Hydration of clays at the molecular scale: the promising perspective of classical density functional theory

We report here how the hydration of complex surfaces can be efficiently studied, thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophyllite clay. After presenting the most recent advances, we show that the strength of this implicit method is that: (1) it is in quantitative or semi-quantitative agreement with reference all-atom simulations (molecular dynamics here) for both the solvation structure and energetics, and (2) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect in that it locally overestimates the polarisation of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry out a systematic study of the electrostatic and van der Waals components of the surface–solvent interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend upon the electrostatics. We conclude on the consequences of such findings on future force-field development.     

采用加权直方图分析和蒙特卡洛重采样法对自由能级的校正研究

本文采用加权直方图分析方法和蒙特卡洛重采样方法进行自由基校正研究. 生成的自由能表面几乎可以收敛到具有足够采样情况的精准表面,并且比常规的加权直方图分析校正方法能更稳定地处理采样不足的情况,为检测能级校正表面的不确定性提供指南,并且定义了明确的标准用以确定能改善其视觉效果的自由能表面平滑程度. 本文通过水中的丙氨酸二肽和KillerRed蛋白质子转移的自由能图证明该方法的优势,说明蒙特卡洛重采样法可以作为在产生自由能表面实际的系统中的实用工具.     

Self-assembly and co-assembly of block polyelectrolytes in aqueous solutions. Dissipative particle dynamics with explicit electrostatics

This topical review outlines the principles of dissipative particle dynamics (DPD) and discusses its use for studying electrically charged systems – particularly its application for investigation of the self-assembly of polyelectrolytes in aqueous solutions. Special emphasis is placed on DPD with incorporation of explicit electrostatic forces (DPD-E). At present, this empowered method is being used by only a few research groups and most studies of polyelectrolyte self-assembly are based on the ‘implicit solvent ionic strength’ approach which completely ignores electrostatics. The inclusion of electrostatics in the DPD machinery not only complicates the calculations and considerably slows down the simulation run, but it also generates some problems of primary importance that have to be solved prior to employing DPD-E to study practically important systems. In the introductory parts, we describe the principles of DPD-E, analyse all the problematic issues and show how they can be resolved or overcome. The later parts demonstrate the successful application of DPD-E. We discuss papers that study the self-assembling behaviour of two different practically important systems and show that they not only closely reproduce all the decisive features of the behaviour, but also reveal new details that are difficult to access for experimentalists. The topical review shows that the tedious calculations are worthwhile: (1) DPD-E simulations are concerned with the true principles of the behaviour of polyelectrolyte systems and therefore provide reliable data and (2) the practically important advantage of computer simulations, i.e. their predictive power (at the level of the employed coarse-graining), which is a questionable aspect in simulations that use physically impoverished models, is not endangered in the case of DPD-E.     

Fluorescence Techniques for Determination of the Membrane Potentials in High Throughput Screening

The characterization of small molecules requires identification and evaluation of several predictive parameters, when selecting compounds for pharmacological applications and/or determining their toxicity. A number of them are correlated with the compound interaction with biological membranes and/or capacity to cross them. The knowledge of the extent of adsorption, partition coefficient and permeability along with the compound ability to alter membrane properties are critical for such studies. Lipid bilayers are frequently used as the adequate experimental models of a biological membrane despite their simple structure and a limited number of components. A significant number of the biologically relevant lipid bilayer properties are related to its electrostatics. Three electrostatic potentials were defined for the lipid bilayer; the intrinsic or induced surface electrostatic potential, the dipole potential and the membrane potential. Each of them was measured with dedicated methodologies. The complex measurement protocols and technically demanding instrumentation made the development of efficient HTS approaches for complete characterization of membrane electrostatics practically impossible. However, the rapid development of fluorescence techniques accompanied by rapid growth in diversity and number of dedicated fluorescent probes enabled characterization of lipid bilayer electrostatics in a moderately simple manner. Technically advanced, compact and automated workstations, capable of measuring practically all fluorescence parameters, are now available. Therefore, the proper selection of fluorescent probes with measuring procedures can be designed to evaluate drug candidates in context of their ability to alter membrane electrostatics. In the paper we present a critical review of available fluorescence methods, useful for the membrane electrostatics evaluation and discuss the feasibility of their adaptation to HTS procedures. The significance of the presented methodology is even greater considering the rapid growth of advanced drug formulations, where electrostatics is an important parameter for production processes and pharmacokinetics of the product. Finally, the potential of the membrane electrostatics to emerge as a viable pharmacological target is indicated and fluorescence techniques capable to evaluate this potential are presented.     

