@article{jang_hall_zhou_2004, title={Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models}, volume={86}, ISSN={["1542-0086"]}, DOI={10.1016/S0006-3495(04)74081-3}, abstractNote={We have performed discontinuous molecular dynamic simulations of the assembly and folding kinetics of a tetrameric β-sheet complex that contains four identical four-stranded antiparallel β-sheet peptides. The potential used in the simulation is a hybrid Go-type potential characterized by the bias gap parameter g, an artificial measure of a model protein's preference for its native state, and the intermolecular contact parameter η, which measures the ratio of intermolecular to intramolecular native attractions. The formation of the β-sheet complex and its equilibrium properties strongly depend on the size of the intermolecular contact parameter η. The ordered β-sheet complex in the folded state and nonaligned β-sheets or tangled chains in the misfolded state are distinguished by measuring the squared radius of gyration Rg2 and the fraction of native contacts Q. The folding yield for the folded state is high at intermediate values of η, but is low at both small and large values of η. The folded state at small η is liquid-like, but is solid-like at both intermediate and large η. The misfolded state at small η contains nonaligned β-sheets and tangled chains with poor secondary structure at large η. Various folding pathways via dimeric and trimeric intermediates are observed, depending on η. Comparison with experimental results on protein aggregation indicates that intermediate η values are most appropriate for modeling fibril formation and small η values are most appropriate for modeling the formation of amorphous aggregates.}, number={1}, journal={BIOPHYSICAL JOURNAL}, author={Jang, HB and Hall, CK and Zhou, YQ}, year={2004}, month={Jan}, pages={31–49} }
 @article{jang_grimson_hall_2003, title={Dynamic phase transitions in thin ferromagnetic films}, volume={67}, ISSN={["1098-0121"]}, DOI={10.1103/physrevb.67.094411}, abstractNote={Monte Carlo simulations have been used to investigate the dynamic phase behavior of a classical Heisenberg spin system with a bilinear exchange anisotropy A in a planar thin film geometry. Studies of the field amplitude, frequency, and temperature dependence show dynamic phase transitions in films subject to a pulsed oscillatory external field. Thin films with competing surface fields show separate and distinct dynamic phase transitions for the bulk and surface layers of the film. Between the two transitions, a mixed state with coexisting dynamically ordered arid dynamically disordered phases is observed in the film. In contrast, the free film with no surface fields show a single dynamic phase transition as in a bulk system.}, number={9}, journal={PHYSICAL REVIEW B}, author={Jang, H and Grimson, MJ and Hall, CK}, year={2003}, month={Mar} }
 @article{jang_hall_zhou_2004, title={Thermodynamics and stability of a beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models}, volume={13}, ISSN={["1469-896X"]}, DOI={10.1110/ps.03162804}, abstractNote={AbstractWe have performed discontinuous molecular dynamics simulations of the thermodynamics and stability of a tetrameric β‐sheet complex that contains four identical four‐stranded antiparallel β‐sheet peptides. The potential used in the simulation is a hybrid Go‐type potential characterized by the bias gap parameter g, an artificial measure of the preference of a model protein for its native state, and the intermolecular contact parameter η, which measures the ratio of intermolecular to intramolecular native attractions. Despite the simplicity of the model, a complex set of thermodynamic transitions for the β‐sheet complex is revealed that shows there are three distinct oligomer (partially ordered, ordered, and highly ordered β‐sheet complex) states and four noninteracting monomers phases. The thermodynamic properties of the three oligomer states strongly depend on both the size of the intermolecular contact parameter η and the temperature. The partially ordered β‐sheet complex is made up of four ordered globules and is observed at intermediate to large η at high temperatures. The ordered β‐sheet complex contains four native β‐sheets and is located at small to intermediate η at low temperatures in the phase diagram. The highly ordered β‐sheet complex has fully‐stiff β‐sheet strands, the same as the global energy minimum structure, and is observed for all η at low temperatures.}, number={1}, journal={PROTEIN SCIENCE}, author={Jang, HB and Hall, CK and Zhou, YQ}, year={2004}, month={Jan}, pages={40–53} }
 @article{jang_hall_zhou_2002, title={Folding thermodynamics of model four-strand antiparallel beta-sheet proteins}, volume={82}, ISSN={["0006-3495"]}, DOI={10.1016/S0006-3495(02)75428-3}, abstractNote={The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration, the root-mean-squared pair separation fluctuation, the specific heat, the internal energy of the system, and the Lindemann disorder parameter. In spite of the simplicity, the protein-like heteropolymers have shown a complex set of protein transitions as observed in experimental studies. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. These transitions strongly depend on the native-state geometry of the model proteins and the size of the bias gap. A strong transition from the disordered globule state to the ordered globule state with large energy change and a weak transition from the ordered globule state to the native state with small energy change were observed for the large gap models. For the small gap models no native structures were observed at any temperature, all three beta-sheet proteins fold into a partially-ordered globule state which is geometrically different from the native state. For small bias gaps at even lower temperatures, all protein motions are frozen indicating an inactive solid-like phase.}, number={2}, journal={BIOPHYSICAL JOURNAL}, author={Jang, H and Hall, CK and Zhou, YQ}, year={2002}, month={Feb}, pages={646–659} }
 @article{jang_hall_zhou_2002, title={Protein folding pathways and kinetics: Molecular dynamics simulations of beta-strand motifs}, volume={83}, ISSN={["0006-3495"]}, DOI={10.1016/S0006-3495(02)75211-9}, abstractNote={The folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel β-strand protein models interacting via a hybrid Go-type potential have been investigated using discontinuous molecular dynamics simulations. The kinetic study of protein folding was conducted by temperature quenching from a denatured or random coil state to a native state. The progress parameters used in the kinetic study include the squared radius of gyration Rg2, the fraction of native contacts within the protein as a whole Q, and between specific strands Qab. In the time series of folding, the denatured proteins undergo a conformational change toward the native state. The model proteins exhibit a variety of kinetic folding pathways that include a fast-track folding pathway without passing through an intermediate and multiple pathways with trapping into more than one intermediate. The kinetic folding behavior of the β-strand proteins strongly depends on the native-state geometry of the model proteins and the size of the bias gap g, an artificial measure of a model protein's preference for its native state.}, number={2}, journal={BIOPHYSICAL JOURNAL}, author={Jang, H and Hall, CK and Zhou, YQ}, year={2002}, month={Aug}, pages={819–835} }
 @article{jang_grimson_2001, title={Hysteresis and the dynamic phase transition in thin ferromagnetic films - art. no. 066119}, volume={6306}, number={6}, journal={Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics}, author={Jang, H. B. and Grimson, M. J.}, year={2001}, pages={6119} }