Browse Articles

The carRS-ompV-virK operon of Vibrio cholerae senses antimicrobial peptides and activates the expression of multiple resistance systems

Multi-objective contextual bandits in recommendation systems for smart tourism

Predictors of Boolean2.0 remission in rheumatoid arthritis identified using smart disease management system data

A study on neutrosophic $$\mathscr {T}_{\textrm{1k}}$$-semantic segmentation for iris image recognition with Gaussian and Poisson noises

Characterization of progressive damage behaviour and failure mechanism of carbon fiber reinforced composite laminates

Quantum dynamics of coupled excitons and phonons in chain-like systems: Tensor train approaches and higher-order propagators

We investigate tensor-train approaches to the solution of the time-dependent Schrödinger equation for chain-like quantum systems with on-site and nearest-neighbor interactions only. Using efficient low-rank tensor train representations, we aim at reducing memory consumption and computational costs. As an example, coupled excitons and phonons modeled in terms of Fröhlich–Holstein type Hamiltonians are studied here. By comparing our tensor-train-based results with semi-analytical results, we demonstrate the key role of the ranks of the quantum state vectors. Typically, an excellent quality of solutions is found only when the maximum number of ranks exceeds a certain value. One class of propagation schemes builds on splitting the Hamiltonian into two groups of interleaved nearest-neighbor interactions commutating within each of the groups. In particular, the fourth-order Yoshida–Neri and the eighth-order Kahan–Li symplectic composition yield results close to machine precision. Similar results are found for fourth and eighth order global Krylov scheme. However, the computational effort currently restricts the use of these four propagators to rather short chains, which also applies to propagators based on the time-dependent variational principle, typically used for matrix product states. Yet, another class of propagators involves explicit, time-symmetrized Euler integrators. Especially, the fourth-order variant is recommended for quantum simulations of longer chains, even though the high precision of the splitting schemes cannot be reached. Moreover, the scaling of the computational effort with the dimensions of the local Hilbert spaces is much more favorable for the differencing than for splitting or variational schemes.

Vibrational second-order perturbation theory based on curvilinear coordinates: Thermochemical applications

This work improves and extends a general and robust workflow for the computation of anharmonic vibrational frequencies to thermodynamic functions, paving the way toward the study of large flexible molecules. The key new feature is the extension of closed-form expressions for both zero-point vibrational energies and partition functions to second-order vibrational perturbation theory based on curvilinear internal coordinates. The use of curvilinear coordinates enables the reduction of couplings between different degrees of freedom, enriching the arsenal of existing vibrational approaches, and can lead to effective, low-dimensional linear-scaling models. The accuracy of the results obtained for some prototypical systems paves the way toward the systematic use of this new implementation in the study of molecules containing a few dozen atoms, as exemplified by the test cases of a molecular motor, a nucleoside, and two hormones.

Exploring the role of hydrodynamic interactions in spherically confined drying colloidal suspensions

We study the distribution of colloidal particles confined in drying spherical freestanding droplets using both dynamic density functional theory (DDFT) and particle-based simulations. In particular, we focus on the advection-dominated regime typical of aqueous droplets drying at room temperature and systematically investigate the role of hydrodynamic interactions (HIs) during this nonequilibrium process. In general, drying produces transient particle concentration gradients within the droplet in this regime, with a considerable accumulation of particles at the droplet’s liquid–vapor interface. We find that these gradients become significantly larger with pairwise HIs between colloidal particles instead of a free-draining hydrodynamic approximation; however, the solvent’s boundary conditions at the droplet’s interface (unbounded, slip, or no-slip) do not have a significant effect on the particle distribution. DDFT calculations leveraging the radial symmetry of the drying droplet are in excellent agreement with particle-based simulations for free-draining hydrodynamics, but DDFT unexpectedly fails for pairwise HIs after the particle concentration increases during drying, manifesting as an ejection of particles from the droplet. We hypothesize that this unphysical behavior originates from an inaccurate approximation of the two-body density correlations based on the bulk pair correlation function, which we support by measuring the confined equilibrium two-body density correlations using particle-based simulations. We identify some potential strategies for addressing this issue in DDFT.

