M. S. Li, P. H. Nguyen, D. Thirumalai, Jan Meinke, Ipan Mohanty, ...
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Beta-amyloid Peptides, N. S. Lam, M. Kouza, H. Zung, M. S. Li, ...
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New method for deciphering free energy landscape of three-state proteins (2008)
Li, Mai Suan, Gabovich, A. M., Voitenko, A. I.
We have developed a new simulation method to estimate the distance between the native state and the first transition state, and the distance between the intermediate state and the second transition...
Probing the Mechanisms of Fibril Formation Using Lattice Models (2008)
Li, Mai Suan, Klimov, D. K., Straub, J. E., Thirumalai, D.
Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at...
Kouza, Maksim, Hu, Chin-Kun, Li, Mai Suan
We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to...
Effect of finite size on cooperativity and rates of protein folding (2006)
Kouza, Maksim, Li, Mai Suan, O'Brien Jr., Edward P., Hu, Chin-Kun, Thirumalai, D.
We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, $N$, using lattice models with side...
Folding of the Protein Domain hbSBD (2006)
Kouza, Maksim, Chang, Chi-Fon, Hayryan, Shura, Yu, Tsan-hung, Li, Mai Suan, Huang, Tai-huang, ...
The folding of the alpha-helice domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex is studied by the circular dichroism technique in absence of...
Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin (2006)
Li, Mai Suan, Kouza, Maksim, Hu, Chin-Kun
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Go model and the Langevin dynamics. It is shown that the refolding...
Finite size effects on calorimetric cooperativity of two-state proteins (2004)
Li, Mai Suan, Klimov, D. K., Thirumalai, D.
Finite size effects on the calorimetric cooperatity of the folding-unfolding transition in two-state proteins are considered using the Go lattice models with and without side chains. We show that for...
Finite size effects on thermal denaturation of globular proteins (2004)
Li, Mai Suan, Klimov, D. K., Thirumalai, D.
Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids....
1/f Noise in a one-dimensional charge density wave system (2004)
Struzik, Zbigniew R., Glatz, Andreas, Li, Mai Suan
The current noise in a classical one-dimensional charge density wave system is studied in the weak pinning regime by solving the overdamped equation of motion numerically. At low temperatures and...
Thermal denaturation and folding rates of single domain proteins: size matters (2003)
Li, Mai Suan, Klimov, D. K., Thirumalai, D.
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1,...
Paramagnetic Meissner effect and related dynamical phenomena (2003)
The present review is given on the paramagnetic Meissner effect observed in conventional and ceramic high-Tc superconductors. We discuss two mechanisms leading to this phenomenon: the d-wave and the...
Flux-lattice melting in two-dimensional disordered superconductors (2002)
Li, Mai Suan, Nattermann, Thomas
The flux line lattice melting transition in two-dimensional pure and disordered superconductors is studied by a Monte Carlo simulation using the lowest Landau level approximation and quasi-periodic...
Dependence of folding rates on protein length (2002)
Li, Mai Suan, Klimov, D. K., Thirumalai, D.
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find...
Folding in lattice models with side chains (2002)
Li, Mai Suan, Klimov, D. K., Thirumalai, D.
The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone...
Nonlinear AC resistivity in s-wave and d-wave disordered granular superconductors (2002)
Li, Mai Suan, Zung, Hoang, Dominguez, Daniel
We model s-wave and d-wave disordered granular superconductors with a three-dimensional lattice of randomly distributed Josephson junctions with finite self-inductance. The nonlinear ac resistivity...
Heat capacity of mesoscopically disordered superconductors:implications to MgB$_{2}$ (2001)
Gabovich, A. M., Voitenko, A. I., Li, Mai Suan, Szymczak, H., Pekala, M.
Electronic heat capacity was calculated for a mesoscopically disordered s-wave superconductor treated as a spatial ensemble of domains with a continuously varying superconducting properties. The...
Microwave absorption in s- and d-wave disordered superconductors (2001)
We model s- and d-wave ceramic superconductors with a three-dimensional lattice of randomly distributed Josephson junctions with finite self-inductance. The field and temperature dependences of the...
Nature of the ordering of the three-dimensional XY spin glass (2001)
Kawamura, Hikaru, Li, Mai Suan
Spin and chirality orderings of a three-dimensional XY spin glass are studied by extensive Monte Carlo simulations. By calculating an appropriately defined spin-overlap distribution function, we show...
Collective Dynamics of One-Dimensional Charge Density Waves (2001)
Glatz, Andreas, Kumar, Sanjay, Li, Mai Suan
The effect of disorder on the static and dynamic behaviour of one-dimensional charge density waves at low temperatures is studied by analytical and numerical approaches. In the low temperature region...
