Advances in Physics-X

Water adsorption and dynamics on graphene and other 2D materials: Computational and experimental advances
Sacchi M and Tamtögl A
The interaction of water and surfaces, at molecular level, is of critical importance for understanding processes such as corrosion, friction, catalysis and mass transport. The significant literature on interactions with single crystal metal surfaces should not obscure unknowns in the unique behaviour of ice and the complex relationships between adsorption, diffusion and long-range inter-molecular interactions. Even less is known about the atomic-scale behaviour of water on novel, non-metallic interfaces, in particular on graphene and other 2D materials. In this manuscript, we review recent progress in the characterisation of water adsorption on 2D materials, with a focus on the nano-material graphene and graphitic nanostructures; materials which are of paramount importance for separation technologies, electrochemistry and catalysis, to name a few. The adsorption of water on graphene has also become one of the benchmark systems for modern computational methods, in particular dispersion-corrected density functional theory (DFT). We then review recent experimental and theoretical advances in studying the single-molecular motion of water at surfaces, with a special emphasis on scattering approaches as they allow an unparalleled window of observation to water surface motion, including diffusion, vibration and self-assembly.
Advances in multi-dimensional coherent spectroscopy of semiconductor nanostructures
Moody G and Cundiff ST
Multi-dimensional coherent spectroscopy (MDCS) has become an extremely versatile and sensitive technique for elucidating the structure, composition, and dynamics of condensed matter, atomic, and molecular systems. The appeal of MDCS lies in its ability to resolve both individual-emitter and ensemble-averaged dynamics of optically created excitations in disordered systems. When applied to semiconductors, MDCS enables unambiguous separation of homogeneous and inhomogeneous contributions to the optical linewidth, pinpoints the nature of coupling between resonances, and reveals signatures of many-body interactions. In this review, we discuss the implementation of MDCS to measure the nonlinear optical response of excitonic transitions in semiconductor nanostructures. Capabilities of the technique are illustrated with recent experimental studies that advance our understanding of optical decoherence and dissipation, energy transfer, and many-body phenomena in quantum dots and quantum wells, semiconductor microcavities, layered semiconductors, and photovoltaic materials.
Density-functional tight-binding: basic concepts and applications to molecules and clusters
Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A and Rapacioli M
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
Computational methods and theory for ion channel research
Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A and Roux B
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
Assessing membrane material properties from the response of giant unilamellar vesicles to electric fields
Aleksanyan M, Faizi HA, Kirmpaki MA, Vlahovska PM, Riske KA and Dimova R
Knowledge of the material properties of membranes is crucial to understanding cell viability and physiology. A number of methods have been developed to probe membranes in vitro, utilizing the response of minimal biomimetic membrane models to an external perturbation. In this review, we focus on techniques employing giant unilamellar vesicles (GUVs), model membrane systems, often referred to as minimal artificial cells because of the potential they offer to mimick certain cellular features. When exposed to electric fields, GUV deformation, dynamic response and poration can be used to deduce properties such as bending rigidity, pore edge tension, membrane capacitance, surface shear viscosity, excess area and membrane stability. We present a succinct overview of these techniques, which require only simple instrumentation, available in many labs, as well as reasonably facile experimental implementation and analysis.
Recent Advancements in Nanophotonics for Optofluidics
Yang S, Hong C, Zhu G, Anyika T, Hong I and Ndukaife JC
Optofluidics is dedicated to achieving integrated control of particle and fluid motion, particularly on the micrometer scale, by utilizing light to direct fluid flow and particle motion. The field has seen significant growth recently, driven by the concerted efforts of researchers across various scientific disciplines, notably for its successful applications in biomedical science. In this review, we explore a range of optofluidic architectures developed over the past decade, with a primary focus on mechanisms for precise control of micro and nanoscale biological objects and their applications in sensing. Regarding nanoparticle manipulation, we delve into mechanisms based on optical nanotweezers using nanolocalized light fields and light-based hybrid effects with dramatically improved performance and capabilities. In the context of sensing, we emphasize those works that used optofluidics to aggregate molecules or particles to promote sensing and detection. Additionally, we highlight emerging research directions, encompassing both fundamental principles and practical applications in the field.