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Chiu Fan Lee

Publications and source records attributed to Chiu Fan Lee.

At least 73 records · Page 4Linked to original sources
arXiv2011

Singular perturbation analysis of a reduced model for collective motion: A renormalization group approach

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.

cond-mat.soft↗
arXiv2010

Predicting rare events in chemical reactions: application to skin cell proliferation

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 {\bf 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.

q-bio.CB↗
arXiv2010

Fluctuation-induced collective motion: A single-particle density analysis

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.

cond-mat.soft↗
arXiv2009

Self-assembly of protein amyloid: a competition between amorphous and ordered aggregation

Protein aggregation in the form of amyloid fibrils has important biological and technological implications. Although the self-assembly process is highly efficient, aggregates not in the fibrillar form would also occur and it is important to include these disordered species when discussing the thermodynamic equilibrium behavior of the system. Here, we initiate such a task by considering a mixture of monomeric proteins and the corresponding aggregates in the disordered form (micelles) and in the fibrillar form (amyloid fibrils). Starting with a model on the respective binding free energies for these species, we calculate their concentrations at thermal equilibrium. We then discuss how the incorporation of the disordered structure furthers our understanding on the various amyloid promoting factors observed empirically, and on the kinetics of fibrilization.

cond-mat.soft↗
arXiv2009

Isotropic-nematic phase transition in amyloid fibrilization

We carry out a theoretical study on the isotropic-nematic phase transition and phase separation in amyloid fibril solutions. Borrowing the thermodynamic model employed in the study of cylindrical micelles, we investigate the variations in the fibril length distribution and phase behavior with respect to changes in the protein concentration, fibril's rigidity, and binding energy. We then relate our theoretical findings to the nematic ordering observed in Hen Lysozyme fibril solution.

q-bio.BM↗
arXiv2009

Thermal breakage of a discrete one-dimensional string

We study the thermal breakage of a discrete one-dimensional string, with open and fixed ends, in the heavily damped regime. Basing our analysis on the multidimensional Kramers escape theory, we are able to make analytical predictions on the mean breakage rate, and on the breakage propensity with respect to the breakage location on the string. We then support our predictions with numerical simulations.

cond-mat.stat-mech↗
arXiv2009

Network Automata: Coupling structure and function in real-world networks

We introduce Network Automata, a framework which couples the topological evolution of a network to its structure. It is useful for dealing with networks in which the topology evolves according to some specified microscopic rules and, simultaneously, there is a dynamic process taking place on the network that both depends on its structure but is also capable of modifying it. It is a generic framework for modeling systems in which network structure, dynamics, and function are interrelated. At the practical level, this framework allows for easy implementation of the microscopic rules involved in such systems. To demonstrate the approach, we develop a class of simple biologically inspired models of fungal growth.

physics.soc-ph↗
arXiv2009

Correlated multi-asset portfolio optimisation with transaction cost

We employ perturbation analysis technique to study multi-asset portfolio optimisation with transaction cost. We allow for correlations in risky assets and obtain optimal trading methods for general utility functions. Our analytical results are supported by numerical simulations in the context of the Long Term Growth Model.

q-fin.PM↗
arXiv2009

Elongation dynamics of amyloid fibrils: a rugged energy landscape picture

Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained model of peptides. Our simulation results suggest that the elongation process is dominated by a series of local minimum due to frustration in monomer-fibril interactions. This rugged energy landscape picture indicates that the amount of recycling of monomers at the fibrils' ends before being fibrilized is substantially reduced in comparison to the conventional two-step elongation model. This picture, along with other predictions discussed, can be tested with current experimental techniques.

physics.bio-ph↗
arXiv2009

Rapidly detecting disorder in rhythmic biological signals: A spectral entropy measure to identify cardiac arrhythmias

We consider the use of a running measure of power spectrum disorder to distinguish between the normal sinus rhythm of the heart and two forms of cardiac arrhythmia: atrial fibrillation and atrial flutter. This spectral entropy measure is motivated by characteristic differences in the spectra of beat timings during the three rhythms. We plot patient data derived from ten-beat windows on a "disorder map" and identify rhythm-defining ranges in the level and variance of spectral entropy values. Employing the spectral entropy within an automatic arrhythmia detection algorithm enables the classification of periods of atrial fibrillation from the time series of patients' beats. When the algorithm is set to identify abnormal rhythms within 6 s it agrees with 85.7% of the annotations of professional rhythm assessors; for a response time of 30 s this becomes 89.5%, and with 60 s it is 90.3%. The algorithm provides a rapid way to detect atrial fibrillation, demonstrating usable response times as low as 6 s. Measures of disorder in the frequency domain have practical significance in a range of biological signals: the techniques described in this paper have potential application for the rapid identification of disorder in other rhythmic signals.

