More than one dynamic crossover in protein hydration water

Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water, the binding of water molecules to the protein avoids crystallization. Here we study the dynamics of the hydrogen bond (HB) network of a percolating layer of water molecules, comparing measurements of a hydrated globular protein with the results of a coarse-grained model that has been shown to successfully reproduce the properties of hydration water. With dielectric spectroscopy we measure the temperature dependence of the relaxation time of protons charge fluctuations. These fluctuations are associated to the dynamics of the HB network of water molecules adsorbed on the protein surface. With Monte Carlo (MC) simulations and mean--field (MF) calculations we study the dynamics and thermodynamics of the model. In both experimental and model analyses we find two dynamic crossovers: (i) one at about 252 K, and (ii) one at about 181 K. The agreement of the experiments with the model allows us to relate the two crossovers to the presence of two specific heat maxima at ambient pressure. The first is due to fluctuations in the HB formation, and the second, at lower temperature, is due to the cooperative reordering of the HB network

Diffusing opinions in bounded confidence processes

We study the effects of diffusing opinions on the Deffuant et al. model for continuous opinion dynamics. Individuals are given the opportunity to change their opinion, with a given probability, to a randomly selected opinion inside an interval centered around the present opinion. We show that diffusion induces an order-disorder transition. In the disordered state the opinion distribution tends to be uniform, while for the ordered state a set of well defined opinion clusters are formed, although with some opinion spread inside them. If the diffusion jumps are not large, clusters coalesce, so that weak diffusion favors opinion consensus. A master equation for the process described above is presented. We find that the master equation and the Monte-Carlo simulations do not always agree due to finite-size induced fluctuations. Using a linear stability analysis we can derive approximate conditions for the transition between opinion clusters and the disordered state. The linear stability analysis is compared with Monte Carlo simulations. Novel interesting phenomena are analyzed

Basis set effects on the hyperpolarizability of CHCl_3: Gaussian-type orbitals, numerical basis sets and real-space grids

Calculations of the hyperpolarizability are typically much more difficult to converge with basis set size than the linear polarizability. In order to understand these convergence issues and hence obtain accurate ab initio values, we compare calculations of the static hyperpolarizability of the gas-phase chloroform molecule (CHCl_3) using three different kinds of basis sets: Gaussian-type orbitals, numerical basis sets, and real-space grids. Although all of these methods can yield similar results, surprisingly large, diffuse basis sets are needed to achieve convergence to comparable values. These results are interpreted in terms of local polarizability and hyperpolarizability densities. We find that the hyperpolarizability is very sensitive to the molecular structure, and we also assess the significance of vibrational contributions and frequency dispersion

Phonon transport in large scale carbon-based disordered materials: Implementation of an efficient order-N and real-space Kubo methodology

We have developed an efficient order-N real-space Kubo approach for the calculation of the phonon conductivity which outperforms state-of-the-art alternative implementations based on the Green's function formalism. The method treats efficiently the time-dependent propagation of phonon wave packets in real space, and this dynamics is related to the calculation of the thermal conductance. Without loss of generality, we validate the accuracy of the method by comparing the calculated phonon mean free paths in disordered carbon nanotubes (isotope impurities) with other approaches, and further illustrate its upscalability by exploring the thermal conductance features in large width edge-disordered graphene nanoribbons (up to ~20 nm), which is out of the reach of more conventional techniques. We show that edge-disorder is the most important scattering mechanism for phonons in graphene nanoribbons with realistic sizes and thermal conductance can be reduced by a factor of ~10.Comment: Accepted for publication in Physical Review B - Rapid Communication

An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the hard coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptideComment: 13 pages, 8 figures, published versio

Quantum Simulation of Quantum Field Theories in Trapped Ions

We propose the quantum simulation of a fermion and an antifermion field modes interacting via a bosonic field mode, and present a possible implementation with two trapped ions. This quantum platform allows for the scalable add-up of bosonic and fermionic modes, and represents an avenue towards quantum simulations of quantum field theories in perturbative and nonperturbative regimes.Comment: To be published in Physical Review Letter

Spin canted magnetism, decoupling of charge and spin ordering in NdNiO3_3

We report detailed magnetization measurements on the perovskite oxide NdNiO$_3$. This system has a first order metal-insulator (M-I) transition at about 200 K which is associated with charge ordering. There is also a concurrent paramagnetic to antiferromagnetic spin ordering transition in the system. We show that the antiferromagnetic state of the nickel sublattice is spin canted. We also show that the concurrency of the charge ordering and spin ordering transitions is seen only while warming up the system from low temperature. The transitions are not concurrent while cooling the system through the M-I transition temperature. This is explained based on the fact that the charge ordering transition is first order while the spin ordering transition is continuous. In the magnetically ordered state the system exhibits ZFC-FC irreversibilities, as well as history-dependent magnetization and aging. Our analysis rules out the possibility of spin-glass or superparamagnetism and suggests that the irreversibilities originate from magnetocrystalline anisotropy and domain wall pinning.Comment: 8 pages, 7 figure

Tuning laser-induced bandgaps in graphene

Could a laser field lead to the much sought-after tunable bandgaps in graphene? By using Floquet theory combined with Green's functions techniques, we predict that a laser field in the mid-infrared range can produce observable bandgaps in the electronic structure of graphene. Furthermore, we show how they can be tuned by using the laser polarization. Our results could serve as a guidance to design opto-electronic nano-devices.Comment: 4 pages, 3 figures, to appear in Applied Physics Letter

Self-assembly scenarios of patchy colloidal particles

The rapid progress in precisely designing the surface decoration of patchy colloidal particles offers a new, yet unexperienced freedom to create building entities for larger, more complex structures in soft matter systems. However, it is extremely difficult to predict the large variety of ordered equilibrium structures that these particles are able to undergo under the variation of external parameters, such as temperature or pressure. Here we show that, by a novel combination of two theoretical tools, it is indeed possible to predict the self-assembly scenario of patchy colloidal particles: on one hand, a reliable and efficient optimization tool based on ideas of evolutionary algorithms helps to identify the ordered equilibrium structures to be expected at T = 0; on the other hand, suitable simulation techniques allow to estimate via free energy calculations the phase diagram at finite temperature. With these powerful approaches we are able to identify the broad variety of emerging self-assembly scenarios for spherical colloids decorated by four patches and we investigate and discuss the stability of the crystal structures on modifying in a controlled way the tetrahedral arrangement of the patches.Comment: 11 pages, 7 figures, Soft Matter Communication (accepted

Spin-dependent effective interactions for halo nuclei

We discuss the spin-dependence of the effective two-body interactions appropriate for three-body computations. The only reasonable choice seems to be the fine and hyperfine interactions known for atomic electrons interacting with the nucleus. One exception is the nucleon-nucleon interaction imposing a different type of symmetry. We use the two-neutron halo nucleus 11Li as illustration. We demonstrate that models with the wrong spin-dependence are basically without predictive power. The Pauli forbidden core and valence states must be consistently treated.Comment: TeX file, 6 pages, 3 postscript figure