Absence Of Long-range Interactions Research Articles

Long-Range Prethermal Phases of Nonequilibrium Matter

We prove the existence of non-equilibrium phases of matter in the prethermal regime of periodically-driven, long-range interacting systems, with power-law exponent $\alpha > d$, where $d$ is the dimensionality of the system. In this context, we predict the existence of a disorder-free, prethermal discrete time crystal in one dimension -- a phase strictly forbidden in the absence of long-range interactions. Finally, using a combination of analytic and numerical methods, we highlight key experimentally observable differences between such a prethermal time crystal and its many-body localized counterpart.

Mixed-spin system with supersolid phases: magnetocaloric effect and thermal properties

Recently, it has been shown that two dimensional frustrated mixed-spin systems with anisotropic exchange interactions display supersolid phases in their ground state phase diagrams even in the absence of long-range interactions. In this paper, using cluster mean field theory, we investigate the effects of thermal fluctuations on the ground state phases of this kind of system and show that various thermal solids and thermal insulators emerge around the ground state solid and Mott insulating phases. We also study the thermodynamic properties and magnetocaloric effect of these systems and demonstrate that at low temperatures, a large cooling rate is seen in the vicinity of the solid-supersolid, solid-superfluid and Mott insulator-superfluid critical points, with the large accumulation of the entropy and the minimums of the isentropes. Our results show the sign change of the magnetocaloric parameter inside the solids and the Mott insulator, which is a characteristic of ordered phases.

Kaleidoscope of quantum phases in a long-range interacting spin-1 chain.

Motivated directly by recent trapped-ion quantum simulation experiments, we carry out a comprehensive study of the phase diagram of a spin-1 chain with XXZ-type interactions that decay as 1/rα , using a combination of finite and infinite-size DMRG calculations, spin-wave analysis, and field theory. In the absence of long-range interactions, varying the spin-coupling anisotropy leads to four distinct and well-studied phases: a ferromagnetic Ising phase, a disordered XY phase, a topological Haldane phase, and an antiferromagnetic Ising phase. If long-range interactions are antiferromagnetic and thus frustrated, we find primarily a quantitative change of the phase boundaries. On the other hand, ferromagnetic (nonfrustrated) long-range interactions qualitatively impact the entire phase diagram. Importantly, for α ≲ 3 long-range interactions destroy the Haldane phase, break the conformal symmetry of the XY phase, give rise to a new phase that spontaneously breaks a U(1) continuous symmetry, and introduce a possibly exotic tricritical point with no direct parallel in short-range interacting spin chains. Importantly, we show that the main signatures of all five phases found could be observed experimentally in the near future.

Effects of chain flexibility on the conformational behavior of a single polymer chain

Effects of chain flexibility on conformational behavior as a function of temperature have been investigated by coarse-grained molecular dynamics (MD) simulation. The paper presents simulation results regarding the potential energies and structural parameters of a single polymer chain made of 100, 200, or 300 beads with various chain flexibilities. Our simulations exhibit the conformational transition from a random coil to a folded structure demonstrated by the curves of non-bonded potential energy, bond-orientational order parameters and characteristic ratios of real polymer chains with a cooling temperature. In this paper, the comparison between the real polymer chain model involving non-bonded interaction and the ideal polymer chain model in the absence of long-range interaction has also been made. It shows that the main factor inducing structural transition lies in the non-bonded interaction. This result explains clearly that the long-range interaction plays an important role in the polymer folding process. Moreover, the flexibility, as well as the chain length of a real polymer chain, strongly effects on its transition temperature. It also concludes that the changes of bond-torsional potential energy and characteristic ratio with the reduced temperature in the ideal polymer models are independent of chain length, but present different tendencies according to the chain flexibility.

Dynamical Correlations After a Quantum Quench

We consider dynamic (non-equal-time) correlation functions of local observables after a quantum quench. We show that, in the absence of long-range interactions in the final Hamiltonian, the dynamics is determined by the same ensemble that describes static (equal-time) correlations. For many integrable models, static correlation functions of local observables after a quantum quench relax to stationary values, which are described by a generalized Gibbs ensemble. The same generalized Gibbs ensemble then determines dynamic correlation functions, and the basic form of the fluctuation dissipation theorem holds, although the absorption and emission spectra are not simply related as in the thermal case. For quenches in the transverse field Ising chain, we derive explicit expressions for the time evolution of dynamic order parameter correlators after a quench.

