Using a water-confined carbon nanotube to probe electricity of sequential charged segments of macromolecules

The detection of macromolecular conformation is particularly important in many physical and biological applications. Here we theoretically explore a method for achieving this detection by probing the electricity of sequential charged segments of macromolecules. Our analysis is based on molecular dynamics simulations, and we investigate a single file of water molecules confined in a half-capped single-walled carbon nanotube (SWCNT) with an external electric charge of +e or ?e (e is the elementary charge). The charge is located in the vicinity of the cap of the SWCNT and along the centerline of the SWCNT. We reveal the picosecond timescale for the re-orientation (namely, from one unidirectional direction to the other) of the water molecules in response to a switch in the charge signal, ?e → +e or +e → ?e. Our results are well understood by taking into account the electrical interactions between the water molecules and between the water molecules and the external charge. Because such signals of re-orientations can be magnified and transported according to Tu et al. [2009 Proc. Natl. Acad. Sci. USA 106 18120], it becomes possible to record fingerprints of electric signals arising from sequential charged segments of a macromolecule, which are expected to be useful for recognizing the conformations of some particular macromolecules.     

Using a water-confined carbon nanotube to probe the electricity of sequential charged segments of macromolecules

The detection of macromolecular conformation is particularly important in many physical and biological applications. Here we theoretically explore a method for achieving this detection by probing the electricity of sequential charged segments of macromolecules. Our analysis is based on molecular dynamics simulations, and we investigate a single file of water molecules confined in a half-capped single-walled carbon nanotube (SWCNT) with an external electric charge of +e or -e (e is the elementary charge). The charge is located in the vicinity of the cap of the SWCNT and along the centerline of the SWCNT. We reveal the picosecond timescale for the re-orientation (namely, from one unidirectional direction to the other) of the water molecules in response to a switch in the charge signal, -e → +e or +e →-e. Our results are well understood by taking into account the electrical interactions between the water molecules and between the water molecules and the external charge. Because such signals of re-orientation can be magnified and transported according to Tu et al. [2009 Proc. Natl. Acad. Sci. USA 106 18120], it becomes possible to record fingerprints of electric signals arising from sequential charged segments of a macromolecule, which are expected to be useful for recognizing the conformations of some particular macromolecules.     

Designed chemical structures for supramolecular assembly in polymers

One of the goals of synthetic polymer chemistry, and maybe the most important one, is the synthesis of macromolecules having tailored macroscopic properties. The synthetic strategies involved in the preparation of new polymeric materials usually utilize the formation of covalent bonds. In recent years the ability of molecules to self-organize has gained increased attention for the development of new materials. Self-assembly can be de.ned as a spontaneous intermolecular process involving noncovalent bonds (e.g. electrostatic or solvophobic interactions, hydrogen bonds) that results in the formation of, usually, thermodynamically stable supramolecular structures with well-defined order in the nm to μm scale. A plethora of self-organizing systems can be found in nature e.g. double-helical structures of DNA and bilayers of lipids in cell membranes. In natural systems their organization is closely linked to their biological function. These systems continue to provide inspiration to synthetic chemists. Control over the self-assembling process of synthetic macromolecules opens new fascinating opportunities for fabrication of functional materials for technological applications where manipulation of macroscopic properties is essential e.g. electronic devices, microsensors, separation membranes, catalysts and biomaterials. However, the information needed for self-assembly in a macromolecular system is always stored, in various ways, in its detailed primary chemical structure. It is this structure that defines the nature and strength of the interactions that are more probable to be developed in the system. This special issue contains papers concerned with the evolution of self assembly processes and structures of macromolecules, both in solution and in bulk state, through the control of the macromolecular architecture, the selective and functionalization of polymers with functional groups, the introduction of amphiphilicity and of conformational asymmetry in the di.erent parts of block copolymers, by using specific interactions between polymers and low molecular weight compounds or by changes occurring in the physicochemical properties of the environment around polymer chains. By use of well-developed polymerization routes, especially anionic and controlled free radical polymerization techniques, new synthetic macromolecules can be produced and used successfully in the formation of complex, self assembled nanostructures (i.e. block copolymer mesophases, micelles and vesicles from block copolymers, nanoobjects, etc.), in many cases responsive to their environment and having an internal structural hierarchy. These features allow for their use in immerging technologies and applications. Obviously a wide field like that of self-assembly in polymer containing systems cannot be fully covered in the limited space of a single special issue. However we hope that by the works presented here we have given a flavor of some of the issues that attract current scientific interest in this field. We also hope that we have shown the degree of concerted effort and collaboration that is often required, between scientists of different disciplines, theoreticians and experimentalists, in order to design, synthesize, study and understand self-organizing polymeric systems. It is our goal to initiate discussion in this, to our opinion, interesting and important field. The European Physical Journal E-Soft Matter aims in becoming a place where more related studies will be published, and especially on the synthesis of designed polymeric chemical structures, in the framework of multidisciplinarity that characterizes this Journal and the field of Soft Matter in general. Martin M?ller (Editor) Stergios Pispas (Guest Editor)     

