Prediction of long and short time rheological behavior in soft glassy materials

We present an effective time approach to predict long and short time rheological behavior of soft glassy materials from experiments carried out over practical time scales. Effective time approach takes advantage of relaxation time dependence on aging time that allows time-aging time superposition even when aging occurs over the experimental timescales. Interestingly experiments on variety of soft materials demonstrate that the effective time approach successfully predicts superposition for diverse aging regimes ranging from sub-aging to hyper-aging behaviors. This approach can also be used to predict behavior of any response function in molecular as well as spin glasses.Comment: 13 pages, 4 figure

Stress release mechanisms for Cu on Pd(111) in the submonolayer and monolayer regimes

We study the strain relaxation mechanisms of Cu on Pd(111) up to the monolayer regime using two different computational methodologies, basin-hopping global optimization and energy minimization with a repulsive bias potential. Our numerical results are consistent with experimentally observed layer-by-layer growth mode. However, we find that the structure of the Cu layer is not fully pseudomorphic even at low coverages. Instead, the Cu adsorbates forms fcc and hcp stacking domains, separated by partial misfit dislocations. We also estimate the minimum energy path and energy barriers for transitions from the ideal epitaxial state to the fcc-hcp domain pattern.Comment: 4 pages, 4 figure

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically-relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions---electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters---optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically-relevant molecules. We further focus on hydrogen-bonded complexes---essential but challenging due to their directional nature---where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML in denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.Comment: 15 pages, 9 figure

The Glassy Wormlike Chain

We introduce a new model for the dynamics of a wormlike chain in an environment that gives rise to a rough free energy landscape, which we baptise the glassy wormlike chain. It is obtained from the common wormlike chain by an exponential stretching of the relaxation spectrum of its long-wavelength eigenmodes, controlled by a single stretching parameter. Predictions for pertinent observables such as the dynamic structure factor and the microrheological susceptibility exhibit the characteristics of soft glassy rheology and compare favourably with experimental data for reconstituted cytoskeletal networks and live cells. We speculate about the possible microscopic origin of the stretching, implications for the nonlinear rheology, and the potential physiological significance of our results.Comment: 12 pages, 8 figures. Minor correction

Deceptive signals of phase transitions in small magnetic clusters

We present an analysis of the thermodynamic properties of small transition metal clusters and show how the commonly used indicators of phase transitions like peaks in the specific heat or magnetic susceptibility can lead to deceptive interpretations of the underlying physics. The analysis of the distribution of zeros of the canonical partition function in the whole complex temperature plane reveals the nature of the transition. We show that signals in the magnetic susceptibility at positive temperatures have their origin at zeros lying at negative temperatures.Comment: 4 pages, 5 figures, revtex4, for further information see http://www.smallsystems.d

Energy Landscape and Global Optimization for a Frustrated Model Protein

The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Go model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system.Comparisons are made with the widely studied 46-residue BLN protein.We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure

Aging in a Colloidal Glass in Creep Flow: Time-Stress Superposition

In this work, we study ageing behavior of aqueous laponite suspension, a model soft glassy material, in creep. We observe that viscoelastic behavior is time dependent and is strongly influenced by the deformation field; the effect is known to arise due to ageing and rejuvenation. We show that irrespective of strength of deformation field (shear stress) and age, when imposed time-scale is normalized with dominating relaxation mode of the system, universal ageing behavior is obtained demonstrating time-stress superposition; the phenomena that may be generic in variety of soft materials.Comment: 10 pages, 4 figure

Classification of phase transitions in small systems

We present a classification scheme for phase transitions in finite systems like atomic and molecular clusters based on the Lee-Yang zeros in the complex temperature plane. In the limit of infinite particle numbers the scheme reduces to the Ehrenfest definition of phase transitions and gives the right critical indices. We apply this classification scheme to Bose-Einstein condensates in a harmonic trap as an example of a higher order phase transitions in a finite system and to small Ar clusters.Comment: 12 pages, 4 figures, accepted for publication in Phys. Rev. Let

An investigation of standard thermodynamic quantities as determined via models of nuclear multifragmentation

Both simple and sophisticated models are frequently used in an attempt to understand how real nuclei breakup when subjected to large excitation energies, a process known as nuclear multifragmentation. Many of these models assume equilibriumthermodynamics and produce results often interpreted as evidence of a phase transition. This work examines one class of models and employs standard thermodynamical procedure to explore the possible existence and nature of a phase transition. The role of various terms, e.g. Coulomb and surface energy, is discussed.Comment: 19 two-column format pages with 24 figure

Structural Transitions and Global Minima of Sodium Chloride Clusters

In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we determine reaction pathways between the low energy isomers of one of these clusters, (NaCl)35Cl-. The key process in these structural transitions is a highly cooperative rearrangement in which two parts of the nanocrystal slip past one another on a {110} plane in a direction. In this way the nanocrystals can plastically deform, in contrast to the brittle behaviour of bulk sodium chloride crystals at the same temperatures; the nanocrystals have mechanical properties which are a unique feature of their finite size. We also report and compare the global potential energy minima for (NaCl)NCl- using two empirical potentials, and comment on the effect of polarization.Comment: extended version, 13 pages, 8 figures, revte