Molecular dynamics modelling of nanocarbon cluster properties under conditions close to HE detonation

We use molecular dynamics for modelling properties of carbon nanoclusters. The size of modelled carbon nanoclusters is below 5 nm, which is typical of detonation di- amond nanoclusters. We have found their structural changes at P = 0 to be as follows: Dia- mond → Diamond core + GL-surface → sandwich-type graphite → Graphite-like liquid. In smaller clusters the transformations start at a lower temperature. Adaptive Template Analysis (ATA) was used to determine the structures. We studied evaporation properties at temperatures above 5000 K. For clusters of several thousands of atoms, the simple depen- dence kvap ∼ e −T0/T /N 1/3 (T0 is constant) is quite good. It has been found out that densities of saturated vapour for clusters containing from 4000 to 8000 atoms are very close at T = 5000 K. The structure of nanoclusters was studied at nonzero pressures set by an argon environ- ment. Calculated results suggest that the patterns for different temperatures are qualita- tively similar for three pressures under study (20, 25 and 30 GPa). At T = 1000-1500 K, the initial diamond core is preserved and a thin disordered GL layer is present on the sur- face. At T = 2000-5000 K, graphite grains form in the sample and a thin layer of liquid is present on its surface. The sample is amorphous at 5500 K and 6000 K. The prevalence of the graphite phase at these pressures seems to come from the absence of long-range interaction in REBO-2002.

Secondary structure determines protein topology

Using a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long-range interactions. It has been a long-standing open question whether such information is sufficient to determine a protein's fold. Indeed, even the far simpler problem of reconstructing the three-dimensional structure of a protein from its exact backbone torsion angles has remained a difficult challenge owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, cause large errors in structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm; the longer the arm, the larger the displacement. Here, correct secondary structure assignments (alpha-helix, beta-strand, beta-turn, polyproline II, coil) were used to constrain polypeptide backbone chains devoid of side chains, and the most stable folded conformations were determined, using Monte Carlo simulation. Just three terms were used to assess stability: molecular compaction, steric exclusion, and hydrogen bonding. For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them.

Adsorption of polymers on a brush: Tuning the order of the wetting phase transition

We develop a computational methodology for the direct measurement of a wetting transition and its order via the effective interface potential. The method also allows to estimate contact angles in the nonwet state and to study adsorption isotherms. The proposed methodology is employed in order to study the wetting behavior of polymers on top of a brush consisting of identical polymers. In the absence of long-range forces, the system shows a sequence of nonwet, wet, and nonwet states as the brush density is increased. Including attractive long-range interactions we can make the polymer liquid wet the bush at all grafting densities, and both first- and second-order wetting transitions are observed. The latter case is limited to a small interval of grafting densities where the melt wets the brush in the absence of long-range interactions. Second-order wetting transitions are preceded by a first-order surface transition from a thin to a thick adsorbed layer. The interval of second-order wetting transitions is limited at low grafting densities by a surface critical end point and at high grafting densities by a tricritical wetting point. Our study highlights the rich wetting behavior that results when competing adsorbent-substrate interactions of different scales are tuned over a broad range.

Topological properties of the energy landscape of small peptides

In several works it has been shown that the interplay between short range and long range interactions, mimicking the hydrophobic effect, leads to the formation of the typical secondary structures in proteins, alpha-helices and beta-sheets. In this work we study in detail how the general properties of the energy landscape emerge in a model that presents both components. In this regard it proves useful a sort of perturbative approach. In our model many features of the energy landscape in absence of long range interaction can be determined analytically. The comparison between the energy landscape of this reduced model to that of the complete model gives interesting insight on the role of long range interactions.

Variation in antimicrobial activity of lactoferricin-derived peptides explained by structure modelling

Antimicrobial peptides bovine lactoferricin (LfcinB) and human lactoferricin (LfcinH) are produced from the respective lactoferrin, but are more active than their precursors. Despite sequence homology, the bovine peptide and its derivatives are more active than their human homologs. Such differences between not only the peptides and their precursor but also between the bovine and the human peptides could relate to structural differences. Upon sequence alignment of both peptides with their parental proteins, the structural differences observed between the bovine lactoferrin (BLf) and LfcinB were also found between the human lactoferrin (HLf) and the LfcinH. The helical structures in HLf are replaced by β-strands separated by a strong turn in LfcinH suggesting an antiparallel β-sheet structure similar to LfcinB. MIC assays with HLP-2 and BLP-2, 11-residue peptides derived from the active core of both Lfcins, against Escherichia coli, showed that the bovine derivative, BLP-2, is more active than its human homolog HLP-2. Both 3D models for HLP-2 and BLP-2 showed that the β-strand is centred between the aromatic residues giving both side chains the same orientations. The displacement towards the N-terminus observed for the β-strand in HLP-2, compared with its central location in BLP-2, could be less favourable to membrane interaction and therefore responsible for the decrease in activity. Such a model suggests for LfcinH a mechanism similar to the one observed for LfcinB, where the absence of long-range interaction, present in lactoferrin, destabilises the first alpha helix, as observed in solution and, upon interaction with the membrane, could result in the formation of a β-strand, as observed in the presence of LPS. The location of the β-strand in relation to the positive charges, seems to define the efficiency of the activity of the peptide and may explain the difference in activity obtained between HLP-2 and BLP-2.

