Ligand diffusion in proteins via enhanced sampling in molecular dynamics

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand–protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.     

Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins

Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs(BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics(MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins.     

与HO2和HO3相关的复杂反应的量子动力学

Complex-forming reactions widely exist in gas-phase chemical reactions.Various complexforming bimolecular reactions have been investigated and interesting phenomena have been discovered.The complex-forming reactions usually have small or no barrier in the entrance channel,which leads to obvious differences in kinetic and dynamic characteristics compared with direct reactions.Theoretically,quantum state-resolved reaction dynamics can provide the most detailed microscopic dynamic mechanisms and is now feasible for a direct reaction with only one potential barrier.However,it is of great challenge to construct accurate potential energy surfaces and perform accurate quantum dynamics calculations for a complex polyatomic reaction involving deep potential wells and multi-channels.This paper reviews the most recent progress in two prototypical oxyhydrogen complex-forming reaction systems,HO₂ and HO₃,which are significant in combustion,atmospheric,and interstellar chemistry.We will present a brief survey of both computational and experimental work and emphasize on some unsolved problems existing in these systems.     

Coupled disease–behavior dynamics on complex networks: A review

It is increasingly recognized that a key component of successful infection control efforts is understanding the complex, two-way interaction between disease dynamics and human behavioral and social dynamics. Human behavior such as contact precautions and social distancing clearly influence disease prevalence, but disease prevalence can in turn alter human behavior, forming a coupled, nonlinear system. Moreover, in many cases, the spatial structure of the population cannot be ignored, such that social and behavioral processes and/or transmission of infection must be represented with complex networks. Research on studying coupled disease–behavior dynamics in complex networks in particular is growing rapidly, and frequently makes use of analysis methods and concepts from statistical physics. Here, we review some of the growing literature in this area. We contrast network-based approaches to homogeneous-mixing approaches, point out how their predictions differ, and describe the rich and often surprising behavior of disease–behavior dynamics on complex networks, and compare them to processes in statistical physics. We discuss how these models can capture the dynamics that characterize many real-world scenarios, thereby suggesting ways that policy makers can better design effective prevention strategies. We also describe the growing sources of digital data that are facilitating research in this area. Finally, we suggest pitfalls which might be faced by researchers in the field, and we suggest several ways in which the field could move forward in the coming years.     

Synchronization processes in complex networks

During the last decades the emergence of collective dynamics in large networks of coupled units has been investigated in fields such as optics, chemistry, biology and ecology. Recently, complex networks have provided a challenging framework for the study of synchronization of dynamical units, based on the interplay between complexity in the overall topology and local dynamical properties of the coupled units. In this work, we review the constructive role played by such complex wirings for the synchronization of networks of coupled dynamical systems. We review the main techniques that have been proposed for assessing the propensity for synchronization (synchronizability) of a given networked system. We will also describe the main applications, especially in the view of selecting the optimal topology in the coupling configuration that provides enhancement of the synchronization features.     

Single-molecular methodologies for the physical biology of protein machines

Physical biology is an interdisciplinary field that bridges biology with physical sciences and engineering. Single-molecule physical biology focuses on dynamics of individual biomolecules and complexes, aiming to answering basic questions about their functions and mechanisms. It takes advantages of physical methodologies to gain quantitative understanding of biological processes, often engaging precise physical measurements of reconstructed objects to avoid interference from unnecessary complications. In this review, we (i) briefly introduce concepts of single-molecule physical biology, (ii) describe extensively used single-molecule methodologies that have been developed to address key questions in two important objects of single-molecule physical biology, namely, nucleic acid-interacting proteins and membrane-interacting proteins, and (iii) show by a few successful examples how one may use single-molecule methods to deepen our understanding of protein machines.     

The structure of and interactions in binary acetonitrile + water mixtures

Binary liquid mixtures of acetonitrile (AN) and water (W) are widely used as reaction media in such fields of chemistry as physical organic chemistry, reverse phase liquid chromatography, and electrochemistry, among others. Much information on the structure of these systems and the interactions in them has accumulated since the author's often quoted comprehensive 1990 paper, so that a review is merited. Macroscopic physical properties, results from diffraction and spectroscopic studies, theoretical considerations and computer simulations, and results from the use of solute probes all bear on the structure (and less so on the dynamics) of the mixtures. These are discussed in terms of the microheterogeneity that occurs in them at intermediate contents (that leads eventually to liquid‐liquid phase separation). Copyright © 2012 John Wiley & Sons, Ltd.     

双分子反应中的范德华作用

本文综述了近年来双分子反应中范德华作用的理论和实验研究进展.对于直接的活化反应和形成络合物的反应中范德华力对动力学的显著影响深化了人们的认识的研究工作进行了回顾,并进一步讨论了涉及更多原子的反应以及在低温和超低温条件下的反应.无论是对于从头算还是势能面拟合而言,准确描述势能面的范德华区域的结构以及长程势仍是当前挑战性的工作.此外,本文还对最近提出的"范德华鞍"的概念作了阐明,该概念可能具有一般的意义.     

