Publications
95 results found
Jean L, Lee CF, Vaux DJ, 2012, Enrichment of Amyloidogenesis at an Air-Water Interface, Biophysical Journal, Vol: 102, Pages: 1154-1162, ISSN: 0006-3495
The aggregation of proteins or peptides into amyloid fibrils is a hallmark of protein misfolding diseases (e.g., Alzheimer’s disease) and is under intense investigation. Many of the experiments performed are in vitro in nature and the samples under study are ordinarily exposed to diverse interfaces, e.g., the container wall and air. This naturally raises the question of how important interfacial effects are to amyloidogenesis. Indeed, it has already been recognized that many amyloid-forming peptides are surface-active. Moreover, it has recently been demonstrated that the presence of a hydrophobic interface can promote amyloid fibrillization, although the underlying mechanism is still unclear. Here, we combine theory, surface property measurements, and amyloid fibrillogenesis assays on islet amyloid polypeptide and amyloid-² peptide to demonstrate why, at experimentally relevant concentrations, the surface activity of the amyloid-forming peptides leads to enriched fibrillization at an air-water interface. Our findings indicate that the key that links these two seemingly different phenomena is the surface-active nature of the amyloid-forming species, which renders the surface concentration much higher than the corresponding critical fibrillar concentration. This subsequently leads to a substantial increase in fibrillization.
Lee CF, 2011, Singular perturbation analysis of a reduced model for collective motion: A renormalization group approach, Physical Review E, Vol: 83, Pages: 031127-031127
In a system of noisy self-propelled particles with interactions that favor directional alignment, collective motion will appear if the density of particles is beyond a critical density. Starting with a reduced model for collective motion, we determine how the critical density depends on the form of the initial perturbation. Specifically, we employ a renormalization-group improved perturbative method to analyze the model equations and show analytically, up to first order in the perturbation parameter, how the critical density is modified by the strength of the initial angular perturbation in the system.
Smith DMD, Onnela JP, Lee CF, et al., 2011, NETWORK AUTOMATA: COUPLING STRUCTURE AND FUNCTION IN DYNAMIC NETWORKS, Advances in Complex Systems, Vol: 14, Pages: 317-339
Lee CF, 2010, Predicting rare events in chemical reactions: Application to skin cell proliferation, Physical Review E, Vol: 82, Pages: 021103-021103
In a well-stirred system undergoing chemical reactions, fluctuations in the reaction propensities are approximately captured by the corresponding chemical Langevin equation. Within this context, we discuss in this work how the Kramers escape theory can be used to predict rare events in chemical reactions. As an example, we apply our approach to a recently proposed model on cell proliferation with relevance to skin cancer [ P. B. Warren Phys. Rev. E 80 030903 (2009)]. In particular, we provide an analytical explanation for the form of the exponential exponent observed in the onset rate of uncontrolled cell proliferation.
Lee CF, 2010, Fluctuation-induced collective motion: A single-particle density analysis, Physical Review E, Vol: 81, Pages: 031125-031125
In a system of noisy self-propelled particles with interactions that favor directional alignment, collective motion will appear if the density of particles increases beyond a certain threshold. In this paper, we argue that such a threshold may depend also on the profiles of the perturbation in the particle directions. Specifically, we perform mean-field, linear stability, perturbative, and numerical analyses on an approximated form of the Fokker-Planck equation describing the system. We find that if an angular perturbation to an initially homogeneous system is large in magnitude and highly localized in space, it will be amplified and thus serves as an indication of the onset of collective motion. Our results also demonstrate that high particle speed promotes collective motion.
Jean L, Lee CF, Lee C, et al., 2010, Competing discrete interfacial effects are critical for amyloidogenesis, The FASEB Journal, Vol: 24, Pages: 309-317, ISSN: 1530-6860
Amyloid accumulation is associated with pathological conditions, including type II diabetes and Alzheimer’s disease. Lipids influence amyloidogenesis and are themselves targets for amyloid-mediated cell membrane disruption. Amyloid precursors are surface-active, accumulating at hydrophobic-hydrophilic interfaces (e.g., air-water), where their biophysical and kinetic behaviors differ from those in the bulk solution with significant and underappreciated consequences. Biophysical modeling predicted the probability and rate of β-sheet amyloid dimer formation to be higher and faster at the air-water interface (AWI) than in the bulk (by 14 and ∼1500 times, respectively). Time-course staining experiments with a typical amyloid dye verified our predictions by demonstrating that without AWI, islet amyloid polypeptide (IAPP) fibrilization was abolished or slowed, depending on the conditions. Our controls included undisturbed IAPP reactions, and we ascertained that the AWI removal process (technical or material) did not itself affect the reaction. Furthermore, we showed that the role of membranes in amyloidogenesis has been previously underestimated; in an in vivo-like situation (with no AWI), anionic liposomes (containing dioleoylphosphatidylglycerol) enhanced IAPP fibrilogenesis far more than described previously in conventional assay conditions (in the presence of an AWI). These findings have implications for the protein misfolding field and in assay design to target toxic protein aggregation.—Jean, L., Lee, C. F., Lee, C., Shaw, M., Vaux, D. J. Competing discrete interfacial effects are critical for amyloidogenesis.