Low-temperature behavior of water confined by biological macromolecules and its relation to protein dynamics

Confined water is an essential component of biological entities and processes and its properties differ from the ones of bulk water. Since protein and water dynamics are thought to be strongly coupled, and since macromolecular dynamics is crucial for biological function, the study of water confined by biological macromolecules is not only interesting on its own right but often provides useful information for understanding biological activity at the molecular level. Studies are reviewed that focus on the low-temperature behavior of water confined in protein crystals and in stacks of native biological membranes. Diffraction methods allowed the determination of characteristic changes that relate to the glass transition and crystallization of water. Protein crystallography and energy-resolved neutron scattering are employed to gain further insight into the coupling of solvent and protein dynamics.Received: 1 January 2003, Published online: 14 October 2003PACS: 87.15.He Dynamics and conformational changes - 87.50.Gi Ionizing radiations (ultraviolet, X-rays, gamma-rays, ions, electrons, positrons, neutrons, and mesons, etc.) - 64.70.Pf Glass transitions     

Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics

A method is introduced for simulating long timescale macromolecular structural fluctuations and transitions with atomic-scale detail. The N-atom Liouville equation for the macromolecule/host medium system provides the starting point for the analysis. Order parameters characterizing overall macromolecular architecture are demonstrated to be slowly evolving. For single-stranded macromolecules, a curvilinear coordinate provides a way to introduce the order parameters. Using a multiscale approach, Fokker–Planck equations are derived. A nanocanonical method for constructing the lowest order solution to the Liouville equation and the equivalence of long-time and ensemble averages avoid the tedious bookkeeping needed to preserve the number of degrees of freedom (required in earlier methods). The method overcomes the large energy barriers that plague other approaches for estimating rates of transition between macromolecular conformations. A reduced dynamics is derived for the friction dominated limit. New experimental methods for observing macromolecular dynamics and medical sciences applications are discussed.     

Coulomb self-energy of a uniformly charged three-dimensional cylinder

We calculate exactly the Coulomb self-energy of a uniformly charged three-dimensional cylinder. We derive a general analytical formula which, in the limit of zero length, gives also the correct result for the Coulomb self-energy of a uniformly charged two-dimensional disk. The exact analytical expression that we derive can be used in models that incorporate finite thickness effects in studies of two-dimensional electronic systems in the fractional quantum Hall regime as well as models that describe cylindrical beams of charged particles, certain colloidal suspensions of charged rigid rod-like particles and biological systems consisting of macromolecules with cylindrical symmetry.     

Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations.      

Sensing charged macromolecules with nanocrystalline diamond-based field-effect capacitive sensors

The possibility of a label-free electrical detection of layer-by-layer adsorbed polyelectrolyte (PE) multilayers using a field-effect capacitive electrolyte-diamond-insulator-semiconductor (EDIS) structure is investigated. Positively charged synthetic polyelectrolyte PAH (Poly (allylamine hydrochloride)) and negatively charged PSS (Poly (sodium 4-styrene sulfonate)) have been used as a model system. Nanocrystalline diamond films were grown on p-Si-SiO₂ substrates by a microwave plasma-enhanced chemical vapor deposition from a mixture of methane and hydrogen. The EDIS sensors functionalized with charged macromolecules have been characterized by means of capacitance-voltage and constant-capacitance methods. Alternating shifts in the capacitance-voltage and constant-capacitance curves have been observed after the adsorption of each polyanion and polycation layer, respectively. The effect of the number of the adsorbed PE layers and polarity of the outermost layer on the sensor response is discussed.     