Conformational properties of active polar semiflexible phantom polymers

The conformational properties of semiflexible active polar linear and ring phantom polymers are analyzed analytically to shed light on their dependence on activity. Special attention is paid to the influence of the implemented bond force for discrete and continuous polymer models. In detail, the Gaussian semiflexible polymer model and a model with a harmonic bond potential with finite bond length are considered. The studies reveal the immanent effects of the particular bond model on the polymer conformations as well as on the discrete or continuous representation. For continuum models, activity implies polymer end effects only, whereas for discrete models, all bonds can contribute to activity-dependent conformational changes. Ring polymers lack end effects; hence, continuous rings exhibit the same conformations as passive polymers. Similarly, the conformations of inextensible continuous polymers (Kratky–Porod worm-like chain) are activity-independent. These findings are in contrast to passive polymers, where a wide spectrum of bond potentials capture their generic features. Hence, this universality is broken by activity, and a model must be carefully selected to capture the characteristics observed in experiments.

Tuning partial charges of alkyl alcohols to improve simulated fluid properties

Standard simulation interaction parameters sometimes predict liquid properties at variance with experiment, especially for polar liquids. In this work, we systematically scaled the partial charges of three alkyl alcohols to evaluate whether adjusting the partial charges, and thus the electrostatic interactions, can improve agreement with experimental values of key liquid properties, including the dielectric constant, vapor pressure, density, and self-diffusion coefficient. Changing the partial charges also affects liquid structures, which are evaluated through a hydrogen bond analysis. We found that modest adjustment factors applied to all partial charges improve values for computed properties, but too large an adjustment causes string-like aggregation of molecular dipoles and inhibits system dynamics.

Nonequilibrium friction and free energy estimates for kinetic coarse-graining—Driven particles in responsive media

Predicting the molecular friction and energy landscapes under nonequilibrium conditions is key to coarse-graining the dynamics of selective solute transport through complex, fluctuating, and responsive media, e.g., polymeric materials such as hydrogels, cellular membranes, or ion channels. The analysis of equilibrium ensembles already allows such a coarse-graining for very mild nonequilibrium conditions. However, in the presence of stronger external driving and/or inhomogeneous setups, the transport process is governed apart from a potential of mean force also by a nontrivial position- and velocity-dependent friction. It is therefore important to find suitable and efficient methods to estimate the mean force and the friction landscape, which can then be used in a low-dimensional, coarse-grained Langevin framework to predict the system’s transport properties and timescales. In this work, we evaluate different coarse-graining approaches based on constant-velocity constraint simulations for generating such estimates using two model systems, which are a 1D responsive barrier as a minimalistic model and a single tracer driven through a 3D bead-spring polymer membrane as a more sophisticated problem. Finally, we demonstrate that the estimates from 3D constant-velocity simulations yield the correct velocity-dependent friction, which can be directly utilized for coarse-grained (1D) Langevin simulations with constant external driving forces.

Nonequilibrium dynamics of the helix–coil transition in polyalanine

In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix–coil transition is simulated using molecular dynamics simulations. At the start of the transition, short 310-helices form, seemingly leading to the molecule becoming more aspherical midway through the collapse. After the completed collapse, the formation of α-helices becomes the prevalent ordering mechanism leading to helical bundles, a typical structural motif representative of the equilibrium behavior of longer chains. The dynamics of this transition is quantified in terms of the power-law scaling of two associated relaxation times as a function of chain length.

