discuss some consequences for experimental distinction of true Majorana states, and show that on-site Coulomb interactions support the appearance of topological phase.

Trajectory displacement in a multi beam scanning electron microscope

The analytical theory of statistical Coulomb interactions allows to determine the trajectory displacement in a single rotationally symmetrical beam with well-behaved spatial and angular particle distributions. This can be used to estimate the trajectory displacement in a multi-beam system using the so called fully-filled segment approximation. This approach predicts full compensation of trajectory displacement for a specific setup of the system. We show that this prediction is not consistent with Monte Carlo simulations and we develop a new approach to the calculation, showing that two independent trajectory displacement contributions are present in a multi-beam system. We support this calculation with Monte Carlo simulations as well as with experimental data from a multi-beam system.

Magnetic reorientation transition in a three orbital model for Ca2RuO4-interplay of spin-orbit coupling, tetragonal distortion, and Coulomb interactions

Including the orbital off-diagonal spin and charge condensates in the self consistent determination of magnetic order within a realistic three-orbital model for the 4d4compound Ca2RuO4, reveals a host of novel features including strong and anisotropic spin-orbit coupling (SOC) renormalization, coupling of strong orbital magnetic moments to orbital fields, and a magnetic reorientation transition. Highlighting the rich interplay between orbital geometry and overlap, SOC, Coulomb interactions, tetragonal distortion, and staggered octahedral tilting and rotation, our investigation yields a planar antiferromagnetic (AFM) order for moderate tetragonal distortion, with easya-bplane and easybaxis anisotropies, along with small canting of the dominantlyyz,xzorbital moments. With decreasing tetragonal distortion, we find a magnetic reorientation transition from the dominantly planar AFM order to a dominantlycaxis ferromagnetic order with significantxyorbital moment.

Charge and heat current rectification by a double-dot system within the Coulomb blockade regime

Nanoscale rectifiers are known to have significant nanoelectronic and nanoheatronic applications. In the present work we theoretically analyze rectifying properties of a junction including a couple of quantum dots asymmetrically coupled to the electrodes. The charge and heat current rectification in the system is controlled by the dots occupation numbers and interdot Coulomb interactions. We examine the dependencies of the rectification ratio on the electron energy levels on the dots, on the intensity of electron-electron interactions, on the gate and bias voltages and on the thermal gradients applied across the system. It is shown that the considered double-dot system possesses significant potentialities as a common as well as a heat diode.

Constant Electricity Generation in Nanostructured Silicon by Evaporation-Driven Water Flow

Recently, hydrovoltaic technology emerged as a novel renewable energy harvesting method, which dramatically extends the capability to harvest water energy. However, the urgent issue restricting its device performance is poor carrier transport properties of the solid surface if large charged interface is considered simultaneously. Herein, a hydrovoltaic device based on silicon nanowire arrays (SiNWs), which provide large charged surface/volume ratio and excellent carrier transport properties, yields sustained electricity by a carrier concentration gradient induced by evaporation-induced water flow inside nanochannels. The device can yield direct current with a short-circuit current density of over 55 μA cm^-2 , which is three orders larger than a previously reported analogous device (approximately 40 nA cm^-2 ). Moreover, it exhibits a constant output power density of over 6 μW cm^-2 and an open-circuit voltage of up to 400 mV. Our finding may pave a way for developing energy-harvesting devices from ubiquitous evaporation-driven internal water flow in nature with semiconductor material of silicon.

Short solvent model for ion correlations and hydrophobic association

Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent-solvent and solute-solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

Exciton-Exciton Interactions in Coaxial Double Quantum Rings

We study theoretically the quantum states of two interacting excitons in coaxial double quantum rings. An interplay between exciton–exciton Coulomb interactions and specific geometry of the structure leads to the emergence of peculiar energy spectrum of two exciton system. We develop a semi-analytic approach providing highly accurate energies of system in the wide range of values of geometrical parameters relevant to experimental realizations.

The electrostatic core of the outer membrane protein X from E. coli

Electrostatic side chain contacts can contribute substantial interaction energy terms to the stability of proteins. The impact of electrostatic interactions on the structure and architecture of outer membrane proteins is however not well studied compared to soluble proteins. Here, we report the results of a systematic study of all charged side chains of the E. coli outer membrane protein X (OmpX). The data identify three distinct salt-bridge clusters in the core of OmpX that contribute significantly to protein stability in dodecylphosphocholine detergent micelles. The three clusters form an "electrostatic core" of the membrane protein OmpX, corresponding in its architectural role to the hydrophobic core of soluble proteins. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.