Lee CF, 2009, Isotropic-nematic phase transition in amyloid fibrilization, Physical Review E, Vol: 80, Pages: 031902-031902
We carry out a theoretical study on the isotropic-nematic phase transitionand phase separation in amyloid fibril solutions. Borrowing the thermodynamicmodel employed in the study of cylindrical micelles, we investigate thevariations in the fibril length distribution and phase behavior with respect tochanges in the protein concentration, fibril’s rigidity, and binding energy. Wethen relate our theoretical findings to the nematic ordering observed in HenLysozyme fibril solution.
Lee CF, 2009, Thermal breakage of a discrete one-dimensional string, Physical Review E, Vol: 80, Pages: 031134-031134
We study the thermal breakage of a discrete one-dimensional string, with openand fixed ends, in the heavily damped regime. Basing our analysis on themultidimensional Kramers escape theory, we are able to make analyticalpredictions on the mean breakage rate, and on the breakage propensity withrespect to the breakage location on the string. We then support our predictionswith numerical simulations.
Lee CF, Loken J, Jean L, et al., 2009, Elongation dynamics of amyloid fibrils: a rugged energy landscape picture, Physical Review E, Vol: 80, Pages: 041906-041906
Protein amyloid fibrils are a form of linear protein aggregates that areimplicated in many neurodegenerative diseases. Here, we study the dynamics ofamyloid fibril elongation by performing Langevin dynamic simulations on acoarse-grained model of peptides. Our simulation results suggest that theelongation process is dominated by a series of local minimum due to frustrationin monomer-fibril interactions. This rugged energy landscape picture indicatesthat the amount of recycling of monomers at the fibrils’ ends before beingfibrilized is substantially reduced in comparison to the conventional two-stepelongation model. This picture, along with other predictions discussed, can betested with current experimental techniques.
Malhas AN, Lee CF, Vaux DJ, 2009, Lamin B1 controls oxidative stress responses via Oct-1, J. Cell Biol., Vol: 184, Pages: 45-55
Interaction of lamins with chromatin and transcription factors regulate transcription. Oct-1 has previously been shown to colocalize partly with B-type lamins and is essential for transcriptional regulation of oxidative stress response genes. Using sequential extraction, co-immunoprecipitation (IP), fluorescence loss in photobleaching, and fluorescence resonance energy transfer, we confirm Oct-1-lamin B1 association at the nuclear periphery and show that this association is lost in Lmnb1Delta/Delta cells. We show that several Oct-1-dependent genes, including a subset involved in oxidative stress response, are dysregulated in Lmnb1Delta/Delta cells. Electrophoretic mobility shift assay and chromatin IP reveal that Oct-1 binds to the putative octamer-binding sequences of the dysregulated genes and that this activity is increased in cells lacking functional lamin B1. Like Oct1-/- cells, Lmnb1Delta/Delta cells have elevated levels of reactive oxygen species and are more susceptible to oxidative stress. Sequestration of Oct-1 at the nuclear periphery by lamin B1 may be a mechanism by which the nuclear envelope can regulate gene expression and contribute to the cellular response to stress, development, and aging. 10.1083/jcb.200804155
Lee CF, 2009, Self-assembly of protein amyloids: A competition between amorphous and ordered aggregation, Physical Review E, Vol: 80, Pages: 031922-031922
Staniczenko PPA, Lee CF, Jones NS, 2009, Rapidly detecting disorder in rhythmic biological signals: A spectral entropy measure to identify cardiac arrhythmias, Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol: 79, Pages: 011915-011915
Jean L, Lee CF, Shaw M, et al., 2008, Structural Elements Regulating Amyloidogenesis: A Cholinesterase Model System, PLoS ONE, Vol: 3, Pages: e1834-e1834
Polymerization into amyloid fibrils is a crucial step in the pathogenesis of neurodegenerative syndromes. Amyloid assembly is governed by properties of the sequence backbone and specific side-chain interactions, since fibrils from unrelated sequences possess similar structures and morphologies. Therefore, characterization of the structural determinants driving amyloid aggregation is of fundamental importance. We investigated the forces involved in the amyloid assembly of a model peptide derived from the oligomerization domain of acetylcholinesterase (AChE), AChE586-599, through the effect of single point mutations on β-sheet propensity, conformation, fibrilization, surfactant activity, oligomerization and fibril morphology. AChE586-599 was chosen due to its fibrilization tractability and AChE involvement in Alzheimer’s disease. The results revealed how