Equation-of-motion internally contracted multireference unitary coupled-cluster theory

The accurate computation of excited states remains a challenge in electronic structure theory, especially for systems with a ground state that requires a multireference treatment. In this work, we introduce a novel equation-of-motion (EOM) extension of the internally contracted multireference unitary coupled-cluster framework (ic-MRUCC), termed EOM-ic-MRUCC. EOM-ic-MRUCC follows the transform-then-diagonalize approach, in analogy to its non-unitary counterpart [Datta and Nooijen, J. Chem. Phys. 137, 204107 (2012)]. By employing a projective approach to optimize the ground state, the method retains additive separability and proper scaling with system size. We show that excitation energies are size-intensive if the EOM operator satisfies the “killer” and the projective conditions. Furthermore, we propose to represent changes in the reference state upon electron excitation via projected many-body operators that span the active orbitals and show that the EOM equations formulated in this way are invariant with respect to active orbital rotations. We test the EOM-ic-MRUCC method truncated to single and double excitations by computing the potential energy curves for several excited states of a BeH2 model system, the HF molecule, and water undergoing symmetric dissociation. Across these systems, our method delivers accurate excitation energies and potential energy curves within 5 mEh (∼0.14 eV) from full configuration interaction. We find that truncating the Baker–Campbell–Hausdorff series to fourfold commutators contributes negligible errors (on the order of 10−5Eh or less), offering a practical route to highly accurate excited-state calculations with reduced computational overhead.

A general formalism to describe the stereodynamics of bond axis orientation in the scattering of a linear molecule with an atom

One of the aims of the chemist is to obtain the greatest possible level of control over the outcome of a reaction. A factor that can influence such outcomes is the so-called steric effect. The underpinning idea of this effect is that the mutual orientation of the collision partners at the moment of collision may impact the nature of the products. The steric effect has been studied in a variety of ways, notably using optical methods, as well as making use of both magnetic and electric fields, to orient or align reactants. Here, we present a general framework for interpreting and evaluating steric effects in collisions of open shell linear molecules with an atom in the presence of an electric field. While in previous studies, the theory has been limited to the specific system of interest, such as for the end-on collisions of NO(X), this new formalism provides a fundamental basis for examining any system of this type. Some examples of the utility and power of this formalism are also provided. This theory may then be built on further in the future to provide greater insights into the stereodynamics of collisions and, hence, provide the foundation for deeper study into how the steric effect may be harnessed for control.

pH-antenna residues trigger a large-scale conformational change in the large extracellular loop domain of the CD81 human receptor

CD81 is a human receptor that clusters into microdomains to mediate cell signaling processes. Previous structural studies on the CD81 large-extracellular-loop domain (CD81LEL) proposed that its conformation (ranging from closed to open) may depend on environmental pH conditions. However, the precise mechanism governing CD81LEL plasticity has remained unconfirmed until now. Here, by combining molecular dynamics simulations and spectroscopic experiments on CD81LEL, we show that the mechanism underlying the dependence of the changes in pH to the opening of CD81LEL relates to the modulation of the solvation shell by “antenna” residues. The antenna residues are D139 and E188. Under acidic conditions, such residues generate a signal cascade propagating through the CD81LEL molecule changing the local solvation that, in turn, acts as an effector of the closed-to-open conformational transition. We further proved the key role of D139 and E188 by introducing mutations that switch off their sensitivity to pH. As expected, the mutations stabilize the closed conformation. This signal transduction mechanism might play a role in other cellular receptors that function along the endosomal pathway.

Electronic quenching of N(2D) in collision with CO(1Σ+) via spin-forbidden transitions

In nitrogen-rich atmospheres under extreme conditions, the N2 molecule dissociates into atomic nitrogen in different electronic states. In particular, N(2D) is known to be reactive and to drive a complex chemistry in such regimes. If the atmosphere also contains carbon monoxide (such as Earth and Mars), several collisional processes with nitrogen-, carbon-, and oxygen-bearing species are relevant. Here, we employ a set of three accurate and global potential energy surfaces for the CNO system to study the N(2D) + CO → N(4S) + CO electronic quenching process, using the quasiclassical trajectories approach coupled with two different surface hopping schemes. Experimental measurements of the quenching rate coefficient are available only at room temperature, and our computational predictions show good agreement. We further provide the temperature dependence of the rate coefficients for the first time, extending to the hyperthermal regime. The effect of the initial rovibrational state of CO on the reactivity, as well as the distribution of energy in the products, is also unveiled.