利用中子散射探索生命世界中的物理奥秘

中子散射是利用入射中子与原子核发生碰撞以后中子动量与能量的改变来研究微观世界的一种技术。由于中子对氢原子的散射截面远大于其他元素的独特属性,使得中子散射在研究包含大量氢元素的生物大分子的结构以及动力学特性方面都有卓越的应用。文章对中子散射在生物方面的应用进行了探讨,重点介绍了中子衍射、结合衬度变换技术的小角中子散射、准弹性/非弹性中子散射和中子自旋回波技术,以及它们在研究生物大分子结构、动力学及其功能方面的应用。最后对中子散射未来在生命科学中探索新的物理现象进行了探讨和展望。     

Evaluation of Conformational dynamics properties of spin-labelled proteins at different degrees of nitroxide radicals immobilization

Spin-labelling has found wide applications in elucidation of the dynamic behaviour of biological macromolecules in aqueous media and biomembranes. Most of the proposed methods aimed at estimation of macromolecular correlation times (τ_c) assume, however, spin label molecules rigidly bound within the protein matrix. To avoid this limitation theoretical models which involve additional dynamic parameters to characterize the spin label motion should be considered. We have used ESR spectra analysis technique which permits quantitative separation of slow macromolecular rotation (described by the rotational correlation time, τ_c) and fast anisotropic relative to protein nitroxyl radical motion (described by the “order parameter”,S). This method was applied to study: i) conformational dynamics of covalently and non-covalently spin-labelled human serum albumin (HSA) in solution; ii) protein-protein (antigen-antibody) interactions in a model system containing spin-labelled bovine serum albumin (BSA) and anti-BSA immunoglobulin (IgG) in solution; and iii) dynamic properties of membrane-bound proteins: H⁺-ATPase (CF₁-CF₀ coupling factor of photophosphorylation) and Photosystem I pigment-protein reaction centre complex (PSI RC) isolated from spinach chloroplasts and reconstituted in proteoliposomes.     

The dependence of relaxation rates and chemical shift on the size of the imaged molecules and the concentration of MRI contrast agents

An intriguing phenomenon on enhancement of the relaxation rates and chemical shift of two typical magnetic resonance imaging (MRI) contrast agents based on gadolinium complex is observed. The relaxation enhancement or chemical shift change depends on the size of the molecule where the imaged nuclear species is located: the small molecules show a perfect linear relationship between the concentration and the relaxation enhancement or chemical shift change while for macromolecules pronounced nonlinearity is observed. The phenomenon is also confirmed with real images of a macromolecular sample. A quantitative theoretical interpretation of the phenomenon is proposed and the significance of this phenomenon to MRI of materials and biological systems is discussed.     

微通道中高分子溶液Poiseuille流的耗散粒子动力学模拟

利用耗散粒子动力学(dissipative particle dynamics, DPD)方法模拟了微通道中高分子溶液的Poiseuille流动.研究表明, 微通道中的高分子溶液呈现非牛顿流体特性, 可以用幂律流体来描述流动行为, 高分子浓度越大, 幂律指数n 越小. 高分子链与壁面的流体动力学相互作用以及布朗扩散率梯度控制着高分子链的横向迁移. 由于传统的DPD方法中壁面诱导的流体动力学作用部分被屏蔽, 高分子链将向壁面方向迁移, 并且随着流场增强, 高分子链向壁面方向迁移越明显. 未被屏蔽的流体动力学相互作用和布朗扩散率梯度相互竞争, 使高分子链在微通道内的质心分布呈双峰状, 通道中心处高分子浓度出现局部最小值. 当通道宽度减小、强受限时, 壁面与高分子链间的流体动力学相互作用可能全部被屏蔽, 而布朗扩散运动弱, 高分子向壁面方向有微弱的迁移. 关键词： 耗散粒子动力学 高分子溶液 非牛顿流体 横向迁移     

