Table of contents

Proteins are one of the most versatile modular assembling systems in nature. Experimentally, more than 110 000 protein structures have been identified and more are deposited every day in the Protein Data Bank. Such an enormous structural variety is to a first approximation controlled by the sequence of amino acids along the peptide chain of each protein. Understanding how the structural and functional properties of the target can be encoded in this sequence is the main objective of protein design. Unfortunately, rational protein design remains one of the major challenges across the disciplines of biology, physics and chemistry. The implications of solving this problem are enormous and branch into materials science, drug design, evolution and even cryptography. For instance, in the field of drug design an effective computational method to design protein-based ligands for biological targets such as viruses, bacteria or tumour cells, could give a significant boost to the development of new therapies with reduced side effects. In materials science, self-assembly is a highly desired property and soon artificial proteins could represent a new class of designable self-assembling materials. The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future.

We review a systematic practical implementation of the multiple scattering formalism due to Balian and Duplantier (1977 Ann. Phys. 104300, 1978 Ann. Phys. 112165) for the calculation of the Casimir interaction between arbitrarily shaped smooth conductors. The leading two-point scattering term of the expansion has a simple compact form, amenable to exact or accurate numerical evaluation. It is a general expression which improves upon the proximity force and pairwise summation approximations. We show that for many geometries it captures the bulk of the interaction effect. The inclusion of terms beyond the two-point approximation provides an accuracy check and explains screening. As an illustration of the power and versatility of the method we re-evaluate sphere–sphere and sphere–plane interactions and compared the results with previous findings that employed different methods. We also compute for the first time interaction of a hyperboloid (mimicking an atomic force microscope tip) and a plane. We also analyze the anomalous situations involving long cylindrical conductors where the two-point scattering approximation fails qualitatively. In such cases analytic summation of the entire scattering series is carried out and a topological argument is put forward as an explanation of the result. We give the extension of this theory to the case of finite temperatures where the two-point scattering approximation result has a simple compact form, also amenable to exact or accurate numerical evaluation.

We investigate spin correlations in the dipolar Heisenberg antiferromagnet Gd₂Sn₂O₇ using polarised neutron-scattering measurements in the correlated paramagnetic regime. Using Monte Carlo methods, we show that our data are sensitive to weak further-neighbour exchange interactions of magnitude  ∼0.5% of the nearest-neighbour interaction, and are compatible with either antiferromagnetic next-nearest-neighbour interactions, or ferromagnetic third-neighbour interactions that connect spins across hexagonal loops. Calculations of the magnetic scattering intensity reveal rods of diffuse scattering along [1 1 1] reciprocal-space directions, which we explain in terms of strong antiferromagnetic correlations parallel to the set of $\langle 1\,1\,0\rangle$ directions that connect a given spin with its nearest neighbours. Finally, we demonstrate that the spin correlations in Gd₂Sn₂O₇ are highly anisotropic, and correlations parallel to third-neighbour separations are particularly sensitive to critical fluctuations associated with incipient long-range order.

A theoretical study of a noble surface plasmon resonance (SPR) based sensing probe has been carried out. The sensing probe consists of a magnesium fluoride (MgF₂) prism with its base coated with rarely used noble metal rhodium (Rh) and a bio-compatible layer of graphene. The refractive indices (RIs) of the sensing medium vary from 1.33 to 1.36 refractive index unit (RIU). The thickness of Rh and the number of graphene layers have been optimized for maximum sensitivity in a constraint set by the detection accuracy (DA). For the operating wavelength of 632 nm, the optimized sensing probe Rh (12 nm)/graphene (single layer) demonstrates sensitivity of ~259 degree/RIU with corresponding DA of ~0.32 degree⁻¹ while for 532 nm of excitation, the optimized sensing probe Rh (12 nm)/graphene (three layer) exhibits sensitivity of ~240 degree/RIU and DA of ~0.27 degree⁻¹.

An ordered germanium terminated (1 0 0) diamond surface has been formed and characterised using a combination of low energy electron diffraction and synchrotron-based core level photoemission spectroscopy. A number of preparation methods are explored, in each case inducing a two domain $\left(3\times 1\right)$ surface reconstruction. The surface becomes saturated with bonded germanium such that each $\left(3\times 1\right)$ unit cell hosts 1.26 Ge atoms on average, and possesses a negative electron affinity of  −0.71 eV.

