Analyzing Microdomains in Biological Membranes Using Fluorescence Techniques

It is becoming increasingly clear that various lipids and proteins in the plasma membrane are not distributed homogeneously but are organized in compositionally and functionally variable microdomains. Fluorescence techniques have contributed significantly to our understanding of membrane structure and function. Here we review recent studies using fluorescence methods to detect membrane domains in intact cells. We also discuss the current limitations in the available techniques and the models used to interpret experimental data.     

The application of quasi-elastic neutron scattering techniques (QENS) in surface diffusion studies

Neutron scattering techniques such as quasi-elastic neutron scattering, QENS, have proven to be well-suited tools for studying structure and dynamics of surface adsorbed molecules. In contrast to many more widely used surface science techniques neutron scattering allows the microscopic characterization of samples under a wide range of thermodynamic conditions, as the samples are not constrained to ultra high vacuum environment. Moreover, neutron scattering allows the separation of coherent and incoherent scattering, giving access to different diffusive mechanisms such as single particle diffusion, mass transport, rotations, or vibrations. In this paper we will review recent progress and the state-of-the-art in neutron scattering experiments on surface adsorbed molecules in the sub-monolayer coverage range with a specific emphasis on studies of carbon and other high surface density substrates. We will also cover recent progress in theoretical modeling, since the usefulness of neutron scattering data on surface dynamics can be strongly enhanced by computational modeling, such as molecular dynamics (MD) simulations and the development of analytical models.     

Critical dynamics of magnets

We review our current understanding of the critical dynamics of magnets above and below the transition temperature with focus on the effects due to the dipole-dipole interaction present in all real magnets. Significant progress in our understanding of real ferromagnets in the vicinity of the critical point has been made in the last decade through improved experimental techniques and theoretical advances in taking into account realistic spin-spin interactions. We start our review with a discussion of the theoretical results for the critical dynamics based on recent renormalization group, mode coupling and spin-wave theories. A detailed comparison is made of the theory with experimental results obtained by different measuring techniques, such as neutron scattering, hyperfine interaction, muon spin resonance, electron spin resonance, and magnetic relaxation, in various materials. Furthermore we discuss the effects of dipolar interaction on the critical dynamics of three-dimensional isotropic antiferromagnets and uniaxial ferromagnets. Special attention is also paid to a discussion of the consequences of dipolar anisotropies on the existence of magnetic order and the spin-wave spectrum in two-dimensional ferromagnets and antiferromagnets. We close our review with a formulation of critical dynamics in terms of nonlinear Langevin equations.     

Perspectives of solution NMR spectroscopy for structural and functional studies of integral membrane proteins

This article discusses future perspectives of solution NMR spectroscopy to study structures and functions of integral membrane proteins at atomic resolution, based on a review of recent progress in this area. Several selected examples of structure determinations, as well as functional studies of integral membrane proteins are highlighted. We expect NMR spectroscopy to make future key scientific contributions to understanding membrane protein function, in particular for large membrane protein systems with known three-dimensional structure. Such situations can benefit from the fact that functional NMR studies have substantially less limitations by molecular size than a full de novo structure determination. Therefore, the general potential for NMR spectroscopy to solve biologic key questions associated with integral membrane proteins is very promising.     

用异核多维NMR技术研究蛋白质动力学

蛋白质在溶液中的三维空间结构、动力学与蛋白质生物功能的关系是在分子水平上理解生命现象的重要基础. NMR技术在研究蛋白质动力学方面具有独特的优势,所能表征的运动过程相关时间尺度很广. 文章综述了异核多维NMR技术研究蛋白质动力学的实验技术和理论方法,介绍了描述蛋白质动力学的内运动参量的意义和Model-Free 方法,并举例说明¹⁵N弛豫测量实验被用于研究蛋白质及其与配体复合物的动力学.      

Femtosecond magneto-optical processes in metals

Ultrafast magneto-optical techniques, using femtosecond laser pulses, are a powerful tool for investigating the magnetization dynamics in metallic materials. We review some recent developments in this field, which allow progress in the understanding of the fundamental mechanisms that govern the magnetization changes in ferromagnetic structures. Some fundamental aspects of the magneto-optical response in the frequency and time domain are first considered. Then, we analyze the dynamics of the charges and spins following the optical excitation of quasiparticles in different ferromagnetic thin films. This dynamics is discussed by considering the processes that are involved in the ultrafast magneto-optical response.     

