Now showing items 1-10 of 25
Fluctuating mobility generation and transport in glasses
(American Physical Society, 2013)
In the context of the random first order transition theory we use an extended mode coupling theory of the glass transition that includes activated events to account for spatiotemporal structures in rejuvenating glasses. We numerically solve fluctuating dynamical equations for mobility and fictive temperature fields which capture both mobility generation ...
Chemical physics of protein folding
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
(Oxford University Press, 2016)
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network ...
Dichotomous noise models of gene switches
(AIP Publishing LLC., 2015)
Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from gene state switching, a single molecule event. Stochastic dynamics of gene regulatory circuits appears to be ...
Predictive energy landscapes for folding α-helical transmembrane proteins
(National Academy of Sciences, 2014)
We explore the hypothesis that the folding landscapes of membrane proteins are funneled once the proteins' topology within the membrane is established. We extend a protein folding model, the associative memory, water-mediated, structure, and energy model (AWSEM) by adding an implicit membrane potential and reoptimizing the force field to account for ...
On the hydrodynamics of swimming enzymes
(AIP Publishing LLC, 2015)
Several recent experiments suggest that rather generally the diffusion of enzymes may be augmented through their activity. We demonstrate that such swimming motility can emerge from the interplay between the enzyme energy landscape and the hydrodynamic coupling of the enzyme to its environment. Swimming thus occurs during the transit time of a transient ...
Microscopic theory of the glassy dynamics of passive and active network materials
(American Institute of Physics, 2013)
Signatures of glassy dynamics have been identified experimentally for a rich variety of materials in which molecular networks provide rigidity. Here we present a theoretical framework to study the glassy behavior of both passive and active network materials. We construct a general microscopic network model that incorporates nonlinear elasticity of ...
Active patterning and asymmetric transport in a model actomyosin network
(AIP Publishing LLC, 2013)
Cytoskeletal networks, which are essentially motor-filament assemblies, play a major role in many developmental processes involving structural remodeling and shape changes. These are achieved by nonequilibrium self-organization processes that generate functional patterns and drive intracellular transport. We construct a minimal physical model that ...
Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network
(The Royal Society, 2016)
Eukaryotic transcription factors in the NF-κB family are central components of an extensive genetic network that activates cellular responses to inflammation and to a host of other external stressors. This network consists of feedback loops that involve the inhibitor IκBα, numerous downstream functional targets, and still more numerous binding sites ...
Funneling and frustration in the energy landscapes of some designed and simplified proteins
(American Institute of Physics, 2013)
We explore the similarities and differences between the energy landscapes of proteins that have been selected by nature and those of some proteins designed by humans. Natural proteins have evolved to function as well as fold, and this is a source of energetic frustration. The sequence of Top7, on the other hand, was designed with architecture alone ...