Sensitivity Regulation based on Noise Propagation in Stochastic Reaction Networks (2008)
Kim, Kyung Hyuk, Qian, Hong, Sauro, Herbert M.
In this work we focus on how noise propagates in biochemical reaction networks and affects sensitivities of the system. We discover that the stochastic fluctuations can enhance sensitivities in one...
Heuett, William J, Beard, Daniel A, Qian, Hong
Abstract Background: Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have...
Baross, Ágnes, Delaney, Allen D, Li, H Irene, Nayar, Tarun, Flibotte, Stephane, Qian, Hong, ...
Abstract Background Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in...
Hawkins, Bradford A., Albuquerque, Fabio S., Araujo, Miguel B., Beck, Jan, Mauricio Bini, Luis, Cabrero-Sanudo, Francisco J., ...
We compiled 46 broadscale data sets of species richness for a wide range of terrestrial plant, invertebrate, and ectothermic vertebrate groups in all parts of the world to test the ability of...
Regulation of Hematopoietic Stem and Progenitor Cells by Bone Marrow Niche Components (2007)
Throughout the lifespan of an individual, enormous numbers of mature blood cells are generated by hematopoietic stem cells (HSCs) in the bone marrow (BM). The HSC is a cell that can self-renew to...
Clustering Coefficients of Protein-Protein Interaction Networks (2007)
Miller, Gerald A., Shi, Yi Y., Qian, Hong, Bomsztyk, Karol
The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden...
Mansson, Robert, Hultquist, Anne, Luc, Sidinh, Yang, Liping, Anderson, Kristina, Kharazi, Shabnam, ...
Abstract is not available
Qian, Hong, Georges-Labouesse, Elisabeth, Nystrom, Alexander, Domogatskaya, Anna, Tryggvason, Karl, Jacobsen, Sten Eirik W, ...
Abstract is not available
Essays on Equity Issuance (2006)
This thesis explores two issues regarding corporate equity issuance. The first chapter studies the timing of seasoned equity offerings (SEOs) at the firm level. Descriptive statistics formulated...
Characterization of Metastatic Tumor Formation by the Colony Size Distribution (2006)
Lee, Steve P., Sun, Ji-Rong, Qian, Hong, McBride, William H., Withers, H. Rodney
Knowledge regarding the kinetics of metastatic tumor formation, as related to the growth of the primary tumor, represents a fundamental issue in cancer biology. Using an in vivo mammalian model, we...
Shi, Yi Y., Miller, Gerald A., Qian, Hong, Bomsztyk, Karol
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria....
Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far...
Fluctuation Theorems of Brownian Particles Controlled by a Maxwell's Demon (2006)
We study the stochastic dynamics of Brownian particles in a heat bath and subject to an active feedback control by an external, Maxwell's demon-like agent. The agent uses the information of the...
Qian, Hong, Tryggvason, Karl, Jacobsen, Sten E, Ekblom, Marja
Abstract is not available
Buza-Vidas, Natalija, Antonchuk, Jennifer, Qian, Hong, Månsson, Robert, Luc, Sidinh, Zandi, Sasan, ...
Abstract is not available
"The oxygen evolving complex (OEC) of photosystem II (PSII) requires chloride as a critical cofactor. The Cl- content of PSII was determined to be 1 Cl-/PSII by the AgCl colloid assay. The...
Advisor: Alice Haddy ; submitted to the Dept. of Chemistry.
Essays on equity issuance [electronic resource] / (2006)
The full text of the dissertation is available as a Adobe Acrobat .pdf file (125 p.) ; Adobe Acrobat Reader required to view the file.
Thesis (M.S.)--University of North Carolina at Greensboro, 2006.
Metabolic Futile Cycles and Their Functions: A Systems Analysis of Energy and Control (2005)
It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative...
Applying the method from recently developed fluctuation theorems to the stochastic dynamics of single macromolecules in ambient fluid at constant temperature, we establish two Jarzynski-type...
Enyzme kinetics are cyclic. We study a Markov renewal process model of single-enzyme turnover in nonequilibrium steady-state (NESS) with sustained concentrations for substrates and products. We show...
Qiu-Yun (Jenny) Xiang, Wen Heng Zhang, Robert E. Ricklefs, Hong Qian, Zhi Duan Chen, Jun Wen, ...
The eastern Asian (EAS)–eastern North American (ENA) floristic disjunction is one of the best-known biogeographic patterns in the Northern Hemisphere. Recent paleontological and molecular analyses...
Qian, Hong, Xiao, Yin, Bartold, P. Mark
OBJECTIVE: The aim of this study was to determine the distribution and expression of fibromodulin in adult rat periodontal tissues and inflamed human gingiva. MATERIALS AND METHODS: The distribution...
Xiao, Yin, Qian, Hong, Young, William G., Bartold, P. Mark
Regeneration of osseous defects by a tissue-engineering approach provides a novel means of treatment utilizing cell biology, materials science, and molecular biology. In this study the concept of...
Hong Qian, Karel Klinka, Rune H. Økland, Pavel Krestov, Gordon J. Kayahara
We compared the species composition and species density of vascular plants in the understorey vegetation of boreal forest between Picea mariana (Black spruce) and Populus tremuloides (Trembling...
Entropy Production of Brownian Macromolecules with Inertia (2003)
We investigate the nonequilibrium steady-state thermodynamics of single Brownian macromolecules with inertia under feedback control in isothermal ambient fluid. With the control being represented by...
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal...