Note on the History of Contact Mechanics and Friction: Interplay of Electrostatics,Theory of Gravitation and Elasticity from Coulomb to Johnson-Kendall-Roberts Theory of Adhesion

Great discoveries are often perceived by subsequent generations as sudden insights of genius scientists. Historical studies show, however, that the real mechanism of creation of new theories and paradigms is often a transfer of knowledge from one subject area to the other. Such transfers made the military engineer Coulomb the founder of the theory of electricity, they made the professor for celestial mechanics Poisson the founder of the electrostatics, and the pioneer in electrodynamics Hertz also became the founder of contact mechanics. Transfer of knowledge can be traced as a very effective way of development of science in many other cases. It often leads to breakthrough and rapid development of the whole branches of science. In the present paper we trace such transfers of knowledge in the history of elasticity and contact mechanics on one side and electrostatics on the other side. The participants of this historical process are Coulomb, Poisson, Hertz, Inglis, Griffith and finally the authors of the theory of adhesive contacts Johnson, Kendall and Roberts. Interestingly, the same principle of "exaptation" (use of a property for a function for which it was not originally created) is currently accepted theory of how major innovations happen also in biological evolution.     

Molecular simulations of self-assembly processes of amphiphiles in dilute solutions: the challenge for quantitative modelling

We report on two recent developments in molecular simulations of self-assembly processes of amphiphilic solutions. We focus on the determination of micelle formation of ionic surfactants which exhibit the archetype of self-assembling compounds in solution. The first approach is centred on the challenge in predicting micellisation properties through explicit solvent molecular dynamics simulations. Even with a coarse-grained (CG) approach and the use of highly optimised software packages run on graphics processing unit hardware, it remains in many cases computationally infeasible to directly extract the critical micelle concentration (cmc). However, combined with a recently presented theoretical mean-field model this task becomes resolved. An alternative approach to study self-assembly is through implicit solvent modelling of the surfactants. Here we review some latest results and present new ones regarding capabilities of such a modelling approach in determining the cmc, and the aggregate structures in the dilute regime, that is currently not accessible through explicit solvent simulations, neither through atomistic nor through CG approaches. A special focus is put on surfactant concentration effects and surfactant correlations quantified by scattering intensities that are compared to recently published small-angle X-ray scattering data.     

Permeation of ions through a model biological channel: effect of periodic boundary conditions and cell size

The effect of the simulation cell size and periodic boundary conditions on non-equilibrium molecular dynamics simulations of the structure and dynamics with explicit water molecules and ions in and near a model channel in a biological membrane is considered. The approach seems satisfactory. In particular, the presence of image channels that often contain image ions seems to have little effect on the average structure, channel content, or current for this system.     

Electrostatic charging of single granules by repeated sliding along inclined metal plates

In this work, repeated sliding tests for single granules were investigated for their electrostatics generation. Several factors were considered including granule length-ratio, sliding face shape, sliding times, sliding area, sliding velocity, front-facing edge, plate inclined angle and humidity. Generally, it is found that electrostatics increases with granule length-ratio. Two kinds of granular sliding face shapes were used in this work, half circle and rectangle. Under the same working conditions, a granule with the sliding face shape of half-circle tends to produce more electrostatics than that of rectangle. In addition, the efficiency of granule charge generation increases with sliding times although the amount of impact charge is decreased by the initial charge. Electrostatics increases with sliding area, which is independent of granule sliding-face shape and sliding times. Electrostatics also increases with granule sliding velocity. Front-facing sliding with a short edge tends to generate more electrostatics than that with a long edge. In this work, three sliding-plate angles were chosen as 30°,54°,70°, where granules sliding along the inclined plate at 54° acquired the highest electrostatics in comparison with other two angles. Humidity has significant effect on electrostatics as that electrostatics decreases with humidity. At lower relative humidity, the granule length-ratio is found to have more effect on electrostatics.     

中微子振荡和中微子质量

本文介绍了目前中微子振荡和中微子质量研究的一般状况,其中包括各种实验方法,所取得的结果和今后发展方向。     

Mathematical modeling the formation of a histone octamer

A physical model of the interaction of protein molecules and their ability to form complex biological systems for the in vitro case in a solution of monovalent salt has been developed. Their reactive abilities using the methods of electrostatics based on the example of the step-by-step formation of the histone octamer from the H2A, H2B, H3, and H4 proteins have been studied. To analyze the ability of protein molecules to form compounds the matrix of potential energy of interactions between protein molecules in solutions with different concentrations of monovalent salt has been examined.     

生物传感器的应用

综述了生物传感器的类型、基本原理、目前的研究现状及应用情况。生物传感器是以生物分子作为敏感元件的一类新兴传感器，将化学信号、热信号、光信号转化成电信号或者直接产生电信号予以放大输出，从而得到检测结果。生物传感器广泛应用于食品工业、环境监测、发酵工业、军事领域和临床医学等方面。主要用于一些食品和污染物浓度的测量，微生物呼吸活性的测定，微生物培养方法的选择等，此外，还可以作为水处理设备的终端。可以预料，生物传感器将向着微型化、实用化、多样化和人工智能化的方向发展，并且还将用于对生物功能进行人工模拟，研究人工感官。生物传感器具有快速、准确、方便等优点，具有广阔的应用前景，必将在市场上开辟出一片新的天地。     

A pilgrimage to gravity on GPUs

In this short review we present the developments over the last 5 decades that have led to the use of Graphics Processing Units (GPUs) for astrophysical simulations. Since the introduction of NVIDIA’s Compute Unified Device Architecture (CUDA) in 2007 the GPU has become a valuable tool for N-body simulations and is so popular these days that almost all papers about high precision N-body simulations use methods that are accelerated by GPUs. With the GPU hardware becoming more advanced and being used for more advanced algorithms like gravitational tree-codes we see a bright future for GPU like hardware in computational astrophysics.     