We develop a statistical mechanical framework, based on a variational approximation, to describe closed loop plectonemes. This framework incorporates weak helix structure dependent forces into the determination of the free energy and average structure of a plectoneme. Notably, due to their chiral nature, helix structure dependent forces break the symmetry between left and right handed supercoiling. The theoretical approach, presented here, also provides a systematic way of enforcing the topological constraint of closed loop supercoiling in the variational approximation. At large plectoneme lengths, by considering correlation functions in an expansion in terms of the spatial mean twist density about its thermally averaged value, it can be argued that topological constraint may be approximated by replacing twist and writhe by their thermal averages. A Lagrange multiplier, containing the sum of average twist and writhe, can be added to the free energy to conveniently inforce this result. The average writhe can be calculated through the thermal average of the Gauss' integral in the variational approximation. Furthermore, this approach allows for a possible way to calculate finite size corrections due to the topological constraint. Using interaction energy terms from the mean-field Kornyshev–Leikin theory, for parameter values that correspond to weak helix dependent forces, we calculate the free energy, fluctuation magnitudes and mean geometric parameters for the plectoneme. We see a slight asymmetry, where interestingly, left handed supercoils have a looser structure than right handed ones, although with a lower free energy, unlike what the previous ground state calculations would suggest.

The existence of a network structure consisting of electrically neutral tetrahedral molecules in liquid SnI₄ and GeI₄ at ambient pressure was examined. The liquid structures employed for the examination were obtained from a reverse Monte Carlo analysis. The structures were physically interpreted by introducing an appropriate intermolecular interaction. A 'bond' was then defined as an intermolecular connection that minimizes the energy of intermolecular interaction. However, their 'bond' energy is too weak for the 'bond' and the resulting network structure to be defined statically. The vertex-to-edge orientation between the nearest molecules is so ubiquitous that almost all of the molecules in the system can take part in the network, which is reflected in the appearance of a prepeak in the structure factor.

A self-adaptive accelerated molecular dynamics method is developed to model infrequent atomic-scale events, especially those events that occur on a rugged free-energy surface. Key in the new development is the use of the total displacement of the system at a given temperature to construct a boost-potential, which is slowly increased to accelerate the dynamics. The temperature is slowly increased to accelerate the dynamics. By allowing the system to evolve from one steady-state configuration to another by overcoming the transition state, this self-evolving approach makes it possible to explore the coupled motion of species that migrate on vastly different time scales. The migrations of single vacancy (V) and small He-V clusters, and the growth of nano-sized He-V clusters in Fe for times in the order of seconds are studied by this new method. An interstitial-assisted mechanism is first explored for the migration of a helium-rich He-V cluster, while a new two-component Ostwald ripening mechanism is suggested for He-V cluster growth.

Massless charge carriers in gate potentials modulate graphene quantum well transport in the same way that a electromagnetic wave propagates in optical fibers. A recent experiment by Kim et al (2016 Nat. Phys. 121022) reports valley symmetry preserved transport in a graphene carrier guider. Based on a tight-binding model, the valley-resolved transport coefficients are calculated with the method of scattering matrix theory. For a straight potential well, valley-resolved conductance is quantized with a value of 2n  +  1 and multiplied by 2e²/h with integer n. In the absence of disorder, intervalley scattering, only occurring at both ends of the potential well, is weak. The propagating modes inside the potential well are analyzed with the help of band structure and wave function distribution. The conductance is better preserved for a longer carrier guider. The quantized conductance is barely affected by the boundaries of different types or slightly changing the orientation of the carrier guider. For a curved model, the state with momentum closes to the neutral point is more fragile to boundary scattering and the quantized conductance is ruined as well.

It is possible to confine vibrational modes to a crystal by encapsulating it within thin disordered layers with the same average properties as the crystal. This is not due to an impedance mismatch between materials but, rather, to higher order moments in the distribution of density and stiffness in the disordered phase—i.e. it is a result of material substructure. The concept is elucidated in an idealized one-dimensional setting and then demonstrated for a realistic nanocrystalline geometry. This offers the prospect of specifically engineering higher order property distributions as an alternate means of managing phonons.