Qian, Hong, Qian, Min, Tang, Xiang
The solution to nonlinear Fokker-Planck equation is constructed in terms of the minimal Markov semigroup generated by the equation. The semigroup is obtained by a purely functional analytical method...
We introduce axiomatically a complete thermodynamic formalism for a single macromolecule, either with or without detailed balance, in an isothermal ambient fluid based on its stochastic dynamics....
In recent single-particle tracking (SPT) measurements on {\it Listeria monocytogenes} motility {\em in vitro}, the actin-based stochastic dynamics of the bacterium movement is analyzed statistically...
The Mathematical Theory of Molecular Motor Movement and Chemomechanical Energy Transduction (2001)
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion...
An Analysis of the Thermodynamics of Hydrophobic Solvation Based on Scaled Particle Theory (2001)
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats...
From Discrete Protein Kinetics to Continuous Brownian Dynamics: A New Perspective (2001)
An analysis on the discrete versus continuous views of kinetics of macromolecules is presented. It is shown that the discrete approach traditional to biochemistry is insufficient for understanding...
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the...
Mathematical Formalism for Isothermal Linear Irreversibility (2000)
We prove the equivalence among symmetricity, time reversibility, and zero entropy production of the stationary solutions of linear stochastic differential equations. A sufficient and necessary...
Using a one-dimensional macromolecule in aqueous solution as an illustration, we demonstrate that the relative entropy from information theory, $\sum_k p_k\ln(p_k/p_k^*)$, has a natural role in the...
A Simple Theory of Motor Protein Kinetics and Energetics. II (1999)
A three-state stochastic model of motor protein [Qian, Biophys. Chem., (1997)] is further developed to illustrate the relationship between the external load on an individual motor protein in aqueous...
Single-Particle Tracking Brownian Dynamics of Viscoelastic Materials (1999)
A unifying theoretical framework for analyzing stochastic data from single-particle tracking (SPT) in viscoelastic materials is presented. A generalization of the beadspring model for linear polymers...
Hong Qian, Gary M. Raymond, James B. Bassingthwaighte
Fluctuations in the concentration of Brownian particles in 1- and 2-dimensions, or any reasonable measurement of the concentration such as in fluorescence correlation spectroscopy, is shown to be a...
A Graphical Method for Force Analysis: Macromolecular Mechanics with Atomic Force Microscopy (1999)
this article, we present a unifying, yet graphical and quantitative interpretation for these measurements. The analysis shows that many experimental observations, such as "jumps-on", "snaps-off ",...
Separation of coffee cherries by maturity using difference in bioyield force [microform] / (1999)
Thesis (M.S.)--University of Hawaii at Manoa, 1999.
Separation of coffee cherries by maturity using difference in bioyield force / (1999)
Thesis (M.S.)--University of Hawaii at Manoa, 1999.
Entropy-Enthalpy Compensation: Conformational Fluctuation and Induced-fit (1998)
A localized change in a protein, which occurs as a result of either ligand binding or single amino acid substitution, necessarily encounters the conformational fluctuation of the rest of the protein....
Typescript.
Concentration fluctuations in a mesoscopic oscillating chemical reaction system
Qian, Hong, Saffarian, Saveez, Elson, Elliot L.
Under sustained pumping, kinetics of macroscopic nonlinear biochemical reaction systems far from equilibrium either can be in a stationary steady state or can execute sustained oscillations about a...
In living cells, biochemical reaction networks often function in nonequilibrium steady states. Under these conditions, the networks necessarily have cyclic reaction kinetics that are maintained by...
Energy balance for analysis of complex metabolic networks.
Beard, Daniel A, Liang, Shou-dan, Qian, Hong
Predicting behavior of large-scale biochemical networks represents one of the greatest challenges of bioinformatics and computational biology. Computational tools for predicting fluxes in biochemical...
Concentration fluctuations in a mesoscopic oscillating chemical reaction system
Qian, Hong, Saffarian, Saveez, Elson, Elliot L.
Under sustained pumping, kinetics of macroscopic nonlinear biochemical reaction systems far from equilibrium either can be in a stationary steady state or can execute sustained oscillations about a...
In living cells, biochemical reaction networks often function in nonequilibrium steady states. Under these conditions, the networks necessarily have cyclic reaction kinetics that are maintained by...
Energy balance for analysis of complex metabolic networks.
Beard, Daniel A, Liang, Shou-dan, Qian, Hong
Predicting behavior of large-scale biochemical networks represents one of the greatest challenges of bioinformatics and computational biology. Computational tools for predicting fluxes in biochemical...
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes
Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far...
Buza-Vidas, Natalija, Antonchuk, Jennifer, Qian, Hong, Månsson, Robert, Luc, Sidinh, Zandi, Sasan, ...
The role of cytokines as regulators of hematopoietic stem cell (HSC) expansion remains elusive. Herein, we identify thrombopoietin (THPO) and the cytokine signaling inhibitor LNK, as opposing...
Shi, Yi Y., Miller, Gerald A., Qian, Hong, Bomsztyk, Karol
Major advances in large-scale yeast two-hybrid screening have provided a global view of binary protein–protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably,...
Dixit, Manjusha, Ansseau, Eugénie, Tassin, Alexandra, Winokur, Sara, Shi, Rongye, Qian, Hong, ...
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disorder linked to contractions of the D4Z4 repeat array in the subtelomeric region of chromosome 4q. By comparing genome-wide...
From discrete protein kinetics to continuous Brownian dynamics: A new perspective
This article presents a comparative analysis of two sets of data from recent experiments on kinetics of (i) protein unfolding by mechanical force and (ii) channel gating with membrane electric...