Aging Effect in Ceramic Superconductors (2000)
Li, Mai Suan, Nordblad, Per, Kawamura, Hikaru
A three-dimensional lattice of the Josephson junctions with a finite self-conductance is employed to model ceramic superconductors. Using Monte Carlo simulations it is shown that the aging disappears...
Structural Susceptibilities in Toy Models of Proteins (2000)
New definitions of the structural susceptibilities based on the fluctuations of distances to the native state of toy protein models are proposed. The calculation of such susceptibilities does not...
AC resistivity of d-wave ceramic superconductors (2000)
Li, Mai Suan, Dominguez, Daniel
We model d-wave ceramic superconductors with a three-dimensional lattice of randomly distributed $\pi$ Josephson junctions with finite self-inductance. The linear and nonlinear ac resistivity of the...
Dynamical chaos and power spectra in toy models of heteropolymers and proteins (2000)
Li, Mai Suan, Cieplak, Marek, Sushko, Nazar
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the...
Spin analogs of proteins: scaling of "folding" properties (1999)
Hoang, Trinh Xuan, Sushko, Nazar, Li, Mai Suan, Cieplak, Marek
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic...
Folding in two-dimenensional off-lattice models of proteins (1999)
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The...
Delineation of the Native Basin in Continuum Models of Proteins (1999)
We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories emerging from the...
Scaling of folding properties in simple models of proteins (1999)
Cieplak, Marek, Hoang, Trinh Xuan, Li, Mai Suan
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic...
Chiral Glass Phase in Ceramic Superconductors (1999)
Li, Mai Suan, Kawamura, Hikaru
A three-dimensional lattice of the Josephson junctions with a finite self-conductance is employed to model the ceramic superconductors. By Monte Carlo simulations it is shown that the chiral glass...
Simple models of proteins with repulsive non-native contacts (1999)
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts....
Second harmonics and compensation effect in ceramic superconductors (1999)
A three-dimensional lattice of the Josephson junctions with a finite self-conductance is employed to model the ceramic superconductors. The nonlinear ac susceptibility and the compensation effect are...
Chiral glass: a new equilibrium phase of ceramic high-Tc superconductors (1997)
Kawamura, Hikaru, Li, Mai Suan
Possible occurrence of an equilibrium thermodynamic phase with a spontaneously broken time-reversal symmetry is studied in a model ceramic superconductor with anisotropic pairing symmetry. It is...
ABSENCE OF REENTRANCE IN THE TWO-DIMENSIONAL XY-MODEL WITH RANDOM PHASE SHIFT (1995)
NATTERMANN, Thomas, SCHEIDL, Stefan, KORSHUNOV, Sergey E., LI, Mai Suan
We show, that the 2D XY-model with random phase shifts exhibits for low temperature and small disorder a phase with quasi-long-range order, and that the transition to the disordered phase is {\it...
Li, Mai Suan, Hu, Chin-Kun, Klimov, Dmitri K., Thirumalai, D.
Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy experiments [Fernandez, J. M. & Li, H. (2004)...
Folding of the Protein Domain hbSBD
Kouza, Maksim, Chang, Chi-Fon, Hayryan, Shura, Yu, Tsan-hung, Li, Mai Suan, Huang, Tai-huang, ...
The folding of the α-helix domain hbSBD of the mammalian mitochondrial branched-chain α-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal...
Li, Mai Suan, Hu, Chin-Kun, Klimov, Dmitri K., Thirumalai, D.
Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy experiments [Fernandez, J. M. & Li, H. (2004)...
Folding of the Protein Domain hbSBD
Kouza, Maksim, Chang, Chi-Fon, Hayryan, Shura, Yu, Tsan-hung, Li, Mai Suan, Huang, Tai-huang, ...
The folding of the α-helix domain hbSBD of the mammalian mitochondrial branched-chain α-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal...
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism
Nguyen, Phuong H., Li, Mai Suan, Stock, Gerhard, Straub, John E., Thirumalai, D.
Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct...
Refolding upon Force Quench and Pathways of Mechanical and Thermal Unfolding of Ubiquitin
Li, Mai Suan, Kouza, Maksim, Hu, Chin-Kun
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Cα-Gō model and the Langevin dynamics. It is shown that the refolding...
Secondary Structure, Mechanical Stability, and Location of Transition State of Proteins
It is well known that the unfolding times of proteins, τu, scales with the external mechanical force f as \documentclass[10pt]{article} \usepackage{amsmath} \usepackage{wasysym}...
Probing the mechanisms of fibril formation using lattice models
Li, Mai Suan, Klimov, D. K., Straub, J. E., Thirumalai, D.
Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature (T) and the number of chains (M). While these models...