Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

We discuss aspects of the physics of proteins at low temperature as they are reflected in highly resolved optical spectra of molecular probes. Typical probe molecules are heme-like dyes, aromatic amino acids, but also extended molecular aggregates in light harvesting complexes. We put emphasis on the interactions of the probe with its protein environment, on the range of these interactions, on their specific behavior in external fields, as well as on the characteristic parameters of the protein which can be determined with optical techniques at low temperatures but are not easily accessible otherwise. However, the focus of the review is on spectral diffusion physics of proteins, i.e. on their motion in conformational phase space, and on how this motion is reflected in the optical spectra. These structure changing-processes reflect the non-ergodic nature of low temperature proteins. They are most clearly detected at low temperature where the resolution of the experiment is close to the ultimate limit as given by the natural linewidth and where the dynamics become slow enough to be conveniently measured. In part I we discuss aspects of ensemble experiments, in part II we focus on experiments with single protein complexes. We offer lines of reasoning which may serve as guidelines for an understanding of the phenomena.     

Micro-hydrodynamics

Micro-hydrodynamics is a term used to describe the search for and study of hydrodynamic phenomena at microscopic scales. The principal method used to accomplish this research is molecular dynamic (MD) simulations. Computational limits on MD models restrict the size of the system and simulation time. Typically, the length scales are on the order of 10–1000 Å and time scales 10–1000 psec (thus the qualifier micro). We review the results of our research in this area. We use MD to model channel flow, flow past a plate, flow past a cylinder, and Rayleigh-Benard convection. In general, we find that the behavior in these models agrees with results obtained from experiment and more traditional theoretical approaches, such as solving the Navier-Stokes equations. In addition to the appearance of spatial and temporal patterns, we observe scaling relations in agreement with those predicted by macroscopic hydrodynamics. In some specific situations, we can see the breakdown of Navier-Stokes theory and estimate its limits.     

Catalysis and corrosion: the theoretical surface-science context

Numerous experiments in ultra-high vacuum as well as (T=0 K, p=0) theoretical studies on surfaces have been performed over the last decades in order to gain a better understanding of the mechanisms, which, for example, underlie the phenomena of catalysis and corrosion. Often the results achieved this way cannot be extrapolated directly to the technologically relevant situation of finite temperature and high pressure. Accordingly, modern surface science has realized that bridging the so-called pressure gap (getting out of the vacuum) is the inevitable way to go. Of similar importance are studies in which the temperature is changed systematically (warming up and cooling down). Both aspects are being taken into account in recent experiments and ab initio calculations.

In this paper we stress that there is still much to learn and important questions to be answered concerning the complex atomic and molecular processes which occur at surfaces and actuate catalysis and corrosion, although significant advances in this exciting field have been made over the years. We demonstrate how synergetic effects between theory and experiment are leading to the next step, which is the development of simple concepts and understanding of the different modes of the interaction of chemisorbed species with surfaces. To a large extent this is being made possible by recent developments in theoretical methodology, which allow to extend the ab initio (i.e., starting from the self-consistent electronic structure) approach to poly-atomic complexes with 10,000 and more atoms, time scales of seconds, and involved statistics (e.g., ab initio molecular dynamics with 10,000 and more trajectories). In this paper we will

1. sketch recent density–functional theory based hybrid methods, which bridge the length and time scales from those of electron orbitals to meso- and macroscopic proportions, and

2. present some key results on properties of surfaces, demonstrating their role in corrosion and heterogeneous catalysis. In particular we discuss

◦ the influence of the ambient gas phase on the surface structure and stoichiometry,

◦ adsorbate phase transitions and thermal desorption, and

◦ the role of atoms' dynamics and statistics for the surface chemical reactivity.

Modeling and Analysis of Social Phenomena: Challenges and Possible Research Directions

This opening editorial aims to interest researchers and encourage novel research in the closely related fields of sociophysics and computational social science. We briefly discuss challenges and possible research directions in the study of social phenomena, with a particular focus on opinion dynamics. The aim of this Special Issue is to allow physicists, mathematicians, engineers and social scientists to show their current research interests in social dynamics, as well as to collect recent advances and new techniques in the analysis of social systems.     