Crowding versus molecular seeding: NMR studies of protein aggregation in hen egg white

In living systems, proteins are surrounded by many other macromolecules of different nature, at high total concentrations. In the last few years, there has been an increasing effort to study biological macromolecules directly in natural crowded environments, such as in intact bacterial cells or by mimicking natural crowding by adding proteins, polysaccharides or even synthetic polymers. We have recently proposed hen egg white (HEW) as a suitable, natural medium to study macromolecules in crowding conditions. Here, we show that HEW can increase dramatically the aggregation kinetics of proteins with an in-built tendency to associate. By dissecting the mechanism we demonstrate that only part of this effect is due to crowding, while another factor playing an important role is the interaction with proteins from the milieu. High molecular weight glycoproteins present in HEW act as efficient molecular seeds for aggregation. Our results bear important consequences for in-cell NMR studies and suggest a role of glycosylated proteins in aggregation.     

Kinetically locked-in colloidal transport in an array of optical tweezers

We describe measurements of colloidal transport through arrays of micrometer-scale potential wells created with holographic optical tweezers. Varying the orientation of the trap array relative to the external driving force results in a hierarchy of lock-in transitions analogous to symmetry-selecting processes in a wide variety of systems. Focusing on colloid as a model system provides the first opportunity to observe the microscopic mechanisms of kinetic lock-in transitions and reveals a new class of statistically locked-in states. This particular realization also has immediate applications for continuously fractionating particles, biological cells, and macromolecules.     

Microchameleons: nonlinear chemical microsystems for amplification and sensing

In biological systems, the coupling of nonlinear biochemical kinetics and molecular transport enables functional sensing and "signal" amplification across many length scales. Drawing on biological inspiration, we describe how artificial reaction-diffusion (RD) microsystems can provide a basis for sensing applications, capable of amplifying micro- and nanoscopic events into macroscopic visual readouts. The RD applications reviewed here are based on a novel experimental technique, WETS for Wet Stamping, which offers unprecedented control over RD processes in microscopic and complex geometries. It is discussed how RD can be used to sense subtle differences in the thickness and/or absorptivity of thin absorptive films, amplify macromolecular phase transitions, detect the presence and quality of self-assembled monolayers, and provide dynamic spatiotemporal readouts of chemical "metabolites."     

Label-free detection of charged macromolecules by using a field-effect-based sensor platform: Experiments and possible mechanisms of signal generation

The possibilities and limitations of a direct electrical detection of charged macromolecules using a field-effect-based sensor platform is evaluated, mainly focusing on capacitive EIS (electrolyte-insulator-semiconductor) devices. The experimentally obtained results on the detection of DNA immobilisation and hybridisation as well as the monitoring of layer-by-layer adsorbed charged polyelectrolyte (PE) multilayers have been discussed by using two basic possible mechanisms of signal generation, namely the intrinsic charge of the macromolecules and the charge redistribution within the intermolecular spaces or in the multilayer. The effects of the layer-by-layer adsorption conditions (unbuffered and pH buffer solution), and the number and polarity of charged layers on the sensor response have been systematically investigated by means of capacitance–voltage (C–V), constant–capacitance (ConCap) and impedance spectroscopy (IS) methods. PACS 82.47.Rs; 82.80.Fk; 85.30.Tv; 87.15.Kg; 87.14.Gg     

Thermodynamics,phase transitions and Ruppeiner geometry for Einstein–dilaton–Lifshitz black holes in the presence of Maxwell and Born–Infeld electrodynamics