On the Ising model for the simple cubic lattice

The Ising model was introduced in 1920 to describe a uniaxial system of magnetic moments, localized on a lattice, interacting via nearest-neighbour exchange interaction. It is the generic model for a continuous phase transition and arguably the most studied model in theoretical physics. Since it was solved for a two-dimensional lattice by Onsager in 1944, thereby representing one of the very few exactly solvable models in dimensions higher than one, it has served as a testing ground for new developments in analytic treatment and numerical algorithms. Only series expansions and numerical approaches, such as Monte Carlo simulations, are available in three dimensions. This review focuses on Monte Carlo simulation. We build upon a data set of unprecedented size. A great number of quantities of the model are estimated near the critical coupling. We present both a conventional analysis and an analysis in terms of a Puiseux series for the critical exponents. The former gives distinct values of the high- and low-temperature exponents; by means of the latter we can get these exponents to be equal at the cost of having true asymptotic behaviour being found only extremely close to the critical point. The consequences of this for simulations of lattice systems are discussed at length.     

A nonlocal plate model incorporating interatomic potentials for vibrations of graphene with arbitrary edge conditions

This article presents analytical explicit frequency expressions for investigating the vibrations of single-layer graphene sheets (SLGSs). The interatomic potential is incorporated into a nonlocal continuum plate model through establishing a linkage between the strain energy density induced in the continuum and nonlocal plate constitutive relations. The model which is independent of scattered value of Young's modulus is then applied and explicit frequency formulas for the SLGSs with different edge conditions are derived using static deflection function of the nanoplate under uniformly distributed load. The reliability of the present formulation is verified by the results obtained by the molecular dynamics (MD) simulations and other research workers. The formulas are of a simple short form enabling quick and accurate evaluation of the frequency of the SLGSs and also simple calibration of scale coefficient by the use of MD simulations results.     

Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.     

Effect of solvent on directional drift in Brownian motion of particle/molecule with broken symmetry

The directional drifting of particles/molecules with broken symmetry has received increasing attention. Through molecular dynamics simulations, we investigate the effects of various solvents on the time-dependent directional drifting of a particle with broken symmetry. Our simulations show that the distance of directional drift of the asymmetrical particle is reduced while the ratio of the drift to the mean displacement of the particle is enhanced with increasing mass, size, and interaction strength of the solvent atoms in a short time range. Among the parameters considered, solvent atom size is a particularly influential factor for enhancing the directional drift of asymmetrical particles, while the effects of the interaction strength and the mass of the solvent atoms are relatively weaker. These findings are of great importance to the understanding and control of the Brownian motion of particles in various physical, chemical, and biological processes within finite time spans.     

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K⁺/Na⁺)is about the base stacking free energies indicates that there will be a competition among the binding of M⁺-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.     

Zero constant formula for first-passage observables in bounded domains

In this Letter, we develop an analytical approach which provides an explicit determination of mean first-passage times (MFPTs) for random walks in bounded domains for a wide class of transport processes. In particular, we derive for the first time explicit expressions of MFPTs for emblematic models of transport in complex media, such as diffusion on deterministic and random fractals. This approach relies on a scale-invariance hypothesis and a large volume expansion of the MFPT, which actually proves to be very accurate even for small system sizes as shown by numerical simulations. This explicit determination of MFPTs can be straightforwardly generalized to further useful first-passage observables such as occupation times and splitting probabilities.     

Locally implicit discontinuous Galerkin method for time domain electromagnetics

In the recent years, there has been an increasing interest in discontinuous Galerkin time domain (DGTD) methods for the solution of the unsteady Maxwell equations modeling electromagnetic wave propagation. One of the main features of DGTD methods is their ability to deal with unstructured meshes which are particularly well suited to the discretization of the geometrical details and heterogeneous media that characterize realistic propagation problems. Such DGTD methods most often rely on explicit time integration schemes and lead to block diagonal mass matrices. However, explicit DGTD methods are also constrained by a stability condition that can be very restrictive on highly refined meshes and when the local approximation relies on high order polynomial interpolation. An implicit time integration scheme is a natural way to obtain a time domain method which is unconditionally stable but at the expense of the inversion of a global linear system at each time step. A more viable approach consists of applying an implicit time integration scheme locally in the refined regions of the mesh while preserving an explicit time scheme in the complementary part, resulting in an hybrid explicit–implicit (or locally implicit) time integration strategy. In this paper, we report on our recent efforts towards the development of such a hybrid explicit–implicit DGTD method for solving the time domain Maxwell equations on unstructured simplicial meshes. Numerical experiments for 3D propagation problems in homogeneous and heterogeneous media illustrate the possibilities of the method for simulations involving locally refined meshes.