Geographical networks: geographical effects on network properties

Complex networks describe a wide range of systems in nature and society. Since most real systems exist in certain physical space and the distance between the nodes has influence on the connections, it is helpful to study geographical complex networks and to investigate how the geographical constrains on the connections affect the network properties. In this paper, we briefly review our recent progress on geographical complex networks with respect of statistics, modelling, robustness, and synchronizability. It has been shown that the geographical constrains tend to make the network less robust and less synchronizable. Synchronization on random networks and clustered networks is also studied.      

Geographical networks: geographical effects on network properties

Complex networks describe a wide range of systems in nature and society. Since most real systems exist in certain physical space and the distance between the nodes has influence on the connections, it is helpful to study geographical complex networks and to investigate how the geographical constrains on the connections affect the network properties. In this paper, we briefly review our recent progress on geographical complex networks with respect of statistics, modelling, robustness, and synchronizability. It has been shown that the geographical constrains tend to make the network less robust and less synchronizable. Synchronization on random networks and clustered networks is also studied.     

Use of molecular beams for kinetic measurements of chemical reactions on solid surfaces

In this review we survey the contributions that molecular beam experiments have provided to our understanding of the dynamics and kinetics of chemical interactions of gas molecules with solid surfaces. First, we describe the experimental details of the different instrumental setups and approaches available for the study of these systems under the ultrahigh vacuum conditions and with the model planar surfaces often used in modern surface-science experiments. Next, a discussion is provided of the most important fundamental aspects of the dynamics of chemical adsorption that have been elucidated with the help of molecular beam experiments, which include the development of potential energy surfaces, the determination of the different channels for energy exchange between the incoming molecules and the surface, the identification of adsorption precursor states, the understanding of dissociative chemisorption, the determination of the contributions of corrugation, steps, and other structural details of the surface to the adsorption process, the effect to molecular steering, the identification of avenues for assisting adsorption, and the molecular details associated with the kinetics of the uptake of adsorbates as a function of coverage. We follow with a summary of the work directed at the determination of kinetic parameters and mechanistic details of surface reactions associated with catalysis, mostly those promoted by late transition metals. This discussion we initiate with an overview of what has been learned about simple bimolecular reactions such as the oxidation of CO and H₂ with O₂ and the reaction of CO with NO, and continue with the review of the studies of more complex systems such as the oxidation of alcohols, the conversion of organic acids, the hydrogenation and isomerization of olefins, and the oxidative activation of alkanes under conditions of short contact times. 6 Reactions on supported nanoparticles: Materials gap, 7 Low-probability reactions: Pressure gap of this review deal with the advances made in the use of molecular beams with more realistic models for catalysis, using surfaces comprised of metal nanoparticles dispersed on the oxide surfaces used as catalyst support and high-flux beams to approach the pressures used in catalysis. The next section deals with the study of systems associated with fields other than catalysis, mainly with the etching and oxidation of semiconductor surfaces and with the chemistry used to grow thin solid films by chemical means (chemical vapor deposition, CVD, or atomic layer deposition, ALD). We end with a personal assessment of the past accomplishments, present state, and future promise of the use of molecular beams for the study of the kinetics of surface reactions relevant to practical applications.     

The interplay between chemistry and mechanics in the transduction of a mechanical signal into a biochemical function

There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct an overview of this kind of mechanical transduction, focusing in particular on the multiple layers of complexity displayed by the mechanisms that control and trigger the conversion of a mechanical signal into a biochemical function. Single molecule methodologies, through their capability to introduce the force in studies of biological processes in which mechanical stresses are developed, are unveiling subtle intertwining mechanisms between chemistry and mechanics and in particular are revealing how chemistry can control mechanics. The possibility that chemistry interplays with mechanics should be always considered in biochemical studies.     

Mechanism from isotope effects

Abstract Isotope effects represent perhaps one of the most versatile tools available to investigators interested in the determination of reaction mechanism, particularly in the case of the mechanistic enzymologist. Interpretation of isotope effect data is somewhat more difficult for enzyme reactions, since the chemical or isotope-dependent step(s) is(are) normally not solely rate-limiting as they are for non-enzyme-catalyzed reactions. One can, however, take advantage of rate-limitation by multiple steps in an enzyme-catalyzed reaction to obtain information on a number of aspects of mechanism. In this paper, simple theory for the application of isotope effects to reaction mechanism is developed, and applied to organic reactions and those catalyzed by enzymes. Techniques used to measure isotope effects depend somewhat on the isotope used, that is radioisotope vs. stable isotope, or hydrogen isotope vs. heavier atoms. Techniques to be discussed include competitive and noncompetitive (or internal discrimination) measurements. In enzymecatalyzed reactions, information can be obtained on the order of addition of reactants and release of products, and this will be illustrated using the 6-phosphogluconate and alcohol dehydrogenase reactions. The use of multiple isotope effects can be used to distinguish between stepwise and concerted reactions, and this will be illustrated with the formate and glucose 6-phosphate dehydrogenase and malic enzyme reactions.     

