We consider an atomistic model of thermal welding at the polymer-polymer interface of a polyetherimide/polycarbonate blend, motivated by applications to 3D manufacturing in space. We follow diffusion of semiflexible chains at the interface and analyze strengthening of the samples as a function of the welding time t(w) by simulating the strain-stress and shear viscosity curves. The time scales for initial wetting, and for fast and slow diffusion, are revealed. It is shown that each component of the polymer blend has its own characteristic time of slow diffusion at the interface. Analysis of strain-stress demonstrates saturation of the Young's modulus at t(w) = 240 ns, while the tensile strength continues to increase. The shear viscosity is found to have a very weak dependence on the welding time for t(w) > 60 ns. It is shown that both strain-stress and shear viscosity curves agree with experimental data. Welding dynamics and strengthening of the interface in the polyetherimide blend are analyzed using molecular dynamics. Time scales for initial welding of blend components are revealed. The strengthening is characterized by the strain-stress and shear viscosity curves obtained at different welding times. A way to control welding time in 3D manufacturing is proposed. The revealed features of the dynamics of semiflexible polymer chains are of importance for theoretical developments and practical applications.

Selective permeation through graphene nanopores is attracting increasing interest as an efficient and cost-effective technique for water desalination and purification. In this work, using umbrella sampling and molecular dynamics simulations with constant electric field, we analyze the influence of pore charge on potassium and chloride ion permeation. As pore charge is increased, the barrier of the potential of mean force (PMF) gradually decreases until it turns into a well split in two subminima. While in the case of K+ this pattern can be explained as an increasing electrostatic compensation of the desolvation cost, in the case of Cl- the pattern can be attributed to the accumulation of a concentration polarization layer of potassium ions screening pore charge. The analysis of potassium PMFs in terms of forces revealed a conflicting influence on permeation of van der Waals and electrostatic forces that both undergo an inversion of their direction as pore charge is increased. Even if the most important transition involves the interplay between the electrostatic forces exerted by graphene and water, the simulations also revealed an important role of the changing distribution of potassium and chloride ions. The influence of pore charge on the orientation of water molecules was also found to affect the van der Waals forces they exert on potassium.

In this article we apply our multi-component statistical and linear response theory to the process of mixed-valence ionic transport in a biological sodium ion channel. We analyse the free energy spectra, and statistical fluctuations (which are proportional to the conductivity) to investigate conditions and optimal parameters required for selectivity.

Just lifting a finger involves the coordinated opening and closing of billions of ion channels. These natural nanotubes play an essential role in the physiology of all living creatures, from bacter...

A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena measured in the bacterial NaChBac sodium channel and some of its mutants. Site-directed mutagenesis and the whole-cell patch-clamp technique were used to investigate how the value Q_f of the fixed charge at the selectivity filter (SF) affected both valence and alike-charge selectivity. The new ICB/QD model predicts that increasing Q_f should lead to a shift of selectivity sequences towards larger ion sizes and charges, a result that agrees with the present experiments and with earlier work. Comparison of the model with experimental data provides evidence for an effective charge Q_f^* at the SF that is smaller in magnitude than the nominal Q_f corresponding to the charge on the isolated protein residues. Furthermore, Q_f^* was different for aspartate and glutamate charged rings and also depended on their position within the SF. It is suggested that protonation of the residues within the restricted space is an important factor in significantly reducing the effective charge of the EEEE ring. Values of Q_f^* derived from experiments on the anomalous mole fraction effect (AMFE) agree well with expectations based on the ICB/QD model and have led to the first clear demonstration of the expected ICB oscillations in Ca^2+ conduction as a function of the fixed charge. Pilot studies of the dependence of Ca^2+ conduction on pH are consistent with the predictions of the model.

We consider multispecies conduction and selectivity of narrow biological filters such as KcsA [1] and NaChBac [2]. We use equilibrium statistical theory to find filter occupation and conductivities when coupled to the bath solutions with mixed types of conducting ions. The analysis of the filter conduction and selectivity conduction and selectivity is thus reduced to the analysis of the effective grand canonical distribution of ions within the filter [3], energy spectra, and density of the states within the filter [4]. The effects of energy quantization due to discrete number of ions and due to dehydration are taken into account. To account for the interaction between fluxes of different species within the channel we introduce Maxwell-Stefan theory [5] of the ion channel conduction. The fluxes of various species through the filter are obtained analytically in the limit of weak coupling. The theory is applied to derive Eisenman relations of the filter selectivity from the condition of nearly diffusion limited conduction in KscA channel. The model predictions are compared with experimental results using self-consistent kinetic equations. The transition rates in kinetic model are derived using effective grand canonical ensemble. A good agreement with the experiment is demonstrated. An application of the theory to analysis of the channel mutation experiments are discussed.