Phase Separation in Confined Geometries

The kinetics of phase separation or domain growth, subsequent to temperature quenches of binary mixtures from the one-phase region into the miscibility gap, still remains a challenging problem of nonequilibrium statistical mechanics. We have an incomplete understanding of many aspects of the growth of concentration inhomogeneities, including the effect of surfaces on this process, and the interplay with wetting phenomena and finite-size effects in thin films. In the present paper, an overview of the simulation approaches to this problem is given, with an emphasis on solutions of a diffusive Ginzburg-Landau model. We also discuss two recent alternative approaches: a local molecular field approximation to the Kawasaki spin exchange model on a lattice; and molecular dynamics simulations of a fluid binary Lennard-Jones mixture. A brief outlook to open questions is also given.     

Attractive and Repulsive Gravity

We discuss the circumstances under which gravity might be repulsive rather than attractive. In particular we show why our standard solar system distance scale gravitational intuition need not be a reliable guide to the behavior of gravitational phenomena on altogether larger distance scales such as cosmological, and argue that in fact gravity actually gets to act repulsively on such distance scales. With such repulsion a variety of current cosmological problems (the flatness, horizon, dark matter, universe age, cosmic acceleration and cosmological constant problems) are then all naturally resolved.     

Multi-scale plasma simulation by the interlocking of magnetohydrodynamic model and particle-in-cell kinetic model

Many kinds of simulation models have been developed to understand the complex plasma systems. However, these simulation models have been separately performed because the fundamental assumption of each model is different and restricts the physical processes in each spatial and temporal scales. On the other hand, it is well known that the interactions among the multiple scales may play crucial roles in the plasma phenomena (e.g. magnetic reconnection, collisionless shock), where the kinetic processes in the micro-scale may interact with the global structure in the fluid dynamics. To take self-consistently into account such multi-scale phenomena, we have developed a new simulation model by directly interlocking the fluid simulation of the magnetohyrdodynamics (MHD) model and the kinetic simulation of the particle-in-cell (PIC) model. The PIC domain is embedded in a small part of MHD domain. The both simulations are performed simultaneously in each domain and the bounded data are frequently exchanged each other to keep the consistency between the models. We have applied our new interlocked simulation to Alfvén wave propagation problem as a benchmark test and confirmed that the waves can propagate smoothly through the boundaries of each domain.     

Acoustics of shells

We discuss the physical phenomena that arise in the scattering of acoustic waves from fluid-immersed elastic (metal) shells which may be either evacuated or filled with the same or with a different fluid. The phenomena occurring here include the formation of circumferential (peripheral, or “surface”) waves that circumnavigate the shells, propagating either as elastic waves in the shell material or as fluid-borne waves of the Scholte-Stoneley type in the external or the internal fluid. By phase matching along a closed circuit, these waves may lead to prominent resonances in the acoustic scattering amplitude, and we demonstrate how the set of observed resonance frequencies is related to the dispersive phase velocities of the surface waves, so that one can be determined from the other. In addition, we discuss how the dispersion curves (phase velocity plotted vs. frequency) of the various types of surface waves show repulsion phenomena due to their coupling through the boundary conditions. The cases of spherical and cylindrical shells are investigated here as typical examples, and as an introductory topic we additionally mention surface waves on plates where related phenomena also occur. Both the theoretical and the experimental aspects of the present subject will be considered, including the experimental visualization of the surface waves.     

On non-Fermi liquid quantum critical points in heavy fermion metals

Heavy electron metals on the verge of a quantum phase transition to magnetism show a number of unusual non-Fermi liquid properties which are poorly understood. This article discusses in a general way various theoretical aspects of this phase transition with an eye toward understanding the non-Fermi liquid phenomena. We suggest that the non-Fermi liquid quantum critical state may have a sharp Fermi surface with power law quasiparticles but with a volume not set by the usual Luttinger rule. We also discuss the possibility that the electronic structure change associated with the possible Fermi surface reconstruction may diverge at a different time/length scale from that associated with magnetic phenomena.     

Quantum recurrences in driven power-law potentials

The recurrence phenomena of an initially well-localized wave packet are studied in periodically driven power-law potentials. For our general study we divide the potentials in two kinds, namely tightly binding and loosely binding potentials. In the presence of an external periodically modulating force, these potentials may exhibit classical and quantum chaos. We show that in the dynamics of a quantum wave packet in the modulated power law potentials quantum recurrences occur at various time scales. We develop general analytical relations for these times and discuss their parametric dependence.     