In this paper, we first obtain the higher-dimen-sional dilaton–Lifshitz black hole solutions in the presence of Born–Infeld (BI) electrodynamics. We find that there are two different solutions for the cases of \(z=n+1\) and \(z\ne n+1\) where z is the dynamical critical exponent and n is the number of spatial dimensions. Calculating the conserved and thermodynamical quantities, we show that the first law of thermodynamics is satisfied for both cases. Then we turn to the study of different phase transitions for our Lifshitz black holes. We start with the Hawking–Page phase transition and explore the effects of different parameters of our model on it for both linearly and BI charged cases. After that, we discuss the phase transitions inside the black holes. We present the improved Davies quantities and prove that the phase transition points shown by them are coincident with the Ruppeiner ones. We show that the zero temperature phase transitions are transitions in the radiance properties of black holes by using the Landau–Lifshitz theory of thermodynamic fluctuations. Next, we turn to the study of the Ruppeiner geometry (thermodynamic geometry) for our solutions. We investigate thermal stability, interaction type of possible black hole molecules and phase transitions of our solutions for linearly and BI charged cases separately. For the linearly charged case, we show that there are no phase transitions at finite temperature for the case \( z\ge 2\). For \(z<2\), it is found that the number of finite temperature phase transition points depends on the value of the black hole charge and there are not more than two. When we have two finite temperature phase transition points, there is no thermally stable black hole between these two points and we have discontinuous small/large black hole phase transitions. As expected, for small black holes, we observe finite magnitude for the Ruppeiner invariant, which shows the finite correlation between possible black hole molecules, while for large black holes, the correlation is very small. Finally, we study the Ruppeiner geometry and thermal stability of BI charged Lifshtiz black holes for different values of z. We observe that small black holes are thermally unstable in some situations. Also, the behavior of the correlation between possible black hole molecules for large black holes is the same as for the linearly charged case. In both the linearly and the BI charged cases, for some choices of the parameters, the black hole system behaves like a Van der Waals gas near the transition point.     

Shape transition of semi-flexible macromolecules confined in channel and cavity

Stiff macromolecules entrapped in channels or in spherical cavities undergo a shape transition on increasing confinement as shown by our investigation using molecular simulations. In channels this weak-to-strong confinement transition leads to extended conformations without the hairpin-like back-folding. In cavities, on decrease of cavity radius, the semi-flexible chain in a disordered state starts to self-organize into the torus. As a common rule for both types of confinement the transition to the ordered structures is observed when the radius of cavity and cylindrical channel reaches the lower bound of macromolecular flexibility given by the average typical radius of curvature of the chain, which is approximately equal to the persistence length of the macromolecular chain. This simple geometric rule finds its application in various confinement situations of stiff bio-macromolecules either in micro-channel experiments or in real biophysical situation, such as DNA in viral capsid.     

Anomalous transport of macromolecules in solution

Based on a semi-phenomenological Fokker-Planck approach, we present and discuss a theoretical framework for studying the transport properties of macromolecules in solution. A formally exact expression for the diffusion of macromolecules is derived and utilized in order to show the anomalous character of the macromolecular diffusion, both at very short times, t→ 0, as well as in the asymptotic limit, t→∞. Numerical computations for 50- and 100-bead macromolecules demonstrate moreover a `superdiffusive' behaviour at short and intermediate times when compared with the data from the (Einstein's) phenomenological theory.     

Vibroacoustic processes and structural variations in muscular tissue

This paper reviews the problems and results obtained in the course of experimental and theoretical investigations of the vibroacoustic activity of contracting muscles. Two types of such processes are examined: (1) acoustic vibrations due to the macromolecular recombinations of muscle proteins, which are responsible for the muscle contraction, and (2) acoustic vibrations associated with the finite accuracy and speed of the receptor-effector system that controls the muscle contraction. By investigating the acoustic vibrations, we examine structural recombinations (conformation variations) in macromolecules during mechanochemical reactions. Since chemical reactions of macromolecules are always accompanied by conformational recombinations, the generation mechanism, which is responsible for the contraction processes in a muscular tissue, can also be extended to other macromolecular media. Investigation of infrasound vibrations makes it possible to explore the quality and error of control for the processes in the muscle under different types of loading. Since a living body is controlled via perceptions, the latter can be quantitatively estimated by the parametess of infrasound vibrations.Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 38, Nos. 3–4, pp. 357–367, March–April, 1995.