Challenges in protein folding simulations: Timescale, representation, and analysis

Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.     

Generalized-ensemble simulations of all-atom protein models

We review recent progress in generalized-ensemble simulations of proteins. Focusing on the formation of secondary structure, we show how these techniques can lead to a deeper understanding of the folding mechanism in proteins.     

Optical methods for the study of dynamics in biological membrane models

Membranes are highly complex and heterogeneous interfaces that are the active partition between living cells and the outside world. Many biologically important processes occur at the membrane surface, such as transmembrane transport and signaling. Many of these processes depend on the subtle interactions between the different membrane constituents: lipids, proteins and water. At present, a large body of knowledge exists on the molecular composition and static structure of membranes. However, our understanding of the dynamics of membrane molecules has not yet reached the same level of sophistication. Information on membrane dynamics, such as conformational fluctuations, conformational changes and dynamical interactions between membrane constituents are essential for a full understanding of membrane action. Here, we review a recently developed approach aimed at obtaining such dynamical information. The approach is based on surface-specific femtosecond laser vibrational spectroscopy, and is illustrated for simple membrane model systems.     

生物分子结合水的结构与动力学研究进展

生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.     

Coarsening in fluid phase transitions

We review the understanding of the kinetics of fluid phase separation in various space dimensions. Morphological differences, percolating or disconnected domains, based on overall composition in a binary liquid or on density in a vapor–liquid system, are discussed. Depending upon the morphology, various possible mechanisms for domain growth are pointed out and discussions of corresponding theoretical predictions are provided. On the computational front, useful models and simulation methodologies are presented. Theoretically predicted growth laws have been tested via molecular dynamics simulations of vapor–liquid transitions. In the case of a disconnected structure, the mechanism has been confirmed directly.     

High Probe Intensity Photobleaching Measurement of Lateral Diffusion in Cell Membranes

Lateral diffusion measurements, most commonly accomplished through Fluorescence Photobleaching Recovery (FPR or FRAP), provide important information on cell membrane molecules' size, environment and participation in intermolecular interactions. However, serious difficulties arise when these techniques are applied to weakly expressed proteins of either of two types: fusions of membrane receptors with visible fluorescent proteins or membrane molecules on autofluorescent cells. To achieve adequate sensitivity in these cases, techniques such as interference fringe FPR are needed. However, in such measurements, cytoplasmic species contribute to the fluorescence recovery signal and thus yield diffusion parameters not properly representing the small number of surface molecules. A new method helps eliminate these difficulties. High Probe Intensity (HPI)-FPR measurements retain the intrinsic confocality of spot measurements to eliminate interference from fluorescent cytoplasmic species. However, HPI-FPR methods lift the previous requirement that FPR procedures be performed at probe beam intensities low enough to not induce bleaching in samples during measurements. The high probe intensities now employed provide much larger fluorescence signals and thus more information on molecular diffusion from each measurement. We report successful measurement of membrane dynamics by this technique.     

On the use of slow manifolds in molecular and geophysical fluid dynamics

Constraints typically arise from the elimination of high frequency oscillations in mechanical systems. Examples are provided by bond constraints in molecular simulations and incompressibility constraints in fluid dynamics. A key issue is the accuracy of constrained dynamics with regard to the full dynamics. In this review we focus on the smooth solution components and discuss the concept of slow manifold and soft constraints in molecular and geophysical fluid dynamics. While the formal mathematical derivation of constraints is the same for both molecular and fluid dynamics, the predominant numerical techniques for dealing with constraints are different in the two fields. Semi-implicit time- stepping methods are often used in geophysical fluid dynamics while explicitly enforced constraints are more common in molecular dynamics.     

Recent structural insight into mitochondria gained by microscopy

Novel applications of microscopy have recently provided new insights into mitochondrial structures. Diverse techniques such as high resolution scanning electron microscopy, transmission electron microscopy, electron microscope tomography and light microscopy have contributed a better understanding of mitochondrial compartmentalization, dynamic networks of mitochondria, intermembrane bridges, segregation of mitochondrial DNA and contacts with the endoplasmic reticulum among other aspects. This review focuses on advances reported in the last five years concerning aspects of mitochondrial substructure or dynamics gained through new techniques, whether they be novel microscope methods or new ways to prepare or label specimens. Sometimes these advances have produced surprising results and more often than not, they have challenged current conceptions of how mitochondria work.     