Alkali and alkali-earth metal hydrides have high volumetric and gravimetric hydrogen densities, but due to their high thermodynamic stability, they possess high dehydrogenation temperatures which may be reduced by transforming these compounds into less stable states/configurations. We present a systematic computational study of the electron doping effects on the stability of the alkali metal hydride NaH substituted with Mg, using the self-consistent version of the virtual crystal approximation to model the alloy Na_1−xMg_xH. The phonon dispersions were studied paying special attention to the crystal stability and the correlations with the electronic structure taking into account the zero point energy contribution. We found that substitution of Na by Mg in the hydride invokes a reduction of the frequencies, leading to dynamical instabilities for Mg content of 25%. The microscopic origin of these instabilities could be related to the formation of ellipsoidal Fermi surfaces centered at the L point due to the metallization of the hydride by the Mg substitution. Applying the quasiharmonic approximation, thermodynamic properties like heat capacities, vibrational entropies and vibrational free energies as a function of temperature at zero pressure are obtained. These properties determine an upper temperature for the thermodynamic stability of the hydride, which decreases from 600 K for NaH to 300 K at 20% Mg concentration. This significant reduction of the stability range indicates that dehydrogenation could be favoured by electron doping of NaH.

On the basis of ab initio calculations, we present a new parametrisation of the Vervisch–Mottet–Goniakowski (VMG) potential (Vervisch et al 2002 Phys. Rev. B 24245411) for modelling the oxide–metal interaction. Applying this model to mimic the finite temperature behaviour of large platinum icosahedra deposited on the pristine MgO(1 0 0), we find the nanoparticle undergoes two solid–solid transitions. At 650 K the 'squarisation' of the interface layer, while a full reshaping towards a fcc architecture takes place above 950 K. In between, a quite long-lived intermediate state with a (1 0 0) interface but with an icosahedral cap is observed. Our approach reproduces experimental observations, including wetting behaviour and the lack of surface diffusion.

The occurrence of segregation in dilute alloys under irradiation is a highly unusual phenomenon that has recently attracted attention, stimulated by the interest in the fundamental properties of alloys as well as by their applications. The fact that solute atoms segregate in alloys that, according to equilibrium thermodynamics, should exhibit full solubility, has significant practical implications, as the formation of precipitates strongly affects physical and mechanical properties of alloys. A lattice Hamiltonian, generalizing the so-called 'ABV' Ising model and including collective many-body inter-atomic interactions, has been developed to treat rhenium solute atoms and vacancies in tungsten as components of a ternary alloy. The phase stability of W–Re-vacancy alloys is assessed using a combination of density functional theory (DFT) calculations and cluster expansion (CE) simulations. The accuracy of CE parametrization is evaluated against the DFT data, and the cross-validation error is found to be less than 4.2 meV/atom. The free energy of W–Re-vacancy ternary alloys is computed as a function of temperature using quasi-canonical Monte Carlo simulations, using effective two, three and four-body interactions. In the low rhenium concentration range (<5 at.$\%$Re), solute segregation is found to occur in the form of voids decorated by Re atoms. These vacancy-rhenium clusters remain stable over a broad temperature range from 800 K to 1600 K. At lower temperatures, simulations predict the formation of Re-rich rhenium–vacancy clusters taking the form of sponge-like configurations that contain from 30 to 50 at.$\%$Re. The anomalous vacancy-mediated segregation of Re atoms in W can be rationalized by analyzing binding energy dependence as a function of Re to vacancy ratio as well as chemical Re–W and Re-vacancy interactions and short-range order parameters. DFT calculations show that rhenium–vacancy binding energies can be as high as 1.5 eV if the rhenium/vacancy ratio is in the range from 2.4 to 6.6. The predicted Re clustering agrees with experimental observations of precipitation in self-ion irradiated W-2$\%$ Re alloys and neutron-irradiated alloys containing 1.4 at.$\%$Re.

Regarding the spin field effect transistor (spin FET) challenges such as mismatch effect in spin injection and insufficient spin life time, we propose a silicene based device which can be a promising candidate to overcome some of those problems. Using non-equilibrium Green's function method, we investigate the spin-dependent conductance in a zigzag silicene nanoribbon connected to two magnetized leads which are supposed to be either in parallel or anti-parallel configurations. For both configurations, a controllable spin current can be obtained when the Rashba effect is present; thus, we can have a spin filter device. In addition, for anti-parallel configuration, in the absence of Rashba effect, there is an intrinsic energy gap in the system (OFF-state); while, in the presence of Rashba effect, electrons with flipped spin can pass through the channel and make the ON-state. The current voltage (I–V) characteristics which can be tuned by changing the gate voltage or Rashba strength, are studied. More importantly, reducing the mismatch conductivity as well as energy consumption make the silicene based spin FET more efficient relative to the spin FET based on two-dimensional electron gas proposed by Datta and Das. Also, we show that, at the same conditions, the current and ${{I}_{\text{on}}}/{{I}_{\text{off}}}$ ratio of silicene based spin FET are significantly greater than that of the graphene based one.

