• Publications
  • Influence
Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance
TLDR
A new mathematical model (the amplifier model) is presented that tracks the emergence and evolution of multiple strains of drug-resistant Mycobacterium tuberculosis, and finds that areas with programs that successfully reduced wild-type pansensitive strains often evolved into hot zones.
A Quantitative Affinity-Profiling System That Reveals Distinct CD4/CCR5 Usage Patterns among Human Immunodeficiency Virus Type 1 and Simian Immunodeficiency Virus Strains
TLDR
A system that provides a quantitative and comprehensive characterization of viral entry efficiency as a direct interdependent function of both CD4 and CCR5 levels and revealed heretofore unappreciated complexities underlying CD4/CCR5 usage is presented.
Non-equilibrium statistical mechanics: from a paradigmatic model to biological transport
TLDR
This work provides detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process, regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics.
Clustered bottlenecks in mRNA translation and protein synthesis.
TLDR
Using a model based on the totally asymmetric exclusion process, the effects of slow codons along messenger RNA are investigated, providing a biologically motivated explanation for the experimentally observed clustering of low-usage codons.
Elite Suppressor–Derived HIV-1 Envelope Glycoproteins Exhibit Reduced Entry Efficiency and Kinetics
TLDR
Overall, ES env clones were less efficient at mediating entry than chronic progressor envs, implying that lower env fitness may be established early and may directly contribute to viral suppression in ES individuals.
Totally asymmetric exclusion processes with particles of arbitrary size
The steady-state currents and densities of a one-dimensional totally asymmetric exclusion process (TASEP) with particles that occlude an integer number (d) of lattice sites are computed using various
Statistical thermodynamics of membrane bending-mediated protein-protein attractions.
TLDR
Here, pair interaction potentials and entropic contributions to the two-dimensional osmotic pressure of a collection of noncircular proteins are computed and thermally averaged attractive interactions of order k(B)T are found.
Entropy-driven pumping in zeolites and biological channels
TLDR
Model lattice simulations are used to show that single-file molecular-sized channels (such biomembrane channels and zeolites) can exhibit diffusional pumping, where one type of particle uses its entropy of mixing to drive another up its chemical potential gradient.
Kinetics and thermodynamics across single-file pores: Solute permeability and rectified osmosis
  • T. Chou
  • Chemistry, Physics
  • 29 September 1998
We study the effects of solute-membrane interactions on osmotic transport through pores. By extending single-file, single-species kinetic models to include entrance of solute into membrane pores, we
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