Greener organic synthetic methods: Sonochemistry and heterogeneous catalysis promoted multicomponent reactions

Ultrasound is an essential technique to improve organic synthesis from the point of view of green chemistry, as it can promote better yields and selectivities, in addition to shorter reaction times when compared to the conventional methods. Heterogeneous catalysis is another pillar of sustainable chemistry being the recycling and reuse of the catalysts one of its great advantage. In the other hand, multicomponent reactions provide the synthesis of structurally diverse compounds, in a one-pot fashion, without isolation and purification of intermediates. Thus, the combination of these protocols has proved to be a powerful tool to obtain biologically active organic compounds with lower costs, time and energy consumption. Herein, we provide a comprehensive overview of advances on methods of organic synthesis that have been reported over the past ten years with focus on ultrasound-assisted multicomponent reactions under heterogeneous catalysis. In particular, we present pharmacologically important N- and O-heterocyclic compounds, considering their synthetic methods using green solvents, and catalyst recycling.     

Traffic dynamics on layered complex networks

To minimize traffic congestion, understanding how traffic dynamics depend on network structure is necessary. Many real-world complex systems can be described as multilayer structures. In this paper, we introduce the idea of layers to establish a traffic model of two-layer complex networks. By comparing different two-layer complex networks based on random and scale-free networks, we find that the physical layer is much more important to the network capacity of two-layer complex networks than the logical layer. Two-layer complex networks with a homogeneous physical topology are found to be more tolerant to congestion. Moreover, simulation results show that the heterogeneity of logical and physical topologies makes the packet-delivery process of two-layer networks more efficient in the free-flow state, without the occurrence of traffic congestion.     

Network dynamics and its relationships to topology and coupling structure in excitable complex networks

All dynamic complex networks have two important aspects, pattern dynamics and network topology. Discovering different types of pattern dynamics and exploring how these dynamics depend or/network topologies are tasks of both great theoretical importance and broad practical significance. In this paper we study the oscillatory behaviors of excitable complex networks （ECNs） and find some interesting dynamic behaviors of ECNs in oscillatory probability, the multiplicity of oscillatory attractors, period distribution, and different types of oscillatory patterns （e.g., periodic, quasiperiodic, and chaotic）. In these aspects, we further explore strikingly sharp differences among network dynamics induced by different topologies （random or scale-free topologies） and different interaction structures （symmetric or asymmetric couplings）. The mechanisms behind these differences are explained physically.     

A gentle introduction to the thermodynamics of biochemical stoichiometric networks in steady state

Reaction networks in thermodynamic equilibrium under isothermal and isobaric conditions minimize the Gibbs free energy, but chemical reactions in living organisms operate typically far from equilibrium. Currently, there is no general optimization principle for nonequilibrium systems which can be used in the analysis of biochemical networks. Motivated by the avalailabity of whole genome reconstructions of metabolic reactions, the thermodynamics of biochemical stoichiometric networks has made significant progress in the last decade. These include the consistent formulation of conservation conditions resembling Kirchhoff’s law for electrical networks. In addition, Beard and Qian suggested that the flow force relationship Δμ = RT log(J⁺/J⁻) between the forward and backward fluxes J⁺ and J⁻ and the chemical potential difference of a chemical reaction can be extended from mass action kinetics to more general reactions schemes. In this tutorial review we summarize the recent literature on reaction network thermodynamics and discuss its implications to the analysis of large biochemical systems. In addition, we discuss some recent work on flow-force relationships and global variational principles characterizing nonequilibrium steady states of reaction networks.     

Quantum chemical modelling case studies relevant to metal oxide dissolution and catalysis

Over the past 20 years quantum-chemical methods have been developed sufficiently so that they can now be applied to the elucidation of the complex mechanistic processes that occur during metal oxide dissolution and catalysis reactions. Many of the reactions occurring during these processes are not directly accessible to experimental techniques and therefore quantum-chemical modelling can be applied to probe the individual reaction steps involved in the overall mechanism. Quantum chemistry provides the means of calculating the electronic properties of solids (e.g. band structures) structural properties of solids and surfaces (for instance surface relaxation and rumpling) heats of formation and reaction, activation energies, spectroscopic excitation energies and vibrational frequencies. Three case studies are described, which have been chosen to cover a range of quantum chemical applications and methodologies. These case studies are a) the dissolution mechanism of MgO, b) the parameterisation of titanium dioxide for the determination of electronic properties and c) the mechanism and energetics of adsorption of Pd onto rutile. These case studies utilise Hartree-Fock semiempirical andab initio quantum-chemical methods as well as density functional methodologies. A range of model types are used, namely cluster models embedded in pseudo-atoms, 3-dimensional periodic models and 2-dimensional periodic surface models.