We investigate the influence of slab thickness on the electronic structure of the Si(1 0 0)- p($2\times 2$) surface in density functional theory (DFT) calculations, considering both density of states and band structure. Our calculations, with slab thicknesses of up to 78 atomic layers, reveal that the slab thickness profoundly affects the surface band structure, particularly the dangling bond states of the silicon dimers near the Fermi level. We find that, to precisely reproduce the surface bands, the slab thickness needs to be large enough to completely converge the bulk bands in the slab. In the case of the Si(1 0 0) surface, the dispersion features of the surface bands, such as the band shape and width, converge when the slab thickness is larger than 30 layers. Complete convergence of both the surface and bulk bands in the slab is only achieved when the slab thickness is greater than 60 layers.

We have performed first-principles studies of the electronic properties of Cu-diamond hetero-integrated systems, particularly placing emphasis on elucidating the effects of surface modification of diamond with H or O. It is found that the electronic properties crucially depend on the chemical compositions of the modified atomically thin interface region. The local density of states (LDOS) of the H-terminated diamond moiety near the Cu surface exhibits a clearly different distribution from that near the vacuum region, whereas the LDOS of the O-terminated diamond is almost independent of the Cu deposition. In other words, the effects of the electronic interactions between Cu and diamond on the electronic properties in the interface region are readily controlled by surface modification with only one atomic (i.e. H or O) layer. Electric field (EF) effects on the Cu-diamond systems also strongly depend on the electronic details, i.e. atomistic modification in the interface regions. In particular, at the interface between the H-terminated diamond moiety and the vacuum region, its conduction band energy is strongly affected by an applied EF much more than the valence band energy; that is, the band gap can be varied with an applied EF. The band gap variation is found to be attributed to an atomistic level difference in the spatial extension of the valence and conduction bands and thus is not explained with a macroscopic band diagram model. It has been demonstrated that the electronic properties of hetero-integrated systems are described and controlled well by carefully designing atomically thin interface regions.

Motivated by the report of superconductivity in R₃TiSb₅ (R  =  La and Ce) and possibly Nd₃TiSb₅ at  ∼4 K, we grew single crystals of La₃TiSb₅ and Ce₃TiSb₅ by the high-temperature solution method using Sn as a flux. While in both compounds we observed a superconducting transition at 3.7 K for resistivity and low-field magnetization, our data conclusively show that it arose from residual Sn flux present in the single crystals. In particular, the heat capacity data do not present any of the anomalies expected from a bulk superconducting transition. The anisotropic magnetic properties of Ce₃TiSb₅, crystallizing in a hexagonal P6₃/mcm structure, were studied in detail. We find that the Ce ions in Ce₃TiSb₅ form a Kondo lattice and exhibited antiferromagnetic ordering at 5.5 K with a reduced moment and a moderately normalized Sommerfeld coefficient of 598 mJ/mol K². The characteristic single-ion Kondo energy scale was found to be  ∼8 K. The magnetization data were subjected to a crystal electric field (CEF) analysis. The experimentally observed Schottky peak in the 4f-electron heat capacity of Ce₃TiSb₅ was reproduced fairly well by the energy levels derived from the CEF analysis.

