Biomedical subjects

J P Sethna

Publications and source records attributed to J P Sethna.

6 recordsLinked to original sources

PubMed2005

Bayesian error estimation in density-functional theory.

We present a practical scheme for performing error estimates for density-functional theory calculations. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies for molecules and solids. Fluctuations within the ensemble can then be used to estimate errors relative to experiment on calculated quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.

Bayes Theorem↗

PubMed2005

Vibration-assisted electron tunneling in C140 transistors.

We measure electron tunneling in transistors made from C(140), a molecule with a mass-spring-mass geometry chosen as a model system to study electron-vibration coupling. We observe vibration-assisted tunneling at an energy corresponding to the stretching mode of C(140). Molecular modeling provides explanations for why this mode couples more strongly to electron tunneling than to the other internal modes of the molecule. We make comparisons between the observed tunneling rates and those expected from the Franck-Condon model.

Carbon↗

PubMed2004

The statistical mechanics of complex signaling networks: nerve growth factor signaling.

The inherent complexity of cellular signaling networks and their importance to a wide range of cellular functions necessitates the development of modeling methods that can be applied toward making predictions and highlighting the appropriate experiments to test our understanding of how these systems are designed and function. We use methods of statistical mechanics to extract useful predictions for complex cellular signaling networks. A key difficulty with signaling models is that, while significant effort is being made to experimentally measure the rate constants for individual steps in these networks, many of the parameters required to describe their behavior remain unknown or at best represent estimates. To establish the usefulness of our approach, we have applied our methods toward modeling the nerve growth factor (NGF)-induced differentiation of neuronal cells. In particular, we study the actions of NGF and mitogenic epidermal growth factor (EGF) in rat pheochromocytoma (PC12) cells. Through a network of intermediate signaling proteins, each of these growth factors stimulates extracellular regulated kinase (Erk) phosphorylation with distinct dynamical profiles. Using our modeling approach, we are able to predict the influence of specific signaling modules in determining the integrated cellular response to the two growth factors. Our methods also raise some interesting insights into the design and possible evolution of cellular systems, highlighting an inherent property of these systems that we call 'sloppiness.'

Animals↗

PubMed2002

Fracture in mode I using a conserved phase-field model.

We present a continuum phase-field model of crack propagation. It includes a phase-field that is proportional to the mass density and a displacement field that is governed by linear elastic theory. Generic macroscopic crack growth laws emerge naturally from this model. In contrast to classical continuum fracture mechanics simulations, our model avoids numerical front tracking. The added phase-field smooths the sharp interface, enabling us to use equations of motion for the material (grounded in basic physical principles) rather than for the interface (which often are deduced from complicated theories or empirical observations). The interface dynamics thus emerges naturally. In this paper, we look at stationary solutions of the model, mode I fracture, and also discuss numerical issues. We find that the Griffith's threshold underestimates the critical value at which our system fractures due to long wavelength modes excited by the fracture process.

Journal Article↗

PubMed2001

Crackling noise.

Crackling noise arises when a system responds to changing external conditions through discrete, impulsive events spanning a broad range of sizes. A wide variety of physical systems exhibiting crackling noise have been studied, from earthquakes on faults to paper crumpling. Because these systems exhibit regular behaviour over a huge range of sizes, their behaviour is likely to be independent of microscopic and macroscopic details, and progress can be made by the use of simple models. The fact that these models and real systems can share the same behaviour on many scales is called universality. We illustrate these ideas by using results for our model of crackling noise in magnets, explaining the use of the renormalization group and scaling collapses, and we highlight some continuing challenges in this still-evolving field.

Journal Article↗

PubMed2001

Calculation of quantum tunneling for a spatially extended defect: the dislocation kink in copper has a low effective mass.

Several experiments indicate that there are atomic tunneling defects in plastically deformed metals. How this is possible has not been clear, given the large mass of the metal atoms. Using a classical molecular-dynamics calculation, we determine the structures, energy barriers, effective masses, and quantum tunneling rates for dislocation kinks and jogs in copper screw dislocations. We find that jogs are unlikely to tunnel, but the kinks should have large quantum fluctuations. The kink motion involves hundreds of atoms each shifting a tiny amount, leading to a small effective mass and tunneling barrier.

Journal Article↗