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Biomedical subjects

Tom Chou

Publications and source records attributed to Tom Chou.

11 recordsLinked to original sources

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↗

First passage times of driven DNA hairpin unzipping.

We model the dynamics of voltage-driven transport of DNA hairpins through transmembrane channels. A two-dimensional stochastic model of the DNA translocation process is fit to the measurements of Mathé, who pulled self-hybridized DNA hairpins through lipid-embedded alpha-hemolysin channels. As the channel was too narrow to accommodate hybridized DNA, dehybridization of the hairpin became the rate-limiting step of the transport process. We show that the mean first passage time versus voltage curve for the escape of the DNA from the transmembrane channel can be divided into two regions: (1) a low-voltage region where the DNA slides out of the pore in reverse and without undergoing significant dehybridization, and (2) a region where the DNA dehybridizes under the influence of the applied voltage and translocates across the membrane.

Biological Transport↗

Steady-state properties of a totally asymmetric exclusion process with periodic structure.

We study the steady-state behavior of totally asymmetric simple exclusion processes (TASEPs) that contain periodically varying movement rates. In this model, particles move to the right at one of two rates: p(2) if the particle occupies one of a periodically arranged set of lattice sites; p(1) otherwise. Approximate mean field approaches are used to study the steady-state currents and bulk densities of this model. These mean field methods are found to provide results in good agreement with data derived from Monte Carlo simulations. Finally, the condition for particle-hole symmetry in the TASEP with periodically varying movement rates is specified, and the changes in the locations of the boundary-limited to maximal-current transition lines due to symmetry violation are investigated.

Animals↗

Clustered bottlenecks in mRNA translation and protein synthesis.

Using a model based on the totally asymmetric exclusion process, we investigate the effects of slow codons along messenger RNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size beyond approximately 3-4 codons does not significantly reduce the ribosome current. Our results are verified by both extensive Monte Carlo simulations and numerical calculation, and provide a biologically motivated explanation for the experimentally observed clustering of low-usage codons.

Algorithms↗

Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance.

'Hot zones' are areas that have >5% prevalence (or incidence) of multidrug-resistant tuberculosis (MDRTB). We present a new mathematical model (the amplifier model) that tracks the emergence and evolution of multiple (pre-MDR, MDR and post-MDR) strains of drug-resistant Mycobacterium tuberculosis. We reconstruct possible evolutionary trajectories that generated hot zones over the past three decades, and identify the key causal factors. Results are consistent with recently reported World Health Organization (WHO) data. Our analyses yield three important insights. First, paradoxically we found that areas with programs that successfully reduced wild-type pansensitive strains often evolved into hot zones. Second, some hot zones emerged even when MDR strains were substantially less fit (and thus less transmissible) than wild-type pansensitive strains. Third, levels of MDR are driven by case-finding rates, cure rates and amplification probabilities. To effectively control MDRTB in the hot zones, it is essential that the WHO specify a goal for minimizing the amplification probability.

Biological Evolution↗

Physical mechanisms of gas and perfluoron retinopexy and sub-retinal fluid displacement.

Injection of gas into the eye, followed by face-down positioning, is a common protocol for the reseating of the retina in posterior and superior retinal tears and breaks. The physical mechanism by which injected gas helps reattach retinal flaps is often ascribed to the 'buoyancy' force of the injected gas bubble. The various forces at play in this system (surface tension and buoyancy) were calculated and compared. The results are extended to the case in which the retina is intact (pneumatic displacement of blood) and to the use of intraocular perfluoron (n-perfluorooctane). We show that buoyancy forces are applicable only for gas or n-perfluorooctane bubbles that are smaller than the detached retina and that do not invade underneath the retina. For larger bubbles, as is normally used in reattachment protocols, we show that it is the interfacial tension that reattaches the retina. The range of angles within which patients can position, and still maintain a gas-vitreous interface along a tear is calculated as a function of the volume of injected gas and size of the tear. The maximum retinal flap size that can be reattached using surface tension forces is also estimated.

Fluorocarbons↗

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↗

Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport.

A discrete multistate kinetic model for water-wire proton transport is constructed and analyzed using Monte Carlo simulations. In the model, each water molecule can be in one of three states: oxygen lone-pairs pointing leftward, pointing rightward, or protonated (H(3)O(+)). Specific rules for transitions among these states are defined as protons hop across successive water oxygens. Our model also includes water-channel interactions that preferentially align the water dipoles, nearest-neighbor dipolar coupling interactions, and Coulombic repulsion. Extensive Monte Carlo simulations were performed and the observed qualitative physical behaviors discussed. We find the parameters that allow the model to exhibit superlinear and sublinear current-voltage relationships, and show why alignment fields, whether generated by interactions with the pore interior or by membrane potentials, always decrease the proton current. The simulations also reveal a "lubrication" mechanism that suppresses water dipole interactions when the channel is multiply occupied by protons. This effect can account for an observed sublinear-to-superlinear transition in the current-voltage relationship.

Biological Transport↗

Physics of RecA-mediated homologous recognition.

To accomplish its DNA strand exchange activities, the Escherichia coli protein RecA polymerizes onto DNA to form a stiff helical nucleoprotein filament within which the DNA is extended by 50%. Homology search and recognition occurs between ssDNA within the filament and an external dsDNA molecule. We show that stretching the internal DNA greatly enhances homology recognition by increasing the probability that the homologous regions of a stretched DNA molecule and a parallel, unstretched DNA molecule will be "in register" at some position. We also show that the stretching and stiffness of the filament act together to ensure that initiation of homologous exchange between the substrate DNA molecules at one position precludes initiation of homologous exchange at any other position. This prevents formation of multiple exchange site "topological traps" which would prevent completion of the exchange reaction and resolution of the products.

Adenosine Triphosphatases↗

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↗

Ribosome recycling, diffusion, and mRNA loop formation in translational regulation.

We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to the initiation site, especially if it is held nearby, enhancing overall translation rates. The elongation steps of the mRNA-bound ribosomes are modeled using exact and asymptotic results of the totally asymmetric exclusion process. Since the ribosome injection rates of the totally asymmetric exclusion process depend on the local concentrations at the initiation site, a source of ribosomes emanating from the termination end can feed back to the initiation site, leading to a self-consistent set of equations for the steady-state ribosome throughput. Additional mRNA binding factors can also promote loop formation, or cyclization, bringing the initiation and termination sites into close proximity. The probability distribution of the distance between the initiation and termination sites is described using simple noninteracting polymer models. We find that the initiation, or initial ribosome adsorption binding required for maximal throughput, can vary dramatically depending on certain values of the bulk ribosome concentration and diffusion constant. If cooperative interactions among the loop-promoting proteins and the initiation/termination sites are considered, the throughput can be further regulated in a nonmonotonic manner. Experiments that can potentially test the hypothesized physical mechanisms are discussed.

Adsorption↗