Variation in antimicrobial activity of lactoferricin-derived peptides explained by structure modelling

Antimicrobial peptides bovine lactoferricin (LfcinB) and human lactoferricin (LfcinH) are produced from the respective lactoferrin, but are more active than their precursors. Despite sequence homology, the bovine peptide and its derivatives are more active than their human homologs. Such differences between not only the peptides and their precursor but also between the bovine and the human peptides could relate to structural differences. Upon sequence alignment of both peptides with their parental proteins, the structural differences observed between the bovine lactoferrin (BLf) and LfcinB were also found between the human lactoferrin (HLf) and the LfcinH. The helical structures in HLf are replaced by β-strands separated by a strong turn in LfcinH suggesting an antiparallel β-sheet structure similar to LfcinB. MIC assays with HLP-2 and BLP-2, 11-residue peptides derived from the active core of both Lfcins, against Escherichia coli, showed that the bovine derivative, BLP-2, is more active than its human homolog HLP-2. Both 3D models for HLP-2 and BLP-2 showed that the β-strand is centred between the aromatic residues giving both side chains the same orientations. The displacement towards the N-terminus observed for the β-strand in HLP-2, compared with its central location in BLP-2, could be less favourable to membrane interaction and therefore responsible for the decrease in activity. Such a model suggests for LfcinH a mechanism similar to the one observed for LfcinB, where the absence of long-range interaction, present in lactoferrin, destabilises the first alpha helix, as observed in solution and, upon interaction with the membrane, could result in the formation of a β-strand, as observed in the presence of LPS. The location of the β-strand in relation to the positive charges, seems to define the efficiency of the activity of the peptide and may explain the difference in activity obtained between HLP-2 and BLP-2.

Reduced Spectral Density Mapping of a Partially Folded Fragment of E. coli Thioredoxin

The backbone dynamics of a partially folded, N-terminal fragment of E. coli thioredoxin were investigated using nuclear magnetic resonance spectroscopy (NMR). Relaxation data were collected at three temperatures and analyzed using reduced spectral density mapping. As temperature was increased, the values for the viscosity normalized J(0) and for J(ωH) increased, while J(ωN) decreased. The global trend observed for the viscosity normalized J(0) was consistent with an increase in the hydrodynamic volume of the fragment and suggested the presence of correlated rotational motion in the absence of long range interactions. In addition, the residue specific variation observed for the viscosity normalized J(0) suggested contributions to J(ω) from a range of correlation times that are close to the global correlation time.

Field Induced Dielectric Properties of 0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 Thin Films

ABSTRACTDC electric field induced dielectric properties of 0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 (PMN-PT) thin films were studied as a function of frequency at different temperatures. It was observed that the dielectric constant (ε) and dissipation factor (tanδ) were decreased in presence of bias field. The temperature of dielectric maxima was found to increase with increasing bias level. The low temperature (<Tm) frequency dispersion of dielectric permittivity was suppressed with the application of dc bias. After a certain bias voltage the relaxor property of films was disappeared i.e. the films exhibited normal ferroelectric behavior. Since the absence of long range interaction among the nanopolar clusters in PMN and its family is believed to be the origin of relaxor behavior, disappearance of relaxor nature in PMN-PT (70/30) films could be attributed to manifestation of long-range order at higher bias voltage. This was observed in the temperature dependence of dielectric constant i.e. the films neither exhibited any frequency dispersion in the temperature of dielectric maximum (Tm) nor showed any diffused phase transition. The relaxor property of PMN-PT thin films was studied in terms of diffused phase transition together with frequency dispersion of the temperature of dielectric maximum (Tm). Vogel-Fulcher relation was used to analyze the frequency dependence of temperature of dielectric maximum.

