SearcharxivSearch

arXiv · 1601.01036

Anomalous dimensionality dependence of diffusion in a rugged energy landscape : How pathological is one dimension ?

Abstract

Rugged (or, rough) energy landscape (REL) with spatially distributed maxima and minima are often employed in applications of physics, chemistry and biology (enzyme kinetics, protein folding, diffusion in disordered solids, transport in organic semiconductors, relaxation in random spin systems, in supercooled liquids and glasses). Sometimes the system needs to be modeled as a random walker in high dimensions (like in protein folding/unfolding) where dimensions could be the distances between different amino acid residues (as in unfolding of HP-36). Nevertheless, most of the theoretical studies of these phenomena still employ a one dimensional description. This is despite the prediction that in a rough (or, rugged) energy landscape (REL), diffusion in one dimension (1d) is predicted to be pathologically different from any higher dimension with the increased chance of encountering broken ergodicity (Stein and Newman, 2012). We explore the dimensionality dependent diffusion on REL by carrying out an effective medium approximation based analytical calculations and compare them with the available computer simulation results. We find that at intermediate level of ruggedness (assumed to have a Gaussian distribution), where diffusion is well-defined, the value of the effective diffusion coefficient depends on dimensionality and changes (increases) by several factors (~5-10) in going from 1d to 2d. In contrast, the changes in subsequent transitions (like 2d to 3d and 3d to 4d and so on) are far more modest, of the order of 10-20% only. When ruggedness is given by random traps with an exponential distribution of barrier heights, the mean square displacement is sub-diffusive (a well-known result), but the growth of MSD is described by different exponents in one and higher dimensions. The exponent of growth is larger in higher dimensions than in 1d.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Kazuhiko Seki, Kaushik Bagchi, Biman Bagchi. 2016-04-28. Anomalous dimensionality dependence of diffusion in a rugged energy landscape : How pathological is one dimension ?. https://doi.org/10.1063/1.4948936

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Slow Dynamics and the Geometry of Jammed Packings

Saddle points in the energy landscape of granular packings dominate the discrete steepest descent dynamics and ultimately determine the path that an out of mechanical equilibrium packing will follow and the resulting stable minimum that it will find. The saddle points that ultimately determine the resulting minima tend to be low-index saddle points. For models with an analytic energy landscape, such as the $p$-spin model, the steepest descent minimization path is affected by higher-index saddle points, which pull the system towards saddle points of decreasing index before arriving at the minima. Here, we examine the steepest descent minimization path of granular packings and compare them to the $p$-spin model. We show that the granular packing steepest descent minimization paths act like their smooth energy landscape counterparts and get attracted by saddle points. The index versus time curves for all models follow a shifted, stretched exponential. We further show that the shape parameter for the granular packings is unchanged when the energy landscape is modified to become analytic (Gaussian potential in a harmonic well) or non-local (Mari-Krzakala-Kurchan). The $p$-spin, on the other hand, has a significantly larger shape parameter. The reason is not due to the dimensionality, packing fraction, nonanalyticity, or the locality of the Hamiltonian of the models. The exact reason for the discrepancy in the shape parameter is \st{still} an unsolved mystery.

cond-mat.soft

A Phase-Field Study of Desiccation Crack Pattern Maturation under Drying-Wetting Cycles

The characteristic intersection angle of the desiccation crack relaxes from near \ang{90} toward \ang{120} under repeated drying--wetting cycles. However, the theoretical understanding of this relaxation is insufficient, especially the modeling of the drying--wetting cycles. Here we introduce a phase-field model of desiccation fracture, extending the model proposed in previous studies by adding crack healing and a scar effect left by past cracks. By repeating drying--wetting cycles in a finite element simulation, we find that the angle distribution develops a growing peak near \ang{120} as the cycle number increases, consistent with experiments. The standard deviation of the intersection angle from \ang{120} relaxes exponentially with a characteristic time of about 2.85 cycles. These results are consistent with experiments, except that the characteristic time is slightly smaller than the experimental value. Crack energy dominates the total energy and also relaxes exponentially with nearly the same characteristic cycle as the angle relaxation. This decay is driven mainly by a shortening of the effective crack length rather than a change in effective fracture toughness.

cond-mat.soft

Kinetics of ferritin crystal formation and melting in acoustically levitated droplets

Understanding protein crystallization pathways is essential for controlling crystallization in structural biology, materials science, and pharmaceutical applications. Classical nucleation theory does not fully capture crystallization processes for several proteins, including ferritin. Here, we combine acoustic levitation with small- and wide-angle X-ray scattering (SAXS and WAXS) to monitor ferritin crystallization in evaporating aqueous polyethylene glycol (PEG) solutions. Acoustic levitation rapidly drives the droplets through a broad range of protein and polymer concentrations, enabling time-resolved measurements of crystallization during evaporation. The scattering data show that ferritin crystals form during evaporation and subsequently lose their crystalline order upon further dehydration. Varying the PEG molecular weight switches between distinct crystallization pathways: one dominated by attractive protein-protein interactions and another dominated by repulsive interactions and excluded-volume effects. Furthermore, we find that lower molecular weight PEG (1000 g/mol) suppresses the dehydration-induced loss of crystalline order observed for higher molecular weight PEG (6000 g/mol), providing a simple strategy for improving protein crystal stability.

cond-mat.soft