Theoretical and experimental aspects of chaos control by time-delayed feedback

We review recent developments for the control of chaos by time-delayed feedback methods. While such methods are easily applied even in quite complex experimental context the theoretical analysis yields infinite-dimensional differential-difference systems which are hard to tackle. The essential ideas for a general theoretical approach are sketched and the results are compared to electronic circuits and to high power ferromagnetic resonance experiments. Our results show that the control performance can be understood on the basis of experimentally accessible quantities without resort to any model for the internal dynamics.     

Simulating high energy cascades in metals

Abstract

The processes of radiation damage, from initial defect production to microstructure evolution, occur over a wide spectrum of time and size scales. An understanding of the fundamental aspects of these processes requires a spectrum of theoretical models, each applicable in its own time and distance scales. As elements of this multi-model approach, molecular dynamics and binary collision simulations play complementary roles in the characterization of the primary damage state of high energy collision cascades. Molecular dynamics is needed to describe the individual point defects in the primary damage state with the requisite physical reality. The binary collision approximation is needed to model the gross structure of statistically significant numbers of high energy cascades. Information provided by both models is needed for connecting the defect production in the primary damage state with the appropriate models of defect diffusion and interaction describing the microstructure evolution. Results of binary collision simulations of high energy cascade morphology are reviewed. The energy dependence of freely migrating defect fractions calculated in recent molecular dynamics simulations are compared to results obtained much earlier with a binary collision/annealing simulation approach. The favorable agreement demonstrates the viability of the multi-model approach to defect production in high energy cascades.     

Effects of nano-void density, size and spatial population on thermal conductivity: a case study of GaN crystal

The thermal conductivity of a crystal is sensitive to the presence of surfaces and nanoscale defects. While this opens tremendous opportunities to tailor thermal conductivity, true 'phonon engineering' of nanocrystals for a specific electronic or thermoelectric application can only be achieved when the dependence of thermal conductivity on the defect density, size and spatial population is understood and quantified. Unfortunately, experimental studies of the effects of nanoscale defects are quite challenging. While molecular dynamics simulations are effective in calculating thermal conductivity, the defect density range that can be explored with feasible computing resources is unrealistically high. As a result, previous work has not generated a fully detailed understanding of the dependence of thermal conductivity on nanoscale defects. Using GaN as an example, we have combined a physically motivated analytical model and highly converged large-scale molecular dynamics simulations to study the effects of defects on thermal conductivity. An analytical expression for thermal conductivity as a function of void density, size, and population has been derived and corroborated with the model, simulations, and experiments.     

Regulation of the intermittent release of giant unilamellar vesicles under osmotic pressure

Osmotic pressure can break the fluid balance between intracellular and extracellular solutions. In hypo-osmotic solution, water molecules, which transfer into the cell and burst, are driven by the concentration difference of solute across the semi-permeable membrane. The complicated dynamic processes of intermittent bursts have been previously observed. However, the underlying physical mechanism has yet to be thoroughly explored and analyzed. Here, the intermittent release of inclusion in giant unilamellar vesicles was investigated quantitatively, applying the combination of experimental and theoretical methods in the hypo-osmotic medium. Experimentally, we adopted a highly sensitive electron multiplying charge-coupled device to acquire intermittent dynamic images. Notably, the component of the vesicle phospholipids affected the stretch velocity, and the prepared solution of vesicles adjusted the release time. Theoretically, we chose equations and numerical simulations to quantify the dynamic process in phases and explored the influences of physical parameters such as bilayer permeability and solution viscosity on the process. It was concluded that the time taken to achieve the balance of giant unilamellar vesicles was highly dependent on the molecular structure of the lipid. The pore lifetime was strongly related to the internal solution environment of giant unilamellar vesicles. The vesicles prepared in viscous solution were able to visualize long-lived pores. Furthermore, the line tension was measured quantitatively by the release velocity of inclusion, which was of the same order of magnitude as the theoretical simulation. In all, the experimental values well matched the theoretical values. Our investigation clarified the physical regulatory mechanism of intermittent pore formation and inclusion release, which provides an important reference for the development of novel technologies such as gene therapy based on transmembrane transport as well as controlled drug delivery based on liposomes.