The ability of the potassium channel to conduct K+ at almost the rate of free diffusion, while discriminating strongly against the (smaller) Na+ ion, is of enormous biological importance [1]. Yet its function remains at the center of a “many-voiced debate” [2,3]. In this presentation, a first-principles explanation is provided for the seemingly paradoxical coexistence of high conductivity with high selectivity between monovalent ions within the channel. It is shown that the conductivity of the selectivity filter is described by the generalized Einstein relation. A novel analytic approach to the analysis of the conductivity is proposed, based on the derivation of an effective grand canonical ensemble for ions within the filter. The conditions for barrier-less diffusion-limited conduction through the KcsA filter are introduced, and the relationships between system parameters required to satisfy these conditions are derived. It is shown that the Eisenman selectivity equation is one of these, and that it follows directly from the condition for barrier-less conduction. The proposed theory provides analytical insight into the “knock-on” [1] and Coulomb blockade [4] mechanisms of K+ conduction through the KcsA filter. It confirms and illuminates an earlier argument [3] that the “snug-fit” model cannot describe the fast diffusion-limited conduction seen in experiments. Numerical examples are provided illustrating agreement of the theory with experimentally-measured I-V curves. The results are not restricted to biological systems, but also carry implications for the design of artificial nanopores. [1] Morais-Cabral, J. H. H., Zhou, Y. & MacKinnon, R., Energetic optimization of ion conduction rate by the K+ selectivity filter, Nature 414, 37-42 (2001). [2] Piasta, K. N., Theobald, D. L. & Miller, C., Potassium- selective block of barium permeation through single KcsA channels., J. Gen. Physiol. 138, 421-36 (2011). [3] Horn, R., Roux, B. & Åqvist, J., Permeation Redux: Thermodynamics and Kinetics of Ion Movement through Potassium Channels, Biophys. J. 106, 1859-1863 (2014). Kaufman, I. K., Luchinsky, D. G., Tindjong, R., McClintock, P. V. E. & Eisenberg, R. S., Multi-ion conduction bands in a simple model of calcium ion channels, Phys. Biol. 10, 026007 (2013).

We introduce a self-consistent multi-species kinetic theory based on the structure of the narrow voltage-gated potassium channel. Transition rates depend on a complete energy spectrum with contributions including the dehydration amongst species, interaction with the dipolar charge of the filter and, bulk solution properties. It displays high selectivity between species coexisting with fast conductivity, and Coulomb blockade phenomena, and it fits well to data.

The complex interactions that give rise to heart rate variability (HRV) involve coupled physiological oscillators operating over a wide range of different frequencies and length-scales. Based on the premise that interactions are key to the functioning of complex systems, the time-dependent deterministic coupling parameters underlying cardiac, respiratory and vascular regulation have been investigated at both the central and microvascular levels. Hypertension was considered as an example of a globally altered state of the complex dynamics of the cardiovascular system. Its effects were established through analysis of simultaneous recordings of the electrocardiogram (ECG), respiratory effort, and microvascular blood flow [by laser Doppler flowmetry (LDF)]. The signals were analyzed by methods developed to capture time-dependent dynamics, including the wavelet transform, wavelet-based phase coherence, non-linear mode decomposition, and dynamical Bayesian inference, all of which can encompass the inherent frequency and coupling variability of living systems. Phases of oscillatory modes corresponding to the cardiac (around 1.0 Hz), respiratory (around 0.25 Hz), and vascular myogenic activities (around 0.1 Hz) were extracted and combined into two coupled networks describing the central and peripheral systems, respectively. The corresponding spectral powers and coupling functions were computed. The same measurements and analyses were performed for three groups of subjects: healthy young (Y group, 24.4 ± 3.4 y), healthy aged (A group, 71.1 ± 6.6 y), and aged treated hypertensive patients (ATH group, 70.3 ± 6.7 y). It was established that the degree of coherence between low-frequency oscillations near 0.1 Hz in blood flow and in HRV time series differs markedly between the groups, declining with age and nearly disappearing in treated hypertension. Comparing the two healthy groups it was found that the couplings to the cardiac rhythm from both respiration and vascular myogenic activity decrease significantly in aging. Comparing the data from A and ATH groups it was found that the coupling from the vascular myogenic activity is significantly weaker in treated hypertension subjects, implying that the mechanisms of microcirculation are not completely restored by current anti-hypertension medications.