Thermal properties of two-dimensional materials

Two-dimensional(2D) materials, such as graphene, phosphorene, and transition metal dichalcogenides(e.g., Mo S2 and WS2), have attracted a great deal of attention recently due to their extraordinary structural, mechanical, and physical properties. In particular, 2D materials have shown great potential for thermal management and thermoelectric energy generation. In this article, we review the recent advances in the study of thermal properties of 2D materials. We first review some important aspects in thermal conductivity of graphene and discuss the possibility to enhance the ultra-high thermal conductivity of graphene. Next, we discuss thermal conductivity of Mo S2 and the new strategy for thermal management of Mo S2 device. Subsequently, we discuss the anisotropic thermal properties of phosphorene. Finally, we review the application of 2D materials in thermal devices, including thermal rectifier and thermal modulator.     

Non-equilibrium phenomena and molecular reaction dynamics: mode space,energy space and conformer space

The ability to characterise and control matter far away from equilibrium is a frontier challenge facing modern science. In this article, we sketch out a heuristic structure for thinking about the different ways in which non-equilibrium phenomena can impact molecular reaction dynamics. Our analytical schema includes three different regimes, organised according to increasing dynamical resolution: at the lowest resolution, we have conformer phase space, at an intermediate resolution, we have energy space; and at the highest resolution, we have mode space. Within each regime, we discuss practical definitions of non-equilibrium phenomena, mostly in terms of the corresponding relaxation timescales. Using this analytical framework, we discuss some recent non-equilibrium reaction dynamics studies spanning isolated small-molecule ensembles, gas-phase ensembles and solution-phase ensembles. This includes new results that provide insight into how non-equilibrium phenomena impact the solution-phase alkene–hydroboration reaction. We emphasise that interesting non-equilibrium dynamical phenomena often occur when the relaxation timescales characterising each regime are similar. In closing, we reflect on outstanding challenges and future research directions to guide our understanding of how non-equilibrium phenomena impact reaction dynamics.     

Recent advances on “ordered water monolayer that does not completely wet water” at room temperature

The molecular scales behavior of interfacial water at the solid/liquid interfaces is of a fundamental significance in a diverse set of technical and scientific contexts,ranging from the efficiency of oil mining to the activity of biological molecules.Recently,it has become recognized that,both the physical interactions and the surface morphology have significant impact on the behavior of interfacial water,including the water structures as well as the wetting properties of the surface.In this review,we summarize some of recent advances in the atom-level pictures of the interfacial water,which exhibits the ordered character on various solid surfaces at room or cryogenic temperature.Special focus has been devoted to the wetting phenomenon of"ordered water monolayer that does not completely wet water"and the underlying mechanism on model and some real solid surfaces at room temperature.The possible applications of this phenomenon are also discussed.     

Water reorientation in the hydration shells of hydrophilic and hydrophobic solutes

We discuss some key aspects of our recent theoretical work on water reorientation dynamics,which is important in a wide range of phenomena,including aqueous phase chemical reactions,protein folding,and drug binding to proteins and DNA. It is shown that,contrary to the standard conception that these dynamics are diffusional,the reorientation of a water molecule occurs by sudden,large amplitude angular jumps. The mechanism involves the exchange of one hydrogen bond for another by the reorienting water,and the process can be fruitfully viewed as a chemical reaction. The results for reorientation times,which can be well described analytically,are discussed in the context of the molecular level interpretation of recent ultrafast infrared spectroscopic results,focusing on the concepts of structure making/breaking and solvent 'icebergs'.     

Nature of quantum recurrences in coupled higher dimensional systems

We investigate recurrence phenomena in coupled two degrees of freedom systems. It is shown that an initial well localized wave packet displays recurrences even in the presence of coupling in these systems. We discuss the interdependence of time scales namely classical period and quantum revival time and explain the significance of initial conditions.     

Nanotechnology convergence and modeling paradigm of sustainable energy system using polymer electrolyte membrane fuel cell as a benchmark example

Developments in nanotechnology have led to innovative progress and converging technologies in engineering and science. These demand novel methodologies that enable efficient communications from the nanoscale all the way to decision-making criteria for actual production systems. In this paper, we discuss the convergence of nanotechnology and novel multi-scale modeling paradigms by using the fuel cell system as a benchmark example. This approach includes complex multi-phenomena at different time and length scales along with the introduction of an optimization framework for application-driven nanotechnology research trends. The modeling paradigm introduced here covers the novel holistic integration from atomistic/molecular phenomena to meso/continuum scales. System optimization is also discussed with respect to the reduced order parameters for a coarse-graining procedure in multi-scale model integration as well as system design. The development of a hierarchical multi-scale paradigm consolidates the theoretical analysis and enables large-scale decision-making of process level design, based on first-principles, and therefore promotes the convergence of nanotechnology to sustainable energy technologies.