specific regions and residues can control AChE586-599 assembly. Hydrophobic and/or aromatic residues were crucial for maintaining a high β-strand propensity, for the conformational transition to β-sheet, and for the first stage of aggregation. We also demonstrated that positively charged side-chains might be involved in electrostatic interactions, which could control the transition to β-sheet, the oligomerization and assembly stability. Further interactions were also found to participate in the assembly. We showed that some residues were important for AChE586-599 surfactant activity and that amyloid assembly might preferentially occur at an air-water interface. Consistently with the experimental observations and assembly models for other amyloid systems, we propose a model for AChE586-599 assembly in which a steric-zipper formed through specific interactions (hydrophobic, electrostatic, cation-π, SH-aromatic, metal chelation and polar-polar) would maintain the β-sheets together. We also propose that the stacking between the strands in the β-sheets along the fiber axis could be st
Castro AO, Olsen FF, Lee CF, et al., 2008, Ultrafast quantum dynamics in photosynthesis, Quantum Aspects of Life, Pages: 51-70, ISBN: 9781848162532
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Lee CF, Johnson NF, 2008, Spin-glasses in optical cavity, EPL (Europhysics Letters), Vol: 81, Pages: 37004-37004
Recent advances in nanofabrication and optical control have garnered tremendous interest in multi-qubit-cavity systems. Here we analyze a spin-glass version of such a nanostructure, solving analytically for the phase diagrams in both the matter and radiation subsystems in the replica symmetric regime. Interestingly, the resulting phase transitions turn out to be tunable simply by varying the matter-radiation coupling strength.
Olaya-Castro A, Lee CF, Fassioli-Olsen F, et al., 2008, Efficiency of energy transfer in a light-harvesting system under quantum coherence, Physical Review B (Condensed Matter and Materials Physics), Vol: 78
Smith DMD, Lee CF, Onnela JP, et al., 2008, Link-space formalism for network analysis, Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol: 77
Law SL, Lee CF, Howison S, et al., 2007, Perturbation analysis of multi-asset portfolio optimization with transaction cost
We employ perturbation analysis technique to study trading strategies for multi-asset portfolio and obtain optimal trading methods for wealth maximization under arbitrary utility functions.
Malhas A, Lee CF, Sanders R, et al., 2007, Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression, J. Cell Biol., Vol: 176, Pages: 593-603
Radial organization of nuclei with peripheral gene-poor chromosomes and central gene-rich chromosomes is common and could depend on the nuclear boundary as a scaffold or position marker. To test this, we studied the role of the ubiquitous nuclear envelope (NE) component lamin B1 in NE stability, chromosome territory position, and gene expression. The stability of the lamin B1 lamina is dependent on lamin endoproteolysis (by Rce1) but not carboxymethylation (by Icmt), whereas lamin C lamina stability is not affected by the loss of full-length lamin B1 or its processing. Comparison of wild-type murine fibroblasts with fibroblasts lacking full-length lamin B1, or defective in CAAX processing, identified genes that depend on a stable processed lamin B1 lamina for normal expression. We also demonstrate that the position of mouse chromosome 18 but not 19 is dependent on such a stable nuclear lamina. The results implicate processed lamin B1 in the control of gene expression as well as chromosome position. 10.1083/jcb.200607054
Lerma C, Lee CF, Glass L, et al., 2007, The rule of bigeminy revisited: analysis in sudden cardiac death syndrome, Journal of Electrocardiology, Vol: 40, Pages: 78-88, ISSN: 0022-0736
The rule of bigeminy is commonly explained by a reentrant mechanism. We hypothesize that in patients with prolonged ventricular repolarization, the rule of bigeminy may be caused by premature ventricular complexes (PVCs) due to early afterdepolarizations. We evaluated these ventricular arrhythmias over extended periods in patients with sudden cardiac death syndrome. The electrocardiographic (ECG) characteristics of 15 recordings from the PhysioNet Sudden Cardiac Death Holter Database were analyzed for the persistence of bigeminy, interaction between the underlying cardiac rhythm and the coupling interval, and influence of a prolonged initiating RR cycle on the self-perpetuation of the arrhythmias. We identified a set of ECG characteristics that supports the notion that premature ventricular complexes during self-perpetuating ventricular bigeminy (“rule of bigeminy”) in long QT syndromes may be due to early afterdepolarizations.