Hollow silver nanoparticle formation under ultrafast laser irradiation via single- and multiple-shots

The morphological changes induced in metal nanoparticles by the interaction with laser pulses have an important impact on their optical response. In this work, by means of an atomistic model, we have studied the formation of cavities in spherical silver nanoparticles embedded in amorphous silica using one or more femtosecond laser pulses. The model allows us to identify the different processes that lead to cavity formation and how they affect the variation of the aspect ratio, i.e., the relationship between the size of the cavity and that of the metallic sphere. The model is used to explain experiments revealing the conditions necessary to produce hollow metal nanoparticles. New information on hollow nanoparticle formation both in single shot and multiple shot regimes is reported. The atomistic model in combination with an optical model constitutes a tool to tune the properties of hollow nanoparticles, as shown in this paper. This way, we can achieve a fine control over the aspect ratio and, thus, about the localized surface plasmon resonance of the hollow nanoparticles.

Novel pseudomomentum-translational sum rule for the molecular Berry curvature

The molecular Berry curvature plays an important role for electronic structure calculations within the adiabatic Born–Oppenheimer approximation and is connected to many magnetic phenomena such as the Aharonov–Bohm and the chirality-induced spin selectivity effect. For molecules in external magnetic fields, the Berry curvature is essential to achieve a qualitatively correct description of nuclear motion. Here, it is responsible for screening the Lorentz forces acting on moving nuclear charges. This connection has recently been exploited to derive a new type of population analysis known as Berry charges. In this work, we derive a novel sum rule for the molecular Berry curvature. This pseudomomentum-translational sum rule is then used to reveal the connection between Berry charges and the well-known generalized atomic polar tensor (GAPT) charges. Furthermore, we present an efficient integral-direct implementation of the molecular Berry curvature for molecules in finite magnetic fields into the Turbomole program suite. This is used to further demonstrate the connection between Berry and GAPT charges for a variety of larger molecules, comparing the results to other established types of partial charges.

Parametric sensitivity analysis for models of reaction networks within interacting compartments

Models of reaction networks within interacting compartments (RNIC) are a generalization of stochastic reaction networks. It is most natural to think of the interacting compartments as “cells” that can appear, degrade, split, and even merge, with each cell containing an evolving copy of the underlying stochastic reaction network. Such models have a number of parameters, including those associated with the internal chemical model and those associated with the compartment interactions, and it is natural to want efficient computational methods for the numerical estimation of sensitivities of model statistics with respect to these parameters. Motivated by the extensive work on computational methods for parametric sensitivity analysis in the context of stochastic reaction networks over the past few decades, we provide a number of methods in the basic RNIC setting. Provided methods include the (unbiased) Girsanov transformation method (also called the likelihood ratio method) and a number of coupling methods for the implementation of finite differences, each motivated by methods from previous work related to stochastic reaction networks. We provide several numerical examples comparing the various methods in the new setting. We find that the relative performance of each method is in line with its analog in the “standard” stochastic reaction network setting. We have made all the MATLAB codes used to implement the various methods freely available for download.

The open driven two-level system at conical intersections of quasienergies

We study the stationary state of an ac-driven two-level system under particle exchange with a fermionic environment. A particular question addressed is whether there exist limits in which the populations of the Floquet states are determined by their quasienergies or their mean energies, respectively. The focus lies on parameters in the vicinity of conical intersections of quasienergies at which the two kinds of energies behave rather differently, such that the characteristics of the two intuitive limits are most pronounced. A main finding is a crossover from a Floquet–Gibbs-like state at low temperatures to a mean-energy dominated state at intermediate temperatures. Analytical estimates are confirmed by numerical calculations.