Unique among alkali-doped A₃C₆₀ fullerene compounds, the A15 and fcc forms of Cs₃C₆₀ exhibit superconducting states varying under hydrostatic pressure with highest transition temperatures at $T_{\text{C}}^{\text{meas}}$  =  38.3 and 35.2 K, respectively. Herein it is argued that these two compounds under pressure represent the optimal materials of the A₃C₆₀ family, and that the C₆₀-associated superconductivity is mediated through Coulombic interactions with charges on the alkalis. A derivation of the interlayer Coulombic pairing model of high-T_C superconductivity employing non-planar geometry is introduced, generalizing the picture of two interacting layers to an interaction between charge reservoirs located on the C₆₀ and alkali ions. The optimal transition temperature follows the algebraic expression, T_C0  =  (12.474 nm² K)/ℓζ, where ℓ relates to the mean spacing between interacting surface charges on the C₆₀ and ζ is the average radial distance between the C₆₀ surface and the neighboring Cs ions. Values of T_C0 for the measured cation stoichiometries of Cs_3−xC₆₀ with x  ≈  0 are found to be 38.19 and 36.88 K for the A15 and fcc forms, respectively, with the dichotomy in transition temperature reflecting the larger ζ and structural disorder in the fcc form. In the A15 form, modeled interacting charges and Coulomb potential e²/ζ are shown to agree quantitatively with findings from nuclear-spin relaxation and mid-infrared optical conductivity. In the fcc form, suppression of $T_{\text{C}}^{\text{meas}}$ below T_C0 is ascribed to native structural disorder. Phononic effects in conjunction with Coulombic pairing are discussed.

We have studied the local structure of LaO_0.5F_0.5BiS_2−xSe_x by Bi L₁-edge extended x-ray absorption fine structure (EXAFS). We find a significant effect of Se substitution on the local atomic correlations with a gradual elongation of average in-plane Bi-S bondlength. The associated mean square relative displacement, measuring average local distortions in the BiS₂ plane, hardly shows any change for small Se substitution, but decreases significantly for $x\geqslant 0.6$. The Se substitution appears to suppress the local distortions within the BiS₂ plane that may optimize in-plane orbital hybridization and hence the superconductivity. The results suggest that the local structure of the BiS₂-layer is one of the key ingredients to control the physical properties of the BiS₂-based dichalcogenides.

Investigation of mesoscopically phase-separated Rb_0.85Fe_1.9Se₂ single crystals has been performed and two iron sites: nonmagnetic and magnetic ones, were observed by Mössbauer spectroscopy. The softening of the nonmagnetic one, having clearly more soft dynamics, was found to be gained further by the annealing of the single crystals at phase separation temperature, T_p, leading to the reduction of size of initially separated domains and their more homogenous distribution in the tetragonal matrix of the studied sample. The magnetic Fe sites of Rb_0.85Fe_1.9Se₂ show strong magnetic texture, indicating the perpendicular to the ab-plane orientation of the iron magnetic moments. It was found that the annealing at T_p causes a systematic decrease of the isomer shift of the doublet by 0.02(1) mm s⁻¹.

The structural distortions, orbital ordering, magnetic and electronic properties of double perovskite R₂CoMnO₆ (R  =  rare-earth element) have been systematically calculated by first-principles. Structural distortions, including Co–O and Mn–O bond length splitting, the antiferroelectric motions of R ions, the tilting of octahedral (the resulted Co–O–Mn bond angle) are obviously affected by the rare-earth ions' radius. The bond length splitting behavior of Co–O and Mn–O are rather different because of the Jahn–Teller active ion Co²⁺ and the Jahn–Teller nonactive ion Mn⁴⁺. Taking Gd₂CoMnO₆ as an example, the t_2g orbitals of Co ions are predicted to be orbital ordered. That is, the spin down channel of d_xz orbital for one Co ion and d_yz orbital for another Co ion are basically vacant. Finally, the physical properties, including the magnetic Curie temperature and electronic band gap of R₂CoMnO₆ are almost linear dependent on the average value of cos²θ (θ is the Co–O–Mn exchange-angle).

Using magnetization, dielectric constant, and neutron diffraction measurements on a high quality single crystal of YBaCuFeO₅ (YBCFO), we demonstrate that the crystal shows two antiferromagnetic transitions at ${{T}_{N1}}\sim 475$ K and ${{T}_{N2}}\sim 175$ K, and displays a giant dielectric constant with a characteristic of the dielectric relaxation at T_N2. It does not show the evidence of the electric polarization for the crystal used for this study. The transition at T_N1 corresponds with a paramagnetic to antiferromagnetic transition with a magnetic propagation vector doubling the unit cell along three crystallographic axes. Upon cooling, at T_N2, the commensurate spin ordering transforms to a spiral magnetic structure with a propagation vector of ($\frac{h}{2}$$\frac{k}{2}$$\frac{l}{2}\pm \delta$), where $h$, $k$, and $l$ are odd, and the incommensurability δ is temperature dependent. Around the transition boundary at T_N2, both commensurate and incommensurate spin ordering coexist.