The dynamical systems found in Nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. Here, we aim to present a coherent and comprehensive review encompassing the rapid progress made recently in the analysis, understanding and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally-coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

The highly selective permeation of ions through biological ion channels can be described and explained in terms of fluctuational dynamics under the influence of powerful electrostatic forces. Hence valence selectivity, e.g. between Ca2+ and Na+ in calcium and sodium channels, can be described in terms of ionic Coulomb blockade, which gives rise to distinct conduction bands and stop-bands as the fixed negative charge Q(f) at the selectivity filter of the channel is varied. This picture accounts successfully for a wide range of conduction phenomena in a diversity of ion channels. A disturbing anomaly, however, is that what appears to be the same electrostatic charge and structure (the so-called EEEE motif) seems to select Na+ conduction in bacterial channels but Ca2+ conduction in mammalian channels. As a possible resolution of this paradox it is hypothesised that an additional charged protein residue on the permeation path of the mammalian channel increases |Q(f)| by e, thereby altering the selectivity from Na+ to Ca2+. Experiments are proposed that will enable the hypothesis to be tested.

"Fundamentals of fluorescence microscopy: exploring life with light, by Partha Pratim Mondal and Alberto Diaspro." Contemporary Physics, 58(2), pp. 181–182

Thermonuclear fusion offers the possibility of virtually unlimited, low-carbon, electrical power generation without leaving an extensive legacy of radioactive waste. For almost as long as I can remember, its practical application has been predicted to be about 30 or 40 years in the future, so why does it never seem to come closer to reality?

The precise mechanisms underlying general anaesthesia pose important and still open questions. To address them, we have studied anaesthesia induced by the widely used (intravenous) propofol and (inhalational) sevoflurane anaesthetics, computing cross-frequency coupling functions between neuronal, cardiac and respiratory oscillations in order to determine their mutual interactions. The phase domain coupling function reveals the form of the function defining the mechanism of an interaction, as well as its coupling strength. Using a method based on dynamical Bayesian inference, we have thus identified and analysed the coupling functions for six relationships. By quantitative assessment of the forms and strengths of the couplings, we have revealed how these relationships are altered by anaesthesia, also showing that some of them are differently affected by propofol and sevoflurane. These findings, together with the novel coupling function analysis, offer a new direction in the assessment of general anaesthesia and neurophysiological interactions, in general.

"Physics and biology: from molecules to life, edited by Jean François Allemand and Pierre Desbiolles." Contemporary Physics, 57(2), p. 265

Many physicists enter the profession because, often as children, they felt a burning curiosity about the world. They wanted to know why material objects behave as they do, what they are made of, an...

Neutron reflectometry offers a unique opportunity for the direct observation of nanostratification in 3He-4He mixtures in the ultra-low temperature limit. Unfortunately the results of recent experiments could not be well-modelled on account of a seemingly anomalous variation of reflectivity with momentum transfer. We now hypothesize that this effect is attributable to an optical distortion caused by the liquid's meniscus near the container wall. The validity of this idea is tested and confirmed through a subsidiary experiment on a D2O sample, showing that the meniscus can significantly distort results if the beam size in the horizontal plane is comparable with, or bigger than, the diameter of the container. The meniscus problem can be eliminated if the beam size is substantially smaller than the diameter of the container, such that reflection takes place only from the flat region of the liquid surface thus excluding the meniscus tails. Practical measures for minimizing the meniscus distortion effect are discussed.

Biological ion channels are protein nanotubes embedded in, and passing through, the bilipid membranes of cells. Physiologically, they are of crucial importance in that they allow ions to pass into and out of cells, fast and efficiently, though in a highly selective way. Here we show that the conduction and selectivity of calcium/sodium ion channels can be described in terms of ionic Coulomb blockade in a simplified electrostatic and Brownian dynamics model of the channel. The Coulomb blockade phenomenon arises from the discreteness of electrical charge, the strong electrostatic interaction, and an electrostatic exclusion principle. The model predicts a periodic pattern of Ca2+ conduction versus the fixed charge Q(f) at the selectivity filter (conduction bands) with a period equal to the ionic charge. It thus provides provisional explanations of some observed and modelled conduction and valence selectivity phenomena, including the anomalous mole fraction effect and the calcium conduction bands. Ionic Coulomb blockade and resonant conduction are similar to electronic Coulomb blockade and resonant tunnelling in quantum dots. The same considerations may also be applicable to other kinds of channel, as well as to charged artificial nanopores.

"Essentials of in vivo Biomedical Imaging, edited by Simon R. Cherry, Ramsey D. Badawi and Jinyi Qi." Contemporary Physics, 57(1), pp. 144–145