A semiempirical simulation methodology: atomistic and ionic dissociation of silica

Modeling defects, surfaces and interfaces of silica is complicated by the presence of charged and uncharged states of the atoms, and the existence of local nonstoichiometric structure. The changes in the local molecular environments associated with defects and surfaces are a consequence of changes in the electronic structure away from the bulk values. The ability to capture the electronic structure changes in simulations is highly desirable to study defects and surfaces. Moreover, the properties and problems of interest also require the use of large scale simulations. Hence, a semiempirical methodology is introduced that contains these desirable properties. The model approach is described and results using the model in the absence of long range interactions are presented. The motivation to ignore Coulombic interactions is driven by the desire to understand the model's ability to describe the bonding interactions and to what degree it captures any of the medium and long range order.

Incomplete symmetry breaking and anomolous crystallization kinetics at close-packed crystal-liquid interfaces

Stacking faults in close-packed planes are commonly observed during crystallization. In this paper we demonstrate that this behavior can be described in terms of a simple theoretical description of crystallization kinetics that couples two structural order parameters. We establish that the packing degeneracy that permits such faults also gives rise to a striking kinetic effect. The close-packed surface can freeze only when the symmetry of the two possible in-layer packings is broken, either by fluctuations or longer-range interactions. In the absence of long-range interactions, growth can take place only once the supercooling exceeds a critical depinning value, associated with a second-order phase transition in a single surface layer.

The kinetics of protein-protein recognition

We examine a simple kinetic model for association that incorporates the basic features of protein-protein recognition within the rigid body approximation, that is, when no large conformation change occurs. Association starts with random collision at the rate k(coll) predicted by the Einstein-Smoluchowski equation. This creates an encounter pair that can evolve into a stable complex if and only if the two molecules are correctly oriented and positioned, which has a probability p(r). In the absence of long-range interactions, the bimolecular rate of association is p(r) k(coll). Long-range electrostatic interactions affect both k(coll) and p(r). The collision rate is multiplied by q(t), a factor larger than 1 when the molecules carry net charges of opposite sign as coulombic attraction makes collisions more frequent, and less than 1 in the opposite case. The probability p(r) is multiplied by a factor q(r) that represents the steering effect of electric dipoles, which preorient the molecules before they collide. The model is applied to experimental data obtained by Schreiber and Fersht (Nat. Struct. Biol. 3:427-431, 1996) on the kinetics of barnase-barstar association. When long-range electrostatic interactions are fully screened or mutated away, q(t)q(r) approximately 1, and the observed rate of productive collision is p(r) k(coll) approximately 10(5) M(-1) x s(-1). Under these conditions, p(r) approximately 1.5 x 10(-5) is determined by geometric constraints corresponding to a loss of rotational freedom. Its value is compatible with computer docking simulations and implies a rotational entropy loss deltaS(rot) approximately 22 e.u. in the transition state. At low ionic strength, long-range electrostatic interactions accelerate barnase-barstar association by a factor q(t)q(r) of up to 10(5) as favorable charge-charge and charge-dipole interactions work together to make it much faster than free diffusion would allow.

Static light scattering from κ-carrageenan solutions

The polyelectrolyte behaviour of κ-carrageenan in NaCl and NaI solutions was investigated by static light scattering experiments. The solution properties of κ-carrageenan were found to be dependent upon the way the solutions were prepared. The dependence of the z-average radius of gyration and the second virial coefficient upon salt concentration exhibits normal polyelectrolyte behaviour in NaCl solutions for the range of ionic strengths considered. The persistence length as determined in the absence of long range interactions is found to be similar to values obtained for the majority of other polysaccharides. Within the same constraints of ionic strength a conformational change of the polymer chain is observed in NaI solutions without a noticeable change in molar mass. This observation is supported by measurements of optical rotation and the intrinsic viscosity.

Electrostatic Persistence Length of a Wormlike Polyelectrolyte

Electrostatic Persistence Length of a Wormlike Polyelectrolyte

The structural dependence of the inductive effect. Part I. The calculation of geminal substituent effects upon fluorine-19 chemical shifts

We present a simple method of calculating the effects of geminal substituents upon the differences in shielding between 19F nuclei bonded to sp3 carbon in a variety of compounds. A single experimental parameter is used, the Huggins electronegativity of α-substituents. The method rationalises some hitherto puzzling data, and makes it possible to calculate the chemical shifts (referred to CFCl3 as an arbitrary standard) of 19F nuclei in a variety of molecules containing the elements C, H, N, O, F, Cl, Br, and I; the calculated values (in the absence of long-range interactions) agree with experimental results to within the errors dictated by solvent effects and referencing procedures.