q-bio.QM↗
arXiv2008

Efficiency and formalism of quantum games

We pursue a general theory of quantum games. We show that quantum games are more efficient than classical games, and provide a saturated upper bound for this efficiency. We demonstrate that the set of finite classical games is a strict subset of the set of finite quantum games. We also deduce the quantum version of the Minimax Theorem and the Nash Equilibrium Theorem.

quant-ph↗
arXiv2008

Mechanical properties of the two-filament insulin amyloid fibril: a theoretical study

We study the two-filament insulin fibril's structure by incorporating recent simulation results and mechanical measurements. Our investigation suggests that the persistence length measurement correlates well with the previously proposed structural model, while the elasticity measurement suggests that stretching the fibril may involve hydrogen bond breakage. Our work illustrates an attempt to correlate nanoscale measurements with microscopic information on the quaternary protein structure.

cond-mat.soft↗
arXiv2008

Efficiency of energy transfer in a light-harvesting system under quantum coherence

We investigate the role of quantum coherence in the efficiency of excitation transfer in a ring-hub arrangement of interacting two-level systems, mimicking a light-harvesting antenna connected to a reaction center as it is found in natural photosynthetic systems. By using a quantum jump approach, we demonstrate that in the presence of quantum coherent energy transfer and energetic disorder, the efficiency of excitation transfer from the antenna to the reaction center depends intimately on the quantum superposition properties of the initial state. In particular, we find that efficiency is sensitive to symmetric and asymmetric superposition of states in the basis of localized excitations, indicating that initial state properties can be used as a efficiency control parameter at low temperatures.

quant-ph↗
arXiv2008

Link-Space and Network Analysis

Many networks contain correlations and often conventional analysis is incapable of incorporating this often essential feature. In arXiv:0708.2176, we introduced the link-space formalism for analysing degree-degree correlations in evolving networks. In this extended version, we provide additional mathematical details and supplementary material. We explore some of the common oversights when these correlations are not taken into account, highlighting the importance of the formalism. The formalism is based on a statistical description of the fraction of links l_{i,j} connecting nodes of degrees i and j. To demonstrate its use, we apply the framework to some pedagogical network models, namely, random-attachment, Barabasi-Albert preferential attachment and the classical Erdos and Renyi random graph. For these three models the link-space matrix can be solved analytically. We apply the formalism to a simple one-parameter growing network model whose numerical solution exemplifies the effect of degree-degree correlations for the resulting degree distribution. We also employ the formalism to derive the degree distributions of two very simple network decay models, more specifically, that of random link deletion and random node deletion. The formalism allows detailed analysis of the correlations within networks and we also employ it to derive the form of a perfectly non-assortative network for arbitrary degree distribution.

physics.soc-ph↗
arXiv2008

Link-space formalism for network analysis

We introduce the link-space formalism for analyzing network models with degree-degree correlations. The formalism is based on a statistical description of the fraction of links l_{i,j} connecting nodes of degrees i and j. To demonstrate its use, we apply the framework to some pedagogical network models, namely, random-attachment, Barabasi-Albert preferential attachment and the classical Erdos and Renyi random graph. For these three models the link-space matrix can be solved analytically. We apply the formalism to a simple one-parameter growing network model whose numerical solution exemplifies the effect of degree-degree correlations for the resulting degree distribution. We also employ the formalism to derive the degree distributions of two very simple network decay models, more specifically, that of random link deletion and random node deletion. The formalism allows detailed analysis of the correlations within networks and we also employ it to derive the form of a perfectly non-assortative network for arbitrary degree distribution.

physics.soc-ph↗
arXiv2008

Density functional methods for polymers: a coil-globule transition case study

We consider a free energy functional on the monomer density function that is suitable for the study of coil-globule transition. We demonstrate, with explicitly stated assumptions, why the entropic contribution is in the form of the Kullback-Leibler distance, and that the energy contribution is given by two-body and three-body terms. We then solve for the free energy analytically on a set of trial density functions, and reproduce de Gennes' classical theory on polymer coil-globule transition. We then discuss how our formalism can be applied to study polymer dynamics from the perspective of dynamical density function theory.

cond-mat.soft↗
arXiv2007

Spin-glasses in optical cavity

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.

quant-ph↗