Lemaire V, Lee CF, Lei J, et al., 2006, Sequential Recruitment and Combinatorial Assembling of Multiprotein Complexes in Transcriptional Activation, Physical Review Letters, Vol: 96, Pages: 198102-198102
Wolpert DH, Lee CF, 2006, An adaptive Metropolis-Hastings scheme: Sampling and optimization, EPL (Europhysics Letters), Vol: 76, Pages: 353-359
We propose an adaptive Metropolis-Hastings algorithm in which sampled data are used to update the proposal distribution. We use the samples found by the algorithm at a particular step to form the information-theoretically optimal mean-field approximation to the target distribution, and update the proposal distribution to be that approximation. We employ our algorithm to sample the energy distribution for several spin-glasses and we demonstrate the superiority of our algorithm to the conventional MH algorithm in sampling and in annealing optimization.
Olaya-Castro A, Lee CF, Johnson NF, 2006, Exact simulation of multi-qubit dynamics with only three qubits, EPL (Europhysics Letters), Vol: 74, Pages: 208-214
We present equivalence relations which simplify the dynamics of an important class of interacting multi-qubit systems. We show that a wide class of M + 1 qubit systems, with one or M excitations, can be reduced to an equivalent n + 1 qubit system with n [?] 2, for any M. The equivalent system faithfully reproduces the overall dynamics of the original one including the entanglement properties. In addition to its direct application to qubit-cavity systems, the formalism offers insight into a variety of situations ranging from decoherence due to a spin-bath with its own internal entanglement, through to energy transfer processes in organic systems such as biological photosynthetic units.
Jarrett TC, Lee CF, Johnson NF, 2006, Optically controlled spin glasses in multiqubit cavity systems, Physical Review B (Condensed Matter and Materials Physics), Vol: 74, Pages: 121301(R)-121301(R)
Lee CF, Johnson NF, 2004, Efficient quantum computation within a disordered Heisenberg spin chain, Physical Review A, Vol: 70, Pages: 052322+-052322+
Lee CF, Johnson NF, 2004, First-Order Superradiant Phase Transitions in a Multiqubit Cavity System, Physical Review Letters, Vol: 93, Pages: 083001-083001
Lee CF, Wolpert DH, 2004, Product Distribution Theory for Control of Multi-Agent Systems, Los Alamitos, CA, USA, Publisher: IEEE Computer Society, Pages: 522-529
Product Distribution (PD) theory is a new framework for controlling Multi-Agent Systems (MAS?s). First we review one motivation of PD theory, as the information-theoretic extension of conventional full-rationality game theory to the case of bounded rational agents. In this extension the equilibrium of the game is the optimizer of a Lagrangian of the (probability distribution of) the joint state of the agents. Accordingly we can consider a team game havbing a shared utility which is a performance measure of the behavior of the MAS. For such a scenario the game is at equilibrium — the Lagrangian is optimized — when the joint distribution of the agents optimizes the system?s expected performance. One common way to find that equilibrium is to have each agent run a reinforcement learning algorithm. Here we investigate the alternative of exploiting PD theory to run gradient descent on the Lagrangian. We present computer experiments validating some of the predictions of PD theory for how best to do that gradient descent. We also demonstrate how PD theory can improve performance even when we are not allowed to rerun the MAS from different initial conditions, a requirement implicit in some previous work.
Lee CF, Johnson NF, 2003, Efficiency and formalism of quantum games, Physical Review A, Vol: 67, Pages: 022311-022311
Kemkes G, Lee CF, Merlini D, et al., 2003, Stirling Numbers for Complex Arguments: Asymptotics and Identities, SIAM Journal on Discrete Mathematics, Vol: 16, Pages: 179-191
Lee CF, 2002, Game-theoretic discussion of quantum state estimation and cloning, Physics Letters A, Vol: 319, Pages: 429-433, ISSN: 0375-9601
We present a game-theoretic perspective on the problems of quantum state estimation and quantum cloning. This enables us to show why the focus on universal machines and the different measures of success, as employed in previous works, are in fact legitimite.
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