Biomedical subjects

Maria R D'Orsogna

Publications and source records attributed to Maria R D'Orsogna.

5 recordsLinked to original sources

PubMed2005

First passage and cooperativity of queuing kinetics.

We model the kinetics of ligand-receptor systems, where multiple ligands may bind and unbind to the receptor, either randomly or in a specific order. Equilibrium occupation and first occurrence of complete filling of the receptor are determined and compared. At equilibrium, receptors that bind ligands sequentially are more likely to be saturated than those that bind in random order. Surprisingly however, for low cooperativity, the random process first reaches full occupancy faster than the sequential one. This is true except near a critical binding energy where a "kinetic trap" arises and the random process dramatically slows down when the number of binding sites N > or = 8. These results demonstrate the subtle interplay between cooperativity and sequentiality for a wide class of kinetic phenomena, including chemical binding, nucleation, and assembly line strategies.

Kinetics↗

PubMed2004

Chiral molecule adsorption on helical polymers.

We present a lattice model for helicity induction on an optically inactive polymer due to the adsorption of exogenous chiral amine molecules. The system is mapped onto a one-dimensional Ising model characterized by an on-site polymer helicity variable and an amine occupancy one. The equilibrium properties are analyzed in the limits of strong coupling between helicity induction and amine adsorption and in that of noninteracting adsorbant molecules. We discuss our results in the context of recent experimental results.

Journal Article↗

PubMed2003

Interplay of chemotaxis and chemokinesis mechanisms in bacterial dynamics.

Motivated by observations of the dynamics of Myxococcus xanthus, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but release a chemical chemoattractant at a steady state. The bacteria sense the chemical that they produce. The probability of direction reversals is modeled as a function of both the absolute level of chemoattractant sensed directly under each cell as well as the gradient sensed across the length of the cell. If the chemical does not degrade or diffuse rapidly, the one-dimensional trajectory depends on the entire past history of the trajectory. We derive the corresponding Fokker-Planck equations, use an iterative mean-field approach that we solve numerically for short times, and perform extensive Monte Carlo simulations of the model. Cell positional distributions and the associated moments are computed in this feedback system. Average drift and mean squared displacements are found. Crossover behaviors among different diffusion regimes are found.

Bacterial Physiological Phenomena↗

PubMed2003

Charge transfer, symmetry, and dissipation in donor-acceptor molecules.

We study charge transfer between donor-acceptor molecules subject to a mirror symmetry constraint in the presence of a dissipative environment. The symmetry requirement leads to the breakdown of the standard single reaction coordinate description, and to a new charge transfer model, in the limit of low temperature, based on two independent reaction coordinates of equal relevance. We discuss implications of these results to charge transfer between DNA base pairs, whose geometrical configuration is modified by the addition of the migrating charge in conformity with the discussed symmetry constraint.

DNA↗

PubMed2002

Two-level system with a thermally fluctuating transfer matrix element: application to the problem of DNA charge transfer.

Charge transfer along the base-pair stack in DNA is modeled in terms of thermally assisted tunneling between adjacent base pairs. The key element of the approach in this paper is the notion that this tunneling between base pairs that fluctuate significantly from their nominal orientation is rate limited by the requirement of optimal alignment. We focus on this aspect of the process by modeling two adjacent base pairs in terms of a classical damped oscillator subject to thermal fluctuations as described by a Fokker-Planck equation. We find that the process is characterized by two time scales, a result that is in accord with the experimental findings.

Journal Article↗